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Published & In Press Manuscripts

Cutter, A.D. & J.C. Gray. 2016. Ephemeral ecological speciation and the latitudinal biodiversity gradient.
Evolution. 70: 2171-2181

The richness of biodiversity in the tropics compared to high latitude parts of the world forms one of the most globally conspicuous patterns in biology, and yet few hypotheses aim to explain this phenomenon in terms of explicit micro-evolutionary mechanisms of speciation and extinction. We link population genetic processes of selection and adaptation to speciation and extinction by way of their interaction with environmental factors to drive global scale macro-ecological patterns. High latitude regions are both cradle and grave with respect to species diversification. In particular, we point to a conceptual equivalence of ‘environmental harshness’ and ‘hard selection’ as eco-evolutionary drivers of local adaptation and ecological speciation. By describing how ecological speciation likely occurs more readily at high latitudes, with such nascent species especially prone to extinction by fusion, we derive the ephemeral ecological speciation hypothesis as an integrative mechanistic explanation for latitudinal gradients in species turnover and the net accumulation of biodiversity.  

Vielle, A., N. Callemeyn-Torre, C. Gimond, N. Poullet, N. Soares, J.C. Gray, A.D. Cutter & C. Braendle. 2016. Convergent evolution of sperm gigantism and the developmental origins of sperms size variability in Caenorhabditis nematodes. Evolution. 70: 2485-2503. 

Sperm cells provide essential, if usually diminutive, ingredients to successful sexual reproduction. Despite this conserved function, sperm competition and coevolution with female traits can drive spectacular morphological change in these cells. Here we characterize four repeated instances of convergent evolution of sperm gigantism in Caenorhabditis nematodes using phylogenetic comparative methods on 26 species. Species at the extreme end of the 50-fold range of sperm-cell volumes across the genus have sperm capable of comprising up to 5% of egg-cell volume, representing severe attenuation of the magnitude of anisogamy. Furthermore, we uncover significant differences in mean and variance of sperm size among genotypes, between sexes, and within and between individuals of identical genotypes. We demonstrate that the developmental basis of sperm size variation, both within and between species, becomes established during an early stage of sperm development, i.e. at the formation of primary spermatocytes while subsequent meiotic divisions contribute little further sperm size variability. These findings provide first insights into the developmental determinants of inter- and intraspecific sperm size differences in Caenorhabditis. We hypothesize that life history and ecological differences among species favoured the evolution of alternative sperm competition strategies toward either many smaller sperm or fewer larger sperm.  

Jovelin, R., A. Krizus, B. Taghizada, J.C. Gray, P.C. Phillips, J.M. Claycomb, & A.D. Cutter. 2016. Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis. RNA. 22: 968-978. 

MicroRNAs (miRNAs) comprise a class of short non-coding RNA molecules that play diverse developmental and physiological roles by controlling mRNA abundance and protein output of the vast majority of transcripts. Despite the importance of miRNAs in regulating gene function, we still lack a complete understanding of how miRNAs themselves are transcriptionally regulated. To fill this gap, we predicted regulatory sequences by searching for abundant short motifs located upstream of miRNAs in 8 species of Caenorhabditis nematodes. We identified three conserved motifs across the Caenorhabditis phylogeny that show clear signatures of purifying selection from comparative genomics, patterns of nucleotide changes in motifs of orthologous miRNAs, and correlation between motif incidence and miRNA expression. We then validated our predictions with transgenic green fluorescent protein reporters and site-directed mutagenesis for a subset of motifs located in an enhancer region upstream of let-7. We demonstrate that a CT-dinucleotide motif is sufficient for proper expression of GFP in the seam cells of adult C. elegans, and that two other motifs play incremental roles in combination with the CT-rich motif. Thus, functional tests of sequence motifs identified through analysis of molecular evolutionary signatures provide a powerful path for efficiently characterizing the transcriptional regulation of miRNA genes.  

Jovelin, R. & A.D. Cutter. 2016. Hitting two birds with one stone: the unforeseen consequences of nested gene knockouts in Caenorhabditis elegans. Worm. 5: e1156835. 

Nested genes represent an intriguing form of non-random genomic organization in which the boundaries of one gene are fully contained within another, longer host gene. The C. elegans genome contains over 10,000 nested genes, 92% of which are ncRNAs, which occur inside 16% of the protein coding gene complement. Host genes are longer than non-host coding genes, owing to their longer and more numerous introns. Indel alleles are available for nearly all of these host genes that simultaneously alter the nested gene, raising the possibility of nested gene disruption contributing to phenotypes that might be attributed to the host gene. Such dual-knockouts could represent a source of misinterpretation about host gene function. Dual-knockouts might also provide a novel source of synthetic phenotypes that reveal the functional effects of ncRNA genes, whereby the host gene disruption acts as a perturbed genetic background to help unmask ncRNA phenotypes.  

Ting, J.J. & A.D. Cutter. 2016. Sexual conflict and speciation. In: Encyclopedia of Evolutionary Biology (R. Kliman ed.). Academic Press (Oxford). Volume 4, pp. 192-199. 

Speciation arises from the evolutionary accumulation of barriers to successful reproduction between populations, so any process that accelerates trait evolution among populations along independent genetic trajectories will foster speciation and its maintenance. Sexual conflict mediated by sexually antagonistic co-evolution provides an especially powerful, albeit largely unproven, mechanism compared to other forms of inter-sexual selection capable of driving divergence between, or maintaining the integrity of, nascent species. Under some circumstances, however, sexual conflict could inhibit the evolution of reproductive isolation or accelerate extinction. Assessing the general form of the genetic architecture underlying sexual conflict and discerning conflict from other modes of sexual selection remain persistent challenges to evaluating sexual conflict's role in speciation.  

Cutter, A.D. & R. Jovelin. 2015. When natural selection gives gene function the cold shoulder. Bioessays. 37: 1169-1173. [pdf]

It is tempting to invoke organismal selection as perpetually optimizing the function of any given gene. However, natural selection can drive genic functional change without improvement of biochemical activity, even to the extinction of gene activity. Detrimental mutations can creep in owing to linkage with other selectively favored loci. Selection can promote functional degradation, irrespective of genetic drift, when adaptation occurs by loss of gene function. Even stabilizing selection on a trait can lead to divergence of the underlying molecular constituents. Selfish genetic elements also can proliferate independent of any functional benefits to the host genome. Here we review the logic and evidence for these diverse processes acting in genome evolution. This collection of distinct evolutionary phenomena -- while operating through easily understandable mechanisms -- all contribute to the seemingly counterintuitive notion that maintenance or improvement of a gene's biochemical function sometimes do not determine its evolutionary fate.  

Fierst, J.L., J.H. Willis, C.G. Thomas, W. Wang, R.M. Reynolds, T. Ahearne, A.D. Cutter & P.C. Phillips. 2015. Reproductive mode and the evolution of genome size and structure in Caenorhabditis nematodes. PLoS Genetics. 11: e1005323. [pdf]

The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes ~20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this,we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.  

Cutter, A.D. 2015. Caenorhabditis evolution in the wild. Bioessays. 37: 983-995. [pdf]

Recent research has filled many gaps about Caenorhabditis natural history, simultaneously exposing how much remains to be discovered. This awareness now provides means of connecting ecological and evolutionary theory with diverse biological patterns within and among species in terms of adaptation, sexual selection, breeding systems, speciation, and other phenomena. Moreover, the heralded laboratory tractability of C. elegans, and Caenorhabditis species generally, provides a powerful case study for experimental hypothesis testing about evolutionary and ecological processes to levels of detail unparalleled by most study systems. Here I synthesize pertinent theory with what we know and suspect about Caenorhabditis natural history for salient features of biodiversity, phenotypes, population dynamics, and interactions within and between species. I identify topics of pressing concern to advance Caenorhabditis biology and to study general evolutionary processes, including the key opportunities to tackle problems in dispersal dynamics, competition, and the dimensionality of niche space.  

Bundus, J.D., R. Alaei & A.D. Cutter. 2015. Gametic selection, developmental trajectories and extrinsic heterogeneity in Haldane's rule. Evolution. 69: 2005-2017. [pdf]

Deciphering the genetic and developmental causes of the disproportionate rarity, inviability and sterility of hybrid males, Haldane’s rule, is important for understanding the evolution of reproductive isolation between species. Moreover, extrinsic and pre-zygotic factors can contribute to the magnitude of intrinsic isolation experienced between species with partial reproductive compatibility. Here we use the nematodes Caenorhabditis briggsae and C. nigoni to quantify the sensitivity of hybrid male viability to extrinsic temperature and developmental timing, and test for a role of mito-nuclear incompatibility as a genetic cause. We demonstrate that hybrid male inviability manifests almost entirely as embryonic, not larval, arrest and is maximal at the lowest rearing temperatures, indicating an intrinsic-by-extrinsic interaction to hybrid inviability. Crosses using mitochondrial substitution strains that have reciprocally introgressed mitochondrial and nuclear genomes show that mito-nuclear incompatibility is not a dominant contributor to post-zygotic isolation and does not drive Haldane’s rule in this system. Crosses also reveal that competitive superiority of X-bearing sperm provides a novel means by which post-mating pre-zygotic factors exacerbate the rarity of hybrid males. These findings highlight the important roles of gametic, developmental, and extrinsic factors in modulating the manifestation of Haldane’s rule.  

Thomas, C.G.*, W. Wang*, R. Jovelin, R. Ghosh, T. Lomasko, Q. Trinh, L. Kruglyak, L.D. Stein & A.D. Cutter. 2015. Full-genome evolutionary histories of selfing, splitting and selection in Caenorhabditis.
Genome Research. 25: 667-678. [pdf] [supplement]

The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the “Temperate” and “Tropical” phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.  

Cutter, A.D. 2015. Repeatability, ephemerality, and inconvenient truths in the speciation process. (Commentary) Molecular Ecology. 24: 1643-1644. [pdf]

Everyone appreciates the happy fiction that species conform to the simple theoretical convenience of a single panmictic population. In speciation genetics, a further standard simplification is that it is only those genetic differences that are fixed between diverging populations that need concern us in order to understand the accumulation of intrinsic barriers to reproduction. To a first approximation, of course, both of these assumptions are appropriate and theory based on them provides compelling insights into diverse evolutionary phenomena (Orr & Turelli 2001). But what else can we learn about the begetting of biodiversity, speciation, by considering explicitly some less convenient realities of natural populations? Specifically, how does genetic variation at incompatibility loci within a species influence interspecies hybridization upon secondary contact? And, in nature, how repeatable among distinct bouts of secondary contact are the genomic outcomes of hybridization? Mandeville et al. (2015) tackle exactly this question in their new study in Molecular Ecology on five species of suckers, fish of the genus Catostomus, that overlap sympatrically in different portions of their subdivided ranges that occupy different rivers. They document substantial genomic heterogeneity in realized hybridization in nature, both among species pairs and among the source populations for hybrids of a given species pair. This imperfect repeatability of episodes of hybridization implies greater permeability of species barriers in some parts of their range, with intriguing consequences for how the integrity of species as independently evolving units could be susceptible to collapse. 

Tu, S., M. Wu, J. Wang, A.D. Cutter, Z. Weng & J.M. Claycomb. 2015.Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes. Nucleic Acids Research43: 208-224. [pdf] [supplemental data]

As a champion of small RNA research for two decades, Caenorhabditis elegans has revealed the essential Argonaute CSR-1 to play key nuclear roles in modulating chromatin, chromosome segregation and germline gene expression via 22G-small RNAs. Despite CSR-1 being preserved among diverse nematodes, the conservation and divergence in function of the targets of small RNA pathways remains poorly resolved. Here we apply comparative functional genomic analysis between C. elegans and Caenorhabditis briggsae to characterize the CSR-1 pathway, its targets and their evolution. C. briggsae CSR-1-associated small RNAs that we identified by immunoprecipitation-small RNA sequencing overlap with 22G-RNAs depleted in cbr-csr-1 RNAi-treated worms. By comparing 22G-RNAs and target genes between species, we defined a set of CSR-1 target genes with conserved germline expression, enrichment in operons and more slowly evolving coding sequences than other genes, along with a small group of evolutionarily labile targets. We demonstrate that the association of CSR-1 with chromatin is preserved, and show that depletion of cbr-csr-1 leads to chromosome segregation defects and embryonic lethality. This first comparative characterization of a small RNA pathway in Caenorhabditis establishes a conserved nuclear role for CSR-1 and highlights its key role in germline gene regulation across multiple animal species.

Jovelin, R. & A.D. Cutter. 2014. Microevolution of nematode miRNAs reveals diverse modes of selection.
Genome Biology & Evolution. In press. [pdf]

Micro-RNA (miRNA) genes encode abundant small regulatory RNAs that play key roles during development and in homeostasis by fine-tuning and buffering gene expression. This layer of regulatory control over transcriptional networks is preserved by selection across deep evolutionary time, yet selection pressures on individual miRNA genes in contemporary populations remain poorly characterized in any organism. Here, we quantify nucleotide variability for 129 miRNAs in the genome of the nematode Caenorhabditis remanei to understand the micro-evolution of this important class of regulatory genes. Our analysis of three population samples and C. remanei's sister species revealed ongoing natural selection that constrains evolution of all sequence domains within miRNA hairpins. We also show that new miRNAs evolve faster than older miRNAs but that selection nevertheless favors their persistence. Despite the ongoing importance of purging of new mutations, we discover a trove of >400 natural miRNA sequence variants that include SNPs in seed motifs, indels that ablate miRNA functional domains, and origination of new miRNAs by duplication. Moreover, we demonstrate substantial nucleotide divergence of pre-miRNA hairpin alleles between populations and sister species. These findings from the first global survey of miRNA microevolution in Caenorhabditis support the idea that changes in gene expression, mediated through divergence in miRNA regulation, can contribute to phenotypic novelty and adaptation to specific environments in the present day as well as the distant past.  

Dey, A., Q. Jin, Y.-C. Chen & A.D. Cutter. 2014. Gonad morphogenesis defects drive hybrid male sterility in asymmetric hybrid breakdown of Caenorhabditis nematodes. Evolution & Development. 16: 362-372. [pdf]

Determining the causes and evolution of reproductive barriers to gene flow between populations, speciation, is the key to understanding the origin of diversity in nature. Many species manifest hybrid breakdown when they intercross, characterized by increasingly exacerbated problems in later generations of hybrids. Recently, Caenorhabditis nematodes have emerged as a genetic model for studying speciation, and here we investigate the nature and causes of hybrid breakdown between Caenorhabditis remanei and C. latens. We quantify partial F1 hybrid inviability and extensive F2 hybrid inviability; the ∼75% F2 embryonic arrest occurs primarily during gastrulation or embryonic elongation. Moreover, F1 hybrid males exhibit Haldane's rule asymmetrically for both sterility and inviability, being strongest when C. remanei serves as maternal parent. We show that the mechanism by which sterile hybrid males are incapable of transferring sperm or a copulatory plug involves defective gonad morphogenesis, which we hypothesize results from linker cell defects in migration and/or cell death during development. This first documented case of partial hybrid male sterility in Caenorhabditis follows expectations of Darwin's corollary to Haldane's rule for asymmetric male fitness, providing a powerful foundation for molecular dissection of intrinsic reproductive barriers and divergence of genetic pathways controlling organ morphogenesis.  

Ting, J.J.*, G.C. Woodruff*, G. Leung, N.-R. Shin, A.D. Cutter & E.S. Haag. 2014. Intense sperm-mediated sexual conflict promotes gametic isolation in Caenorhabditis nematodes. PLoS Biology. 12: e1001915. [pdf]
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Conflict between the sexes over reproductive interests can drive rapid evolution of reproductive traits and promote speciation. Here we show that inter-species mating between Caenorhabditis nematodes sterilizes maternal individuals. The principal effectors of male-induced harm are sperm cells, which induce sterility and shorten lifespan by displacing conspecific sperm, invading the ovary, and sometimes breaching the gonad to infiltrate other tissues. This sperm-mediated harm is pervasive across species, but idiosyncrasies in its magnitude implicate both independent histories of sexually antagonistic coevolution within species and differences in reproductive mode (self-fertilizing hermaphrodites versus females) in determining its severity. Consistent with this conclusion, in androdioecious species the hermaphrodites are more vulnerable, the males more benign, or both. Patterns of assortative mating and a low incidence of invasive sperm occurring with conspecific mating are indicative of ongoing intra-specific sexual conflict that results in inter-species reproductive incompatibility.  

Chen, Z.-X. ... A.D. Cutter ... S. Richards (63 authors). 2014. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research. 24: 1209-1223. [pdf]

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community. 

Felix, M.-A., C. Braendle & A.D. Cutter. 2014. A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species. PLoS One. 9: e97423. [pdf]

The rapid pace of species discovery outstrips the rate of species description in many taxa. This problem is especially acute for Caenorhabditis nematodes, where the naming of distinct species would greatly improve their visibility and usage for biological research, given the thousands of scientists studying Caenorhabditis. Species description and naming has been hampered in Caenorhabditis, in part due to the presence of morphologically cryptic species despite complete biological reproductive isolation and often enormous molecular divergence. With the aim of expediting species designations, here we propose and apply a revised framework for species diagnosis and description in this group. Our solution prioritizes reproductive isolation over traditional morphological characters as the key feature in delineating and diagnosing new species, reflecting both practical considerations and conceptual justifications. DNA sequence divergence criteria help prioritize crosses for establishing patterns of reproductive isolation among the many species of Caenorhabditis known to science, such as with the ribosomal internal transcribed spacer-2 (ITS2) DNA barcode. By adopting this approach, we provide new species name designations for 15 distinct biological species, thus increasing the number of named Caenorhabditis species in laboratory culture by nearly 3-fold. We anticipate that the improved accessibility of these species to the research community will expand the opportunities for study and accelerate our understanding of diverse biological phenomena.  

Gray, J.C. & A.D. Cutter. 2014. Mainstreaming C. elegans in experimental evolution. Proceedings B (Royal Society of London). 281: 20133055. [pdf]

Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with their own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as molecular genetics and systems biology. To date, C. elegans and related species have proven themselves in experimental evolution studies of the process of mutation, host-pathogen coevolution, mating system evolution, and life history theory. And yet, these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here we outline this experimental evolution work undertaken so far in Caenorhabditis, detail simple methodological tricks that can be exploited, and identify research areas that are ripe for future discovery.  

Li, S.*, R. Jovelin*, T. Yoshiga, R. Tanaka & A.D. Cutter. 2014. Specialist versus generalist life histories and nucleotide diversity in Caenorhabditis nematodes. Proceedings B (Royal Society of London). 281: 20132858. [pdf]

Species with broad ecological amplitudes with respect to a key focal resource, niche generalists, should maintain larger and more connected populations than niche specialists, leading to the prediction that nucleotide diversity will be lower and more subdivided in specialists relative to their generalist relatives. This logic describes the specialist-generalist variation hypothesis (SGVH). Some outbreeding species of Caenorhabditis nematodes use a variety of invertebrate dispersal vectors and have high molecular diversity. In contrast, Caenorhabditis japonica lives in a strict association and synchronized life cycle with its dispersal host, the shield bug Parastrachia japonensis, itself a diet specialist. Here we characterize sequence variation for 20 nuclear loci to investigate how C. japonica’s life history shapes nucleotide diversity. We find that C. japonica has >3-fold lower polymorphism than other outbreeding Caenorhabditis species, but that local populations are not genetically disconnected. Coupled with its restricted range, we propose that its specialist host association contributes to a smaller effective population size and lower genetic variation than host generalist Caenorhabditis species with outbreeding reproductive modes. A literature survey of diverse organisms provides broader support for the SGVH. These findings encourage further testing of ecological and evolutionary hypotheses with comparative population genetics in Caenorhabditis and other taxa. 

Dey, A., C.K.W. Chan, C.G. Thomas & A.D. Cutter. 2013. Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri. PNAS. 110: 11056-11060. [pdf]
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The biology of Sydney Brenner’s eponymous species of nematode, Caenorhabditis brenneri, is little known to science, despite its famous sibling Caenorhabditis elegans. Here we demonstrate that C. brenneri harbors the most molecular diversity of any eukaryote, with its 14.1% of polymorphic synonymous sites between individuals being 150-fold greater than humans and most comparable to hyperdiverse bacteria. This diversity is not an artifact of cryptic species divergence but reflects an enormous pan-tropical population, confirmed by fully viable genetic crosses between continents, extensive intralocus recombination, selection on codon use, and only weak geographic genetic structure. These findings in an animal galvanize tests of theory about the evolution of complexity in genomes and phenotypes and enable molecular population genetics methods to finely resolve uncharacterized functional noncoding elements. 

Gimond, C., R. JovelinS. Han, C. Ferrari, A.D. Cutter & C. Braendle. 2013. Outbreeding depression with low genetic variation in selfing Caenorhabditis nematodes. Evolution. 67: 3087-3101.  [pdf]

Theory and empirical study produce clear links between mating system evolution and inbreeding depression. The connections between mating systems and outbreeding depression, whereby fitness is reduced in crosses of less related individuals, however, are less well defined. Here we investigate inbreeding and outbreeding depression in self-fertile androdioecious nematodes, focusing on Caenorhabditis sp. 11. We quantify nucleotide polymorphism for nine nuclear loci for strains throughout its tropical range, and find some evidence of genetic differentiation despite the lowest sequence diversity observed in this genus. Controlled crosses between strains from geographically separated regions show strong outbreeding depression, with reproductive output of F1s reduced by 36% on average. Outbreeding depression is therefore common in self-fertilizing Caenorhabditis species, each of which evolved androdioecious selfing hermaphroditism independently, but appears strongest in C. sp. 11. Moreover, the poor mating efficiency of androdioecious males extends to C. sp. 11. We propose that self-fertilization is a key driver of outbreeding depression, but that it need not evolve as a direct result of local adaptation per se. Our verbal model of this process highlights the need for formal theory, and C. sp. 11 provides a convenient system for testing the genetic mechanisms that cause outbreeding depression, negative epistasis, and incipient speciation. 

Cutter, A.D. 2013. Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory. Molecular Phylogenetics and Evolution. 69: 1172-1185. [pdf]

Evolutionary theory is primed to synthesize microevolutionary processes with macroevolutionary divergence by taking advantage of multilocus multispecies genomic data in the molecular evolutionary analysis of biodiversity. While coalescent theory bridges across timescales to facilitate this integration, it is important to appreciate the assumptions, caveats, and recent theoretical advances so as to most effectively exploit genomic analysis. Here I outline the connections between population processes and phylogeny, with special attention to how genomic features play into underlying predictions. I discuss empirical and theoretical complications, and solutions, relating to recombination and multifurcating genealogical processes, predictions about how genome structure affects gene tree heterogeneity, and practical choices in genome sequencing and analysis. I illustrate the conceptual implications and practical benefits of how genomic features generate predictable patterns of discordance of gene trees and species trees along genomes, for example, as a consequence of how regions of low recombination and sex linkage interact with natural selection and with the accumulation of reproductive incompatibilities in speciation. Moreover, treating population genetic parameters as characters to be mapped onto phylogenies offers a new way to understand the evolutionary drivers of diversity within and differentiation between populations. Despite a number of challenges conferred by genomic information, the melding of phylogenetics, phylogeography and population genetics into integrative molecular evolution is poised to improve our understanding of biodiversity at all levels. 

Cutter, A.D. & B.A. Payseur. 2013. Genomic signatures of selection at linked sites: unifying the disparity among species. Nature Reviews Genetics. 14: 262-274. [pdf]

Population genetics theory supplies powerful predictions about how natural selection interacts with genetic linkage to sculpt the genomic landscape of nucleotide polymorphism. Both the spread of beneficial mutations and the removal of deleterious mutations act to depress polymorphism levels, especially in low-recombination regions. However, empiricists have documented extreme disparities among species. Here we characterize the dominant features that could drive differences in linked selection among species — including roles for selective sweeps being 'hard' or 'soft' — and the concealing effects of demography and confounding genomic variables. We advocate targeted studies of closely related species to unify our understanding of how selection and linkage interact to shape genome evolution. 

Jovelin, R. & A.D. Cutter. 2013. Fine-scale signatures of molecular evolution reconcile models of indel-associated mutation. Genome Biology and Evolution. 5: 978-986. [pdf]

Genomic structural alterations that vary within species, known as large copy number variants, represent an unanticipated and abundant source of genetic diversity that associates with variation in gene expression and susceptibility to disease. Even short insertions and deletions (indels) can exert important effects on genomes by locally increasing the mutation rate, with multiple mechanisms proposed to account for this pattern. To better understand how indels promote genome evolution, we demonstrate that the single nucleotide mutation rate is elevated in the vicinity of indels, with a resolution of tens of base pairs, for the two closely related nematode species Caenorhabditis remanei and C. sp. 23. In addition to indels being clustered with single nucleotide polymorphisms and fixed differences, we also show that transversion mutations are enriched in sequences that flank indels and that many indels associate with sequence repeats. These observations are compatible with a model that reconciles previously proposed mechanisms of indel-associated mutagenesis, implicating repeat sequences as a common driver of indel errors, which then recruit error-prone polymerases during DNA repair, resulting in a locally elevated single nucleotide mutation rate. The striking influence of indel variants on the molecular evolution of flanking sequences strengthens the emerging general view that mutations can induce further mutations. 

Cutter, A.D., R. Jovelin & A. Dey. 2013. Molecular hyperdiversity and evolution in very large populations. Molecular Ecology. 22: 2074-2095. [pdf]

The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements. 

Jovelin, R., A. Dey, & A.D. Cutter. 2013. Fifteen years of evolutionary genomics in Caenorhabditis elegans. In: Encyclopedia of Life Sciences. John Wiley & Sons (Chichester). [pdf]

The nematode worm Caenorhabditis elegans, introduced by Sydney Brenner for the genetic analysis of nervous system formation, is now a powerful model organism for studying nearly all aspects of biology, from development to diseases to evolution. Sequencing and analysis of the worm genome revealed intriguing nonrandom patterns of genome organisation and unusual features such as abundant operons. Surprising upon first discovery, worms and humans have a similar number of genes that are comprised of a similar proportion of transcription factors to regulate their genomes. However, differences in small ribonucleic acid content may contribute to differences in organismal complexity. In nature, the bacterivorous C. elegans is found primarily on rotting vegetation in temperate regions across the world. Natural selection, combined with the low effective recombination rate associated with selfing, strongly reduces nucleotide variation across the genome, yielding similarly low polymorphism to other selfing hermaphrodite species of Caenorhabditis. The genus Caenorhabditis provides a superb model system for ecological and evolutionary genetics, benefiting from C. elegans tools and information when applied to investigations of species with a higher polymorphism and better known ecological context. 

Felix, M.A., R. Jovelin, C. Ferrari, S. Han, Y.R. Cho, E.C. Andersen, A.D. Cutter & C. Braendle. 2013. Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest. BMC Evolutionary Biology. 13: 10. [pdf]

In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species. 

Stegeman, G.W., M. Bueno de Mesquita, W.S. Ryu & A.D. Cutter. 2013. Temperature-dependent behaviors are genetically variable in the nematode Caenorhabditis briggsaeJournal of Experimental Biology. 216: 850-858. [pdf]

Temperature-dependent behaviours in Caenorhabditis elegans, such as thermotaxis and isothermal tracking, are complex behavioural responses that integrate sensation, foraging and learning, and have driven investigations to discover many essential genetic and neural pathways. The ease of manipulation of the Caenorhabditis model system also has encouraged its application to comparative analyses of phenotypic evolution, particularly contrasts of the classic model C. elegans with C. briggsae. And yet few studies have investigated natural genetic variation in behaviour in any nematode. Here we measure thermotaxis and isothermal tracking behaviour in genetically distinct strains of C. briggsae, further motivated by the latitudinal differentiation in C. briggsae that is associated with temperature-dependent fitness differences in this species. We demonstrate that C. briggsae performs thermotaxis and isothermal tracking largely similar to that of C. elegans, with a tendency to prefer its rearing temperature. Comparisons of these behaviours among strains reveal substantial heritable natural variation within each species that corresponds to three general patterns of behavioural response. However, intraspecific genetic differences in thermal behaviour often exceed interspecific differences. These patterns of temperature-dependent behaviour motivate further development of C. briggsae as a model system for dissecting the genetic underpinnings of complex behavioural traits. 

Dey, A., Y. Jeon, G.-X. Wang & A.D. Cutter. 2012. Global population genetic structure of Caenorhabditis remanei reveals incipient speciation. Genetics. 191: 1257-1269. [pdf]

Mating system transitions dramatically alter the evolutionary trajectories of genomes that can be revealed by contrasts of species with disparate modes of reproduction. For such transitions in Caenorhabditis nematodes, some major causes of genome variation in selfing species have been discerned. And yet, we have only limited understanding of species-wide population genetic processes for their outcrossing relatives, which represent the reproductive state of the progenitors of selfing species. Multilocus-multipopulation sequence polymorphism data provide a powerful means to uncover the historical demography and evolutionary processes that shape genomes. Here we survey nucleotide polymorphism across the X chromosome for three populations of the outcrossing nematode C. remanei and demonstrate its divergence from a fourth population describing a closely-related new species from China, C. sp. 23. We find high genetic variation globally and within each local population sample. Despite geographic barriers and moderate genetic differentiation between Europe and North America, considerable gene flow connects C. remanei populations. We discovered C. sp. 23 while investigating C. remanei, observing strong genetic differentiation characteristic of reproductive isolation that was confirmed by substantial F2 hybrid breakdown in inter-specific crosses. That C. sp. 23 represents a distinct biological species provides a cautionary example of how standard practice can fail for mating tests of species identity in this group. This species pair permits full application of divergence population genetic methods to obligately-outcrossing species of Caenorhabditis and also presents a new focus for interrogation of the genetics and evolution of speciation with the Caenorhabditis model system. 

Cutter, A.D., G.-X. Wang, H. Ai, & Y. Peng. 2012. Influence of finite-sites mutation, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversityMolecular Ecology. 21: 1345-1359. [pdf]

Molecular hyperdiversity has been documented in viruses, prokaryotes and eukaryotes. Such organisms undermine the assumptions of the infinite-sites mutational model, because multiple mutational events at a site comprise a non-negligible portion of polymorphisms. Moreover, different sampling schemes of individuals from species with subdivided populations can profoundly influence resulting patterns and interpretations of molecular variation. Inspired by molecular hyperdiversity in the nematode Caenorhabditis sp. 5, which exhibits average pairwise differences among synonymous sites of >5% as well as modest population structure, we investigated via coalescent simulation the joint effects of a finite-sites mutation (FSM) process and population subdivision on the variant frequency spectrum. From many demes interconnected through a stepping-stone migration model, we constructed local samples from a single deme, pooled samples from several demes and scattered samples of a single individual from numerous demes. Compared with a single panmictic population at equilibrium, we find that high population mutation rates induce a deficit of rare variants (positive Tajima’s D) under a FSM model. Population structure also induces such a skew for local samples when migration is high and for pooled samples when migration is low. Contrasts of sampling schemes for C. sp. 5 imply high mutational input coupled with high migration. We propose that joint analysis of local, pooled and scattered samples for species with subdivided populations provides a means of improving inference of demographic history, by virtue of the partially distinct patterns of polymorphism that manifest when sequences are analyzed according to differing sampling schemes. 

Wyman, M.J., A.D. Cutter & L. Rowe. 2012. Gene duplication in the evolution of sexual dimorphism. Evolution. 66: 1556-1566. [pdf]

Males and females share most of the same genes, so selection in one sex will typically produce a correlated response in the other sex. Yet, the sexes have evolved to differ in a multitude of behavioral, morphological, and physiological traits. How did this sexual dimorphism evolve despite the presence of a common underlying genome? We investigated the potential role of gene duplication in the evolution of sexual dimorphism. Because duplication events provide extra genetic material, the sexes each might use this redundancy to facilitate sex-specific gene expression, permitting the evolution of dimorphism. We investigated this hypothesis at the genome-wide level in Drosophila melanogaster, using the presence of sex-biased expression as a proxy for the sex-specific specialization of gene function. We expected that if sexually antagonistic selection is a potent force acting upon individual genes, duplication will result in paralog families whose members differ in sex-biased expression. Gene members of the same duplicate family can have different expression patterns in males versus females. In particular, duplicate pairs containing a male-biased gene are found more frequently than expected, in agreement with previous studies. Furthermore, when the singleton ortholog is unbiased, duplication appears to allow one of the paralog copies to acquire male-biased expression. Conversely, female-biased expression is not common among duplicates; fewer duplicate genes are expressed in the female-soma and ovaries than in the male-soma and testes. Expression divergence exists more in older than in younger duplicates pairs, but expression divergence does not correlate with protein sequence divergence. Finally, genomic proximity may have an effect on whether paralogs differ in sex-biased expression. We conclude that the data are consistent with a role of gene duplication in fostering male-biased, but not female-biased, gene expression, thereby aiding the evolution of sexual dimorphism. 

Cutter, A.D. 2012. The polymorphic prelude to Bateson-Dobzhansky-Muller incompatibilities. Trends in Ecology & Evolution. 27: 209-218. [pdf]

Speciation research has largely assumed that the genetic causes of reproductive isolation are the work of fixed, divergent alleles that interact to cause genetic problems in hybrids: Bateson–Dobzhansky–Muller incompatibilities. However, many recent studies demonstrate substantial heritable polymorphism within species for hybrid incompatibility, herein called variable reproductive isolation (VRI). In this review, I outline the causes and importance of this general phenomenon. I also identify the new challenges of quantifying the relative contributions to reproductive isolation of fixed alleles versus polymorphisms, and the change in these contributions over the course of speciation. Explicit integration of VRI into speciation theory will help to quantify the relative roles of genetic drift and selection in speciation, but this synthesis requires substantial new contributions from both theory and empirical studies. 

Kozlowska, J.L., A.R. Ahmad, E. Jahesh & A.D. Cutter. 2012. Genetic variation for post-zygotic reproductive isolation between Caenorhabditis briggsae and Caenorhabditis sp. 9. Evolution. 66: 1180-1195. [pdf]

The process of speciation is key to the origins of biodiversity, and yet the Caenorhabditis nematode model system has contributed little to this topic. Genetic studies of speciation in the genus are now feasible, owing to crosses between the recently discovered Caenorhabditis sp. 9 and the well-known C. briggsae producing fertile F1 hybrid females. We dissected patterns of postzygotic reproductive isolation between these species by crossing eight isogenic strains of C. briggsae reciprocally with six strains of C. sp. 9. We determined that overall patterns of reproductive isolation are robust across these genetic backgrounds. However, we also quantified significant heritable variation within each species for interspecific hybrid incompatibilities for total adult progeny, egg-to-adult viability, and the percentage of male progeny. This demonstrates that intraspecific variation for interspecific hybrid incompatibility occurs despite extensive, albeit incomplete, reproductive isolation. Therefore, this emerging general phenomenon of variable reproductive isolation is not restricted to highly interfertile, early-stage incipient species, but also applies to species in the latest stages of the speciation process. Furthermore, we confirm Haldane's rule and demonstrate strongly asymmetric parent-of-origin effects (Darwin's corollary) that consistently manifest more extremely when hermaphroditic C. briggsae serves as maternal parent. These findings highlight Caenorhabditis as an emerging system for understanding the genetics of general patterns of reproductive isolation. 

Jovelin, R. & A.D. Cutter. 2011. MicroRNA sequence variation potentially contributes to within-species functional divergence in the nematode Caenorhabditis briggsae. Genetics189: 967-976. [pdf]

Mounting evidence points to differences in gene regulation as a major source of phenotypic variation. MicroRNA-mediated post-transcriptional regulation, in particular, has emerged recently as a key factor controlling gene activity during development. MicroRNA genes are abundant in genomes, acting as managers of gene expression by directing translational repression. Thus, understanding the role of microRNA sequence variation within populations is essential for dissecting the origin and maintenance of phenotypic diversity in nature. In this study, we investigate naturally-occurring allelic variation at microRNA loci in the nematode Caenorhabditis briggsae, a close relative of C. elegans. Phylogeographic structure in C. briggsae partitions most strains from around the globe into a “temperate” or a “tropical” clade, with a few strains having divergent, geographically-restricted genotypes. Remarkably, strains that follow this latitudinal dichotomy also differ in temperature-associated fitness. With this phylogeographic pattern in mind, we examined polymorphisms in 18 miRNAs in a global sample of C. briggsae isolates and tested whether newly-isolated strains conform to this phylogeography. By quantifying levels of allelic variation and identifying divergent alleles, we demonstrate unexpected nucleotide diversity in this class of genes that generally experiences strong purifying selection. We find that half of the polymorphisms are found specifically in those few strains from geographically-restricted locations and that some mutations suggest functional divergence, based on computational prediction of the effects of the polymorphisms on RNA folding. These findings demonstrate the potential for miRNA polymorphisms to contribute to phenotypic variation within a species. 

Murray, R.L., J.L. Kozlowska & A.D. Cutter. 2011. Heritable determinants of male fertilization success in the nematode Caenorhabditis elegans. BMC Evolutionary Biology. 11:99. [pdf]

Sperm competition is a driving force in the evolution of male sperm characteristics in many species. In the nematode Caenorhabditis elegans, larger male sperm evolve under experimentally increased sperm competition and larger male sperm outcompete smaller hermaphrodite sperm for fertilization within the hermaphrodite reproductive tract. To further elucidate the relative importance of sperm-related traits that contribute to differential reproductive success among males, we quantified within- and among-strain variation in sperm traits (size, rate of production, number transferred, competitive ability) for seven male genetic backgrounds known previously to differ with respect to some sperm traits. We also quantified male mating ability in assays for rates of courtship and successful copulation, and then assessed the roles of these pre- and post-mating traits in first- and second-male fertilization success. We document significant variation in courtship ability, mating ability, sperm size and sperm production rate.  Sperm size and production rate were strong indicators of early fertilization success for males that mated second, but male genetic backgrounds conferring faster sperm production make smaller sperm, despite virgin males of all genetic backgrounds transferring indistinguishable numbers of sperm to mating partners. We have demonstrated that sperm size and the rate of sperm production represent dominant factors in determining male fertilization success and that C. elegans harbors substantial heritable variation for traits contributing to male reproductive success. C. elegans provides a powerful, tractable system for studying sexual selection and for dissecting the genetic basis and evolution of reproduction-related traits. 

Murray, R.L. & A.D. Cutter. 2011. Experimental evolution of sperm count in protandrous self-fertilizing hermaphrodites. Journal of Experimental Biology. 214: 1740-1747. [pdf]

Sperm count evolution is driven by sexual selection, with an added role of selection on gamete resource allocation for hermaphrodite spermatogenesis. However, self-fertilization by hermaphrodites retards sexual selection and results in the evolution of reduced investment in sperm or pollen and, contrasting with reproduction limited by female gametes (Bateman's Principle), Caenorhabditis elegans self-fertilizing hermaphrodites exhibit sperm-limited reproduction. C. elegans hermaphrodites are thought to experience a fitness trade-off between lifetime fecundity and generation time: longer sperm production decreases the risk of self-sperm depletion, but at the same time delays the onset of selfing and thus increases egg-to-egg generation time. Theory predicts that shorter larval development will favor lower sperm counts and longer development will favor more sperm. To investigate how developmental trajectories affect the evolution of sperm production, we performed experimental evolution by directly competing alleles controlling hermaphrodite sperm count, conducted under different environmental conditions that alter development time. Results are partially consistent with theory, where rapid larval development generally favored alleles encoding production of few sperm. However, we identify some previously-unrecognized simplifications of the theory and its application to our experimental system. In addition, we evaluated the generality of sperm-limitation in C. elegans. Although optimal growth conditions yield sperm-limitation, non-optimal conditions induce oocyte-limitation, suggesting that this species might conform to Bateman's Principle under many natural settings. These findings demonstrate how developmental trajectories can shape the fitness landscape for the evolution of reproduction and sperm traits, even without sexual selection.

Cutter, A.D. & A.M. Moses. 2011. Polymorphism, divergence and the role of recombination in Saccharomyces cerevisiae genome evolutionMolecular Biology and Evolution. 28: 1745-1754. [pdf]

A contentious issue in molecular evolution and population genetics concerns the roles of recombination as a facilitator of natural selection and as a potential source of mutational input into genomes. The budding yeast Saccharomyces cerevisiae, in particular, has injected both insights and confusion into this topic, as an early system subject to genomic analysis with subsequent conflicting reports. Here, we revisit the role of recombination in mutation and selection with recent genome-wide maps of population polymorphism and recombination for S. cerevisiae. We confirm that recombination-associated mutation (RAM) does not leave a genomic signature in yeast, and conclude that a previously-observed, enigmatic, negative recombination-divergence correlation is largely a consequence of weak selection and other genomic covariates. We also corroborate the presence of biased gene conversion from patterns of polymorphism. Moreover, we identify significant positive relations between recombination and population polymorphism at putatively neutrally-evolving sites, independent of other factors and the genomic scale of interrogation. We conclude that widespread natural selection across the yeast genome has left its imprint on segregating genetic variation, but that this signature is much weaker than in Drosophila and Caenorhabditis.

Prasad, A., M. Croydon-Sugarman, R.L. Murray & A.D. Cutter. 2011. Temperature-dependent fecundity associates with latitude in Caenorhabditis briggsae. Evolution. 65: 52-63. [pdf]

Populations of organisms separated by latitude provide striking examples of local adaptation, by virtue of ecological gradients that correlate with latitudinal position on the globe. Ambient temperature forms one key ecological variable that varies with latitude, and here we investigate its effects on the fecundity of self-fertilizing nematodes of the species Caenorhabditis briggsae that exhibits strong genetically-based differentiation in association with latitude. We find that isogenic strains from a Tropical phylogeographic clade have greater lifetime fecundity when reared at extreme high temperatures and lower lifetime fecundity at extreme low temperatures than do strains from a Temperate phylogeographic clade, consistent with adaptation to local temperature regimes. Further, we determine experimentally that the mechanism underlying reduced fecundity at extreme temperatures differs for low versus high temperature extremes, but that the total number sperm produced by the gonad is unaffected by rearing temperature. Low rearing temperatures result in facultatively reduced oocyte production by hermaphrodites, whereas extreme high temperatures experienced during development induce permanent defects in sperm fertility. Available and emerging genetic tools for this organism will permit the characterization of the evolutionary genetic basis to this putative example of adaptation in latitudinally-separated populations. 

Wang, G.-X., S. Ren, Y. Ren, H. Ai & A.D. Cutter. 2010. Extremely high molecular diversity within the East Asian nematode Caenorhabditis sp. 5. Molecular Ecology. 19: 5022-5029. [pdf] 

Most relatives of the self-fertilizing hermaphroditic nematode model organism Caenorhabditis elegans reproduce via obligate outbreeding between males and females, which also represents the ancestral mode of reproduction within the genus. However, little is known about the scope of genetic diversity and differentiation within such gonochoristic species, especially those found outside of temperate Europe and North America. It is critical to understand the evolutionary processes operating in these species to provide a framework for deciphering the evolution of hermaphroditism and a baseline for the application of outcrossing Caenorhabditis to diverse problems in evolutionary genetics. Here we investigate for the first time molecular sequence variation for Caenorhabditis sp. 5, a species found commonly in eastern Asia. We identify enormous levels of standing genetic variation that approach the levels observed in the marine broadcast-spawning sea squirt, Ciona savignyi. Although we document significant isolation by distance, we demonstrate that the high polymorphism within C. sp. 5 is not due to strong differentiation among populations or to the presence of cryptic species. These findings illustrate that molecular population genetic approaches to studying obligately outbreeding species of Caenorhabditis will prove powerful in identifying and characterizing functionally and evolutionarily important features of the genome. 

Cutter, A.D. & J.Y. Choi. 2010. Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsaeGenome Research. 20: 1103-1111. [pdf

The combined action of natural selection, mutation and recombination forge the landscape of genetic variation across genomes. One frequently-observed manifestation of these processes is a positive association between neutral genetic variation and local recombination rates. Two selective mechanisms and/or recombination-associated mutation (RAM) could generate this pattern, and the relative importance of these alternative possibilities remains unresolved generally. Here we quantify nucleotide differences within populations, between populations, and between species to test for genome-wide effects of selection and RAM in the partially-selfing nematode Caenorhabditis briggsae. We find that nearly half of genome-wide variation in nucleotide polymorphism is explained by differences in local recombination rates. By quantifying divergence between several reproductively-isolated lineages, we demonstrate that ancestral polymorphism generates a spurious signal of RAM for closely-related lineages, with implications for analyses of humans and primates; RAM is, at most, a minor factor in C. briggsae. We conclude that the positive relation between nucleotide polymorphism and the rate of crossover represents the footprint of natural selection across the C. briggsae genome and demonstrate that background selection against deleterious mutations is sufficient to explain this pattern. Hill-Robertson interference also leaves a signature of more effective purifying selection in high-recombination regions of the genome. Finally, we identify an emerging contrast between widespread adaptive hitchhiking effects in species with large outcrossing populations (e.g. Drosophila) versus pervasive background selection effects on the genomes of organisms with self-fertilizing lifestyles and/or small population sizes (e.g. C. elegans, C. briggsae, Arabidopsis thaliana, Lycopersicon, human). These results illustrate how recombination, mutation, selection and population history interact in important ways to shape molecular heterogeneity within and between genomes. 

Cutter, A.D. & A.F. Agrawal. 2010. The evolutionary dynamics of operon distributions in eukaryote genomes. Genetics. 185: 685-693.[pdf]

Genes in nematode and ascidian genomes frequently occur in operons – multiple genes sharing a common promoter to generate a polycistronic primary transcript – and such genes comprise 15-20% of the coding genome for Caenorhabditis elegans and Ciona intestinalis. Recent work in nematodes has demonstrated that the identity of genes within operons are highly conserved among species and that the unifying feature of genes within operons is that they are expressed in germline tissue. However, it is generally unknown what processes are responsible for generating the distribution of operon sizes across the genome, which are comprised of up to 8 genes per operon. Here we investigate several models for operon evolution to better understand their abundance, distribution of sizes, and evolutionary dynamics over time. We find that birth-death models of operon evolution reasonably describe the relative abundance of operons of different sizes in the C. elegans and Ciona genomes and generate predictions about the number of monocistronic, non-operon genes that likely participate in the birth-death process. This theory, and applications to C. elegans and Ciona, motivates several new and testable hypotheses about eukaryote operon evolution. 

Cutter, A.D. 2010. Molecular evolution inferences from the C. elegans genome. In: WormBook, The C. elegans Research Community, ed. doi/10.1895/wormbook.1.149.1 [pdf

An understanding of evolution at the molecular level requires the simultaneous consideration of the 5 fundamental evolutionary processes: mutation, recombination, natural selection, genetic drift, and population dynamic effects. Experimental, comparative genomic, and population genetic work in C. elegans has greatly expanded our understanding of these core processes, as well as of C. elegans biology. This chapter presents a brief overview of some of the most salient features of molecular evolution elucidated by the C. elegans system. 

Cutter, A.D., W. Yan, N. Tsvetkov, S. Sunil & M.A. Felix. 2010. Molecular population genetics and phenotypic sensitivity to ethanol for a globally diverse sample of the nematode Caenorhabditis briggsae. Molecular Ecology. 19: 798-809. [pdf]  

New genomic resources and genetic tools of the past few years have advanced the nematode genus Caenorhabditis as a model for comparative biology. However, understanding of natural genetic variation at molecular and phenotypic levels remains rudimentary for most species in this genus, and for C. briggsae in particular. Here we characterize phenotypic variation in C. briggsae's sensitivity to the potentially important and variable environmental toxin, ethanol, for globally-diverse strains. We also quantify nucleotide variation in a new sample of 32 strains from four continents, including small islands, and for the closest-known relative of this species (C. sp. 9). We demonstrate that C. briggsae exhibits little heritable variation for the effects of ethanol on the norm of reaction for survival and reproduction and, moreover, that C. briggsae does not differ significantly from C. elegans in its response to this substance that they likely encounter regularly in habitats of rotting fruit and vegetation. However, we uncover drastically more molecular genetic variation than was known previously for this species, despite most strains, including all island strains, conforming to the broad biogeographic patterns described previously. Using patterns of sequence divergence between populations and between species, we estimate that the self-fertilizing mode of reproduction by hermaphrodites in C. briggsae likely evolved sometime between 0.9 - 10 million generations ago. These insights into C. briggsae's natural history and natural genetic variation greatly expand the potential of this organism as an emerging model for studies in molecular and quantitative genetics, the evolution of development, and ecological genetics. 

Cutter, A.D., A. Dey & R.L. Murray. 2009. Evolution of the C. elegans genomeMolecular Biology & Evolution. 26: 1199-1234. [pdf

A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating non-random patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, C. elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution, and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess non-adaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns. 

Reinke, V. & A.D. Cutter. 2009. Germline expression influences operon organization in the C. elegans genome. Genetics. 181: 1219-1228. [pdf] [supplementary data]

Operons are found across multiple kingdoms and phyla, from prokaryotes to chordates. In the nematode C. elegans, the genome contains over 1000 operons that comprise roughly 15% of the protein-coding genes. However, determination of the force(s) promoting the origin and maintenance of operons in C. elegans has proved elusive. Compared to bacterial operons, genes within a C. elegans operon often show poor co-expression and only sometimes encode proteins with related functions. Using analysis of microarray and large-scale in situ hybridization data, we demonstrate that almost all operon-encoded genes are expressed in germline tissue. However, genes expressed during spermatogenesis are excluded from operons. Operons group together along chromosomes in local clusters that also contain monocistronic germline-expressed genes. Additionally, germline expression of genes in operons is largely independent of the molecular function of the encoded proteins. These analyses demonstrate that mechanisms governing germline gene expression influence operon origination and/or maintenance. Thus, gene expression in a specific tissue can have profound effects on the evolution of genome organization.

Cutter, A.D. 2008. Reproductive evolution: symptom of a selfing syndrome (Dispatch). Current Biology. 18: R1056-R1058. [pdf]

In the nematode Caenorhabditis elegans, a single gene (plg-1) encodes the dominant protein found in mating-plugs -- a means of inhibiting multiple matings. Naturally occurring loss of plg-1 function results in males that fail to deposit mating plugs -- a manifestation of relaxed sexual selection since the evolution of self-fertilization in this species.

Dolgin, E.S., B. Charlesworth & A.D. Cutter. 2008. Population frequencies of transposable elements in selfing and outcrossing Caenorhabditis nematodes. Genetics Research. 90: 317-329.  [pdf]

Population genetics theory predicts that differences in breeding systems should be an important factor in the dynamics of selfish genetic elements, because of different intensities of selection on both hosts and elements. We examined population frequencies of transposable elements in natural populations of the self-fertilising nematode Caenorhabditis elegans and its outcrossing relative C. remanei. We identified a Tc1-like class of elements in the C. remanei genome with homology to the terminal inverted repeats of the C. elegans Tc1 transposon, which we name mTcre1. We measured levels of insertion polymorphism for all 32 Tc1 elements present in the genome sequence of the C. elegans N2 strain, and 16 mTcre1 elements from the genome sequence of the C. remanei PB4641 strain. We show that transposons are less polymorphic and segregate at higher frequencies in C. elegans compared with C. remanei. Estimates of the intensity of selection based on the population frequencies of polymorphic elements suggest that transposons are selectively neutral in C. elegans, but subject to purifying selection in C. remanei. These results are consistent with a reduced efficacy of natural selection against transposable elements in selfing populations, but may in part be explained by non-equilibrium TE dynamics.

Loewe, L. & A.D. Cutter. 2008. On the potential for extinction by Muller's ratchet in Caenorhabditis elegans. BMC Evolutionary Biology. 8: 125. [pdf]

The self-fertile hermaphrodite worm C. elegans is an important model organism for biology, yet little is known about the origin and persistence of the self-fertilizing mode of reproduction in this lineage. Recent work has demonstrated an extraordinary degree of selfing combined with a high deleterious mutation rate in contemporary populations. These observations raise the question as to whether the mutation load might rise to such a degree as to eventually threaten the species with extinction. The potential for such a process to occur would inform our understanding of the time since the origin of self-fertilization in C. elegans history. To address this issue, here we quantify the rate of fitness decline expected to occur via Muller's ratchet for a purely selfing population, using both analytical approximations and globally distributed individual-based simulations from the evolution@home system to compute the rate of deleterious mutation accumulation. Using the best available estimates for parameters of how C. elegans evolves, we conclude that pure selfing can persist for only short evolutionary intervals, and is expected to lead to extinction within thousands of years for a plausible portion of parameter space. Credible lower-bound estimates of nuclear mutation rates do not extend the expected time to extinction much beyond a million years. Thus we conclude that either the extreme self-fertilization implied by current patterns of genetic variation in C. elegans arose relatively recently or that low levels of outcrossing and other factors are key to the persistence of C. elegans into the present day. We also discuss results for the mitochondrial genome and the implications for C. briggsae, a close relative that made the transition to selfing independently of C. elegans

Cutter, A.D. 2008. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Molecular Biology & Evolution. 25: 778-786. [pdf] [supplementary tables]

Accurate inference of the dates of common ancestry among species forms a central problem in understanding the evolutionary history of organisms. Molecular estimates of divergence time rely on the molecular evolutionary prediction that neutral mutations and substitutions occur at the same constant rate in genomes of related species. This underlies the notion of a molecular clock. Most implementations of this idea depend on paleontological calibration to infer dates of common ancestry, but taxa with poor fossil records must rely on external, potentially inappropriate, calibration with distantly related species. The classic biological models Caenorhabditis and Drosophila are examples of such problem taxa. Here, I illustrate internal-calibration in these groups with direct estimates of the mutation rate from contemporary populations that are corrected for interfering effects of selection on the assumption of neutrality of substitutions. Divergence times are inferred among six species each of Caenorhabditis and Drosophila based on thousands of orthologous groups of genes. I propose that the two closest known species of Caenorhabditis shared a common ancestor <24 Mya (C. briggsae and C. sp. 5) and that C. elegans diverged from its closest known relatives <30 Mya, assuming that these species pass through at least 6 generations per year; these estimates are much more recent than reported previously with molecular clock calibrations from non-nematode phyla. Dates inferred for the common ancestor of D. melanogaster and D. simulans are roughly concordant with previous studies. These revised dates have important implications for rates of genome evolution and the origin of self-fertilization in Caenorhabditis.

Cutter, A.D., J.D. Wasmuth & N.L. Washington. 2008. Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing. Genetics. 178: 2093-2104. [pdf] [supplementary data]

The evolution of self-fertilization can mediate pronounced changes in genomes as a byproduct of a drastic reduction in effective population size and the concomitant accumulation of slightly deleterious mutations by genetic drift. In the nematode genus Caenorhabditis, a highly selfing lifestyle has evolved twice independently, thus permitting an opportunity to test for the effects of mode of reproduction on patterns of molecular evolution on a genomic scale. Here we contrast rates of nucleotide substitution and codon usage bias among thousands of orthologous groups of genes in six species of Caenorhabditis, including the classic model organism C. elegans. Despite evidence that weak selection on synonymous codon usage is pervasive in the history of all species in this genus, we find little difference among species in the patterns of codon usage bias and in replacement-site substitution. Applying a model of relaxed selection on codon usage to the C. elegans and C. briggsae lineages suggests that self-fertilization is unlikely to have evolved more than ~4 million years ago, which is less than a quarter of the time since they shared a common ancestor with outcrossing species. We conclude that the profound changes in mating behavior, physiology, and developmental mechanisms that accompanied the transition from an obligately outcrossing to primarily selfing mode of reproduction evolved in the not-too-distant past.

Cutter, A.D. 2008. Multilocus patterns of polymorphism and selection across the X-chromosome of Caenorhabditis remanei. Genetics. 178: 1661-1672. [pdf] [supplementary tables]

Natural selection and neutral processes such as demography, mutation, and gene conversion, all contribute to patterns of polymorphism within genomes. Identifying the relative importance of these varied components in evolution provides the principle challenge for population genetics. To address this issue in the nematode Caenorhabditis remanei, I sampled nucleotide polymorphism at 40 loci across the X-chromosome. The site frequency spectrum for these loci provide no evidence for population size change, and one locus presents a candidate for linkage to a target of balancing selection. Selection for codon usage bias leads to the non-neutrality of synonymous sites, and despite its weak magnitude of effect (Nes ~ 0.1), is responsible for profound patterns of diversity and divergence in the C. remanei genome. Although gene conversion is evident for many loci, biased gene conversion is not identified as a significant evolutionary process in this sample. No consistent association is observed between synonymous-site diversity and linkage disequilibrium-based estimators of the population recombination parameter, despite theoretical predictions about background selection or widespread genetic hitchhiking, but genetic map-based estimates of recombination are needed to rigorously test for a diversity-recombination relationship. Coalescent simulations also illustrate how a spurious correlation between diversity and linkage disequilibrium-based estimators of recombination can occur, due in part to the presence of unbiased gene conversion. These results illustrate the influence that subtle natural selection can exert on polymorphism and divergence, in the form of codon usage bias, and demonstrate the potential of C. remanei for detecting natural selection from genomic scans of polymorphism.

Dolgin, E.S., M.A. Felix & A.D. Cutter. 2008. Hakuna nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae. Heredity. 100: 304-315. [pdf]

Caenorhabditis elegans and C. briggsae have many parallels in terms of morphology, life history and breeding system. Both species also share similar low levels of molecular diversity, although the global sampling of natural populations has been limited and geographically biased. In this study, we describe the first cultured isolates of C. elegans and C. briggsae from sub-Saharan Africa. We characterize these samples for patterns of nucleotide polymorphism and vulva precursor cell lineage, and conduct a series of hybrid crosses in C. briggsae to test for genetic incompatibilities. The distribution of genetic diversity confirms a lack of geographic structure to C. elegans sequences but shows genetic differentiation of C. briggsae into three distinct clades that may correspond to three latitudinal ranges. Despite low levels of molecular diversity, we find considerable variation in cell division frequency in African C. elegans for the P3.p vulva precursor cell, and in African C. briggsae for P4.p, a variation that was not previously observed in this species. Hybrid crosses did not reveal major incompatibilities between C. briggsae strains from Africa and elsewhere, and there was some evidence of inbreeding depression. These new African isolates suggest that important ecological factors may be shaping the patterns of diversity in C. briggsae, and that despite many similarities between C. elegans and C. briggsae, there may be more subtle differences in their natural histories than previously appreciated.

Dolgin, E.S., B. Charlesworth, S.E. Baird & A.D. Cutter. 2007. Inbreeding and outbreeding depression in Caenorhabditis nematodes. Evolution. 61: 1339-1352. [pdf]

The nematode Caenorhabditis elegans reproduces primarily by self-fertilization of hermaphrodites, yet males are present at low frequencies in natural populations (androdioecy). The ancestral state of C. elegans was probably gonochorism (separate males and females), as in its relative C. remanei. Males may be maintained in C. elegans because outcrossed individuals escape inbreeding depression. The level of inbreeding depression is, however, expected to be low in such a highly selfing species, compared with an outcrosser like C. remanei. To investigate these issues, we measured life-history traits in the progeny of inbred versus outcrossed C. elegans and C. remanei individuals derived from recently isolated natural populations. In addition, we maintained inbred lines of C. remanei through 13 generations of full-sib mating. Highly inbred C. remanei showed dramatic reductions in brood size and relative fitness compared to outcrossed individuals, with evidence of both direct genetic and maternal-effect inbreeding depression. This decline in fitness accumulated over time, causing extinction of nearly 90% of inbred lines, with no evidence of purging of deleterious mutations from the remaining lines. In contrast, pure strains of C. elegans performed better than crosses between strains, indicating outbreeding depression. The results are discussed in relation to the evolution of androdioecy and the effect of mating system on the level of inbreeding depression.

LaMunyon, C., O. Bouban & A.D. Cutter. 2007. Post-copulatory sexual selection reduces genetic diversity in experimental populations of C. elegans. Journal of Heredity. 98: 67-72. [pdf]

Post-copulatory sexual selection affects the evolution of numerous features ranging from mating behavior to seminal fluid toxicity to the size of gametes. In an earlier study of the effect of sperm competition risk on sperm size evolution, experimental populations of the nematode C. elegans were maintained either by outcrossing (sperm competition present) or by selfing (no sperm competition), and after 60 generations, significantly larger sperm had evolved in the outcrossing populations. To determine the effects of this selection on population genetic variation, we assessed genetic diversity in a large number of loci using RAPD-PCR. Nearly 80% of the alleles present in parental strain populations persisted in the six experimental populations after the 60 generations and, despite a 2.2-fold difference in expected heterozygosity, the resulting levels of genetic variation were equivalent between the outcrossing and selfing experimental populations. By inference, we conclude that genetic hitchhiking due to sexual selection in the experimental populations dramatically reduced genetic diversity. We use the levels of variation in the selfing populations as a control for the effects of drift, and estimate the strength of sexual selection to be strong in obligatorily outcrossing populations. While sequential hermaphrodites like C. elegans probably experience little sexual selection in nature, these data suggest that sexual selection can profoundly affect diversity in outcrossing taxa.

Cutter, A.D. & B. Charlesworth. 2006. Selection intensity on preferred codons correlates with overall codon usage bias in Caenorhabditis remanei. Current Biology. 16: 2053-2057. [pdf]

Adaptive codon usage provides evidence of natural selection in one of its most subtle forms: a fitness benefit of one synonymous codon relative to another. Codon usage bias is evident in the coding sequences of a broad array of taxa, reflecting selection for translational efficiency and/or accuracy as well as mutational biases. Here, we quantify the magnitude of selection acting on alternative codons in genes of the nematode Caenorhabditis remanei, an outcrossing relative of the model organism C. elegans, by fitting the expected mutation-selection-drift equilibrium frequency distribution of preferred and unpreferred codon variants to the empirical distribution. This method estimates the intensity of selection on synonymous codons in genes with high codon bias as Nes = 0.17, a value significantly greater than zero. In addition, we demonstrate for the first time that estimates of ongoing selection on codon usage among genes, inferred from nucleotide polymorphism data, correlate strongly with long-term patterns of codon usage bias, as measured by the frequency of optimal codons in a gene. From the pattern of polymorphisms in introns, we also infer that these findings do not result from the operation of biased gene conversion toward G or C nucleotides. We therefore conclude that coincident patterns of current and ancient selection are responsible for shaping biased codon usage in the C. remanei genome.

Cutter, A.D., J. Wasmuth & M. Blaxter. 2006. The evolution of biased codon and amino acid usage in nematode genomes. Molecular Biology and Evolution. 23: 2303-2315. [pdf]

Despite the degeneracy of the genetic code, whereby different codons encode the same amino acid, alternative codons and amino acids are utilized non-randomly within and between genomes.  Such biases in codon and amino acid usage have been demonstrated extensively in prokaryote genomes and likely reflect a balance between the action of mutation, selection, and genetic drift.  Here, we quantify the effects of selection and mutation-drift as causes of codon and amino acid usage bias in a large collection of nematode partial genomes from 37 species spanning approximately 700 My of evolution, as inferred from expressed sequence tag (EST) measures of gene expression and from base composition variation.  Average G+C content at silent sites among these taxa ranges from 10% to 63% and EST counts range more than 100-fold, underlying marked differences between the identities of major codons and optimal codons for a given species as well as influencing patterns of amino acid abundance among taxa.  Few species in our sample demonstrate a dominant role of selection in shaping intra-genomic codon usage biases, and these are principally free-living rather than parasitic nematodes.  This suggests that deviations in effective population size among species, with small effective sizes among parasites, are partly responsible for species differences in the extent to which selection shapes patterns of codon usage.  Nevertheless, a consensus set of optimal codons emerges that is common to most taxa, indicating that, with some notable exceptions, selection for translational efficiency and accuracy favors similar sets of codons regardless of the major codon usage trends defined by base compositional properties of individual nematode genomes.

Cutter, A.D., S.E. Baird & D. Charlesworth. 2006. Patterns of nucleotide polymorphism and the decay of linkage disequilibrium in wild populations of Caenorhabditis remanei. Genetics. 174: 901-913. [pdf]

The common ancestor of the self-fertilizing nematodes Caenorhabditis elegans and C. briggsae must have reproduced by obligate outcrossing, like most species in this genus.  However, we have only a limited understanding about how genetic variation is patterned in such male-female (gonochoristic) Caenorhabditis species.  Here, we report results from surveying nucleotide variation of six nuclear loci in a broad geographic sample of wild isolates of the gonochoristic C. remanei.  We find high levels of diversity in this species, with silent-site diversity averaging 4.7%, implying an effective population size close to one million.  Additionally, the pattern of polymorphisms reveals little evidence for population structure or deviation from neutral expectations, suggesting that the sampled C. remanei populations approximate panmixis and demographic equilibrium.  Combined with the observation that linkage disequilibrium between pairs of polymorphic sites decays rapidly with distance, this suggests that C. remanei will provide an excellent system for identifying the genetic targets of natural selection from deviant patterns of polymorphism and linkage disequilibrium.  The patterns revealed in this obligately outcrossing species may provide a useful model of the evolutionary circumstances in C. elegans’ gonochoristic progenitor.  This will be especially important if self-fertilization evolved recently in C. elegans history, because most of the evolutionary time separating C. elegans from its known relatives would have occurred in a state of obligate outcrossing.

Cutter, A.D., M.A. Felix, A. Barriere & D. Charlesworth. 2006. Patterns of nucleotide polymorphism distinguish temperate and tropical wild isolates of Caenorhabditis briggsae. Genetics. 173: 2021-2031. [pdf]

Caenorhabditis briggsae provides a natural comparison species for the model nematode C. elegans, given their similar morphology, life history, and hermaphroditic mode of reproduction.  Despite C. briggsae boasting a published genome sequence and establishing Caenorhabditis as a model genus for genetics and development, little is known about genetic variation across the geographic range of this species.  In this study, we greatly expand the collection of natural isolates and characterize patterns of nucleotide variation for six loci in 63 strains from three continents.  The pattern of polymorphisms reveals differentiation between C. briggsae strains found in temperate localities in the northern hemisphere from those sampled near the Tropic of Cancer, with diversity within the tropical region comparable to what is found for C. elegans in Europe.  As in C. elegans, linkage disequilibrium is pervasive, although recombination is evident among some variant sites, indicating that outcrossing has occurred at a low rate in the history of the sample.  In contrast to C. elegans, temperate regions harbor extremely little variation, perhaps reflecting colonization and recent expansion of C. briggsae into northern latitudes.  We discuss these findings in relation to their implications for selection, demographic history, and the persistence of self-fertilization.

Payseur, B.A. & A.D. Cutter. 2006. Integrating patterns of polymorphism at SNPs and STRs. Trends in Genetics. 22: 424-429. [pdf]

Single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) differ in mutation rate and mechanism.  These differences have led most researchers to analyze variation separately at these two types of loci.  However, the simultaneous consideration of polymorphism at SNPs and STRs can provide important insights that are difficult to extract from analysis of either marker type in isolation.  Here, we use coalescent simulations to model the opposing effects of contrasting mutational dynamics and of shared genealogical history on the correlation between polymorphism at linked SNPs and STRs.  Results show that polymorphism patterns are correlated only weakly despite the shared underlying genealogy, underscoring the importance of divergent mutational processes.  Examples illustrate how knowledge of this weak correlation may aid population genetic inference.  The inter-digitation of SNPs and STRs throughout genomes, as well as the complex factors that contribute to their co-variation, suggest the need for thorough theoretical studies in the future. 

Cutter, A.D. 2006. Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans. Genetics. 172: 171-184. [pdf]

An understanding of the relative contributions of different evolutionary forces on an organism's genome requires an accurate description of the patterns of genetic variation within and between natural populations. To this end, I report a survey of nucleotide polymorphism in six loci from 118 strains of the nematode Caenorhabditis elegans. These strains derive from wild populations of several regions within France, Germany, and new localities in Scotland, in addition to stock center isolates. Overall levels of silent-site diversity are low within and between populations of this self-fertile species, averaging 0.2% in European samples and 0.3% worldwide. Population structure is present despite a lack of association of sequences with geography, and migration appears to occur at all geographic scales. Linkage disequilibrium is extensive in the C. elegans genome, even extending between chromosomes. Nevertheless, recombination is clearly present in the pattern of polymorphisms, indicating that outcrossing is an infrequent, but important, feature in this species ancestry. The range of outcrossing rates consistent with the data is inferred from linkage disequilibrium, using "scattered" samples representing the collecting phase of the coalescent process in a subdivided population. I propose that genetic variation in this species is largely shaped by population subdivision due to self-fertilization coupled with long- and short-range migration between subpopulations.  

Cutter, A.D., J.M. Good, C. Pappas, M.A. Saunders, D. Starrett, & T.J. Wheeler. 2005. Transposable element orientation bias in the Drosophila melanogaster genome. Journal of Molecular Evolution. 61: 733-741. [pdf]

Non-random distributions of transposable elements can be generated by a variety of genomic features.  Using the full D. melanogaster genome as a model, we characterize the orientations of different classes of transposable elements in relation to the directionality of genes.  DNA-mediated transposable elements are more likely to be in the same orientation as neighboring genes when they occur in the nontranscribed regions flanking genes.  However, RNA-mediated transposable elements located in an intron are more often oriented in the direction opposite to that of the host gene.  These orientation biases are strongest for genes with highly biased codon usage, probably reflecting the ability of such loci to respond to weak positive or negative selection.  The leading hypothesis for selection against transposable elements in the coding orientation proposes that transcription termination poly-(A) signal motifs within retroelements interfere with normal gene transcription.  However, after accounting for differences in base composition between the strands, we find no evidence for global selection against spurious transcription termination signals in introns.  We therefore conclude that premature termination of host gene transcription due to the presence of poly-(A) signal motifs in retroelements might only partially explain strand-specific detrimental effects in the D. melanogaster genome.  

Cutter, A.D. & S. Ward. 2005. Sexual and temporal dynamics of molecular evolution in C. elegans development. Molecular Biology and Evolution. 22: 178-188. [pdf]

Dissection of the phenotypic and molecular details of development and differentiation is a centuries-old topic in evolutionary biology.  However, an adequate understanding is missing for the molecular evolution of genes that are expressed differentially throughout development – across time, tissues, and the sexes.  In this study, we investigate the dynamics of gene evolution across Caenorhabditis elegans ontogeny and among genes expressed differentially between each sex and gamete type.  Using gene classes identified by genome-wide gene expression developmental time series and comparative sequence analysis with the congener C. briggsae, we demonstrate that genes expressed predominantly after reproductive maturity evolve more rapidly than genes expressed earlier in development and that genes expressed transiently during embryogenesis evolve faster than other embryonic transcripts.  These results are indicative of relaxed selection on genes expressed following maturity, in accord with the mutation accumulation model of aging.  Furthermore, genes involved in spermatogenesis reveal more rapid evolution than other phenotypic classes of genes.  Average rates of evolution among male soma-related genes indicates that selection acts to maintain males in these androdioecious species, despite their rarity, and the rapid evolution of sperm genes suggests that sexual selection acts on sperm development and function.

Cutter, A.D. 2005. Mutation and the experimental evolution of outcrossing in Caenorhabditis elegans. Journal of Evolutionary Biology. 18: 27-34. [pdf]

An understanding of the forces that contribute to the phylogenetically widespread phenomenon of sexual reproduction has posed a longstanding problem in evolutionary biology.  Mutational theories contend that sex can be maintained when the deleterious mutation rate is sufficiently high, although empirical evidence is equivocal and experimental studies are rare.  To test the influence of mutation on the evolution of obligate outcrossing, I introduced a genetic polymorphism for breeding system into populations of the nematode Caenorhabditis elegans with high- and low-mutation rate genetic backgrounds and tracked the change in frequency of females, hermaphrodites, and males over ~21 generations.  Hermaphrodites invaded all populations, regardless of mutational background.  However, experimental populations with elevated mutation rates experienced more outcrossing and greater retention of females.  This provides experimental evidence consistent with deleterious mutational explanations for the evolution of sex in principle, but the action of other processes is required to explain the evolution of sex in entirety.

Avilés, L., J.A. Fletcher, & A.D. Cutter. 2004. The kin composition of social groups: Trading group size for degree of altruism. American Naturalist. 164: 132-144. [pdf]

The question of why some social systems form groups with kin, while others don't has gone largely untreated in the literature. Using an individual-based simulation model, we explore the demographic consequences of making kinship a criterion for group formation. We find that systems where social groups consist of one-generation breeding associations may face a serious trade-off between degree of altruism and group size that is largely mediated by their kin composition. On the one hand, restricting groups to close kin allows the evolution of highly altruistic behaviors, but limits group size, the more severely so the smaller the intrinsic fecundity of the species and the stricter the kin-admission rule. Group size requirements, on the other hand, can be met by admitting nonkin into groups, but not without limiting the degree of altruism that can evolve. As a solution to this conundrum, we show that if helping roles within groups are assigned through a lottery, rather than being genetically determined, maximum degrees of altruism can evolve in groups of nonrelatives of any size. Such a "lottery" mechanism may explain reproductive and helping patterns in organisms as varied as the cellular slime molds, polygynous wasps, and Galapagos hawks.

Miller, M.A., A.D. Cutter, I. Yamamoto, S. Ward, & D. Greenstein. 2004. Clustered organization of reproductive genes in the C. elegans genome. Current Biology. 14: 1284-1290. [pdf]

Defining the forces that sculpt genome organization is fundamental for understanding the origin, persistence, and diversification of species [1,2]. The genomic sequences of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae provide an excellent opportunity to explore the dynamics of chromosome evolution [3,4]. Extensive chromosomal rearrangement has accompanied divergence from their common ancestor, an event occurring roughly 100 Mya [4]; yet morphologically these species are nearly indistinguishable and both reproduce primarily by self-fertilization. Here we show that genes expressed during spermatogenesis (sperm genes) are nonrandomly distributed across the C. elegans genome into three large clusters located on two autosomes. In addition to sperm genes, these chromosomal regions are enriched for genes involved in the hermaphrodite sperm/oocyte switch and in the reception of sperm signals that control fertilization. Most loci are present in single copy, suggesting that cluster formation is largely due to gene aggregation and not to tandem duplication. Comparative mapping indicates that the C. briggsae genome differs significantly dramatically from the C. elegans genome in clustering. Since Because clustered genes have a direct role in reproduction and thus fitness, their aggregated pattern might have been shaped by natural selection, perhaps as hermaphroditism evolved.

Cutter, A.D. 2004. Sperm-limited fecundity in nematodes: how many sperm are enough? Evolution. 58: 651-655. [pdf]

The Bateman Principle, in which oocytes are assumed to be the limiting gamete in reproduction, is violated in a variety of species. Self-fertilizing hermaphrodites of the nematode species Caenorhabditis elegans provide an example of a system in which sperm number limits lifetime reproductive output. Sperm number limits reproduction, in this species, due to the protandrous nature of sperm production which in turn delays the onset of fertilization. This reproductive delay forms the basis of a trade-off between generation time and total fecundity, in which sperm number plays a pivotal role. I use an age-structured population model to describe the number of sperm that will maximize growth rate, given larval development time and rates of gamete production. The model yields sperm numbers consistent with empirical data for C. elegans provided that precocious larval sperm production is taken into account. Several testable hypotheses follow from the model regarding how natural selection and environmental variation may influence sperm production among populations or species with a similar mode of reproduction.

Cutter, A.D., B.A. Payseur, T. Salcedo, A.M. Estes, J.M. Good, E. Wood, T. Hartl, H. Maughan, J. Strempel, B. Wang, A.C. Bryan, & M. Dellos. 2003. Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans. Genome Research. 13: 2651-2657. [pdf]

Understanding genome-wide links between genotype and phenotype has generally been difficult due to both the complexity of phenotypes and, until recently, inaccessibility to large numbers of genes that might underlie a trait. To address this issue, we establish the association between particular RNAi phenotypes in C. elegans and sequence characteristics of the corresponding proteins and DNA. We find that genes showing RNAi phenotypes are long and highly expressed with little noncoding DNA and high rates of synonymous site substitution (KS). In addition, genes conferring RNAi phenotypes have significantly lower rates of non-synonymous site substitution (KA). Collectively, these sequence features explain nearly 20% of the difference between the sets of loci that display or lack an RNAi-mediated effect and reflect aspects both of the RNAi mechanism and the biological function of the genes. For example, the particularly low rate of evolution of genes in the sterility RNAi phenotype class suggests a role of C. elegans life history in shaping these patterns of sequence and expression characteristics on phenotypes. This approach also allows prediction of a set of heretofore-uncharacterized loci for which we expect future RNAi studies to reveal phenotypic effects (i.e. false negatives in present screens).

Cutter, A.D. & B.A. Payseur. 2003. Rates of deleterious mutation and the evolution of sex in Caenorhabditis. 16: 812-822. Journal of Evolutionary Biology. [pdf]

A variety of models propose that the accumulation of deleterious mutations plays an important role in the evolution of breeding systems. These models make predictions regarding the relative rates of protein evolution and deleterious mutation in taxa with contrasting modes of reproduction. Here we compare available coding sequences from one obligately outcrossing and two primarily selfing species of Caenorhabditis to explore the potential for mutational models to explain the evolution of breeding system in this clade. If deleterious mutations interact synergistically, the mutational deterministic hypothesis predicts that a high genomic deleterious mutation rate (U) will offset the reproductive disadvantage of outcrossing relative to asexual or selfing reproduction. Therefore, C. elegans and C. briggsae (both largely selfing) should both exhibit lower rates of deleterious mutation than the obligately outcrossing relative C. remanei. We estimate U to be equivalent (and less than one) among all three related species. Stochastic mutational models, Muller’s ratchet and Hill-Robertson interference, are expected to cause reductions in the effective population size in species that rarely outcross, thereby allowing deleterious mutations to accumulate at an elevated rate. Contrary to this prediction, we find that rates of protein evolution are generally equivalent among lineages. Overall, our analyses indicate that the evolution of breeding system in this group is unlikely to be explained solely by available mutational models.

Cutter, A.D., L. Avilés, & S. Ward. 2003. The proximate determinants of sex ratio in C. elegans populations. Genetical Research. 81: 91-102. [pdf]

The soil nematode Caenorhabditis elegans is an example of a species in which self-fertilizing hermaphrodites predominate, but functional males continue to persist—allowing outcrossing to persevere at low levels. Hermaphrodites can produce male progeny as a consequence of sex-chromosome non-disjunction or via outcrossing with males. Consequently, the genetics of sex determination coupled with the efficiency by which males find, inseminate, and obtain fertilizations with hermaphrodites will influence the frequency at which males and outcrossing occurs in such populations. Behavioral and physiological traits with a heritable basis, as well as ecological characters, may influence male reproductive success and therefore sex ratio. Because sex ratio is tied to male reproductive success, sex ratio greatly impacts outcrossing rates, patterns of genetic variation, and the ability of natural selection to act within populations. In this paper we explore the determinants of male frequency in C. elegans with a mathematical model and experimental data. We address the role of the genetic machinery of sex determination via sex-chromosome non-disjunction on sex ratio and the influence of physiological components of C. elegans’ life history that contribute to variation in sex ratio by way of male reproductive success. Finally, we discuss the short-term and long-term factors that are likely to affect sex ratio and breeding system evolution in species like C. elegans.

Cutter, A.D. & B.A. Payseur. 2003. Selection at linked sites in the partial selfer Caenorhabditis elegans. Molecular Biology & Evolution. 20: 665-673. [pdf]

Natural selection can produce a correlation between local recombination rates and levels of neutral DNA polymorphism as a consequence of genetic hitchhiking and background selection. Theory suggests that selection at linked sites should affect patterns of neutral variation in partially selfing populations more dramatically than in outcrossing populations. However, empirical investigations of selection at linked sites have focused primarily on outcrossing species. To assess the potential role of selection as a determinant of neutral polymorphism in the context of partial self-fertilization, we conducted a multivariate analysis of single nucleotide polymorphism (SNP) density throughout the genome of the nematode Caenorhabditis elegans. We based the analysis on a published SNP data set and partitioned the genome into windows to calculate SNP densities, recombination rates, and gene densities across all six chromosomes. Our analyses identify a strong, positive correlation between recombination rate and neutral polymorphism (as estimated by non-coding SNP density) across the genome of C. elegans. Furthermore, we find that levels of neutral polymorphism are lower in gene-dense regions than in gene-poor regions in some analyses. Analyses incorporating local estimates of divergence between C. elegans and C. briggsae indicate that a mutational explanation alone is unlikely to explain the observed patterns. Consequently, we interpret these findings as evidence that natural selection shapes genome-wide patterns of neutral polymorphism in C. elegans. Our study provides the first demonstration of such an effect in a partially selfing animal. Explicit models of genetic hitchhiking and background selection can each adequately describe the relationship between recombination rate and SNP density, but only when they incorporate selfing rate. Clarification of the relative roles of genetic hitchhiking and background selection in C. elegans awaits the development of specific theoretical predictions that account for partial self-fertilization and biased sex ratios.

Payseur, B.A., A.D. Cutter, & M.W. Nachman. 2002. Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. Molecular Biology & Evolution. 19: 1143-1153. [pdf]

Natural selection and non-equilibrium population-level processes can both lead to a skew in the frequency distribution of polymorphisms. Population processes are expected to affect all loci in a roughly equal fashion while selection will affect only some regions of the genome. We conducted a sliding window analysis of the frequency distribution of microsatellite polymorphisms across the human genome to identify regions that may be under positive selection. The analysis was based on a published dataset of 5,257 mapped microsatellites in individuals of European ancestry. Observed and expected numbers of alleles were compared under a stepwise mutation model using analytical formulae. Observed and expected heterozygosities were compared under a stepwise mutation model using coalescent simulations. Both analyses gave similar results. Approximately one fourth of all loci showed a significant deficit of heterozygosity, consistent with a recent population expansion. Forty-three windows were identified with extreme skews in the frequency distribution of polymorphisms (in the direction of a deficit of heterozygosity given the number of alleles). If these extreme windows are tracking selection at linked sites, theory predicts that they should be more common in regions of the genome with less recombination. We tested this prediction by comparing recombination rates in these extreme windows and in other regions of the genome, and found that extreme windows had a significantly lower recombination rate than the genomic average. The proportion of extreme windows was significantly higher on the X chromosome than on the autosomes. Moreover, all of the windows with extreme skews on the X chromosome were found in two clusters on either side of the centromere; both of these clusters exhibit markedly reduced recombination rates. These analyses point to regions of the genome that may have been recently subject to positive selection. These analyses also suggest that the effects of positive selection may be more pronounced on the X chromosome than on the autosomes in humans.

Avilés, L., P. Abbot, & A.D. Cutter. 2002. Population ecology, nonlinear dynamics, and social evolution. I. Associations among nonrelatives. American Naturalist. 159: 115-127. [pdf]

Using an individual-based and genetically explicit simulation model, we explore the evolution of sociality within a population-ecology and nonlinear-dynamics framework. Assuming that individual fitness is a unimodal function of group size and that cooperation may carry a relative fitness cost, we consider the evolution of one-generation breeding associations among nonrelatives. We explore how parameters such as the intrinsic rate of growth and group and global carrying capacities may influence social evolution and how social evolution may, in turn, influence and be influenced by emerging group-level and population-wide dynamics. We find that group living and cooperation evolve under a wide range of parameter values, even when cooperation is costly and the interactions can be defined as altruistic. Greater levels of cooperation, however, did evolve when cooperation carried a low or no relative fitness cost. Larger group carrying capacities allowed the evolution of larger groups but also resulted in lower cooperative tendencies. When the intrinsic rate of growth was not too small and control of the global population size was density dependent, the evolution of large cooperative tendencies resulted in dynamically unstable groups and populations. These results are consistent with the existence and typical group sizes of organisms ranging from the pleometrotic ants to the colonial birds and the global population outbreaks and crashes characteristic of organisms such as the migratory locusts and the tree-killing bark beetles.

Wilf, P., C.C. Labandeira, K. Johnson, P.D. Coley, & A.D. Cutter. 2001. Insect herbivory, plant defense, and early Cenozoic climate change. Proc. Nat. Acad. Sci. 98: 6221-6226. [pdf]

Insect damage on fossil leaves from the Central Rocky Mountains, United States, documents the response of herbivores to changing regional climates and vegetation during the late Paleocene (humid, warm temperate to subtropical, predominantly deciduous), early Eocene (humid subtropical, mixed deciduous and evergreen), and middle Eocene (seasonally dry, subtropical, mixed deciduous and thick-leaved evergreen). During all three time periods, greater herbivory occurred on taxa considered to have short rather than long leaf life spans, consistent with studies in living forests that demonstrate the insect resistance of long-lived, thick leaves. Variance in herbivory frequency and diversity was highest during the middle Eocene, indicating the increased representation of two distinct herbivory syndromes: one for taxa with deciduous, palatable foliage, and the other for hosts with evergreen, thick-textured, small leaves characterized by elevated insect resistance. Leaf galling, which is negatively correlated with moisture today, apparently increased during the middle Eocene, whereas leaf mining decreased.

Avilés, L., J. McCormack, A. Cutter, & T. Bukowski. 2000. Precise, highly female-biased sex ratios in a social spider. Proceedings: Biological Sciences (Royal Society). 267: 1445-1449. [pdf]

It has been recognized for some time that the risk of producing maleless clutches should select for a lower than binomial variance in the sex ratio of organisms with female-biased sex ratios, small clutches and breeding groups containing the clutch of a single female. However, to date, precise sex ratios have only been reported for organisms with haplodiploid sex determination, a system which allows direct control of the sex of individual offspring. In contrast, under heterogametic sex determination chance is expected to play a crucial role in determining the sex composition of any one family, in particular when males are the heterogametic sex. Here, we present evidence of precise or underdispersed primary sex ratios in the Neotropical social spider Anelosimus domingo Levi. We show that this diplodiploid species with male heterogamety has not only beaten the odds of meiosis by producing mostly daughters, but has also attained relative precision in the proportion of sons and daughters produced in any one clutch. The latter finding suggests the existence of mechanisms that allow sorting of the two types of sperm in this spider species.

King, J.R., A.N. Andersen, & A.D. Cutter. 1998. Response of rainforest ant communities in Australia's humid tropics to disturbance: validation of the functional group model. Biodiversity and Conservation 7: 1627-1638. [pdf]

A functional group model of ant community composition has been widely used in Australia to analyse biogeographical patterns of ant community structure and the responses of ant communities to disturbance. The model has provided valuable support to the widespread use of ant communities as bioindicators of ecological change. However, the model was developed from studies of arid-zone faunas, and its applicability to the World Heritage rainforests of Queensland‘s humid tropics has not yet been validated. Here we test predictions based on the functional group model for ant communities in Queensland‘s humid rainforests, by documenting ant community composition and its responses to disturbance on the Atherton Tablelands. Five sites were studied, comprising two relatively undisturbed reference sites representing contrasting rainforest types, and three previously cleared sites, two of which were undergoing revegetation. A variety of sampling techniques were employed, including pitfall trapping, litter extractions, baiting, and general searching. A total of 50 ant species from 29 genera were collected. Site species richness was highest at the reference sites, and lowest at the unvegetated disturbed site, and overall was negatively related to mean ground temperature. As predicted by the functional group model, behaviorally dominant dolichoderines were uncommon or absent at the reference sites, and the most common ants were Generalized myrmicines and Opportunists. Also as predicted, habitat disturbance favored Opportunists, and, as the disturbance involved canopy clearance, this led to colonization by Iridomyrmex and other Dominant dolichoderines. Opportunists represented about 40% of total ants in traps at the reference sites, compared with 80–95% at the disturbed sites. Except one species, Tropical Climate Specialists and Specialist Predators were absent from disturbed sites.In conclusion, patterns of ant composition in relation to disturbance on the Atherton Tablelands conform to the functional group model that has been widely applied to ant faunas elsewhere in Australia. The model may therefore play an important role in the use of ants as bioindicators of ecological change in the World Heritage rainforests of this region.
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