Extraordinarily rapid life-history divergence between Cryptasterina sea star species

Minor Genetic Consequences of a Major Mass Mortality: Short-Term Effects in Pisaster ochraceus

AbstractMass mortality events are increasing globally in frequency and magnitude, largely as a result of human-induced change. The effects of these mass mortality events, in both the long and short term, are of imminent concern because of their ecosystem impacts. Genomic data can be used to reveal some of the population-level changes associated with mass mortality events. Here, we use reduced-representation sequencing to identify potential short-term genetic impacts of a mass mortality event associated with a sea star wasting outbreak. We tested for changes in the population for genetic differentiation, diversity, and effective population size between pre-sea star wasting and post-sea star wasting populations of Pisaster ochraceus-a species that suffered high sea star wasting-associated mortality (75%-100% at 80% of sites). We detected no significant population-based genetic differentiation over the spatial scale sampled; however, the post-sea star wasting population tended toward more differentiation across sites than the pre-sea star wasting population. Genetic estimates of effective population size did not detectably change, consistent with theoretical expectations; however, rare alleles were lost. While we were unable to detect significant population-based genetic differentiation or changes in effective population size over this short time period, the genetic burden of this mass mortality event may be borne by future generations, unless widespread recruitment mitigates the population decline. Prior results from P. ochraceus indicated that natural selection played a role in altering allele frequencies following this mass mortality event. In addition to the role of selection found in a previous study on the genomic impacts of sea star wasting on P. ochraceus, our current study highlights the potential role the stochastic loss of many individuals plays in altering how genetic variation is structured across the landscape. Future genetic monitoring is needed to determine long-term genetic impacts in this long-lived species. Given the increased frequency of mass mortality events, it is important to implement demographic and genetic monitoring strategies that capture baselines and background dynamics to better contextualize species' responses to large perturbations.

Ecological and Evolutionary Implications of Microbial Dispersal

Dispersal is simply defined as the movement of species across space and time. Despite this terse definition, dispersal is an essential process with direct ecological and evolutionary implications that modulate community assembly and turnover. Seminal ecological studies have shown that environmental context (e.g., local edaphic properties, resident community), dispersal timing and frequency, and species traits, collectively account for patterns of species distribution resulting in either their persistence or unsuccessful establishment within local communities. Despite the key importance of this process, relatively little is known about how dispersal operates in microbiomes across divergent systems and community types. Here, we discuss parallels of macro- and micro-organismal ecology with a focus on idiosyncrasies that may lead to novel mechanisms by which dispersal affects the structure and function of microbiomes. Within the context of ecological implications, we revise the importance of short- and long-distance microbial dispersal through active and passive mechanisms, species traits, and community coalescence, and how these align with recent advances in metacommunity theory. Conversely, we enumerate how microbial dispersal can affect diversification rates of species by promoting gene influxes within local communities and/or shifting genes and allele frequencies via migration or de novo changes (e.g., horizontal gene transfer). Finally, we synthesize how observed microbial assemblages are the dynamic outcome of both successful and unsuccessful dispersal events of taxa and discuss these concepts in line with the literature, thus enabling a richer appreciation of this process in microbiome research.

Cloning and Selfing Affect Population Genetic Variation in Simulations of Outcrossing, Sexual Sea Stars

AbstractMany sea stars are well known for facultative or obligate asexual reproduction in both the adult and larval life-cycle stages. Some species and lineages are also capable of facultative or obligate hermaphroditic reproduction with self-fertilization. However, models of population genetic variation and empirical analyses of genetic data typically assume only sexual reproduction and outcrossing. A recent reanalysis of previously published empirical data (microsatellite genotypes) from two studies of one of the most well-known sea star species (the crown-of-thorns sea star; Acanthaster sp.) concluded that cloning and self-fertilization in that species are rare and contribute little to patterns of population genetic variation. Here we reconsider that conclusion by simulating the contribution of cloning and selfing to genetic variation in a series of models of sea star demography. Simulated variation in two simple models (analogous to previous analyses of empirical data) was consistent with high rates of cloning or selfing or both. More realistic scenarios that characterize population flux in sea stars of ecological significance, including outbreaks of crown-of-thorns sea stars that devastate coral reefs, invasions by Asterias amurensis, and epizootics of sea star wasting disease that kill Pisaster ochraceus, also showed significant but smaller effects of cloning and selfing on variation within subpopulations and differentiation between subpopulations. Future models or analyses of genetic variation in similar study systems might benefit from simulation modeling to characterize possible contributions of cloning or selfing to genetic variation in population samples or to understand the limits on inferring the effects of cloning or selfing in nature.

Selection on genes associated with the evolution of divergent life histories: Gamete recognition or something else?

Gamete compatibility, and fertilization success, is mediated by gamete-recognition genes (GRGs) that are expected to show genetic evidence of a response to sexual selection associated with mating system traits. Changes in the strength of sexual selection can arise from the resolution of sperm competition among males, sexual conflicts of interest between males and females, or other mechanisms of sexual selection. To assess these expectations, we compared patterns of episodic diversifying selection among genes expressed in the gonads of Cryptasterina pentagona and C. hystera, which recently speciated and have evolved different mating systems (gonochoric or hermaphroditic), modes of fertilization (outcrossing or selfing), and dispersal (planktonic larvae or internal brooding). Cryptasterina spp. inhabit the upper intertidal of the coast of Queensland and coral islands of the Great Barrier Reef. We found some evidence for positive selection on a GRG in the outcrossing C. pentagona, and we found evidence of loss of gene function in a GRG of the self-fertilizing C. hystera. The modification or loss of gene functionality may be evidence of relaxed selection on some aspects of gamete interaction in C. hystera. In addition to these genes involved in gamete interactions, we also found genes under selection linked to abiotic stress, chromosomal regulation, polyspermy, and egg-laying. We interpret those results as possible evidence that Cryptasterina spp. with different mating systems may have been adapting in divergent ways to oxidative stress or other factors associated with reproduction in the physiologically challenging environment of the high intertidal. RESEARCH HIGHLIGHTS: Recent speciation between two sea stars was unlikely the result of selection on gamete-recognition genes annotated in this study. Instead, our results point to selection on genes linked to the intertidal environment and reproduction.

Genetic homogeneity, lack of larvae recruitment, and clonality in absence of females across western Mediterranean populations of the starfish Coscinasterias tenuispina

We here analysed the populations' genetic structure of Coscinasterias tenuispina, an Atlantic-Mediterranean fissiparous starfish, focusing on the western Mediterranean, to investigate: the distribution and prevalence of genetic variants, the relative importance of asexual reproduction, connectivity across the Atlantic-Mediterranean transition, and the potential recent colonisation of the Mediterranean Sea. Individuals from 11 Atlantic-Mediterranean populations of a previous study added to 172 new samples from five new W Mediterranean sites. Individuals were genotyped at 12 microsatellite loci and their gonads histologically analysed for sex determination. Additionally, four populations were genotyped at two-time points. Results demonstrated genetic homogeneity and low clonal richness within the W Mediterranean, due to the dominance of a superclone, but large genetic divergence with adjacent areas. The lack of new genotypes recruitment over time, and the absence of females, confirmed that W Mediterranean populations were exclusively maintained by fission and reinforced the idea of its recent colonization. The existence of different environmental conditions among basins and/or density-depend processes could explain this lack of recruitment from distant areas. The positive correlation between clonal richness and heterozygote excess suggests that most genetic diversity is retained within individuals in the form of heterozygosity in clonal populations, which might increase their resilience.

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.

Genomic landscape of geographically structured colour polymorphism in a temperate marine fish

The study of phenotypic variation patterns among populations is fundamental to elucidate the drivers of evolutionary processes. Empirical evidence that supports ongoing genetic divergence associated with phenotypic variation remains very limited for marine species where larval dispersal is a common homogenizing force. We present a genome‐wide analysis of a marine fish, Labrus bergylta, comprising 144 samples distributed from Norway to Spain, a large geographical area that harbours a gradient of phenotypic differentiation. We analysed 39,602 biallelic single nucleotide polymorphisms and found a clear latitudinal gradient of genomic differentiation strongly correlated with the variation in phenotypic morph frequencies observed across the North Atlantic. We also detected a strong association between the latitude and the number of loci that appear to be under divergent selection, which increased with differences in coloration but not with overall genetic differentiation. Our results demonstrate that strong reproductive isolation is occurring between sympatric colour morphs of L. bergylta found at the southern areas and provide important new insights into the genomic changes shaping early stages of differentiation that might precede speciation with gene flow.

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.

The developmental transcriptomes of two sea biscuit species with differing larval types

BACKGROUND

Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of larval development, to provide a resource for investigating the evolution of alternate life cycles. One species (Clypeaster subdepressus) develops via an obligately feeding larva which metamorphoses 3-4 weeks after fertilization; the other (Clypeaster rosaceus) develops via a rare, intermediate larval type-facultative feeding- and can develop through metamorphosis entirely based on egg provisioning in under one week.

RESULTS

Overall, the two transcriptomes are highly similar, containing largely orthologous contigs with similar functional annotation. However, we found distinct differences in gene expression patterns between the two species. Larvae from C. rosaceus, the facultative planktotroph, turned genes on at earlier stages and had less differentiation in gene expression between larval stages, whereas, C. subdepressus showed a higher degree of stage-specific gene expression.

CONCLUSION

This study is the first genetic analysis of a species with facultatively feeding larvae. Our results are consistent with known developmental differences between the larval types and raise the question of whether earlier onset of developmental genes is a key step in the evolution of a reduced larval period. By publishing a transcriptome for this rare, intermediate, larval type, this study adds developmental breadth to the current genetic resources, which will provide a valuable tool for future research on echinoderm development as well as studies on the evolution of development in general.

Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish

Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species' distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the southwestern Atlantic and the other along the northeastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo-Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations were found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intrapopulation genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations' genetic divergence could be observed between some populations.

Looking for morphological evidence of cryptic species in Asterina Nardo, 1834 (Echinodermata: Asteroidea). The redescription of Asterina pancerii (Gasco, 1870) and the description of two new species

Three species of the genus Asterina are known to inhabit the Mediterranean Sea and the north-eastern Atlantic Ocean: Asterina gibbosa (Pennant, 1777), A. pancerii (Gasco, 1870) and A. phylactica Emson & Crump, 1979. Differentiation of these species has primarily been based only on subtle characters (some highly debatable), such as colour or size. Therefore, this study aimed to review the morphological data characterising members of the genus, to incorporate new characters that may clarify morphological analyses and to couple morphological data with molecular evidence of differentiation based on the analysis of partial sequences of the cytochromec oxidase subunitI (COI) and 18S rDNA (18S) genes and two anonymous nuclear loci (AgX2 and AgX5). The different lineages and cryptic species identified from the molecular analysis were then morphologically characterised, which was challenging given the limited number of diagnostic characters. Two of the five monophyletic lineages obtained molecularly (COI divergence >4%), further supported by differences in morphological characters and reproductive behaviour, are proposed as new species: Asterina martinbarriosi, sp. nov. from the Canary Islands, Spain (eastern central Atlantic Ocean) and Asterina vicentae, sp. nov. from Tarragona, north-eastern Spain (western Mediterranean Sea).

Extraordinarily rapid speciation in a marine fish

Divergent selection may initiate ecological speciation extremely rapidly. How often and at what pace ecological speciation proceeds to yield strong reproductive isolation is more uncertain. Here, we document a case of extraordinarily rapid speciation associated with ecological selection in the postglacial Baltic Sea. European flounders (Platichthys flesus) in the Baltic exhibit two contrasting reproductive behaviors: pelagic and demersal spawning. Demersal spawning enables flounders to thrive in the low salinity of the Northern Baltic, where eggs cannot achieve neutral buoyancy. We show that demersal and pelagic flounders are a species pair arising from a recent event of speciation. Despite having a parapatric distribution with extensive overlap, the two species are reciprocally monophyletic and show strongly bimodal genotypic clustering and no evidence of contemporary migration, suggesting strong reproductive isolation. Divergence across the genome is weak but shows strong signatures of selection, a pattern suggestive of a recent ecological speciation event. We propose that spawning behavior in Baltic flounders is the trait under ecologically based selection causing reproductive isolation, directly implicating a process of ecological speciation. We evaluated different possible evolutionary scenarios under the approximate Bayesian computation framework and estimate that the speciation process started in allopatry ∼2,400 generations ago, following the colonization of the Baltic by the demersal lineage. This is faster than most known cases of ecological speciation and represents the most rapid event of speciation ever reported for any marine vertebrate.

No association between plant mating system and geographic range overlap

PREMISE OF THE STUDY

Automatic self-fertilization may influence the geography of speciation, promote reproductive isolation between incipient species, and lead to ecological differentiation. As such, selfing taxa are predicted to co-occur more often with their closest relatives than are outcrossing taxa. Despite suggestions that this pattern may be general, the extent to which mating system influences range overlap in close relatives has not been tested formally across a diverse group of plant species pairs.

METHODS

We tested for a difference in range overlap between species pairs for which zero, one, or both species are selfers, using data from 98 sister species pairs in 20 genera across 15 flowering plant families. We also used divergence time estimates from time-calibrated phylogenies to ask how range overlap changes with divergence time and whether this effect depends on mating system.

KEY RESULTS

We found no evidence that automatic self-fertilization influenced range overlap of closely related plant species. Sister pairs with more recent divergence times had modestly greater range overlap, but this effect did not depend on mating system.

CONCLUSIONS

The absence of a strong influence of mating system on range overlap suggests that mating system plays a minor or inconsistent role compared with many other mechanisms potentially influencing the co-occurrence of close relatives.

Reduced genetic diversity and increased reproductive isolation follow population-level loss of larval dispersal in a marine gastropod

Population-level consequences of dispersal ability remain poorly understood, especially for marine animals in which dispersal is typically considered a species-level trait governed by oceanographic transport of microscopic larvae. Transitions from dispersive (planktotrophic) to nondispersive, aplanktonic larvae are predicted to reduce connectivity, genetic diversity within populations, and the spatial scale at which reproductive isolation evolves. However, larval dimorphism within a species is rare, precluding population-level tests. We show the sea slug Costasiella ocellifera expresses both larval morphs in Florida and the Caribbean, regions with divergent mitochondrial lineages. Planktotrophy predominated at 11 sites, 10 of which formed a highly connected and genetically diverse Caribbean metapopulation. Four populations expressed mainly aplanktonic development and had markedly reduced connectivity, and lower genetic diversity at one mitochondrial and six nuclear loci. Aplanktonic dams showed partial postzygotic isolation in most interpopulation crosses, regardless of genetic or geographic distance to the sire's source, suggesting that outbreeding depression affects fragmented populations. Dams from genetically isolated and neighboring populations also exhibited premating isolation, consistent with reinforcement contingent on historical interaction. By increasing self-recruitment and genetic drift, the loss of dispersal may thus initiate a feedback loop resulting in the evolution of reproductive isolation over small spatial scales in the sea.

Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex

Closely related species with divergent life history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatric and ecologically syntopic, making them particularly suitable to study the consequences of their trait differences. At the scale of the geographic distribution of the broadcasters (Mediterranean Sea and northeastern Atlantic), we sequenced the mitochondrial marker COI and genotyped an intron (i51) for 788 individuals. In addition, we sequenced 10 nuclear loci newly developed from transcriptome sequences, for six sympatric populations of brooders and broadcasters from Greece. At the large scale, we found a high genetic structure within the brooders (COI: 0.07 < F(ST) < 0.65) and no polymorphism at the nuclear locus i51. In contrast, the broadcasters displayed lower genetic structure (0 < F(ST) < 0.14) and were polymorphic at locus i51. At the regional scale, the multilocus analysis confirmed the contrasting genetic structure between species, with no structure in the broadcasters (global F(ST) < 0.001) and strong structure in the brooders (global F(ST) = 0.49), and revealed a higher genetic diversity in broadcasters. Our study showed that the lecithotrophic larval stage allows on average a 50-fold increase in migration rates, a 280-fold increase in effective size and a threefold to fourfold increase in genetic diversity. Our work, investigating complementary genetic markers on sympatric and syntopic taxa, highlights the strong impact of the larval phase on connectivity and genetic diversity.

Environmental influences on the Indo-Pacific octocoral Isis hippuris Linnaeus 1758 (Alcyonacea: Isididae): genetic fixation or phenotypic plasticity?

As conspicuous modular components of benthic marine habitats, gorgonian (sea fan) octocorals have perplexed taxonomists for centuries through their shear diversity, particularly throughout the Indo–Pacific. Phenotypic incongruence within and between seemingly unitary lineages across contrasting environments can provide the raw material to investigate processes of disruptive selection. Two distinct phenotypes of the Isidid Isis hippurisLinnaeus, 1758 partition between differing reef environments: long-branched bushy colonies on degraded reefs, and short-branched multi/planar colonies on healthy reefs within the Wakatobi Marine National Park (WMNP), Indonesia. Multivariate analyses reveal phenotypic traits between morphotypes were likely integrated primarily at the colony level with increased polyp density and consistently smaller sclerite dimensions at the degraded site. Sediment load and turbidity, hence light availability, primarily influenced phenotypic differences between the two sites. This distinct morphological dissimilarity between the two sites is a reliable indicator of reef health; selection primarily acting on colony morphology, porosity through branching structure, as well as sclerite diversity and size. ITS2 sequence and predicted RNA secondary structure further revealed intraspecific variation between I. hippuris morphotypes relative to such environments (Φ_ST = 0.7683, P < 0.001). This evidence suggests—but does not confirm—that I. hippuris morphotypes within the WMNP are two separate species; however, to what extent and taxonomic assignment requires further investigation across its full geographic distribution. Incongruence between colonies present in the WMNP with tenuously described Isis alternatives (Isis reticulataNutting, 1910, Isis minorbrachyblastaZou, Huang & Wang, 1991), questions the validity of such assignments. Furthermore, phylogenetic analyses confirm early taxonomic suggestion that the characteristic jointed axis of the Isididae is in fact a convergent trait. Thus the polyphyletic nature of the Isididae lies in its type species I. hippuris, being unrelated to the rest of its family members.

To brood or not to brood: Are marine invertebrates that protect their offspring more resilient to ocean acidification?

Anthropogenic atmospheric carbon dioxide (CO₂) is being absorbed by seawater resulting in increasingly acidic oceans, a process known as ocean acidification (OA). OA is thought to have largely deleterious effects on marine invertebrates, primarily impacting early life stages and consequently, their recruitment and species’ survival. Most research in this field has been limited to short-term, single-species and single-life stage studies, making it difficult to determine which taxa will be evolutionarily successful under OA conditions. We circumvent these limitations by relating the dominance and distribution of the known polychaete worm species living in a naturally acidic seawater vent system to their life history strategies. These data are coupled with breeding experiments, showing all dominant species in this natural system exhibit parental care. Our results provide evidence supporting the idea that long-term survival of marine species in acidic conditions is related to life history strategies where eggs are kept in protected maternal environments (brooders) or where larvae have no free swimming phases (direct developers). Our findings are the first to formally validate the hypothesis that species with life history strategies linked to parental care are more protected in an acidifying ocean compared to their relatives employing broadcast spawning and pelagic larval development.

Spore germination determines yeast inbreeding according to fitness in the local environment

Gene combinations conferring local fitness may be destroyed by mating with individuals that are adapted to a different environment. This form of outbreeding depression provides an evolutionary incentive for self-fertilization. We show that the yeast Saccharomyces paradoxus tends to self-fertilize when it is well adapted to its local environment but tends to outcross when it is poorly adapted. This behavior could preserve combinations of genes when they are beneficial and break them up when they are not, thereby helping adaptation. Haploid spores must germinate before mating, and we found that fitter spores had higher rates of germination across a 24-hour period, increasing the probability that they mate with germinated spores from the same meiotic tetrad. The ability of yeast spores to detect local conditions before germinating and mating suggests the novel possibility that these gametes directly sense their own adaptation and plastically adjust their breeding strategy accordingly.

The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes

Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.

Selection and demographic history shape the molecular evolution of the gamete compatibility protein bindin in Pisaster sea stars

Reproductive compatibility proteins have been shown to evolve rapidly under positive selection leading to reproductive isolation, despite the potential homogenizing effects of gene flow. This process has been implicated in both primary divergence among conspecific populations and reinforcement during secondary contact; however, these two selective regimes can be difficult to discriminate from each other. Here, we describe the gene that encodes the gamete compatibility protein bindin for three sea star species in the genus Pisaster. First, we compare the full-length bindin-coding sequence among all three species and analyze the evolutionary relationships between the repetitive domains of the variable second bindin exon. The comparison suggests that concerted evolution of repetitive domains has an effect on bindin divergence among species and bindin variation within species. Second, we characterize population variation in the second bindin exon of two species: We show that positive selection acts on bindin variation in Pisaster ochraceus but not in Pisaster brevispinus, which is consistent with higher polyspermy risk in P. ochraceus. Third, we show that there is no significant genetic differentiation among populations and no apparent effect of sympatry with congeners that would suggest selection based on reinforcement. Fourth, we combine bindin and cytochrome c oxidase 1 data in isolation-with-migration models to estimate gene flow parameter values and explore the historical demographic context of our positive selection results. Our findings suggest that positive selection on bindin divergence among P. ochraceus alleles can be accounted for in part by relatively recent northward population expansions that may be coupled with the potential homogenizing effects of concerted evolution.

Incipient speciation of sea star populations by adaptive gamete recognition coevolution

Reproductive isolation--the key event in speciation--can evolve when sexual conflict causes selection favoring different combinations of male and female adaptations in different populations. Likely targets of such selection include genes that encode proteins on the surfaces of sperm and eggs, but no previous study has demonstrated intraspecific coevolution of interacting gamete recognition genes under selection. Here, we show that selection drives coevolution between an egg receptor for sperm (OBi1) and a sperm acrosomal protein (bindin) in diverging populations of a sea star (Patiria miniata). We found positive selection on OBi1 in an exon encoding part of its predicted substrate-binding protein domain, the ligand for which is found in bindin. Gene flow was zero for the parts of bindin and OBi1 in which selection for high rates of amino acid substitution was detected; higher gene flow for other parts of the genome indicated selection against immigrant alleles at bindin and OBi1. Populations differed in allele frequencies at two key positively selected sites (one in each gene), and differences at those sites predicted fertilization rate variation among male-female pairs. These patterns suggest adaptively evolving loci that influence reproductive isolation between populations.

Shallow gene pools in the high intertidal: extreme loss of genetic diversity in viviparous sea stars (Parvulastra)

We document an extreme example of reproductive trait evolution that affects population genetic structure in sister species of Parvulastra cushion stars from Australia. Self-fertilization by hermaphroditic adults and brood protection of benthic larvae causes strong inbreeding and range-wide genetic poverty. Most samples were fixed for a single allele at nearly all nuclear loci; heterozygotes were extremely rare (0.18%); mitochondrial DNA sequences were more variable, but few populations shared haplotypes in common. Isolation-with-migration models suggest that these patterns are caused by population bottlenecks (relative to ancestral population size) and low gene flow. Loss of genetic diversity and low potential for dispersal between high-intertidal habitats may have dire consequences for extinction risk and potential for future adaptive evolution in response to climate and other selective agents.

Evolutionary consequences of self-fertilization in plants

The transition from outcrossing to self-fertilization is one of the most common evolutionary changes in plants, yet only about 10-15% of flowering plants are predominantly selfing. To explain this phenomenon, Stebbins proposed that selfing may be an 'evolutionary dead end'. According to this hypothesis, transitions from outcrossing to selfing are irreversible, and selfing lineages suffer from an increased risk of extinction owing to a reduced potential for adaptation. Thus, although selfing can be advantageous in the short term, selfing lineages may be mostly short-lived owing to higher extinction rates. Here, we review recent results relevant to the 'dead-end hypothesis' of selfing and the maintenance of outcrossing over longer evolutionary time periods. In particular, we highlight recent results regarding diversification rates in self-incompatible and self-compatible taxa, and review evidence regarding the accumulation of deleterious mutations in selfing lineages. We conclude that while some aspects of the hypothesis of selfing as a dead end are supported by theory and empirical results, the evolutionary and ecological mechanisms remain unclear. We highlight the need for more studies on the effects of quantitative changes in outcrossing rates and on the potential for adaptation, particularly in selfing plants. In addition, there is growing evidence that transitions to selfing may themselves be drivers of speciation, and future studies of diversification and speciation should investigate this further.

Structure and evolution of the sea star egg receptor for sperm bindin

Selection on coevolving sperm- and egg-recognition molecules is a potent engine of population divergence leading to reproductive isolation and speciation. The study of receptor-ligand pairs can reveal co-evolution of male- and female-expressed genes or differences between their evolution in response to selective factors such as sperm competition and sexual conflict. Phylogeographical studies of these patterns have been limited by targeted gene methods that favour short protein-coding sequences amplifiable by PCR. Here, I use high-throughput transcriptomic methods to characterize the structure and divergence of full-length coding sequences for the gene encoding the protein component of a large complex egg surface glycopeptide receptor for the sperm acrosomal protein bindin from the sea star Patiria miniata. I used a simple but effective method for resolving nucleotide polymorphisms into haplotypes for phylogeny-based analyses of selection. The protein domain organization of sea star egg bindin receptor (EBR1) was similar to sea urchins and included a pair of protein-recognition domains plus a series of tandem repeat domains of two types. Two populations separated by a well-characterized phylogeographical break included lineages of EBR1 alleles under positive selection at several codons (similar to selection on sperm bindin in the same populations). However, these populations shared the same alleles that were under selection for amino acid differences at multiple codons (unlike the pattern of selection for population divergence in sperm bindin). The significance of positively selected EBR1 domains and alleles could be tested in functional analyses of fertilization rates associated with EBR1 (and bindin) polymorphisms.