Consequences of a poecilogonous life history for genetic structure in coastal populations of the polychaete Streblospio benedicti

Assortative mating and mate-choice contributes to the maintenance of a developmental dimorphism in Streblospio benedicti

Assortative mating, where individuals non-randomly mate with respect to phenotype or genotype, can occur when preferences between potential mates have evolved. When such mate preferences occur in a population it can drive evolutionary and phenotypic divergence. But the extent to which assortative mating, mate preference, and development are evolutionarily linked remains unclear. Here we use Streblospio benedicti, a marine annelid with a rare developmental dimorphism, to investigate if mate-choice could contribute to developmental evolution. For S. benedicti two types of ecologically and phenotypically similar adults persist in natural populations, but they give rise to distinctly different offspring with alternative life-histories. This dimorphism persists despite the absence of post-zygotic reproductive barriers, where crosses between the developmental types can produce phenotypically intermediate offspring. How this life-history strategy evolved remains unknown, but assortative mating is a typical first step in evolutionary divergence. Here we investigate if female mate-choice is occurring in this species. We find that mate preferences could be contributing to the maintenance of alternative developmental and life-history strategies.

Latitudinal variation and plasticity in response to temperature in Geukensia demissa

As global temperatures warm, species must adapt to a changing climate or transition to a different location suitable for their survival. Understanding the extent to which species are able to do so, particularly keystone species, is imperative to ensuring the survival of key ecosystems. The ribbed mussel Geukensia demissa is an integral part of salt marshes along the Atlantic coast of North America. Spatial patterns of genomic and phenotypic divergence have been previously documented, although their link with coastal environmental variation is unknown. Here, we study how populations of G. demissa in the northern (Massachusetts) and southern (Georgia) portions of the species range respond to changes in temperature. We combine assays of variation in oxygen consumption and RNA transcriptomic data with genomic divergence analyses to identify how separate populations of G. demissa may vary in distinct thermal environments. Our results show differences in constitutive oxygen consumption between mussels from Georgia and Massachusetts, as well as shared and disparate patterns of gene expression across temperature profiles. We also find that metabolic genes seem to be a strong component of divergence between these two populations. Our analysis highlights the importance of studying integrative patterns of genomic and phenotypic variation in species that are key for particular ecosystems, and how they might respond to further changes in climate.

Streblospio benedicti: A genetic model for understanding the evolution of development and life-history

Investigating developmental evolution usually requires comparing differences across related species to infer how phenotypic change results from embryological modifications. However, when comparing organisms from different environments, ecologies, and evolutionary histories there can be many confounding factors to finding a genetic basis for developmental differences. In the marine annelid Streblospio benedicti, there are two distinct types of offspring with independent developmental pathways that converge on the same adult phenotype. To my knowledge, S. benedicti is the only known species that has heritable (additive) genetic variation in developmental traits that results in alternative life-history strategies. Females produce either hundreds of small, swimming and feeding larvae, or dozens of large, nonfeeding larvae. The larvae differ in their morphology, ecology, and dispersal potential. This developmental dimorphism makes S. benedicti a unique and useful model for understanding how genetic changes result in developmental modifications that ultimately lead to overall life-history differences. Because the offspring phenotypes of S. benedicti are heritable, we can use forward genetics within a single evolutionary lineage to disentangle how development evolves, and which genes and regulatory mechanisms are involved.

The genome of the poecilogonous annelid Streblospio benedicti

Streblospio benedicti is a common marine annelid that has become an important model for developmental evolution. It is the only known example of poecilogony (where two distinct developmental modes occur within a single species) that is due to a heritable difference in egg size. The dimorphic developmental programs and life-histories exhibited in this species depend on differences within the genome, making it an optimal model for understanding the genomic basis of developmental divergence. Studies using S. benedicti have begun to uncover the genetic and genomic principles that underlie developmental uncoupling, but until now they have been limited by the lack of availability of genomic tools. Here we present an annotated chromosomal-level genome assembly of S. benedicti generated from a combination of Illumina reads, Nanopore long reads, Chicago and Hi-C chromatin interaction sequencing, and a genetic map from experimental crosses. At 701.4 Mb, the S. benedicti genome is the largest annelid genome to date that has been assembled to chromosomal scaffolds. The complete genome of S. benedicti is valuable for functional genomic analyses of development and evolution, as well as phylogenetic comparison within the annelida and the Lophotrochozoa. Despite having two developmental modes, there is no evidence of genome duplication or substantial gene number expansions. Instead, lineage specific repeats account for much of the expansion of this genome compared to other annelids.

Plasticity and artificial selection for developmental mode in a poecilogonous sea slug

The contribution of phenotypically plastic traits to evolution depends on the degree of environmental influence on the target of selection (the phenotype) as well as the underlying genetic structure of the trait and plastic response. Likewise, maternal effects can help or hinder evolution through affects to the response to selection. The sacoglossan sea slug Alderia willowi exhibits intraspecific variation for developmental mode (= poecilogony) that is environmentally modulated with populations producing more yolk-feeding (lecithotrophic) larvae during the summer, and more planktonic-feeding (planktotrophic) larvae in the winter. I found significant family-level variation in the reaction norms between 17 maternal families of A. willowi when reared in a split-brood design in low (16 ppt) versus high (32 ppt) salinity, conditions which mimic seasonal variation in salinity of natural populations. I documented a significant response to selection for lecithotrophic larvae in high and low salinity. The slope of the reaction norm was maintained following one generation of selection for lecithotrophy. When the maternal environment was controlled in the laboratory, I found significant maternal effects, which reduced the response to selection. These results suggest there is standing genetic variation for egg-mass type in A. willowi, but the ability of selection to act on that variation may depend on the environment in which the phenotype is expressed in preceding generations.

Behavioral Variability of Hatchlings Modifies Dispersal Potential in Crown Conch (Melongena corona): Why Do Larvae Crawl Away but Sometimes Swim?

AbstractThe diversity and consequences of development in marine invertebrates have, for a long time, provided the opportunity to understand different evolutionary solutions to living in variable environments. However, discrete classifications of development can impede a full understanding of adaptation to variable environments when behavioral, morphological, or physiological flexibility and variation exist within traditionally defined modes of development. We report here novel behavioral variability in hatchlings of a marine gastropod, the Florida crown conch (Melongena corona), that has broad significance for understanding the correlated evolution of development, dispersal, and reproductive strategies in variable environments. All hatchlings crawl away from egg capsules after emergence as larval pediveligers. Some subsequently swim for a brief period (seconds to minutes) before crawling again. From detailed observations of 120 individuals over 30 days, we observed 28 (23.3%) hatchlings swimming at least once (8%-50% per maternal brood). The propensity to swim was unrelated to time spent encapsulated or size at hatching and lasted for 22 days. We manipulated hypothesized environmental cues and found that the proportion of hatchlings that swam was highest in the absence of cues related to habitat or juvenile food and lowest when only habitat cues were present. The relative growth rate of hatchlings was highest when habitats contained a putative juvenile food source. About 44% of hatchlings were competent to metamorphose at emergence but did not metamorphose at this time in the lab or the field. The rate of metamorphosis increased with age and depended on the presence of unknown cues in the field. Crawl-away larvae with prolonged swimming ability may be an adaptation to balance the unpredictable risks of exclusively benthic or pelagic development and to allow the option to disperse to higher-quality habitat.

Baby makes three: Maternal, paternal, and zygotic genetic effects shape larval phenotypic evolution

The evolutionary potential of a population is shaped by the genetic architecture of its life-history traits. Early-life phenotypes are influenced by both maternal and offspring genotype, and efforts to understand life-history evolution therefore require consideration of the interactions between these separate but correlated genomes. We used a four-generation experimental pedigree to estimate the genetic architecture of early-life phenotypes in a species with dramatic variation in larval size and morphology. In the polychaete annelid Streblospio benedicti, females make either many small eggs that develop into complex larvae that feed in the plankton or few large eggs that develop into benthic juveniles without having to feed as larvae. By isolating the contributions of maternal, paternal, and zygotic genotype to larval traits, we determined that larval anatomical structures are governed by the offspring genotype at a small number of large-effect loci. Larval size is not shaped by the larva's own genotype but instead depends on loci that act in the mother, and at two genomic locations, by loci that act in the father. The overall phenotype of each larva thus depends on three separate genomes, and a population's response to selection on larval traits will reflect the interactions among them.

First genetic assessment of brackish water polychaete Tylorrhynchus heterochaetus: mitochondrial COI sequences reveal strong genetic differentiation and population expansion in samples collected from southeast China and north Vietnam

Tylorrhynchus heterochaetus is a widespread benthic polychaete worm found in coastal brackish waters of the west Pacific. It has high ecological and economic value as a biomarker of water quality and as a high-quality feed in aquaculture and fisheries and is considered a delicacy in some areas of Asia. However, it has experienced a marked reduction in recent years due to overexploitation as well as changes in the environment and climate. Here, to comprehensively understand its genetic background and thus provide insights for better conservation and utilization of this species, we assessed the genetic variability and demographic history of T. heterochaetus individuals sampled from eight locations along the coasts of southeast China and north Vietnam based on mitochondrial cytochrome c oxidase I ( COI) sequences. We observed high haplotype diversity ( Hd), with an average of 0.926, but relatively low nucleotide diversity ( π), with a mean of 0.032 across all samples. A total of 94 polymorphic sites and 85 haplotypes were identified among 320 individuals. The pairwise genetic distances among haplotypes ranged from 0.001 to 0.067, with the high intraspecific divergence possibly reflecting geographic isolation and gene pool fragmentation. Significant genetic structures were revealed among the studied locations; specifically, the eight locations could be treated as six genetically different populations based on pairwise Φ ST results (0.026-0.951, P<0.01). A significant pattern of isolation-by-distance was detected between the genetic and geographic distances ( r=0.873, P=0.001). Three geographic lineages were defined based on phylogenetic tree and network analyses of COI haplotypes. AMOVA results indicated that genetic variations mainly occurred among the three lineages (89.96%). Tests of neutrality and mismatch distribution suggested that T. heterochaetus underwent recent population expansion. These results provide the first report on the genetic status of T. heterochaetus and will be valuable for the management of genetic resources and better understanding of the ecology and evolution in this species.

Decoupled maternal and zygotic genetic effects shape the evolution of development

Evolutionary transitions from indirect to direct development involve changes in both maternal and zygotic genetic factors, with distinctive population-genetic implications, but empirical data on the genetics of such transitions are lacking. The polychaete Streblospio benedicti provides an opportunity to dissect a major transition in developmental mode using forward genetics. Females in this species produce either small eggs that develop into planktonic larvae or large eggs that develop into benthic juveniles. We identify large-effect loci that act maternally to influence larval size and independent, unlinked large-effect loci that act zygotically to affect discrete aspects of larval morphology. The likely fitness of zygotic alleles depends on their maternal background, creating a positive frequency-dependence that may homogenize local populations. Developmental and population genetics interact to shape larval evolution.

Discrete phenotypes are not underpinned by genome-wide genetic differentiation in the squat lobster Munida gregaria (Crustacea: Decapoda: Munididae): a multi-marker study covering the Patagonian shelf

BACKGROUND

DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers. The widespread squat lobster Munida gregaria comprises two discrete ecotypes, gregaria s. str. and subrugosa, which were long regarded as different species due to marked differences in morphological, ecological and behavioral traits. We studied the morphometry and genetics of M. gregaria s. l. and tested (1) whether the phenotypic differences remain stable after continental-scale sampling and inclusion of different life stages, (2) and whether each phenotype is underpinned by a specific genotype.

RESULTS

A total number of 219 gregaria s. str. and subrugosa individuals from 25 stations encompassing almost entire range in South America were included in morphological and genetic analyses using nine unlinked hypervariable microsatellites and new COI sequences. Results from the PCA and using discriminant functions demonstrated that the morphology of the two forms remains discrete. The mitochondrial data showed a shallow, star-like haplotype network and complete overlap of genetic distances within and among ecotypes. Coalescent-based species delimitation methods, PTP and GMYC, coherently suggested that haplotypes of both ecotypes forms a single species. Although all microsatellite markers possess sufficient genetic variation, AMOVA, PCoA and Bayesian clustering approaches revealed no genetic clusters corresponding to ecotypes or geographic units across the entire South-American distribution. No evidence of isolation-by-distance could be detected for this species in South America.

CONCLUSIONS

Despite their pronounced bimodal morphologies and different lifestyles, the gregaria s. str. and subrugosa ecotypes form a single, dimorphic species M. gregaria s. l.. Based on adequate geographic coverage and multiple independent polymorphic loci, there is no indication that each phenotype may have a unique genetic basis, leaving phenotypic plasticity or localized genomic islands of speciation as possible explanations.

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.

A new case of poecilogony from South America and the implications of nurse eggs, capsule structure, and maternal brooding behavior on the development of different larval types

Poecilogony is the production of different larval types within the same species. Although rare, poecilogonous species are ideal systems for testing the evolutionary and ecological implication of different developmental modes in marine invertebrates. Here, we described a new case of poecilogony, the Southern Hemisphere spionid Boccardia wellingtonensis. We used a combination of common-garden experiments, video recordings, and in vitro manipulations of individuals from three sites to (1) document the type of poecilogony, the brooding behavior of the mother, and the hatching process; (2) experimentally measure the effect of nurse eggs on the growth and type of larvae produced; and (3) document variation in the length of the brooding period, number of capsules, larvae, and nurse eggs of mothers from three sites to explore the potential for plasticity in reproductive traits. These results were compared to the previously reported poecilogonous species B. proboscidea, which resembles B. wellingtonensis in size, morphology, ecology, and reproductive strategy but differs in capsule structure. We found that in contrast to B. proboscidea, B. wellingtonensis produced larvae that, in isolation and in the presence of nurse eggs, developed into a wide range of offspring sizes. Mothers brood and hatch the larvae with frequent partial hatching of the brood during the brooding period. Although larvae could not liberate themselves, larvae crossed to other capsules as interconnections between capsules broke during the developmental period, potentially affecting food availability, sibling competition for nurse eggs, and cannibalism. Variation in brooding time and number of capsules deposited among sites suggest local adaptations.

Homogeneous nuclear background for mitochondrial cline in northern range of Notochthamalus scabrosus

A mitochondrial cline along the Chilean coast in the barnacle Notochthamalus scabrosus suggests a species history of transient allopatry and secondary contact. However, previous studies of nuclear sequence divergence suggested population genetic homogeneity across northern and central Chile. Here, we collect single-nucleotide polymorphism data from pooled population samples sequenced with restriction site−associated DNA sequencing procedures, confirm these data with the use of a GoldenGate array, and identify a discordance between population genetic patterns in the nuclear and mitochondrial genomes. This discordance was noted in previous work on this species, but here it is confirmed that the nuclear genome exhibits only slight phylogeographic variation across 3000 km of coastline, in the presence of a strong and statistically significant mitochondrial cline. There are nevertheless markers (approximately 5% of nuclear single-nucleotide polymorphisms) exhibiting cytonuclear disequilibrium relative to mitotype. Although these data confirm our previous explorations of this species, it is likely that some of the nuclear genomic diversity of this species has yet to be explored, as comparison with other barnacle phylogeography studies suggest that a divergence of similar magnitude should be found in the nuclear genome somewhere else in the species range.