Correlated evolution of larval development, egg size and genome size across two genera of snapping shrimp.

Across plants and animals, genome size is often correlated with life-history traits: large genomes are correlated with larger seeds, slower development, larger body size and slower cell division. Among decapod crustaceans, caridean shrimps are among the most variable both in terms of genome size variation and life-history characteristics such as larval development mode and egg size, but the extent to which these traits are associated in a phylogenetic context is largely unknown. In this study, we examine correlations among egg size, larval development and genome size in two different genera of snapping shrimp, Alpheus and Synalpheus, using phylogenetically informed analyses. In both Alpheus and Synalpheus, egg size is strongly linked to larval development mode: species with abbreviated development had significantly larger eggs than species with extended larval development. We produced the first comprehensive dataset of genome size in Alpheus (n = 37 species) and demonstrated that genome size was strongly and positively correlated with egg size in both Alpheus and Synalpheus. Correlated trait evolution analyses showed that in Alpheus, changes in genome size were clearly dependent on egg size. In Synalpheus, evolutionary path analyses suggest that changes in development mode (from extended to abbreviated) drove increases in egg volume; larger eggs, in turn, resulted in larger genomes. These data suggest that variation in reproductive traits may underpin the high degree of variation in genome size seen in a wide variety of caridean shrimp groups more generally.

Patterns of genome size variation in snapping shrimp.

Although crustaceans vary extensively in genome size, little is known about how genome size may affect the ecology and evolution of species in this diverse group, in part due to the lack of large genome size datasets. Here we investigate interspecific, intraspecific, and intracolony variation in genome size in 39 species of Synalpheus shrimps, representing one of the largest genome size datasets for a single genus within crustaceans. We find that genome size ranges approximately 4-fold across Synalpheus with little phylogenetic signal, and is not related to body size. In a subset of these species, genome size is related to chromosome size, but not to chromosome number, suggesting that despite large genomes, these species are not polyploid. Interestingly, there appears to be 35% intraspecific genome size variation in Synalpheus idios among geographic regions, and up to 30% variation in Synalpheus duffyi genome size within the same colony.

Phylogenetic relationships within the snapping shrimp genus Synalpheus (Decapoda: Alpheidae).

The snapping shrimp genus Synalpheus (Alpheidae) is one of the most speciose decapod genera, with over 160 described species worldwide. Most species live in symbiotic relationships with other marine organisms, such as sponges, corals and crinoids, and some sponge-dwelling species have a highly organized, social structure. The present study is the first worldwide molecular phylogenetic analysis of Synalpheus, based on >2,200 bp of sequence data from two mitochondrial (COI and 16S) and two nuclear (PEPCK and 18S) loci. Our molecular data show strong support for monophyly of three out of six traditionally recognized morphology-based species groups: the S. brevicarpus, S. comatularum and S. gambarelloides groups. The remaining three species groups (S. paulsoni, S. neomeris and S. coutierei groups) are non-monophyletic in their current composition and will need to be either abandoned or taxonomically redefined. We also identified potential cryptic species of Synalpheus in our dataset, using intraspecific and interspecific sequence variation in COI from the taxonomically well-studied S. gambarelloides group to establish a genetic divergence threshold. We then used both genetic divergence and tree-based criteria (reciprocal monophyly) to identify potential cryptic species in the remaining taxa of the genus. Our results suggest the presence of multiple cryptic lineages in Synalpheus, underlining the need for more integrative taxonomic studies-including morphological, ecological, molecular, and color pattern data-in this biologically interesting genus.

A new sponge-dwelling species of Synalpheus Spence Bate, 1888 (Decapoda: Caridea: Alpheidae) from the Persian Gulf.

The present study is based on material collected in the intertidal and shallow subtidal areas of two Islands in the Persian Gulf, Abu-Musa and Larak. The new species, Synalpheus pentaspinosus n. sp., is closely related to S. quinquedens Tattersall, 1921. These two species share a very characteristic, sixth pleonite armed posteriorly with five stout sharp teeth, a feature unique within the genus. The color of ovaries or freshly laid eggs, red-orange in S. pentaspinosus n. sp. vs. green in S. quinquedens, is the most obvious character, by which the new species may be distinguished from S. quinquedens in the field. In addition, the two species can be separated by two characters on the dactylus of the minor cheliped. In the new species, the dactylus is furnished with two prominent rows of setae, one dorsally and one mesially, and has a small concavity on the cutting edge, contrasting to only one mesial row of setae and no obvious concavity in S. quinquedens.

TERAD: Extraction of transposable element composition from RADseq data.

Transposable elements (TEs) - selfish DNA sequences that can move within the genome - comprise a large proportion of the genomes of many organisms. Although low-coverage whole-genome sequencing can be used to survey TE composition, it is noneconomical for species with large quantities of DNA. Here, we utilize restriction-site associated DNA sequencing (RADSeq) as an alternative method to survey TE composition. First, we demonstrate in silico that double digest restriction-site associated DNA sequencing (ddRADseq) markers contain the same TE compositions as whole genome assemblies across arthropods. Next, we show empirically using eight Synalpheus snapping shrimp species with large genomes that TE compositions from ddRADseq and low-coverage whole-genome sequencing are comparable within and across species. Finally, we develop a new bioinformatic pipeline, TERAD, to extract TE compositions from RADseq data. Our study expands the utility of RADseq to study the repeatome, making comparative studies of genome structure for species with large genomes more tractable and affordable.

Synalpheus amintae sp. nov., a new species of sponge-dwelling snapping shrimp (Crustacea: Decapoda: Alpheidae) from Parque Nacional Natural Isla Gorgona, Pacific Coast of Colombia.

A new species of sponge-dwelling snapping shrimp, Synalpheus amintae sp. nov. from the Parque Nacional Natural Isla Gorgona, Pacific coast of Colombia, is described. This new species pertains to the denominated Synalpheus "Gambarelloides" species group sensu Coutière (1909)-previously known as "Laevimanus" group. It was collected in the southern part of the Island, during episodes of extreme low tides, known locally as "puja". Synalpheus amintae sp. nov. is closely related to the only two other known species of the S. "Gambarelloides" species group from the eastern Pacific: Synalpheus occidentalis Coutière, 1909, from Gulf of San José, Lower California, and Synalpheus mulegensis Ríos, 1992, from Bahía Concepción, Gulf of California, and can be differentiated from them by the poorly developed distal portion of pollex of the major cheliped, the armature of the distal segment of third maxilliped, and the number of acute teeth of exopodal uropod. A discriminative analysis dealing with other three species of Synalpheus from the western Atlantic, with distinctive pollex of major chela reduced, is presented. A dichotomous key was elaborated to identify the species of Synalpheus "Gambarelloides" species group from the eastern Pacific. The number of valid species described of Synalpheus from the eastern Pacific is increased to 23.

Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes.

Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes.

RESOURCE-ASSOCIATED POPULATION SUBDIVISION IN A SYMBIOTIC CORAL-REEF SHRIMP.

The importance of sympatric speciation remains controversial. An empirical observation frequently offered in its support is the occurrence of sister taxa living in sympatry but using different resources. To examine the possibility of sympatric differentiation in producing such cases, I measured genetic, behavioral, and demographic differentiation between populations of the tropical sponge-dwelling shrimp Synalpheus brooksi occupying two alternate host species on three reefs in Caribbean Panama. This species belongs to an apparently monophyletic group of ≥ 30 species of mostly obligate, host-specific sponge-dwellers, many of which occur in sympatry. Demographic data demonstrated the potential for disruptive selection imposed by the two host species: shrimp demes from the sponge Agelas clathrodes were consistently denser, poorer in mature females, more heavily parasitized by branchial bopyrid isopods, and less parasitized by thoracic isopods, than conspecific shrimp from the sponge Spheciospongia vesparium. Laboratory assays demonstrated divergence in host preference: shrimp on all three reefs tended to choose their native sponge species more often than did conspecific shrimp from the other host. Because S. brooksi mates within the host, this habitat selection should foster assortative mating by host species. A hierarchical survey of protein-electrophoretic variation also supported host-mediated divergence, revealing the following: (1) shrimp from the two hosts are conspecific, as evidenced by absence of fixed allelic differences at any of nine allozyme loci scored; (2) strong genetic subdivision among populations of this philopatric shrimp on reefs separated by 1-3 km; and (3) significant host-associated genetic differentiation within two of the three reefs. Finally, intersexual aggression (a proxy for mating incompatibility) between shrimp from different host species was significantly elevated on the one reef where host-associated genetic differences were strongest, demonstrating concordance between genetic and behavioral estimates of divergence. Adjacent reefs appear to be semi-independent sites of host-associated differentiation, as evidenced by differences in the degree of host-associated behavioral and genetic differentiation, and in the specific loci involved, on different reefs. In philopatric organisms with highly subdivided populations, such as S. brooksi, resource-associated differentiation can occur independently in different populations, thus providing multiple "experiments" in differentiation and resulting in a mosaic pattern of polymorphism as reflected by neutral genetic markers. Several freshwater fishes, an amphipod, and a snail similarly show independent but remarkably convergent patterns of resource-associated divergence in different conspecific populations, often in the absence of obvious spatial barriers. In each case, substantial differentiation has occurred in the face of continuing gene flow.