Molecular characterization reveals the complexity of previously overlooked coral-exosymbiont interactions and the implications for coral-guild ecology

Genomic Insights From Natural History Collections Reveal Cryptic Speciation in Coral Guard Crabs (Family: Trapeziidae)

Mutualistic relationships such as the one between Trapezia crabs and coral colonies are common in reef organisms and play a crucial role in coral resilience and resistance to climate-induced stressor, yet very little is known about the taxonomic diversity and evolutionary history of the species involved. Despite being essential actors of coral reefs and threatened by the ongoing degradation of their habitat, little genetic information is available for Trapezia crabs, including the exact number of species and their relationships. To overcome this limitation, we sampled Natural History Collections, an important and underutilized source of genomic data. We used a novel approach optimized for degraded DNA to generate high-quality genomic data from a combination of 166 museum tissues and freshly collected samples and recovered a strongly supported phylogeny of the Trapezia genus, clarifying species relationships of a majority of taxa and suggesting the potential division of Trapezia into two genera. We then focused on the most widespread species T. bidentata and identified four distinct genetic clusters, suggesting high divergence and cryptic speciation in the Indian Ocean and the Marquesas Islands. Populations of the Central and West Pacific showed signs of admixture across a heterogeneous seascape, attributing to a potentially long pelagic dispersal phase and expansive gene pool. Our results highlight the need to further explore the genetic diversity within other Trapezia species and other coral-associated organisms, as they are likely to exhibit more complex genetic patterns than previously understood.

An integrative phylogeography for inferring cryptic speciation in the Alpheus lottini species complex, an important coral mutualist

We use molecular analyses, color patterns, and records of distribution of mating pairs to reconstruct the global phylogeography of Alpheus lottini, a complex of cryptic coral-associated snapping shrimp species. Molecular data support the delineation of ancestral clades A, B, and C, and suggest five additional subdivisions within clades A and B. Clades A, B1, B2, and C exhibit color pattern differences and/or evidence of assortative mating, and thus merit species-level recognition. There is no evidence for assortative mating within clades A and B1, with likely reproductive compatibility (i.e., fertile clutches) in areas of sympatry. The clade diversity peaks in the Mariana Islands and the early branching clade C is restricted to the northern periphery of the Central and Western Pacific suggesting a Pacific origin of this group outside of the Coral Triangle. These findings underscore the prevalence of allopatric processes with possible ecological or microallopatric speciation in areas where clades overlap.

First worldwide molecular phylogeny of the morphologically and ecologically hyperdiversified snapping shrimp genus Alpheus (Malacostraca: Decapoda)

Hyperdiverse animal groups raise intriguing questions regarding the factors that generate and maintain their diversity. The snapping shrimp genus Alpheus (with >300 described species) is a spectacularly diversified group of decapod crustaceans that serves as an exemplary system for addressing evolutionary questions regarding morphological adaptations, symbiosis, cryptic diversity and molecular divergence. A lack of information regarding evolutionary relationships among species has limited investigations into the mechanisms that drive the diversification of Alpheus. Previous phylogenetic studies of Alpheus have been restricted in scope, while molecular datasets used for phylogenetic reconstructions have been based solely on mitochondrial and a handful of nuclear markers. Here we use an anchored hybrid enrichment (AHE) approach to resolve phylogenetic relationships among species of Alpheus. The AHE method generated sequence data for 240 loci (>72,000 bp) for 65 terminal species that span the geographic, ecological and taxonomic diversity of Alpheus. Our resulting, well-supported phylogeny demonstrates a lack of monophyly for five out of seven morphologically defined species groups that have traditionally been used as a framework in Alpheus taxonomy. Our results also suggest that symbiotic associations with a variety of other animals have evolved independently in at least seven lineages in this genus. Our AHE phylogeny represents the most comprehensive phylogenetic treatment of Alpheus to date and will provide a useful evolutionary framework to further investigate questions, such as various modifications of the snapping claw and the role of habitat specialization and symbiosis in promoting speciation. Running head: PHYLOGENY OF THE SNAPPING SHRIMP GENUS ALPHEUS.

Recent and old duplications in crustaceans "Internal Transcribed Spacer 1″: structural and phylogenetic implications

Internal Transcribed Spacer structures are important in preserving accessibility to specific enzymes for the maturation of rRNAs. ITS1 sequences reported in the literature in Crustaceans range between 182 and 820 bp and are characterized by the absence of repeats or the presence of only a limited number of microsatellites. Here, we sequenced ITS1 for a range of shrimp families (infraorder Caridea) and show that most taxa have much larger ITS1 sequences. We find a high number of microsatellites in Alpheus hebes and Crangon crangon and we report repeat units in Pandalidae, Palaemonidae and mainly in Alpheidae species. Up to four repeats were found in A. vanderbilti (1915 bp), A. rostratus (1635 bp) and A. lottini (1625 bp). In general, four helices were found in ITS1. Repeat units led to extra hairpins and loops. No conserved positions occurred except in helix 4. Three clades were defined in A. lottini for the first time. We estimated the ITS1 divergence rate for the three clades of A. lottini collected in French Polynesia using existing calibrations of substitution rates. Rates of sequence evolution are largely influenced by repeat units, which likely evolve separately. By comparison with COI marker, we estimated the divergence rate of the whole ITS1 sequence to range from 0.5 to 1.4% Pmy and between 0.12 and 0.5% for the 3' end of ITS1 located outside the repeat units. Given the degree of identity between repeats, we suggest that a duplication event recently occurred in A. floridanus (98% identity) whereas an ancient duplication happened in A. sulcatus (50% identity) early at the origination of the group Alpheidae, approximately 50 mya ago. In conclusion, our results highlight an over representation of shorter ITS1 sequences in public repositories, and underlines the importance to further understand patterns of molecular evolution of this functionally important gene.