Ecological speciation in anemone-associated snapping shrimps (Alpheus armatusspecies complex)

Bellactis lux n. sp. (Cnidaria: Anthozoa: Actiniaria: Aiptasiidae), a new sea anemone from the Gulf of Mexico

Here we describe a new species of sea anemone from the family Aiptasiidae based on specimens collected from the Gulf of Mexico (USA: Florida & Alabama). Accounts of this species have been known since the early 1990s, primarily from an underwater field guide and hobbyist aquarium literature under the name Lightbulb Anemone. We describe it as a new species from the genus Bellactis based on anatomy, histology, and cnidom. Members of this species are small in size, with a smooth, typically contracted column divided into regions based on color and bearing rows of two or three elevated cinclides in the mid column. Their tentacles are distinctive, translucent, distally inflated and can be bulbous in shape, with sub annular rings. This description synthesizes information about Bellactis and contextualizes what is known about its diversity in light of other members of the Aiptasiidae.

Ecological speciation by sympatric host shifts in a clade of herbivorous sea slugs, with introgression and localized mitochondrial capture between species

Host shifting in insect-plant systems was historically important to the development of ecological speciation theory, yet surprisingly few studies have examined whether host shifting drives diversification of marine herbivores. When small-bodied consumers feed and also mate on a preferred host, disruptive selection can split a population into host races despite gene flow. Support for host shifts is notably lacking for invertebrates associated with macroalgae, where the scale of dispersal by planktonic larvae often far exceeds the grain of host patchiness, and adults are typically less specialized than terrestrial herbivores. Here, we present a candidate example of ecological speciation in a clade of sea slugs that primarily consume green algae in the genus Caulerpa, including highly invasive species. Ancestral character state reconstructions supported 'sea grapes' (C. racemosa, C. lentillifera) as the ancestral host for a tropical radiation of 12 Elysia spp., with one shift onto alternative Caulerpa spp. in the Indo-Pacific. A Caribbean radiation of three species included symaptric host shifts to Rhipocephalus brevicaulis in the ancestor of E. pratensis Ortea & Espinosa, 1996, and to C. prolifera in E. hamanni Krug, Vendetti & Valdes 2016, plus a niche expansion to a range of Caulerpa spp. in E. subornata Verrill, 1901. All three species are broadly sympatric across the Caribbean but are host-partitioned at a fine grain, and distinct by morphology and at nuclear loci. However, non-recombining mtDNA revealed a history of gene flow between E. pratensis and E. subornata: COI haplotypes from E. subornata were 10.4% divergent from E. pratensis haplotypes from four sites, but closely related to all E. pratensis haplotypes sampled from six Bahamian islands, indicating historical introgression and localized "mitochondrial capture." Disruptive selective likely fueled divergence and adaptation to distinct host environments, indicating ecological speciation may be an under-appreciated driver of diversification for marine herbivores as well as epibionts and other resource specialists.

Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

Background

The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome.

Results

To estimate the genome-wide neutral mutation rate (µ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. A range of bioinformatic filtering parameters were evaluated in order to minimize potential bias in mutation rate estimates that may result from SNP filtering. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated µ to be 2.64E−9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. Post-divergence gene flow was detected in one species pair. Failure to account for this post-split migration inflates our substitution rate estimates, emphasizing the importance of demographic methods that can accommodate gene flow.

Conclusions

Results from our study, both parameter estimates and bioinformatic explorations, have broad-ranging implications for phylogeographic studies in other non-model taxa using reduced representation datasets. Our best estimate of µ that accounts for coalescent and demographic processes is remarkably similar to experimentally derived mutation rates in model arthropod systems. These results contradicted recent suggestions that the closure of the Isthmus was completed much earlier (around 10 Ma), as mutation rates based on an early calibration resulted in uncharacteristically low genomic mutation rates. Also, stricter filtering parameters resulted in biased datasets that generated lower mutation rate estimates and influenced demographic parameters, serving as a cautionary tale for the adherence to conservative bioinformatic strategies when generating reduced-representation datasets at the species level. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01836-3.

Surveying keratose sponges (Porifera, demospongiae, Dictyoceratida) reveals hidden diversity of host specialist barnacles (Crustacea, Cirripedia, Balanidae)

Sponges represent one of the most species-rich hosts for commensal barnacles yet host utilisation and diversity have not been thoroughly examined. This study investigated the diversity and phylogenetic relationships of sponge-inhabiting barnacles within a single, targeted host group, primarily from Western Australian waters. Specimens of the sponge order Dictyoceratida were surveyed and a total of 64 host morphospecies, representing four families, were identified as barnacle hosts during the study. Utilising molecular (COI, 12S) and morphological methods 42 molecular operational taxonomic units (MOTUs) of barnacles, representing Acasta, Archiacasta, Euacasta and Neoacasta were identified. Comparing inter- and intra-MOTU genetic distances showed a barcode gap between 2.5% and 5% for COI, but between 1% and 1.5% in the 12S dataset, thus demonstrating COI as a more reliable barcoding region. These sponge-inhabiting barnacles were demonstrated to show high levels of host specificity with the majority being found in a single sponge species (74%), a single genus (83%) or a single host family (93%). Phylogenetic relationships among the barnacles were reconstructed using mitochondrial (12S, COI) and nuclear (H3, 28S) markers. None of the barnacle genera were recovered as monophyletic. Euacasta was paraphyletic in relation to the remaining Acastinae genera, which were polyphyletic. Six well-supported clades of molecular operational taxonomic units, herein considered to represent species complexes, were recovered, but relationships between them were not well supported. These complexes showed differing patterns of host usage, though most were phylogenetically conserved with sister lineages typically occupying related hosts within the same genus or family of sponge. The results show that host specialists are predominant, and the dynamics of host usage have played a significant role in the evolutionary history of the Acastinae.

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.

Speciation-by-depth on coral reefs: Sympatric divergence with gene flow or cryptic transient isolation?

The distributions of many sister species in the sea overlap geographically but are partitioned along depth gradients. The genetic changes leading to depth segregation may evolve in geographic isolation as a prerequisite to coexistence or may emerge during primary divergence leading to new species. These alternatives can now be distinguished via the power endowed by the thousands of scorable loci provided by second-generation sequence data. Here, we revisit the case of two depth-segregated, genetically isolated ecotypes of the nominal Caribbean candelabrum coral Eunicea flexuosa. Previous analyses based on a handful of markers could not distinguish between models of genetic exchange after a period of isolation (consistent with secondary contact) and divergence with gene flow (consistent with primary divergence). Analyses of the history of isolation, genetic exchange and population size based on 15,640 new SNP markers derived from RNAseq data best support models where divergence began 800K BP and include epochs of divergence with gene flow, but with an intermediate period of transient isolation. Results also supported the previous conclusion that recent exchange between the ecotypes occurs asymmetrically from the Shallow lineage to the Deep. Parallel analyses of data from two other corals with depth-segregated populations (Agaricia fragilis and Pocillopora damicornis) suggest divergence leading to depth-segregated populations may begin with a period of symmetric exchange, but that an epoch of population isolation precedes more complete isolation marked by asymmetric introgression. Thus, while divergence-with-gene flow may account for much of the differentiation that separates closely related, depth-segregated species, it remains to be seen whether any critical steps in the speciation process only occur when populations are isolated.

Mitochondrial heteroplasmy and pseudogenes in the freshwater prawn, Macrobrachium amazonicum (Heller, 1862): DNA barcoding and phylogeographic implications

The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of Macrobrachium amazonicum, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.

Genomic signatures of host-associated divergence and adaptation in a coral-eating snail, Coralliophila violacea (Kiener, 1836)

The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail, Coralliophila violacea (Kiener 1836), that specializes on Porites corals in the Indo-Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we examined the mechanisms promoting and maintaining the snails' adaptation to their coral hosts. Genome-wide single nucleotide polymorphism (SNP) data from type II restriction site-associated DNA (2b-RAD) sequencing revealed two differentiated clusters of C. violacea that were largely concordant with coral host, consistent with previous genetic results. However, the presence of some admixed genotypes indicates gene flow from one lineage to the other. Combined, these results suggest that differentiation between host-associated lineages of C. violacea is occurring in the face of ongoing gene flow, requiring strong selection. Indeed, 2.7% of all SNP loci were outlier loci (73/2,718), indicative of divergence with gene flow, driven by adaptation of each C. violacea lineage to their specific coral hosts.

Cryptic ecological and geographic diversification in coral-associated nudibranchs

Coral reefs are among the most biologically diverse ecosystems of the world, yet little is known about the processes creating and maintaining their diversity. Ecologically, corallivory in nudibranchs resembles phytophagy in insects- a process that for decades has served as a model for ecological speciation via host shifting. This study uses extensive field collections, DNA sequencing, and phylogenetic analyses to reconstruct the evolutionary history of coral-associated nudibranchs and assess the relative roles that host shifting and geography may have played in their diversification. We find that the number of species is three times higher than the number previously known to science, with evidence for both allopatric and ecological divergence through host shifting and host specialization. Results contribute to growing support for the importance of ecological diversification in marine environments and provide evidence for new species in the genus Tenellia.

Amplicon sequencing of 42 nuclear loci supports directional gene flow between South Pacific populations of a hydrothermal vent limpet

In the past few decades, population genetics and phylogeographic studies have improved our knowledge of connectivity and population demography in marine environments. Studies of deep-sea hydrothermal vent populations have identified barriers to gene flow, hybrid zones, and demographic events, such as historical population expansions and contractions. These deep-sea studies, however, used few loci, which limit the amount of information they provided for coalescent analysis and thus our ability to confidently test complex population dynamics scenarios. In this study, we investigated population structure, demographic history, and gene flow directionality among four Western Pacific hydrothermal vent populations of the vent limpet Lepetodrilus aff. schrolli. These vent sites are located in the Manus and Lau back-arc basins, currently of great interest for deep-sea mineral extraction. A total of 42 loci were sequenced from each individual using high-throughput amplicon sequencing. Amplicon sequences were analyzed using both genetic variant clustering methods and evolutionary coalescent approaches. Like most previously investigated vent species in the South Pacific, L. aff. schrolli showed no genetic structure within basins but significant differentiation between basins. We inferred significant directional gene flow from Manus Basin to Lau Basin, with low to no gene flow in the opposite direction. This study is one of the very few marine population studies using >10 loci for coalescent analysis and serves as a guide for future marine population studies.

Observations on the symbiotic relationship between the caridean shrimp Odontonia sibogae (Bruce, 1972) and its ascidian host Herdmania momus (Savigny, 1816)

Symbiotic relationships between shrimps and other invertebrates are a very common phenomenon in tropical environments. Although the caridean shrimp-ascidian association has been known for many years, the nature of this relationship is still unclear. The current study investigated the association between the caridean shrimp Odontonia sibogae (Bruce, 1972) and solitary ascidians. A combination of field work conducted along the Red Sea coast of Israel and laboratory experiments, conducted during 2015–2016, revealed a clear preference of the shrimps for the ascidian species Herdmania momus (Savigny, 1816), with a low survival ability of the shrimp outside their host's body. The shrimps usually inhabit their host as pairs of male and female or pair of females, but never as pairs of males. Out of the 53 studied females, 51% were observed to bear between 156–1,146 embryos, throughout the course of the year. As these ascidian hosts are known to create large aggregates, we suggest that males may possibly wander among the ascidians occupied by females in order to increase their reproductive success. To date, this is the first study to record the shrimp Dactylonia ascidicola (Borradaile, 1898) inhabiting the ascidian H. momus; and the first study to investigate in depth the ascidian-shrimp association in the Red Sea. It thus provides a platform for future research into the physiological and behavioral adaptations required for such a unique association.

Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)

Background

The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversity. In this context, shifts between major prey types could constitute important factors explaining the biodiversity of marine taxa, particularly in groups with highly specialized diets. However, the scarcity of marine specialized consumers for which reliable phylogenies exist hampers attempts to test the role of trophic specialization in evolution. In this study, RNA-Seq data is used to produce a phylogeny of Cladobranchia, a group of marine invertebrates that feed on a diverse array of prey taxa but mostly specialize on cnidarians. The broad range of prey type preferences allegedly present in two major groups within Cladobranchia suggest that prey type shifts are relatively common over evolutionary timescales.

Results

In the present study, we generated a well-supported phylogeny of the major lineages within Cladobranchia using RNA-Seq data, and used ancestral state reconstruction analyses to better understand the evolution of prey preference. These analyses answered several fundamental questions regarding the evolutionary relationships within Cladobranchia, including support for a clade of species from Arminidae as sister to Tritoniidae (which both preferentially prey on Octocorallia). Ancestral state reconstruction analyses supported a cladobranchian ancestor with a preference for Hydrozoa and show that the few transitions identified only occur from lineages that prey on Hydrozoa to those that feed on other types of prey.

Conclusions

There is strong phylogenetic correlation with prey preference within Cladobranchia, suggesting that prey type specialization within this group has inertia. Shifts between different types of prey have occurred rarely throughout the evolution of Cladobranchia, indicating that this may not have been an important driver of the diversity within this group.

Electronic supplementary material

The online version of this article (10.1186/s12862-017-1066-0) contains supplementary material, which is available to authorized users.

Comprehensive analysis and reinterpretation of Cenozoic mesofossils reveals ancient origin of the snapping claw of alpheid shrimps

Alpheid snapping shrimps (Decapoda: Caridea: Alpheidae) constitute one of the model groups for inferences aimed at understanding the evolution of complex structural, behavioural, and ecological traits among benthic marine invertebrates. Despite being a super-diverse taxon with a broad geographical distribution, the alpheid fossil record is still poorly known. However, data presented herein show that the strongly calcified fingertips of alpheid snapping claws are not uncommon in the fossil record and should be considered a novel type of mesofossil. The Cenozoic remains analysed here represent a compelling structural match with extant species of Alpheus. Based on the presence of several distinct snapping claw-fingertip morphotypes, the major radiation of Alpheus lineages is estimated to have occurred as early as 18 mya. In addition, the oldest fossil record of alpheids in general can now be confirmed for the Late Oligocene (27–28 mya), thus providing a novel minimum age for the entire group as well as the first reliable calibration point for deep phylogenetic inferences.