Molecular systematics of the deep-sea hydrothermal vent endemic Brachyuran family Bythograeidae: a comparison of three Bayesian species tree methods

Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least 7 and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways. [Brachyura; convergent evolution; crustaceans; divergence times; fossil calibration; molecular phylogeny; terrestrialization; threshold model.].

Cryptic diversity and phylogeographic patterns of Deto echinata (Isopoda: Detonidae) in southern Africa

Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopod Deto echinata is of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterize D. echinata individuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whether D. echinata harbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggest D. echinata is a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.

Beta diversity differs among hydrothermal vent systems: Implications for conservation

Deep-sea hydrothermal vent habitats are small, rare and support unique species through chemosynthesis. As this vulnerable ecosystem is increasingly threatened by human activities, management approaches should address biodiversity conservation. Diversity distribution data provide a useful basis for management approaches as patterns of β-diversity (the change in diversity from site to site) can guide conservation decisions. Our question is whether such patterns are similar enough across vent systems to support a conservation strategy that can be deployed regardless of location. We compile macrofaunal species occurrence data for vent systems in three geological settings in the North Pacific: volcanic arc, back-arc and mid-ocean ridge. Recent discoveries in the Mariana region provide the opportunity to characterize diversity at many vent sites. We examine the extent to which diversity distribution patterns differ among the systems by comparing pairwise β-diversity, nestedness and their additive components. A null model approach that tests whether species compositions of each site pair are more or less similar than random provides insight into community assembly processes. We resolve several taxonomic uncertainties and find that the Mariana arc and back-arc share only 8% of species despite their proximity. Species overlap, species replacement and richness differences create different diversity distributions within the three vent systems; the arc system exhibits much greater β-diversity than both the back-arc and mid-ocean ridge systems which, instead, show greater nestedness. The influence of nestedness on β-diversity also increased from the arc to back-arc to ridge. Community assembly processes appear more deterministic in the arc and ridge systems while back-arc site pairs deviate little from the null expectation. These analyses reflect the need for a variety of management strategies that consider the character of diversity distribution to protect hydrothermal vents, especially in the context of mining hydrothermal deposits.

Complete mitochondrial genome sequence of the genus Austinograea (Malacostraca: Brachyura: Bythograeidae) and its phylogenetic analysis

Austinograea species are restricted to hydrothermal vents and are typically considered to be omnivorous predators in vent communities. Here we present the complete mitochondrial genome of Austinograea sp. which was collected from Carlsberg Ridge, the mid-ocean ridge in the northwestern Indian Ocean. The genome is 15,584 bp in length with a 68.11% AT content. It contains 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis shows that the present species is closest to Austinograea rodriguezensis. This study contributes to further phylogenetic analysis within Eubrachyura.

Population genetic differentiation of the hydrothermal vent crab Austinograea alayseae (Crustacea: Bythograeidae) in the Southwest Pacific Ocean

To understand the origin, migration, and distribution of organisms across disjunct deep-sea vent habitats, previous studies have documented the population genetic structures of widely distributed fauna, such as gastropods, bivalves, barnacles, and squat lobsters. However, a limited number of investigations has been conducted in the Southwest Pacific Ocean, and many questions remain. In this study, we determined the population structure of the bythograeid crab Austinograea alayseae from three adjacent vent systems (Manus Basin, North Fiji Basin, and Tonga Arc) in the Southwest Pacific Ocean using the sequences of two mitochondrial genes (COI and 16S rDNA) and one nuclear gene (28S rDNA). Populations were divided into a Manus clade and a North Fiji-Tonga clade, with sequence divergence values in the middle of the barcoding gap for bythograeids. We inferred that hydrographic and/or physical barriers act on the gene flow of A. alayseae between the Manus and North Fiji basins. Austinograea alayseae individuals interact freely between the North Fiji Basin and the Lau Basin (Tonga Arc). Although further studies of genetic differentiation over a geological time scale, life-history attributes, and genome-based population genetics are needed to improve our understanding of the evolutionary history of A. alayseae, our results contribute to elucidating the phylogeny, evolution, and biogeography of bythograeids.

Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents

BACKGROUND

Chemolithoautotrophic primary production sustains dense invertebrate communities at deep-sea hydrothermal vents and hydrocarbon seeps. Symbiotic bacteria that oxidize dissolved sulfur, methane, and hydrogen gases nourish bathymodiolin mussels that thrive in these environments worldwide. The mussel symbionts are newly acquired in each generation via infection by free-living forms. This study examined geographical subdivision of the thiotrophic endosymbionts hosted by Bathymodiolus mussels living along the eastern Pacific hydrothermal vents. High-throughput sequencing data of 16S ribosomal RNA encoding gene and fragments of six protein-coding genes of symbionts were examined in the samples collected from nine vent localities at the East Pacific Rise, Galápagos Rift, and Pacific-Antarctic Ridge.

RESULTS

Both of the parapatric sister-species, B. thermophilus and B. antarcticus, hosted the same numerically dominant phylotype of thiotrophic Gammaproteobacteria. However, sequences from six protein-coding genes revealed highly divergent symbiont lineages living north and south of the Easter Microplate and hosted by these two Bathymodiolus mussel species. High heterogeneity of symbiont haplotypes among host individuals sampled from the same location suggested that stochasticity associated with initial infections was amplified as symbionts proliferated within the host individuals. The mussel species presently contact one another and hybridize along the Easter Microplate, but the northern and southern symbionts appear to be completely isolated. Vicariance associated with orogeny of the Easter Microplate region, 2.5-5.3 million years ago, may have initiated isolation of the symbiont and host populations. Estimates of synonymous substitution rates for the protein-coding bacterial genes examined in this study were 0.77-1.62%/nucleotide/million years.

CONCLUSIONS

Our present study reports the most comprehensive population genetic analyses of the chemosynthetic endosymbiotic bacteria based on high-throughput genetic data and extensive geographical sampling to date, and demonstrates the role of the geographical features, the Easter Microplate and geographical distance, in the intraspecific divergence of this bacterial species along the mid-ocean ridge axes in the eastern Pacific. Altogether, our results provide insights into extrinsic and intrinsic factors affecting the dispersal and evolution of chemosynthetic symbiotic partners in the hydrothermal vents along the eastern Pacific Ocean.

Exploring the molecular basis of adaptive evolution in hydrothermal vent crab Austinograea alayseae by transcriptome analysis

Elucidating the genetic mechanisms of adaptation to the hydrothermal vent in organisms at genomic level is significant for understanding the adaptive evolution process in the extreme environment. We performed RNA-seq on four different tissues of a vent crab species, Austinograea alayseae, producing 725,461 unigenes and 134,489 annotated genes. Genes related to sensory, circadian rhythm, hormone, hypoxia stress, metal detoxification and immunity were identified. It was noted that in the degenerated eyestalk, transcription of phototransduction related genes which are important for retinal function was greatly reduced; three crucial neuropeptide hormones, one molt-inhibiting and two crustacean hyperglycemic hormone precursors were characterized with conserved domains; hypoxia-inducible factor 1 and two novel isoforms of metallothioneins in the vent crabs were discovered. An analysis of 6,932 orthologs among three crabs A. alayseae, Portunus trituberculutus and Eriocheir sinensis revealed 19 positive selected genes (PSGs). Most of the PSGs were involved in immune responses, such as crustins and anti-lipopolysaccharide factor, suggesting their function in the adaptation to environment. The characterization of the first vent crab transcriptome provides abundant resources for genetic and evolutionary studies of this species, and paves the way for further investigation of vent adaptation process in crabs.

Population subdivision of hydrothermal vent polychaete Alvinella pompejana across equatorial and Easter Microplate boundaries

Background

The Equator and Easter Microplate regions of the eastern Pacific Ocean exhibit geomorphological and hydrological features that create barriers to dispersal for a number of animals associated with deep-sea hydrothermal vent habitats. This study examined effects of these boundaries on geographical subdivision of the vent polychaete Alvinella pompejana. DNA sequences from one mitochondrial and eleven nuclear genes were examined in samples collected from ten vent localities that comprise the species’ known range from 23°N latitude on the East Pacific Rise to 38°S latitude on the Pacific Antarctic Ridge.

Results

Multi-locus genotypes inferred from these sequences clustered the individual worms into three metapopulation segments — the northern East Pacific Rise (NEPR), southern East Pacific Rise (SEPR), and northeastern Pacific Antarctic Ridge (PAR) — separated by the Equator and Easter Microplate boundaries. Genetic diversity estimators were negatively correlated with tectonic spreading rates. Application of the isolation-with-migration (IMa2) model provided information about divergence times and demographic parameters. The PAR and NEPR metapopulation segments were estimated to have split roughly 4.20 million years ago (Mya) (2.42–33.42 Mya, 95 % highest posterior density, (HPD)), followed by splitting of the SEPR and NEPR segments about 0.79 Mya (0.07–6.67 Mya, 95 % HPD). Estimates of gene flow between the neighboring regions were mostly low (2 Nm < 1). Estimates of effective population size decreased with southern latitudes: NEPR > SEPR > PAR.

Conclusions

Highly effective dispersal capabilities allow A. pompejana to overcome the temporal instability and intermittent distribution of active hydrothermal vents in the eastern Pacific Ocean. Consequently, the species exhibits very high levels of genetic diversity compared with many co-distributed vent annelids and mollusks. Nonetheless, its levels of genetic diversity in partially isolated populations are inversely correlated with tectonic spreading rates. As for many other vent taxa, this pioneering colonizer is similarly affected by local rates of habitat turnover and by major dispersal filters associated with the Equator and the Easter Microplate region.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0807-9) contains supplementary material, which is available to authorized users.

Strong Ion Regulatory Abilities Enable the Crab Xenograpsus testudinatus to Inhabit Highly Acidified Marine Vent Systems

Hydrothermal vent organisms have evolved physiological adaptations to cope with extreme abiotic conditions including temperature and pH. To date, acid-base regulatory abilities of vent organisms are poorly investigated, although this physiological feature is essential for survival in low pH environments. We report the acid-base regulatory mechanisms of a hydrothermal vent crab, Xenograpsus testudinatus, endemic to highly acidic shallow-water vent habitats with average environment pH-values ranging between 5.4 and 6.6. Within a few hours, X. testudinatus restores extracellular pH (pHe) in response to environmental acidification of pH 6.5 (1.78 kPa pCO₂) accompanied by an increase in blood HCO3- levels from 8.8 ± 0.3 to 31 ± 6 mM. Branchial Na⁺/K⁺-ATPase (NKA) and V-type H⁺-ATPase (VHA), the major ion pumps involved in branchial acid-base regulation, showed dynamic increases in response to acidified conditions on the mRNA, protein and activity level. Immunohistochemical analyses demonstrate the presence of NKA in basolateral membranes, whereas the VHA is predominantly localized in cytoplasmic vesicles of branchial epithelial- and pillar-cells. X. testudinatus is closely related to other strong osmo-regulating brachyurans, which is also reflected in the phylogeny of the NKA. Accordingly, our results suggest that the evolution of strong ion regulatory abilities in brachyuran crabs that allowed the occupation of ecological niches in euryhaline, freshwater, and terrestrial habitats are probably also linked to substantial acid-base regulatory abilities. This physiological trait allowed X. testudinatus to successfully inhabit one of the world's most acidic marine environments.

Conflicting genomic signals affect phylogenetic inference in four species of North American pines

Adaptive evolutionary processes in plants may be accompanied by episodes of introgression, parallel evolution and incomplete lineage sorting that pose challenges in untangling species evolutionary history. Genus Pinus (pines) is one of the most abundant and most studied groups among gymnosperms, and a good example of a lineage where these phenomena have been observed. Pines are among the most ecologically and economically important plant species. Some, such as the pines of the southeastern USA (southern pines in subsection Australes), are subjects of intensive breeding programmes. Despite numerous published studies, the evolutionary history of Australes remains ambiguous and often controversial. We studied the phylogeny of four major southern pine species: shortleaf (Pinus echinata), slash (P. elliottii), longleaf (P. palustris) and loblolly (P. taeda), using sequences from 11 nuclear loci and maximum likelihood and Bayesian methods. Our analysis encountered resolution difficulties similar to earlier published studies. Although incomplete lineage sorting and introgression are two phenomena presumptively underlying our results, the phylogenetic inferences seem to be also influenced by the genes examined, with certain topologies supported by sets of genes sharing common putative functionalities. For example, genes involved in wood formation supported the clade echinata-taeda, genes linked to plant defence supported the clade echinata-elliottii and genes linked to water management properties supported the clade echinata-palustris The support for these clades was very high and consistent across methods. We discuss the potential factors that could underlie these observations, including incomplete lineage sorting, hybridization and parallel or adaptive evolution. Our results likely reflect the relatively short evolutionary history of the subsection that is thought to have begun during the middle Miocene and has been influenced by climate fluctuations.

Complete mitochondrial genome of the blind vent crab Gandalfus puia (Crustacea: Bythograeidae) from the Tonga Arc

The brachyuran crab Gandalfus puia is a species endemic to the hydrothermal vent fields in the Tonga-Kermadec Arc. In order to understand G. puia at the genomic level, we sequenced its mitochondrial genome (mitogenome) and then compared to other bythograeids. The mitogenome is 15,548 bp in length and exhibits brachyuran-typical gene arrangement. Its protein-coding genes were very similar to other bythograeid species with respect to length, AT content and start and stop codons. Additionally, we compared the mitogenomes of Gandalfus and the closely related Austinograea. The inter-specific nucleotide divergence was 13.4% in Gandalfus and 13.7-14.0% in Austinograea. The inter-generic nucleotide divergence between Gandalfus and Austinograea was 16.3-19.7%. Based on the phylogenetic tree constructed with maximum likelihood and Bayesian inference, bythograeid crabs were recognized as the monophyletic taxon with the high supporting values (100% bootstrap proportions and 1.00 posterior probabilities). These results are useful for understanding the phylogenetic relationships and evolution of bythograeid crabs.

A complex evolutionary history in a remote archipelago: phylogeography and morphometrics of the Hawaiian endemic Ligia isopods

Compared to the striking diversification and levels of endemism observed in many terrestrial groups within the Hawaiian Archipelago, marine invertebrates exhibit remarkably lower rates of endemism and diversification. Supralittoral invertebrates restricted to specific coastal patchy habitats, however, have the potential for high levels of allopatric diversification. This is the case of Ligia isopods endemic to the Hawaiian Archipelago, which most likely arose from a rocky supralittoral ancestor that colonized the archipelago via rafting, and diversified into rocky supralittoral and inland lineages. A previous study on populations of this isopod from O'ahu and Kaua'i revealed high levels of allopatric differentiation, and suggested inter-island historical dispersal events have been rare. To gain a better understanding on the diversity and evolution of this group, we expanded prior phylogeographic work by incorporating populations from unsampled main Hawaiian Islands (Maui, Moloka'i, Lana'i, and Hawai'i), increasing the number of gene markers (four mitochondrial and two nuclear genes), and conducting Maximum likelihood and Bayesian phylogenetic analyses. Our study revealed new lineages and expanded the distribution range of several lineages. The phylogeographic patterns of Ligia in the study area are complex, with Hawai'i, O'ahu, and the Maui-Nui islands sharing major lineages, implying multiple inter-island historical dispersal events. In contrast, the oldest and most geographically distant of the major islands (Kaua'i) shares no lineages with the other islands. Our results did not support the monophyly of all the supralittoral lineages (currently grouped into L. hawaiensis), or the monophyly of the terrestrial lineages (currently grouped into L. perkinsi), implying more than one evolutionary transition between coastal and inland forms. Geometric-morphometric analyses of three supralittoral clades revealed significant body shape differences among them. A taxonomic revision of Hawaiian Ligia is warranted. Our results are relevant for the protection of biodiversity found in an environment subject to high pressure from disturbances.

Nuclear mitochondrial pseudogenes in Austinograea alayseae hydrothermal vent crabs (Crustacea: Bythograeidae): effects on DNA barcoding

Members of the brachyuran crab family, Bythograeidae, are among the most abundant and common crabs in vent fields. However, their identification based on morphological characteristics often leads to incorrect species recognition due to a lack of taxonomic factors and the existence of sibling (or cryptic) species. For these reasons, we used DNA barcoding for vent crabs using mitochondrial cytochrome c oxidase subunit 1 (CO1). However, several nuclear mitochondrial pseudogenes (Numts) were amplified from Austinograea alayseae Guinot, 1990, using universal primers (Folmer primers). The Numts were characterized in six haplotypes, with 13.58-14.11% sequence divergence from A. alayseae, a higher nonsynonymous substitution ratio than true CO1, and the formation of an independent clade in bythograeids. In a neighbour-joining tree, the origin of the Numts would be expected to incorporate into the nucleus at an ancestral node of Austinograea, and they mutated more slowly in the nucleus than CO1 in the mitochondria. This evolutionary process may have resulted in the higher binding affinity of Numts for the Folmer primers than CO1. In the present study, we performed long PCR for the amplification of CO1 in A. alayseae. We also present evidence that Numts can introduce serious ambiguity into DNA barcoding, including overestimating the number of species in bythograeids. These results may help in conducting taxonomic studies using mitochondrial genes from organisms living in hydrothermal vent fields.