Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species

The Impact of Whole Genome Duplication on the Evolution of the Arachnids

The proliferation of genomic resources for Chelicerata in the past 10 years has revealed that the evolution of chelicerate genomes is more dynamic than previously thought, with multiple waves of ancient whole genome duplications affecting separate lineages. Such duplication events are fascinating from the perspective of evolutionary history because the burst of new gene copies associated with genome duplications facilitates the acquisition of new gene functions (neofunctionalization), which may in turn lead to morphological novelties and spur net diversification. While neofunctionalization has been invoked in several contexts with respect to the success and diversity of spiders, the overall impact of whole genome duplications on chelicerate evolution and development remains imperfectly understood. The purpose of this review is to examine critically the role of whole genome duplication on the diversification of the extant arachnid orders, as well as assess functional datasets for evidence of subfunctionalization or neofunctionalization in chelicerates. This examination focuses on functional data from two focal model taxa: the spider Parasteatoda tepidariorum, which exhibits evidence for an ancient duplication, and the harvestman Phalangium opilio, which exhibits an unduplicated genome. I show that there is no evidence that taxa with genome duplications are more successful than taxa with unduplicated genomes. I contend that evidence for sub- or neofunctionalization of duplicated developmental patterning genes in spiders is indirect or fragmentary at present, despite the appeal of this postulate for explaining the success of groups like spiders. Available expression data suggest that the condition of duplicated Hox modules may have played a role in promoting body plan disparity in the posterior tagma of some orders, such as spiders and scorpions, but functional data substantiating this postulate are critically missing. Spatiotemporal dynamics of duplicated transcription factors in spiders may represent cases of developmental system drift, rather than neofunctionalization. Developmental system drift may represent an important, but overlooked, null hypothesis for studies of paralogs in chelicerate developmental biology. To distinguish between subfunctionalization, neofunctionalization, and developmental system drift, concomitant establishment of comparative functional datasets from taxa exhibiting the genome duplication, as well as those that lack the paralogy, is sorely needed.

Conserving migratory waterbirds and the coastal zone: the future of South-east Asia's intertidal wetlands

South-east Asia's diverse coastal wetlands, which span natural mudflats and mangroves to man-made salt pans, offer critical habitat for many migratory waterbird species in the East Asian–Australasian Flyway. Species dependent on these wetlands include nearly the entire population of the Critically Endangered spoon-billed sandpiper Calidris pygmaea and the Endangered spotted greenshank Tringa guttifer, and significant populations of several other globally threatened and declining species. Presently, more than 50 coastal Important Bird and Biodiversity Areas (IBAs) in the region (7.4% of all South-east Asian IBAs) support at least one threatened migratory species. However, recent studies continue to reveal major knowledge gaps on the distribution of migratory waterbirds and important wetland sites along South-east Asia's vast coastline, including undiscovered and potential IBAs. Alongside this, there are critical gaps in the representation of coastal wetlands across the protected area networks of many countries in this region (e.g. Viet Nam, Indonesia, Malaysia), hindering effective conservation. Although a better understanding of the value of coastal wetlands to people and their importance to migratory species is necessary, governments and other stakeholders need to do more to strengthen the conservation of these ecosystems by improving protected area coverage, habitat restoration, and coastal governance and management. This must be underpinned by the judicious use of evidence-based approaches, including satellite-tracking of migratory birds, ecological research and ground surveys.

Enhanced immunity and hemocytes proliferation by three immunostimulants in tri-spine horseshoe crab Tachypleus tridentatus

Tachypleus amebocyte lysate (TAL) is crucial in medical testing, but its industry in China has been restricted due to the decline of horseshoe crab population in recent years. Exploring methods of enhancing immunity and rapid hemocytes proliferation is urgent for the industrial horseshoe crab culture. In this study, β-glucan (G), peptidoglycan (P), and squalene (S) were injected to horseshoe crabs at two concentrations (5 and 10 mg/kg), in order to compare their effects on total hemocyte count (THC), reactive oxygen species (ROS), and non-specific immune enzyme activities. Results showed that the THC, superoxide dismutase (SOD), catalase (CAT), and total antioxidant capacity (T-AOC) were significantly increased by three immunostimulants at different points of time; ROS was significantly increased except at two squalene groups; lysozyme (LZM) and alkaline phosphatase (AKP) activity were increased except at low dose (5 mg/kg) squalene group; malondialdehyde (MDA) activity was decreased in all treatments; and hemocyanin concentration (HC) changed little during the experiment. At the 48th hour, THC, ROS, SOD, CAT, T-AOC, LZM, and AKP activities were significantly higher in the two peptidoglycan groups than those in the control group; the low dose β-glucan and squalene groups showed significantly higher SOD and CAT, but their THC and AKP were not significantly different from those of the control group. In general, all three immunostimulants stimulated the hemolymph parameters of horseshoe crabs, notably, peptidoglycan could significantly increase the THC and enzyme activities, suggesting that peptidoglycan can be developed as an efficient immunostimulant for horseshoe crabs.

Mitochondrial DNA sequence of the horseshoe crab Tachypleus gigas

This paper reports on the complete mitochondrial (mt) genome of a horseshoe crab, Tachypleus gigas (T. gigas), in Kuala Kemaman, Terengganu, Malaysia. Whole-genome sequencing of hemocyte DNA was performed with Illumina HiSeq system and the generated reads were de novo assembled with ABySS 2.1.5 and reassembled using mitoZ against Carcinoscorpius rotundicauda and Limulus polyphemus, resulting in a contig of 15 Kb. Phylogenetic analysis of the assembled mt genome suggests that the Tachypleus gigas is closely related to Tachypleus tridentatus than to Carcinoscorpius rotundicauda.

Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes

Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.

Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7 Gb, N50 = 90.2 Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7 Gb, N50 = 109.7 Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD. Comparison of C. rotundicauda and T. tridentatus genomes from populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for improving our understanding of invertebrate WGD events on the evolutionary fates of genes and microRNAs, at both the individual and population level. We also provide improved genomic resources for horseshoe crabs, of applied value for breeding programs and conservation of this fascinating and unusual invertebrate lineage.

The phylogeny and systematics of Xiphosura

Xiphosurans are aquatic chelicerates with a fossil record extending into the Early Ordovician and known from a total of 88 described species, four of which are extant. Known for their apparent morphological conservatism, for which they have gained notoriety as supposed 'living fossils', recent analyses have demonstrated xiphosurans to have an ecologically diverse evolutionary history, with several groups moving into non-marine environments and developing morphologies markedly different from those of the modern species. The combination of their long evolutionary and complex ecological history along with their paradoxical patterns of morphological stasis in some clades and experimentation among others has resulted in Xiphosura being of particular interest for macroevolutionary study. Phylogenetic analyses have shown the current taxonomic framework for Xiphosura-set out in the Treatise of Invertebrate Paleontology in 1955-to be outdated and in need of revision, with several common genera such as Paleolimulus Dunbar, 1923 and Limulitella Størmer, 1952 acting as wastebasket taxa. Here, an expanded xiphosuran phylogeny is presented, comprising 58 xiphosuran species as part of a 158 taxon chelicerate matrix coded for 259 characters. Analysing the matrix under both Bayesian inference and parsimony optimisation criteria retrieves a concordant tree topology that forms the basis of a genus-level systematic revision of xiphosuran taxonomy. The genera Euproops Meek, 1867, Belinurus König, 1820, Paleolimulus, Limulitella, and Limulus are demonstrated to be non-monophyletic and the previously synonymized genera Koenigiella Raymond, 1944 and Prestwichianella Cockerell, 1905 are shown to be valid. In addition, nine new genera (Andersoniella gen. nov., Macrobelinurus gen. nov., and Parabelinurus gen. nov. in Belinurina; Norilimulus gen. nov. in Paleolimulidae; Batracholimulus gen. nov. and Boeotiaspis gen. nov. in Austrolimulidae; and Allolimulus gen. nov., Keuperlimulus gen. nov., and Volanalimulus gen. nov. in Limulidae) are erected to accommodate xiphosuran species not encompassed by existing genera. One new species, Volanalimulus madagascarensis gen. et sp. nov., is also described. Three putative xiphosuran genera-Elleria Raymond, 1944, Archeolimulus Chlupáč, 1963, and Drabovaspis Chlupáč, 1963-are determined to be non-xiphosuran arthropods and as such are removed from Xiphosura. The priority of Belinurus König, 1820 over Bellinurus Pictet, 1846 is also confirmed. This work is critical for facilitating the study of the xiphosuran fossil record and is the first step in resolving longstanding questions regarding the geographic distribution of the modern horseshoe crab species and whether they truly represent 'living fossils'. Understanding the long evolutionary history of Xiphosura is vital for interpreting how the modern species may respond to environmental change and in guiding conservation efforts.

Chromosome-level genome assembly of the coastal horseshoe crab (Tachypleus gigas)

Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability of genomic resources for these species will be valuable in planning appropriate conservation measures. Whole-genome sequences are currently available for three species. In this study, we have generated a chromosome-level genome assembly of the fourth species, the Asian coastal horseshoe crab (Tachypleus gigas; genome size 2.0 Gb). The genome assembly has a scaffold N50 value of 140 Mb with ~97% of the assembly mapped to 14 scaffolds representing 14 chromosomes of T. gigas. In addition, we have generated the complete mitochondrial genome sequence and deep-coverage transcriptome assemblies for four tissues. A total of 26,159 protein-coding genes were predicted in the genome. The T. gigas genome contains five Hox clusters similar to the mangrove horseshoe crab (Carcinoscorpius rotundicauda), suggesting that the common ancestor of horseshoe crabs already possessed five Hox clusters. Phylogenomic and divergence time analysis suggested that the American and Asian horseshoe crab lineages shared a common ancestor around the Silurian period (~436 Ma). Comparison of the T. gigas genome with those of other horseshoe crab species with chromosome-level assemblies provided insights into the chromosomal rearrangement events that occurred during the emergence of these species. The genomic resources of T. gigas will be useful for understanding their genetic diversity and population structure and would help in designing strategies for managing and conserving their stocks across Asia.

Phylogenomics indicates the "living fossil" Isoetes diversified in the Cenozoic

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution

The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species. Here we report a chromosome-level genome assembly for the mangrove horseshoe crab (Carcinoscorpius rotundicauda) using PacBio reads and Hi-C data. The assembly spans 1.67 Gb with contig N50 of 7.8 Mb and 98% of the genome assigned to 16 chromosomes. The genome contains five Hox clusters with 34 Hox genes, the highest number reported in any invertebrate. Detailed analysis of the genome provides evidence that suggests three rounds of whole-genome duplication (WGD), raising questions about the relationship between WGD and species radiation. Several gene families, particularly those involved in innate immunity, have undergone extensive tandem duplication. These expanded gene families may be important components of the innate immune system of horseshoe crabs, whose amebocyte lysate is a sensitive agent for detecting endotoxin contamination.

Horseshoe crabs have been morphologically stable across evolutionary time. Here, the authors generate a chromosome-level assembly for the mangrove horseshoe crab, with implications for innate immunity, and challenging assumptions about the role of genome duplication in adaptive radiation.

On the appendicular anatomy of the xiphosurid Tachypleus syriacus and the evolution of fossil horseshoe crab appendages

Xiphosurida-crown group horseshoe crabs-are a group of morphologically conservative marine chelicerates (at least since the Jurassic). They represent an idealised example of evolutionary stasis. Unfortunately, body fossils of horseshoe crabs seldom preserve appendages and their associated features; thus, an important aspect of their morphology is absent in explorations of their conservative Bauplan. As such, fossil horseshoe crab appendages are rarely considered within a comparative framework: previous comparisons have focussed almost exclusively on extant taxa to the exclusion of extinct taxa. Here, we examine eight specimens of the xiphosurid Tachypleus syriacus (Woodward, 1879) from the Cenomanian (ca 100 Ma) Konservat-Lagerstätten of Lebanon, five of which preserve the cephalothoracic and thoracetronic appendages in exceptional detail. Comparing these appendages of T. syriacus with other fossil xiphosurids highlights the conserved nature of appendage construction across Xiphosurida, including examples of Austrolimulidae, Paleolimulidae, and Limulidae. Conversely, Belinuridae have more elongate cephalothoracic appendages relative to body length. Differences in appendage sizes are likely related to the freshwater and possible subaerial life modes of belinurids, contrasting with the primarily marine habits of other families. The morphological similarity of T. syriacus to extant members of the genus indicates that the conserved nature of the generic lineage can be extended to ecological adaptations, notably burrowing, swimming, possible diet, and sexual dimorphism.

The inhibitory effect of tachyplesin I on thrombosis and its mechanisms

Thrombotic diseases are major cause of cardiovascular diseases. This study was designed to investigate the effect of tachyplesin I on platelet aggregation and thrombosis. Platelet aggregation was analysed with a whole blood aggregometer. The mice were employed to investigate the effect of tachyplesin I on thrombosis in vivo. Tachyplesin I inhibited thrombin-induced platelet aggregation in a dose-dependent manner. Furthermore, tachyplesin I significantly reduced thrombosis in carrageenan-induced tail thrombosis model by intraperitoneal injection (0.1, 0.2 or 0.4 mg/kg) or intragastric administration (15, 30 or 60 mg/kg). Tachyplesin I also prolonged the bleeding time (BT) and clotting time (CT). The results revealed that tachyplesin I inhibited platelet aggregation and thrombosis by interfering the PI3K/AKT pathway. Tachyplesin I did not show significantly toxicity to mice under 300 mg/kg via intravenous injection. The results show that tachyplesin I inhibits thrombosis and has low toxicity. It is suggested that tachyplesin I has the potential to develop a new anti-thrombotic drug.

Rethinking Living Fossils

Biologists would be mistaken if they relegated living fossils to paleontological inquiry or assumed that the concept is dead. It is now used to describe entities ranging from viruses to higher taxa, despite recent warnings of misleading inferences. Current work on character evolution illustrates how analyzing living fossils and stasis in terms of parts (characters) and wholes (e.g., organisms and lineages) advances our understanding of prolonged stasis at many hierarchical levels. Instead of viewing the concept's task as categorizing living fossils, we show how its primary role is to mark out what is in need of explanation, accounting for the persistence of both molecular and morphological traits. Rethinking different conceptions of living fossils as specific hypotheses reveals novel avenues for research that integrate phylogenetics, ecological and evolutionary modeling, and evo-devo to produce a more unified theoretical outlook.

A revised dated phylogeny of scorpions: Phylogenomic support for ancient divergence of the temperate Gondwanan family Bothriuridae

The scorpion family Bothriuridae occupies a subset of landmasses formerly constituting East and West temperate Gondwana, but its relationship to other scorpion families is in question. Whereas morphological data have strongly supported a sister group relationship of Bothriuridae and the superfamily Scorpionoidea, a recent phylogenomic analysis recovered a basal placement of bothriurids within Iurida, albeit sampling only a single exemplar. Here we reexamined the phylogenetic placement of the family Bothriuridae, sampling six bothriurid exemplars representing both East and West Gondwana, using transcriptomic data. Our results demonstrate that the sister group relationship of Bothriuridae to the clade ("Chactoidea" + Scorpionoidea) is supported by the inclusion of additional bothriurid taxa, and that this placement is insensitive to matrix completeness or partitioning by evolutionary rate. We also estimated divergence times within the order Scorpiones using multiple fossil calibrations, to infer whether the family Bothriuridae is sufficiently old to be characterized as a true Gondwanan lineage. We show that scorpions underwent ancient diversification between the Devonian and early Carboniferous. The age interval of the bothriurids sampled (a derived group that excludes exemplars from South Africa) spans the timing of breakup of temperate Gondwana.

Opsins and Their Expression Patterns in the Xiphosuran Limulus polyphemus

The American horseshoe crab Limulus polyphemus (Linnaeus, 1758) is one of four extant species of xiphosuran chelicerates, the sister group to arachnids. Because of their position in the arthropod family tree and because they exhibit many plesiomorphic characteristics, Xiphosura are considered a proxy for the euchelicerate ancestor and therefore important for understanding the evolution and diversification of chelicerates and arthropods. Limulus polyphemus is the most extensively studied xiphosuran, and its visual system has long been a focus of studies critical for our understanding of basic mechanisms of vision and the evolution of visual systems in arthropods. Building upon a wealth of information about the anatomy and physiology of its visual system, advances in genetic approaches have greatly expanded possibilities for understanding its biochemistry. This review focuses on studies of opsin expression in L. polyphemus, which have been significantly advanced by the availability of transcriptomes and a recent high-quality assembly of its genome. These studies show that the repertoire of expressed opsins in L. polyphemus is far larger than anticipated, that the regulation of their expression in rhabdoms is far more complex than anticipated, and that photosensitivity may be distributed widely throughout the L. polyphemus central nervous system. The visual system of L. polyphemus is now arguably the best understood among chelicerates, and as such, it is a critical resource for furthering our understanding of the evolution and diversification of visual systems in arthropods.

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.

Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

Background

Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” As arthropods, they belong to the Ecdysozoa, an ancient super-phylum whose sequenced genomes (including insects and nematodes) have thus far shown more divergence from the ancestral pattern of eumetazoan genome organization than cnidarians, deuterostomes and lophotrochozoans. However, much of ecdysozoan diversity remains unrepresented in comparative genomic analyses.

Results

Here we apply a new strategy of combined de novo assembly and genetic mapping to examine the chromosome-scale genome organization of the Atlantic horseshoe crab, Limulus polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers grouped into 1,876 distinct genetic intervals and 5,775 candidate conserved protein coding genes.

Conclusions

Comparison with other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient whole genome duplications 300 million years ago, followed by extensive chromosome fusion. These results provide a counter-example to the often noted correlation between whole genome duplication and evolutionary radiations. The new, low-cost genetic mapping method for obtaining a chromosome-scale view of non-model organism genomes that we demonstrate here does not require laboratory culture, and is potentially applicable to a broad range of other species.

Complete mitochondrial genomes of Carcinoscorpius rotundicauda and Tachypleus tridentatus (Xiphosura, Arthropoda) and implications for chelicerate phylogenetic studies

Horseshoe crabs (order Xiphosura) are often referred to as an ancient order of marine chelicerates and have been considered as keystone taxa for the understanding of chelicerate evolution. However, the mitochondrial genome of this order is only available from a single species, Limulus polyphemus. In the present study, we analyzed the complete mitochondrial genomes from two Asian horseshoe crabs, Carcinoscorpius rotundicauda and Tachypleus tridentatus to offer novel data for the evolutionary relationship within Xiphosura and their position in the chelicerate phylogeny. The mitochondrial genomes of C. rotundicauda (15,033 bp) and T. tridentatus (15,006 bp) encode 13 protein-coding genes, two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. Overall sequences and genome structure of two Asian species were highly similar to that of Limulus polyphemus, though clear differences among three were found in the stem-loop structure of the putative control region. In the phylogenetic analysis with complete mitochondrial genomes of 43 chelicerate species, C. rotundicauda and T. tridentatus were recovered as a monophyly, while L. polyphemus solely formed an independent clade. Xiphosuran species were placed at the basal root of the tree, and major other chelicerate taxa were clustered in a single monophyly, clearly confirming that horseshoe crabs composed an ancestral taxon among chelicerates. By contrast, the phylogenetic tree without the information of Asian horseshoe crabs did not support monophyletic clustering of other chelicerates. In conclusion, our analyses may provide more robust and reliable perspective on the study of evolutionary history for chelicerates than earlier analyses with a single Atlantic species.

Into the deep: a phylogenetic approach to the bivalve subclass Protobranchia

A molecular phylogeny of Protobranchia, the subclass of bivalve mollusks sister to the remaining Bivalvia, has long proven elusive, because many constituent lineages are deep-sea endemics, which creates methodological challenges for collecting and preserving genetic material. We obtained 74 representatives of all 12 extant protobranch families and investigated the internal phylogeny of this group using sequence data from five molecular loci (16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, and histone H3). Model-based and dynamic homology parsimony approaches to phylogenetic reconstruction unanimously supported four major clades of Protobranchia, irrespective of treatment of hypervariable regions in the nuclear ribosomal genes 18S rRNA and 28S rRNA. These four clades correspond to the superfamilies Nuculoidea (excluding Sareptidae), Nuculanoidea (including Sareptidae), Solemyoidea, and Manzanelloidea. Salient aspects of the phylogeny include (1) support for the placement of the family Sareptidae with Nuculanoidea; (2) the non-monophyly of the order Solemyida (Solemyidae+Nucinellidae); (3) and the non-monophyly of most nuculoid and nuculanoid genera and families. In light of this first family-level phylogeny of Protobranchia, we present a revised classification of the group. Estimation of divergence times in concert with analyses of diversification rates demonstrate the signature of the end-Permian mass extinction in the phylogeny of extant protobranchs.

Multiple global radiations in tadpole shrimps challenge the concept of 'living fossils'

'Living fossils', a phrase first coined by Darwin, are defined as species with limited recent diversification and high morphological stasis over long periods of evolutionary time. Morphological stasis, however, can potentially lead to diversification rates being underestimated. Notostraca, or tadpole shrimps, is an ancient, globally distributed order of branchiopod crustaceans regarded as 'living fossils' because their rich fossil record dates back to the early Devonian and their morphology is highly conserved. Recent phylogenetic reconstructions have shown a strong biogeographic signal, suggesting diversification due to continental breakup, and widespread cryptic speciation. However, morphological conservatism makes it difficult to place fossil taxa in a phylogenetic context. Here we reveal for the first time the timing and tempo of tadpole shrimp diversification by inferring a robust multilocus phylogeny of Branchiopoda and applying Bayesian divergence dating techniques using reliable fossil calibrations external to Notostraca. Our results suggest at least two bouts of global radiation in Notostraca, one of them recent, so questioning the validity of the 'living fossils' concept in groups where cryptic speciation is widespread.