Multi-omics for studying and understanding polar life.

Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.

Population Genomics of Nymphon australe Hodgson, 1902 (Pycnogonida, Nymphonidae) in the Western Antarctic.

Within the Southern Ocean, the Antarctic Circumpolar Current is hypothesized to facilitate a circumpolar distribution for many taxa, even though some, such as pycnogonids, are assumed to have limited ability to disperse, based on brooding life histories and adult ambulatory capabilities. With a number of contradictions to circumpolarity reported in the literature for other pycnogonids, alternative hypotheses have been explored, particularly for Nymphon australe, the most common species of Pycnogonida (sea spider) in the Southern Ocean. Glacial events have been hypothesized to impact the capacity of organisms to colonize suitable areas without ice coverage as refuge and without the eurybathic capacity to colonize deeper areas. In this study, we examine populations of one presumed circumpolar species, the pycnogonid N. australe, from throughout the Western Antarctic, using a 2b-RAD approach to detect genetic variation with single-nucleotide polymorphisms. Using this approach, we found that N. australe included two distinct groups from within >5000-km sampling region. By using a discriminant analysis of principle components, sparse nonnegative matrix factorization, and admixture coefficient analysis, two distinctive populations were revealed in the Western Antarctic: one covered distances greater than 5000 km (Weddell, Western Antarctic Peninsula, and Ross Sea), and the other shared limited connectivity entrained within the Amundsen Sea. Under further scrutiny of the 3086 single-nucleotide polymorphisms in the data set, only 78 loci had alignment stacks between the two populations. We propose that the populations analyzed are divergent enough to constitute two different species from within this common Antarctic genus known for its phenotypic plasticity.

Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal.

BACKGROUND: Although recent studies have greatly advanced understanding of deep molluscan phylogeny, placement of some taxa remains uncertain as different datasets support competing class-relationships. Traditionally, morphologists have placed Monoplacophora, a group of morphologically simple, limpet-like molluscs as sister group to all other conchiferans (shelled molluscs other than Polyplacophora), a grouping that is supported by the latest large-scale phylogenomic study that includes Laevipilina. However, molecular datasets dominated by nuclear ribosomal genes support Monoplacophora + Polyplacophora (Serialia). Here, we evaluate the potential of mitochondrial genome data for resolving placement of Monoplacophora. RESULTS: Two complete (Laevipilina antarctica and Vema ewingi) and one partial (Laevipilina hyalina) mitochondrial genomes were sequenced, assembled, and compared. All three genomes show a highly similar architecture including an unusually high number of non-coding regions. Comparison of monoplacophoran gene order shows a gene arrangement pattern not previously reported; there is an inversion of one large gene cluster. Our reanalyses of recently published polyplacophoran mitogenomes show, however, that this feature is also present in some chiton species. Maximum Likelihood and Bayesian Inference analyses of 13 mitochondrial protein-coding genes failed to robustly place Monoplacophora and hypothesis testing could not reject any of the evaluated placements of Monoplacophora. CONCLUSIONS: Under both serialian or aculiferan-conchiferan scenarios, the observed gene cluster inversion appears to be a convergent evolution of gene arrangements in molluscs. Our phylogenetic results are inconclusive and sensitive to taxon sampling. Aculifera (Polyplacophora + Aplacophora) and Conchifera were never recovered. However, some analyses recovered Serialia (Monoplacophora + Polyplacophora), Diasoma (Bivalvia + Scaphopoda) or Pleistomollusca (Bivalvia + Gastropoda). Although we could not shed light on deep evolutionary traits of Mollusca we found unique patterns of gene arrangements that are common to monoplacophoran and chitonine polyplacophoran species but not to acanthochitonine Polyplacophora. Complete mitochondrial genome of Laevipilina antarctica.

Opsin evolution in the Ambulacraria.

Opsins--G-protein coupled receptors involved in photoreception--have been extensively studied in the animal kingdom. The present work provides new insights into opsin-based photoreception and photoreceptor cell evolution with a first analysis of opsin sequence data for a major deuterostome clade, the Ambulacraria. Systematic data analysis, including for the first time hemichordate opsin sequences and an expanded echinoderm dataset, led to a robust opsin phylogeny for this cornerstone superphylum. Multiple genomic and transcriptomic resources were surveyed to cover each class of Hemichordata and Echinodermata. In total, 119 ambulacrarian opsin sequences were found, 22 new sequences in hemichordates and 97 in echinoderms (including 67 new sequences). We framed the ambulacrarian opsin repertoire within eumetazoan diversity by including selected reference opsins from non-ambulacrarians. Our findings corroborate the presence of all major ancestral bilaterian opsin groups in Ambulacraria. Furthermore, we identified two opsin groups specific to echinoderms. In conclusion, a molecular phylogenetic framework for investigating light-perception and photobiological behaviors in marine deuterostomes has been obtained.

Molecular phylogeny of the model annelid Ophryotrocha.

Annelids of the genus Ophryotrocha are small opportunistic worms commonly found in polluted and nutrient-rich habitats such as harbors. Within this small group of about 40 described taxa a large variety of reproductive strategies are found, ranging from gonochoristic broadcast spawners to sequential hermaphroditic brooders. Many of the species have a short generation time and are easily maintained as laboratory cultures. Thus they have become a popular system for exploring a variety of biological questions including developmental genetics, ethology, and sexual selection. Despite considerable behavioral, reproductive, and karyological studies, a phylogenetic framework is lacking because most taxa are morphologically similar. In this study we use 16S mitochondrial gene sequence data to infer the phylogeny of Ophryotrocha strains commonly used in the laboratory. The resulting mtDNA topologies are generally well resolved and support a genetic split between hermaphroditic and gonochoristic species. Although the ancestral state could not be unambiguously identified, a change in reproductive strategy (i.e., hermaphroditism and gonochorism) occurred once within Ophryotrocha. Additionally, we show that sequential hermaphroditism evolved from a simultaneous hermaphroditic ancestor, and that characters previously used in phylogenetic reconstruction (i.e., jaw morphology and shape of egg mass) are homoplasic within the group.

Molecular evidence that Sclerolinum brattstromi is closely related to vestimentiferans, not to frenulate pogonophorans (Siboglinidae, Annelida).

Siboglinids, previously referred to as pogonophorans, have typically been divided into two groups, frenulates and vestimentiferans. Adults of these marine protostome worms lack a functional gut and harbor endosymbiotic bacteria. Frenulates usually live in deep, sedimented reducing environments, and vestimentiferans inhabit hydrothermal vents and sulfide-rich hydrocarbon seeps. Taxonomic literature has often treated frenulates and vestimentiferans as sister taxa. Sclerolinum has traditionally been thought to be a basal siboglinid that was originally regarded as a frenulate and later as a third lineage of siboglinids, Monilifera. Evidence from the 18S nuclear rDNA gene and the 16S mitochondrial rDNA gene presented here shows that Sclerolinum is the sister clade to vestimentiferans although it lacks the characteristic morphology (i.e., a vestimentum). The rDNA data confirm the contention that Sclerolinum is different from frenulates, and further supports the idea that siboglinid evolution has been driven by a trend toward increased habitat specialization. The evidence now available indicates that vestimentiferans lack the molecular diversity expected of a group that has been argued to have Silurian or possibly Cambrian origins.

Miocene radiation of deep-sea hydrothermal vent shrimp (Caridea: Bresiliidae): evidence from mitochondrial cytochrome oxidase subunit I.

The evolutionary history of deep-sea shrimp (Caridea: Bresiliidae) inhabiting deep-sea hydrothermal vent and hydrocarbon seep environments was assessed using the mitochondrial Cytochrome c Oxidase subunit I (COI) gene (600 bp). Phylogenetic analyses (parsimony, likelihood, and neighbor-joining) recovered three distinct clades (A, Rimicaris/Chorocaris/Opaepele; B, Alvinocaris; and C, Mirocaris) consistent with higher level taxonomy based on morphology. However, robust phylogenetic results suggested that Chorocaris is paraphyletic and that Mirocaris fortunata and M. keldyshi may not be genetically distinct. A Kishino-Hasegawa likelihood approach was used to test alternative phylogenetic hypotheses based on biogeography and morphology. Evolutionary relationships of vent-endemic shrimp species did not appear to be correlated either with their extant biogeographic distribution or with the history of sea floor spreading. Additionally, COI data suggested that these vent-endemic organisms are not remnants of a Mesozoic vent assemblage; instead, they radiated in the Miocene.

Cytochrome b phylogeny of North American hares and jackrabbits (Lepus, lagomorpha) and the effects of saturation in outgroup taxa.

Jackrabbits and hares, members of the genus Lepus, comprise over half of the species within the family Leporidae (Lagomorpha). Despite their ecological importance, potential economic impact, and worldwide distribution, the evolution of hares and jackrabbits has been poorly studied. We provide an initial phylogenetic framework for jackrabbits and hares so that explicit hypotheses about their evolution can be developed and tested. To this end, we have collected DNA sequence data from a 702-bp region of the mitochondrial cytochrome b gene and reconstructed the evolutionary history (via parsimony, neighbor joining, and maximum likelihood) of 11 species of Lepus, focusing on North American taxa. Due to problems of saturation, induced by multiple substitutions, at synonymous coding positions between the ingroup taxa and the outgroups (Oryctolagus and Sylvilagus), both rooted and unrooted trees were examined. Variation in tree topologies generated by different reconstruction methods was observed in analyses including the outgroups, but not in the analyses of unrooted ingroup networks. Apparently, substitutional saturation hindered the analyses when outgroups were considered. The trees based on the cytochrome b data indicate that the taxonomic status of some species needs to be reassessed and that species of Lepus within North America do not form a monophyletic entity.

Multiple substitutions affect the phylogenetic utility of cytochrome b and 12S rDNA data: examining a rapid radiation in leporid (Lagomorpha) evolution.

Partial sequences of two mitochondrial genes, the 12S ribosomal gene (739 bp) and the cytochrome b gene (672 bp), were analyzed in hopes of reconstructing the evolutionary relationships of 11 leporid species, representative of seven genera. However, partial cytochrome b sequences were of little phylogenetic value in this study. A suite of pairwise comparisons between taxa revealed that at the intergeneric level, the cytochrome b gene is saturated at synonymous coding positions due to multiple substitution events. Furthermore, variation at the nonsynonymous positions is limited, rendering the cytochrome b gene of little phylogenetic value for assessing the relationships between leporid genera. If the cytochrome b data are analyzed without accounting for these two classes of nucleotides (i.e., synonymous and nonsynonymous sites), one may incorrectly conclude that signal exists in the cytochrome b data. The mitochondrial 12S rRNA gene, on the other hand, has not experienced excessive saturation at either stem or loop positions. Phylogenies reconstructed from the 12S rDNA data support hypotheses based on fossil evidence that African rock rabbits (Pronolagus) are outside of the main leporid stock and that leporids experienced a rapid radiation. However, the molecular data suggest that this radiation event occurred in the mid-Miocene several millions of years earlier than the Pleistocene dates suggested by paleontological evidence.

Phylogenetic relationships of cottontails (Sylvilagus, Lagomorpha): congruence of 12S rDNA and cytogenetic data.

The genus Sylvilagus, which comprises the New World cottontail rabbits, contains several commercially important as well as endangered (or threatened) species. Understanding the evolution of this group is pertinent to their management and conservation. The purpose of this study was to examine the evolutionary history of the cottontails using sequence data from the mitochondrial 12S rRNA gene. The 12S data provide a robust phylogeny which was supported under a variety of phylogenetic approaches and transition/transversion (Ti/Tv) weighting schemes. Stem and loop regions of the gene were analyzed separately and two different methods of estimating Ti/Tv ratios were employed. The phylogeny obtained was consistent with available cytogenetic information. The 12S data indicate that separate generic status for the pygmy rabbit, Brachylagus idahoensis, is warranted based on its phylogenetic position and sequence divergence values. Additionally, the taxa which are geographically adjacent are also phylogenetically closely related; for example, the marsh rabbit, S. palustris, and the swamp rabbit, S. aquaticus, are sister taxa, as are the mountain cottontail, S. nuttallii, and desert cottontail, S. audubonii. This finding suggests that recent vicariance events might explain the diversification of several cottontail lineages.

Convergence in the Feeding Apparatuses of Lophophorates and Pterobranch Hemichordates Revealed by 18S rDNA: An Interpretation.

Homology of the feeding apparatus of pterobranch hemichordates and the lophophore of bryozoans, brachiopods, and phoronids has been postulated but never rigorously tested. I employ Patterson's (1, 2) three criteria of conjunction, similarity, and congruence to test this putative homology. Although the conjunction and similarity criteria are satisfied, congruence is not. The congruence test is based on a phylogeny derived from 18s rDNA sequence data which show that pterobranchs and lophophorates are in diRerent metazoan subkingdoms and are not closely related. This finding indicates that a lophophore-like apparatus has evolved at least twice in metazoans even though the gross morphology, feeding mechanics, ultrastructure, and ciliary patterns of these organisms are very similar. The high degree of morphological convergence presumably results from similar selective regimes acting on these taxa. These findings indicate that major clades of organisms can evolve in a correspondingfashion despite independent origins.

Evidence from 18S ribosomal DNA that the lophophorates are protostome animals.

The suspension-feeding metazoan subkingdom Lophophorata exhibits characteristics of both deuterostomes and protostomes. Because the morphology and embryology of lophophorates are phylogenetically ambiguous, their origin is a major unsolved problem of metazoan phylogenetics. The complete 18S ribosomal DNA sequences of all three lophophorate phyla were obtained and analyzed to clarify the phylogenetic relationships of this subkingdom. Sequence analyses show that lophophorates are protostomes closely related to mollusks and annelids. This conclusion deviates from the commonly held view of deuterostome affinity.

The phylogenetic position of the pterobranch hemichordates based on 18S rDNA sequence data.

Pterobranchs are a class of deuterostome metazoans that are sessile marine suspension feeders. Although this group has been poorly studied, understanding their phylogenetic affinities is central to understanding early metazoan evolution. Sequence data from the 5' end of the 18S rDNA gene was collected from a pterobranch, Rhabdopleura normani, and combined with other available 18S sequences. Using standard phylogenetic methods, the evolutionary relationships of deuterostome metazoans were reconstructed. The pterobranchs are most closely related to the enteropneust hemichordates. This was confirmed by bootstrap analyses and a topology-dependent cladistic permutation tail probability (T-PTP) test. My analysis agrees with Turbeville et al.'s (1994) and Wada and Satoh's (1994) finding that hemichordates are more closely related to echinoderms than to chordates, and it is proposed that Metschnikoff's (1881) name Ambulacraria be adopted for the clade defined by the last common ancestor of the hemichordates and echinoderms. These findings suggest that ciliated gill slits and the dorsal hollow nerve chord are pleisomorphic features of the Deuterostomia.

Suspension Feeding by the Lophophore-like Apparatus of the Pterobranch Hemichordate Rhabdopleura normani.

Selective forces acting on feeding mechanisms have played an important role in the evolution of metazoans. To develop a more accurate understanding of the evolution of feeding within the deuterostome and lophophorate clades, I used video analysis and electron microscopy to examine suspension-feeding behavior and ciliation patterns in Rhabdopleura normani, a pterobranch hemichordate. In R. normani, local reversals of ciliary beat capture food particles, and the normal feeding activity does not involve the use of mucus to capture particles. Also, several different methods of particle rejection are identified. Lateral, frontal, and frontolateral ciliary bands, which are composed of cilia 8-13 µm in length, are present on the tentacles. In R. normani from Bermuda, ciliated perforations occur along the length of the arms, specifically between the bases of adjacent tentacles. These structures are previously undescribed in suspension-feeding organisms. My findings are consistent with the hypothesis that the tentaculated arms of pterobranchs are homologous to the lophophores of brachiopods, phoronids, and bryozoans. The similarities in the feeding biology of these groups are discussed.