Chester J. Sands

Is the Scotia Sea a centre of Antarctic marine diversification? Some evidence of cryptic speciation in the circum-Antarctic bivalve Lissarca notorcadensis (Arcoidea: Philobryidae)

The bivalve Lissarca notorcadensis is one of the most abundant species in Antarctic waters and has colonised the entire Antarctic shelf and Scotia Sea Islands. Its brooding reproduction, low dispersal capabilities and epizoic lifestyle predict limited gene flow between geographically isolated populations. Relationships between specimens from seven regions in the Southern Ocean and outgroups were assessed with nuclear 28S rDNA and mitochondrial cytochrome oxidase subunit I (COI) genes. The 28S dataset indicate that while Lissarca appears to be a monophyletic genus, there is polyphyly between the Limopsidae and Philobryidae. Thirteen CO1 haplotypes were found, mostly unique to the sample regions, and two distinct lineages were distinguished. Specimens from the Weddell and Ross Sea form one lineage while individuals from the banks and islands of the Scotia Sea form the other. Within each lineage, further vicariance was observed forming six regionally isolated groups. Our results provide initial evidence for reproductively isolated populations of L. notorcadensis. The islands of the Scotia Sea appear to act as centres of speciation in the Southern Ocean.

Phylum Tardigrada: an “individual” approach

Phylum Tardigrada consists of ∼1000 tiny, hardy metazoan species distributed throughout terrestrial, limno‐terrestrial and oceanic habitats. Their phylogenetic status has been debated, with current evidence placing them in the Ecdysozoa. Although there have been efforts to explore tardigrade phylogeny using both morphological and molecular data, limitations such as their few morphological characters and low genomic DNA concentrations have resulted in restricted taxonomic coverage. Using a protocol that allows us to identify and extract DNA from individuals, we have sequenced 18S rDNA from 343 tardigrades from across the globe. Using maximum parsimony and Bayesian analyses we have found support for dividing Order Parachela into three super‐families and further evidence that indicates the traditional taxonomic perspective of families in the class Eutardigrada are nonmonophyletic and require re‐working. It appears that conserved morphology within Tardigrada has resulted in conservative taxonomy as we have found cases of several discrete lineages grouped into single genera. Although this work substantially adds to the understanding of the evolution and taxonomy of the phylum, we highlight that inferences gained from this work are likely to be refined with the inclusion of further taxa—specifically representatives of the nine families yet to be sampled.

Assessing meiofaunal variation among individuals utilising morphological and molecular approaches: an example using the Tardigrada

BackgroundMeiofauna – multicellular animals captured between sieve size 45 μm and 1000 μm – are a fundamental component of terrestrial, and marine benthic ecosystems, forming an integral element of food webs, and playing a critical roll in nutrient recycling. Most phyla have meiofaunal representatives and studies of these taxa impact on a wide variety of sub-disciplines as well as having social and economic implications. However, studies of variation in meiofauna are presented with several important challenges. Isolating individuals from a sample substrate is a time consuming process, and identification requires increasingly scarce taxonomic expertise. Finding suitable morphological characters in many of these organisms is often difficult even for experts. Molecular markers are extremely useful for identifying variation in morphologically conserved organisms. However, for many species markers need to be developed de novo, while DNA can often only be extracted from pooled samples in order to obtain sufficient quantity and quality. Importantly, multiple independent markers are required to reconcile gene evolution with species evolution. In this primarily methodological paper we provide a proof of principle of a novel and effective protocol for the isolation of meiofauna from an environmental sample. We also go on to illustrate examples of the implications arising from subsequent screening for genetic variation at the level of the individual using ribosomal, mitochondrial and single copy nuclear markers.ResultsTo isolate individual tardigrades from their habitat substrate we used a non-toxic density gradient media that did not interfere with downstream biochemical processes. Using a simple DNA release technique and nested polymerase chain reaction with universal primers we were able amplify multi-copy and, to some extent, single copy genes from individual tardigrades. Maximum likelihood trees from ribosomal 18S, mitochondrial cytochrome oxidase subunit 1, and the single copy nuclear gene Wingless support a recent study indicating that the family Hypsibiidae is a non-monophyletic group. From these sequences we were able to detect variation between individuals at each locus that allowed us to identify the presence of cryptic taxa that would otherwise have been overlooked.ConclusionMolecular results obtained from individuals, rather than pooled samples, are a prerequisite to enable levels of variation to be placed into context. In this study we have provided a proof of principle of this approach for meiofaunal tardigrades, an important group of soil biota previously not considered amenable to such studies, thereby paving the way for more comprehensive phylogenetic studies using multiple nuclear markers, and population genetic studies.

Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology

High throughput sequencing technologies are revolutionizing genetic research. With this “rise of the machines”, genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02–25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers.

Environmental Complexity and Biodiversity: The Multi-Layered Evolutionary History of a Log-Dwelling Velvet Worm in Montane Temperate Australia

Phylogeographic studies provide a framework for understanding the importance of intrinsic versus extrinsic factors in shaping patterns of biodiversity through identifying past and present microevolutionary processes that contributed to lineage divergence. Here we investigate population structure and diversity of the Onychophoran (velvet worm) Euperipatoides rowelli in southeastern Australian montane forests that were not subject to Pleistocene glaciations, and thus likely retained more forest cover than systems under glaciation. Over a ~100 km transect of structurally-connected forest, we found marked nuclear and mitochondrial (mt) DNA genetic structuring, with spatially-localised groups. Patterns from mtDNA and nuclear data broadly corresponded with previously defined geographic regions, consistent with repeated isolation in refuges during Pleistocene climatic cycling. Nevertheless, some E. rowelli genetic contact zones were displaced relative to hypothesized influential landscape structures, implying more recent processes overlying impacts of past environmental history. Major impacts at different timescales were seen in the phylogenetic relationships among mtDNA sequences, which matched geographic relationships and nuclear data only at recent timescales, indicating historical gene flow and/or incomplete lineage sorting. Five major E. rowelli phylogeographic groups were identified, showing substantial but incomplete reproductive isolation despite continuous habitat. Regional distinctiveness, in the face of lineages abutting within forest habitat, could indicate pre- and/or postzygotic gene flow limitation. A potentially functional phenotypic character, colour pattern variation, reflected the geographic patterns in the molecular data. Spatial-genetic patterns broadly match those in previously-studied, co-occurring low-mobility organisms, despite a variety of life histories. We suggest that for E. rowelli, the complex topography and history of the region has led to interplay among limited dispersal ability, historical responses to environmental change, local adaptation, and some resistance to free admixture at geographic secondary contact, leading to strong genetic structuring at fine spatial scale.

Antarctic Tardigrada: a first step in understanding molecular operational taxonomic units (MOTUs) and biogeography of cryptic meiofauna

Recent studies have suggested that some resident Antarctic biota are of ancient origin and may have been isolated for millions of years. The phylum Tardigrada, which is part of the Antarctic terrestrial meiofauna, is of particular interest due to an impressive array of biochemical abilities to withstand harsh environmental conditions. Tardigrades are one of the few widespread Antarctic terrestrial animals that have the potential to be used as a model for evolution and biogeography on the Antarctic continent. We isolated 126 individual tardigrades from four geographically isolated soil samples from two remote nunataks in the Sør Rondane Mountains, Dronning Maud Land, Antarctica. We examined genetic variation among individuals utilising three gene regions: cytochrome c oxidase subunit I gene (COI), 18S rDNA (18S), and the wingless (Wg) gene. Comparison of sequences from worldwide and Antarctic tardigrades indicated long-term survival and isolation over glacially dominated periods in ice-free habitats in the Sør Rondane Mountains.

The need to implement the Convention on Biological Diversity at the high latitude site, South Georgia

Abstract The multilateral failure to apply the Convention on Biological Diversity (CBD) by the target year 2010 was headline news as are the accelerating climatic changes which dictate its urgency. Some ecosystems that are vulnerable to anthropogenic change have few species listed as endangered because too little is known about their biota. The highest vulnerability may correspond to where hotspots of species endemism, range limits and physiological sensitivity overlap with areas of most rapid physical change. The old, large and remote archipelago of South Georgia is one such location. Sea-surface temperatures around South Georgia are amongst the most rapidly warming reported. Furthermore oceanographic projections are highlighting the region as extremely vulnerable to ocean acidification. We outline the first polar Darwin Initiative project and the technical advances in generating an interactive and fully integrated georeferenced map of marine biodiversity, seabed topography and physical oceanography at South Georgia. Mapping marine mega and macro-faunal biodiversity onto multiple physical variables has rarely been attempted. This should provide a new tool in assessing the processes driving biological variability, the importance of marine areas in terms of ecosystem services, the threats and vulnerabilities of Polar Regions and should greatly aid implementation of the CBD.

Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single-nucleotide polymorphism data

Abstract Marine systems have traditionally been thought of as “open” with few barriers to gene flow. In particular, many marine organisms in the Southern Ocean purportedly possess circumpolar distributions that have rarely been well verified. Here, we use the highly abundant and endemic Southern Ocean brittle star Ophionotus victoriae to examine genetic structure and determine whether barriers to gene flow have existed around the Antarctic continent. Ophionotus victoriae possesses feeding planktotrophic larvae with presumed high dispersal capability, but a previous study revealed genetic structure along the Antarctic Peninsula. To test the extent of genetic differentiation within O. victoriae, we sampled from the Ross Sea through the eastern Weddell Sea. Whereas two mitochondrial DNA markers (16S rDNA and COI) were employed to allow comparison to earlier work, a 2b‐RAD single‐nucleotide polymorphism (SNP) approach allowed sampling of loci across the genome. Mitochondrial data from 414 individuals suggested three major lineages, but 2b‐RAD data generated 1,999 biallelic loci that identified four geographically distinct groups from 89 samples. Given the greater resolution by SNP data, O. victoriae can be divided into geographically distinct populations likely representing multiple species. Specific historical scenarios that explain current population structure were examined with approximate Bayesian computation (ABC) analyses. Although the Bransfield Strait region shows high diversity possibly due to mixing, our results suggest that within the recent past, dispersal processes due to strong currents such as the Antarctic Circumpolar Current have not overcome genetic subdivision presumably due to historical isolation, questioning the idea of large open circumpolar populations in the Southern Ocean.

Against the flow: evidence of multiple recent invasions of warmer continental shelf waters by a Southern Ocean brittle star

The Southern Ocean is anomalously rich in benthos. This biodiversity is native, mostly endemic and perceived to be uniquely threatened from climate- and anthropogenically- mediated invasions. Major international scientific effort throughout the last decade has revealed more connectivity than expected between fauna north and south of the worlds strongest marine barrier – the Polar Front (the strongest jet of the Antarctic Circumpolar Current). To date though, no research has demonstrated any radiations of marine taxa out from the Southern Ocean, except at abyssal depths (where conditions differ much less). Our phylogeographic investigation of one of the most ubiquitous and abundant clades at high southern latitudes, the ophiuroids (brittlestars), shows that one of them, Ophiura lymani, has gone against the flow. Remarkably our genetic data suggest that O. lymani has successfully invaded the South American shelf from Antarctica at least three times, in recent (Pleistocene) radiation. Many previous studies have demonstrated links within clades across the PF this is the first in which northwards directional movement of a shelf-restricted species is the only convincing explanation. Rapid, recent, regional warming is likely to facilitate multiple range shift invasions into the Southern Ocean, whereas movement of cold adapted fauna (considered highly stenothermal) out of the Antarctic to warmer shelves has, until now, seemed highly unlikely.

Observations of the ophiuroids from the West Antarctic sector of the Southern Ocean

Abstract Ophiuroids are a conspicuous and often dominant component of the Antarctic continental shelf benthos. Here we report on the ophiuroids collected from the Burdwood Bank, off the Patagonian Shelf, through the shallow water areas of the Scotia Arc, down the west Antarctic Peninsula and as far south as Pine Island Bay in the eastern Amundsen Sea. This preliminary and primarily pattern based study identifies some regional differences in assemblages and highlights the role of the Antarctic Circumpolar Current as a barrier, as well as a facilitator, to dispersal. In order to effectively compare between studies we highlight the need for accurate, expert taxonomic identification of specimens.