Origins and Functional Significance of Eukaryotic Protein Folds.

Folds are the architecture and topology of a protein domain. Categories of folds are very few compared to the astronomical number of sequences. Eukaryotes have more protein folds than Archaea and Bacteria. These folds are of two types: shared with Archaea and/or Bacteria on one hand and specific to eukaryotic clades on the other hand. The first kind of folds is inherited from the first endosymbiosis and confirms the mixed origin of eukaryotes. In a dataset of 1073 folds whose presence or absence has been evidenced among 210 species equally distributed in the three super-kingdoms, we have identified 28 eukaryotic folds unambiguously inherited from Bacteria and 40 eukaryotic folds unambiguously inherited from Archaea. Compared to previous studies, the repartition of informational function is higher than expected for folds originated from Bacteria and as high as expected for folds inherited from Archaea. The second type of folds is specifically eukaryotic and associated with an increase of new folds within eukaryotes distributed in particular clades. Reconstructed ancestral states coupled with dating of each node on the tree of life provided fold appearance rates. The rate is on average twice higher within Eukaryota than within Bacteria or Archaea. The highest rates are found in the origins of eukaryotes, holozoans, metazoans, metazoans stricto sensu, and vertebrates: the roots of these clades correspond to bursts of fold evolution. We could correlate the functions of some of the fold synapomorphies within eukaryotes with significant evolutionary events. Among them, we find evidence for the rise of multicellularity, adaptive immune system, or virus folds which could be linked to an ecological shift made by tetrapods.

Musculotendinous system of mesopelagic fishes: Stomiiformes (Teleostei).

Every night the greatest migration on Earth starts in the deep pelagic oceans where organisms move up to the meso- and epipelagic to find food and return to the deeper zones during the day. One of the dominant fish taxa undertaking vertical migrations are the dragonfishes (Stomiiformes). However, the functional aspects of locomotion and the architecture of the musculotendinous system (MTS) in these fishes have never been examined. In general, the MTS is organized in segmented blocks of specific three-dimensional 'W-shaped' foldings, the myomeres, separated by thin sheets of connective tissue, the myosepta. Within a myoseptum characteristic intermuscular bones or tendons may be developed. Together with the fins, the MTS forms the functional unit for locomotion in fishes. For this study, microdissections of cleared and double stained specimens of seven stomiiform species (Astronesthes sp., Chauliodus sloani, Malacosteus australis, Eustomias simplex, Polymetme sp., Sigmops elongatus, Argyropelecus affinis) were conducted to investigate their MTS. Soft tissue was investigated non-invasively in E. schmidti using a micro-CT scan of one specimen stained with iodine. Additionally, classical histological serial sections were consulted. The investigated stomiiforms are characterized by the absence of anterior cones in the anteriormost myosepta. These cones are developed in myosepta at the level of the dorsal fin and elongate gradually in more posterior myosepta. In all but one investigated stomiiform taxon the horizontal septum is reduced. The amount of connective tissue in the myosepta is very low anteriorly, but increases gradually with body length. Red musculature overlies laterally the white musculature and exhibits strong tendons in each myomere within the muscle bundles dorsal and ventral to the horizontal midline. The amount of red musculature increases immensely towards the caudal fin. The elongated lateral tendons of the posterior body segments attach in a highly complex pattern on the caudal-fin rays, which indicates that the posterior most myosepta are equipped for a multisegmental force transmission towards the caudal fin. This unique anatomical condition might be essential for steady swimming during diel vertical migrations, when prey is rarely available.

LIMES: a tool for comparing species partition.

MOTIVATION: Species delimitation (SD) is on the verge of becoming a fully fledged research field in systematics, but the variety of available approaches tends to result in significant-sometimes striking-incongruences, when tested comparatively with a given taxonomic sampling. RESULTS: We present LIMES, an automatic calculation tool which qualitatively compares species partitions obtained by distinct SD approaches, regardless of their respective theoretical backgrounds, and even in absence of reference topology. The program implements four different previously published indexes, and allows their automated calculation. AVAILABILITY AND IMPLEMENTATION: LIMES is freely downloadable at www.limes.cnrs.fr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Finding our way through phenotypes.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

Phylogenetic classification of bony fishes.

BACKGROUND: Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. RESULTS: The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. CONCLUSIONS: This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.

Revisiting Nature's "Unifying Patterns": A Biological Appraisal.

Effective bioinspiration requires dialogue between designers and biologists, and this dialogue must be rooted in a shared scientific understanding of living systems. To support learning from "nature's overarching design lessons" the Biomimicry Institute has produced ten "Unifying Patterns of Nature". These patterns have been developed to engage with those interested in finding biologically inspired solutions to human challenges. Yet, although well-intentioned and appealing, they are likely to dishearten biologists. The aim of this paper is to identify why and propose alternative principles based on evolutionary theory.

Genome structures resolve the early diversification of teleost fishes.

Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.

Origins of specificity and promiscuity in metabolic networks.

How enzymes have evolved to their present form is linked to the question of how pathways emerged and evolved into extant metabolic networks. To investigate this mechanism, we have explored the chemical diversity present in a largely unbiased data set of catalytic reactions processed by modern enzymes across the tree of life. In order to get a quantitative estimate of enzyme chemical diversity, we measure enzyme multispecificity or promiscuity using the reaction molecular signatures. Our main finding is that reactions that are catalyzed by a highly specific enzyme are shared by poorly divergent species, suggesting a later emergence of this function during evolution. In contrast, reactions that are catalyzed by highly promiscuous enzymes are more likely to appear uniformly distributed across species in the tree of life. From a functional point of view, promiscuous enzymes are mainly involved in amino acid and lipid metabolisms, which might be associated with the earliest form of biochemical reactions. In this way, results presented in this paper might assist us with the identification of primeval promiscuous catalytic functions contributing to life's minimal metabolism.

Protein folds as synapomorphies of the tree of life.

Several studies showed that folds (topology of protein secondary structures) distribution in proteomes may be a global proxy to build phylogeny. Then, some folds should be synapomorphies (derived characters exclusively shared among taxa). However, previous studies used methods that did not allow synapomorphy identification, which requires congruence analysis of folds as individual characters. Here, we map SCOP folds onto a sample of 210 species across the tree of life (TOL). Congruence is assessed using retention index of each fold for the TOL, and principal component analysis for deeper branches. Using a bicluster mapping approach, we define synapomorphic blocks of folds (SBF) sharing similar presence/absence patterns. Among the 1232 folds, 20% are universally present in our TOL, whereas 54% are reliable synapomorphies. These results are similar with CATH and ECOD databases. Eukaryotes are characterized by a large number of them, and several SBFs clearly support nested eukaryotic clades (divergence times from 1100 to 380 mya). Although clearly separated, the three superkingdoms reveal a strong mosaic pattern. This pattern is consistent with the dual origin of eukaryotes and witness secondary endosymbiosis in their phothosynthetic clades. Our study unveils direct analysis of folds synapomorphies as key characters to unravel evolutionary history of species.

Multilocus analyses of an Antarctic fish species flock (Teleostei, Notothenioidei, Trematominae): phylogenetic approach and test of the early-radiation event.

Clades that have undergone episodes of rapid cladogenesis are challenging from a phylogenetic point of view. They are generally characterised by short or missing internal branches in phylogenetic trees and by conflicting topologies among individual gene trees. This may be the case of the subfamily Trematominae, a group of marine teleosts of coastal Antarctic waters, which is considered to have passed through a period of rapid diversification. Despite much phylogenetic attention, the relationships among Trematominae species remain unclear. In contrast to previous studies that were mostly based on concatenated datasets of mitochondrial and/or single nuclear loci, we applied various single-locus and multilocus phylogenetic approaches to sequences from 11 loci (eight nuclear) and we also used several methods to assess the hypothesis of a radiation event in Trematominae evolution. Diversification rate analyses support the hypothesis of a period of rapid diversification during Trematominae history and only a few nodes in the hypothetical species tree were consistently resolved with various phylogenetic methods. We detected significant discrepancies among trees from individual genes of these species, most probably resulting from incomplete lineage sorting, suggesting that concatenation of loci is not the most appropriate way to investigate Trematominae species interrelationships. These data also provide information about the possible effects of historic climate changes on the diversification rate of this group of fish.

rely.py, a python script to detect reliable clades.

rely.py is a program implementing the method to detect independently repeated clades by comparing phylogenies as described in Li and Lecointre (2009) and adapted to incompletely overlapping datasets in Li et al. (2009). The comparison can be performed on trees obtained by any inference method (maximum parsimony, Bayesian inference, maximum likelihood). The program computes repetition indices, provides greedy summary trees for each validity domain and a nexus matrix representation of the clades weighted by their repetition indices. The additional script concatnexus.py assists the user in preparing the primary analyses, but it can also be used separately to concatenate nexus datasets.

The "street light syndrome", or how protein taxonomy can bias experimental manipulations.

In the genomics era, bioinformatic analysis, especially in non-model species, facilitates the identification and naming of numerous new proteins, the function of which is then inferred through homology searches. Here, we question certain aspects of these approaches. What are the criteria that permit such a determination? What are their limits? Naming is classifying. We review the different criteria that are used to name a protein and discuss their constraints. We observe that the name given to a protein often introduces a bias for further functional analyses, a bias that is not often taken into account when analysing results. Last but not least, the heterogeneity of criteria used for naming proteins leads to self-inconsistent or contradictory protein classification that is potentially misleading. Finally, we recommend a wider use of phylogenetic criteria in protein naming.

Hierarchical analysis of ontogenetic time to describe heterochrony and taxonomy of developmental stages.

Even though an accurate description of early life stages is available for some teleostean species in form of embryonic and post-embryonic developmental tables, there is poor overlap between species-specific staging vocabularies beyond the taxonomic family level. What is called "embryonic period", "larval period", "metamorphosis", or "juvenile" is anatomically different across teleostean families. This problem, already pointed out 50 years ago, challenges the consistency of developmental biology, embryology, systematics, and hampers an efficient aquaculture diversification. We propose a general solution by producing a proof-of-concept hierarchical analysis of ontogenetic time using a set of four freshwater species displaying strongly divergent reproductive traits. With a parsimony analysis of a matrix where "operational taxonomic units" are species at a given ontogenetic time segment and characters are organs or structures which are coded present or absent at this time, we show that the hierarchies obtained have both very high consistency and retention index, indicating that the ontogenetic time is correctly grasped through a hierarchical graph. This allows to formally detect developmental heterochronies and might provide a baseline to name early life stages for any set of species. The present method performs a phylogenetic segmentation of ontogenetic time, which can be correctly seen as depicting ontophylogenesis.

The treeness of the tree of historical trees of life.

This paper compares and categorizes historical ideas about trees showing relationships among biological entities. The hierarchical structure of a tree is used to test the global consistency of similarities among these ideas; in other words we assess the "treeness" of the tree of historical trees. The collected data are figures and ideas about trees showing relationships among biological entities published or drawn by naturalists from 1555 to 2012. They are coded into a matrix of 235 historical trees and 141 descriptive attributes. From the most parsimonious "tree" of historical trees, treeness is measured by consistency index, retention index and homoplasy excess ratio. This tree is used to create sets or categories of trees, or to study the circulation of ideas. From an unrooted network of historical trees, treeness is measured by the delta-score. This unrooted network is used to measure and visualize treeness. The two approaches show a rather good treeness of the data, with respectively a retention idex of 0.83 and homoplasy excess ratio of 0.74, on one hand, and a delta-score of 0.26 on the other hand. It is interpreted as due to vertical transmission, i.e. an inheritance of shared ideas about biological trees among authors. This tree of trees is then used to test categories previously made. For instance, cladists and gradists are « paraphyletic ¼. The branches of this tree of trees suggest new categories of tree-thinkers that could have been overlooked by historians or systematists.

RNF213, a new nuclear marker for acanthomorph phylogeny.

We show that RNF213 is a nuclear gene suitable for investigating large scale acanthomorph teleosteans interrelationships. The gene recovers many clades already found by several independent studies of acanthomorph molecular phylogenetics and considered as reliable. Moreover, we performed phylogenetic analyses of three other independent nuclear markers, first separately and then of all possible combinations (Dettaï, A., Lecointre, G., 2004. In search of nothothenioid (Teleostei) relatives. Antarct. Sci. 16 (1), 71-85. URL http://dx.doi.org/10.1017/S0954102004) of the four genes. This was coupled with an assessment of the reliability of clades using the repetition index of Li and Lecointre (Li, B., Lecointre, G., 2008. Formalizing reliability in the taxonomic congruence approach. Article accepted by Zoologica Scripta. URL http://dx.doi.org/10.1111/j.1463-6409.2008.00361.x). This index was improved here to handle the incomplete taxonomic overlap among datasets. The results lead to the identification of new reliable clades within the 'acanthomorph bush'. Within a clade containing the Atherinomorpha, the Mugiloidei, the Plesiopidae, the Blennioidei, the Gobiesocoidei, the Cichlidae and the Pomacentridae, the Plesiopidae is the sister-group of the Mugiloidei. The Apogonidae are closely related to the Gobioidei. A clade named 'H' grouping a number of families close to stromateids and scombrids (Stromateidae, Scombridae, Trichiuridae, Chiasmodontidae, Nomeidae, Bramidae, Centrolophidae) is related to another clade named 'E' (Aulostomidae, Macrorhamphosidae, Dactylopteridae). The Sciaenidae is closely related to the Haemulidae. Within clade 'X' (Dettaï, A., Lecointre, G., 2004. In search of nothothenioid (Teleostei) relatives. Antarct. Sci. 16 (1), 71-85. URL http://dx.doi.org/10.1017/S0954102004), the Cottoidei, the Zoarcoidei, the Gasterosteidae, the Triglidae, the Scorpaenidae, the Sebastidae, the Synanceiidae, and the Congiopodidae form a clade. Within clade 'L' (Chen, W.-J., Bonillo, C., Lecointre, G., 2003. Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa. Mol. Phylogenet. Evol. 26, 262-288; Dettaï, A., Lecointre, G., 2004. In search of nothothenioid (Teleostei) relatives. Antarct. Sci. 16 (1), 71-85. URL http://dx.doi.org/10.1017/S0954102004) grouping carangoids with flatfishes and other families (Centropomidae, Menidae, Sphyraenidae, Polynemidae, Echeneidae, Toxotidae, Xiphiidae), carangids are the stem-group of echeneids and coryphaenids, and sphyraenids are the sister-group to the Carangoidei. The Howellidae, the Epigonidae and the Lateolabracidae are closely related. We propose names for most of the clades repeatedly found in acanthomorph phylogenetic studies of various teams of the past decade.

Empathy and compassion toward other species decrease with evolutionary divergence time.

Currently the planet is inhabited by several millions of extremely diversified species. Not all of them arouse emotions of the same nature or intensity in humans. Little is known about the extent of our affective responses toward them and the factors that may explain these differences. Our online survey involved 3500 raters who had to make choices depending on specific questions designed to either assess their empathic perceptions or their compassionate reactions toward an extended photographic sampling of organisms. Results show a strong negative correlation between empathy scores and the divergence time separating them from us. However, beyond a certain time of divergence, our empathic perceptions stabilize at a minimum level. Compassion scores, although based on less spontaneous choices, remain strongly correlated to empathy scores and time of divergence. The mosaic of features characterizing humans has been acquired gradually over the course of the evolution, and the phylogenetically closer a species is to us, the more it shares common traits with us. Our results could be explained by the fact that many of these traits may arouse sensory biases. These anthropomorphic signals could be able to mobilize cognitive circuitry and to trigger prosocial behaviors usually at work in human relationships.

Inferring evolution of fish proteins: the globin case study.

Because hemoglobins (Hbs) of all animal species have the same heme group, differences in their properties, including oxygen affinity, electrophoretic mobility, and pH sensitivity, must result from the interaction of the prosthetic group with specific amino acid residues in the primary structure. For this reason, fish globins have been the object of extensive studies in the past few years, not only for their structural characteristics but also because they offer the possibility to investigate the evolutionary history of Hbs in marine and freshwater species living in a large variety of environmental conditions. For such a purpose, phylogenetic analysis of globin sequences can be combined with knowledge of the phylogenetic relationships between species. In addition, Type I functional-divergence analysis is aimed toward predicting the amino acid residues that are more likely responsible for biochemical diversification of different Hb families. These residues, mapped on the three-dimensional Hb structure, can provide insights into functional and structural divergence.

New insights into the organization and evolution of vertebrate IRBP genes and utility of IRBP gene sequences for the phylogenetic study of the Acanthomorpha (Actinopterygii: Teleostei).

The interphotoreceptor retinoid-binding protein (IRBP) coding gene has been used with success for the large-scale phylogeny of mammals. However, its phylogenetic worth had not been explored in Actinopterygians. We explored the evolution of the structure of the gene and compared the structure predicted from known sequences with that of a basal vertebrate lineage, the sea lamprey Petromyzon marinus. This sequence is described here for the first time. The structure made up of four tandem repeats (or modules) arranged in a single gene, as present in Chondrichthyes (sharks and rays) and tetrapods, is also present in sea lamprey. In teleosts, one to two paralogous copies of IRBP gene have been identified depending on the genomes. When the sequences from all modules for a wide sampling of vertebrates are compared and analyzed, all sequences previously assigned to a particular module appear to be clustered together, suggesting that the divergence among modules is older than the split between lampreys and other vertebrates. Finally, 92 acanthomorph teleosts were sequenced for the partial module 1 of the gene 2 (713 bp) to assess for the first time the use of this marker for the systematic studies of the Teleostei. The partial sequence is slightly more variable than other markers currently used for this group, and the resulting trees from our sequences recover most of the clades described in the recent molecular multi-marker studies of the Acanthomorpha. We recommend the use of partial sequences from the IRBP gene 2 as a marker for phylogenetic inference in teleosts.

Understanding processes at the origin of species flocks with a focus on the marine Antarctic fauna.

Species flocks (SFs) fascinate evolutionary biologists who wonder whether such striking diversification can be driven by normal evolutionary processes. Multiple definitions of SFs have hindered the study of their origins. Previous studies identified a monophyletic taxon as a SF if it displays high speciosity in an area in which it is endemic (criterion 1), high ecological diversity among species (criterion 2), and if it dominates the habitat in terms of biomass (criterion 3); we used these criteria in our analyses. Our starting hypothesis is that normal evolutionary processes may provide a sufficient explanation for most SFs. We thus clearly separate each criterion and identify which biological (intrinsic) and environmental (extrinsic) traits are most favourable to their realization. The first part focuses on evolutionary processes. We highlight that some popular putative causes of SFs, such as key innovations or ecological speciation, are neither necessary nor sufficient to fulfill some or all of the three criteria. Initial differentiation mechanisms are diverse and difficult to identify a posteriori because a primary differentiation of one type (genetic, ecological or geographical) often promotes other types of differentiation. Furthermore, the criteria are not independent: positive feedbacks between speciosity and ecological diversity among species are expected whatever the initial cause of differentiation, and ecological diversity should enhance habitat dominance at the clade level. We then identify intrinsic and extrinsic factors that favour each criterion. Low dispersal emerges as a convincing driver of speciosity. Except for a genomic architecture favouring ecological speciation, for which assessment is difficult, high effective population sizes are the single intrinsic factor that directly enhances speciosity, ecological diversity and habitat dominance. No extrinsic factor appeared to enhance all criteria simultaneously but a combination of factors (insularity, fragmentation and environmental stability) may favour the three criteria, although the effect is indirect for habitat dominance. We then apply this analytical framework to Antarctic marine environments by analysing data from 18 speciose clades belonging to echinoderms (five unrelated clades), notothenioid fishes (five clades) and peracarid crustaceans (eight clades). Antarctic shelf environments and history appear favourable to endemicity and speciosity, but not to ecological specialization. Two main patterns are distinguished among taxa. (i) In echinoderms, many brooding, species-rich and endemic clades are reported, but without remarkable ecological diversity or habitat dominance. In these taxa, loss of the larval stage is probably a consequence of past Antarctic environmental factors, and brooding is suggested to be responsible for enhanced allopatric speciation (via dispersal limitation). (ii) In notothenioids and peracarids, many clades fulfill all three SF criteria. This could result from unusual features in fish and crustaceans: chromosome instability and key innovations (antifreeze proteins) in notothenioids, ecological opportunity in peracarids, and a genomic architecture favouring ecological speciation in both groups. Therefore, the data do not support our starting point that normal evolutionary factors or processes drive SFs because in these two groups uncommon intrinsic features or ecological opportunity provide the best explanation. The utility of the three-criterion SF concept is therefore questioned and guidelines are given for future studies.

Did glacial advances during the Pleistocene influence differently the demographic histories of benthic and pelagic Antarctic shelf fishes?--Inferences from intraspecific mitochondrial and nuclear DNA sequence diversity.

BACKGROUND: Circum-Antarctic waters harbour a rare example of a marine species flock - the Notothenioid fish, most species of which are restricted to the continental shelf. It remains an open question as to how they survived Pleistocene climatic fluctuations characterised by repeated advances of continental glaciers as far as the shelf break that probably resulted in a loss of habitat for benthic organisms. Pelagic ecosystems, on the other hand, might have flourished during glacial maxima due to the northward expansion of Antarctic polar waters. In order to better understand the role of ecological traits in Quaternary climatic fluctuations, we performed demographic analyses of populations of four fish species from the tribe Trematominae, including both fully benthic and pelagic species using the mitochondrial cytochrome b gene and an intron from the nuclear S7 gene. RESULTS: Nuclear and cytoplasmic markers showed differences in the rate and time of population expansions as well as the likely population structure. Neutrality tests suggest that such discordance comes from different coalescence dynamics of each marker, rather than from selective pressure. Demographic analyses based on intraspecific DNA diversity suggest a recent population expansion in both benthic species, dated by the cyt b locus to the last glacial cycle, whereas the population structure of pelagic feeders either did not deviate from a constant-size model or indicated that the onset of the major population expansion of these species by far predated those of the benthic species. Similar patterns were apparent even when comparing previously published data on other Southern Ocean organisms, but we observed considerable heterogeneity within both groups with regard to the onset of major demographic events and rates. CONCLUSION: Our data suggest benthic and pelagic species reacted differently to the Pleistocene ice-sheet expansions that probably significantly reduced the suitable habitat for benthic species. However, the asynchronous timing of major demographic events observed in different species within both "ecological guilds", imply that the species examined here may have different population and evolutionary histories, and that more species should be analysed in order to more precisely assess the role of life history in the response of organisms to climatic changes.