The tuatara genome reveals ancient features of amniote evolution.

The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2-is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.

Publisher Correction: The tuatara genome reveals ancient features of amniote evolution.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A general theory for temperature dependence in biology.

At present, there is no simple, first principles-based, and general model for quantitatively describing the full range of observed biological temperature responses. Here we derive a general theory for temperature dependence in biology based on Eyring-Evans-Polanyi's theory for chemical reaction rates. Assuming only that the conformational entropy of molecules changes with temperature, we derive a theory for the temperature dependence of enzyme reaction rates which takes the form of an exponential function modified by a power law and that describes the characteristic asymmetric curved temperature response. Based on a few additional principles, our model can be used to predict the temperature response above the enzyme level, thus spanning quantum to classical scales. Our theory provides an analytical description for the shape of temperature response curves and demonstrates its generality by showing the convergence of all temperature dependence responses onto universal relationships-a universal data collapse-under appropriate normalization and by identifying a general optimal temperature, around 25 ∘C, characterizing all temperature response curves. The model provides a good fit to empirical data for a wide variety of biological rates, times, and steady-state quantities, from molecular to ecological scales and across multiple taxonomic groups (from viruses to mammals). This theory provides a simple framework to understand and predict the impact of temperature on biological quantities based on the first principles of thermodynamics, bridging quantum to classical scales.

The circadian clock of teleost fish: a comparative analysis reveals distinct fates for duplicated genes.

The circadian clock is a central oscillator that coordinates endogenous rhythms. Members of six gene families underlie the metabolic machinery of this system. Although this machinery appears to correspond to a highly conserved genetic system in metazoans, it has been recognized that vertebrates possess a more diverse gene inventory than that of non-vertebrates. This difference could have originated in the two successive rounds of whole-genome duplications that took place in the common ancestor of the group. Teleost fish underwent an extra event of whole-genome duplication, which is thought to have provided an abundance of raw genetic material for the biological innovations that facilitated the radiation of the group. In this study, we assessed the relative contributions of whole-genome duplication and small-scale gene duplication to generate the repertoire of genes associated with the circadian clock of teleost fish. To achieve this goal, we annotated genes from six gene families associated with the circadian clock in eight teleost fish species, and we reconstructed their evolutionary history by inferring phylogenetic relationships. Our comparative analysis indicated that teleost species possess a variable repertoire of genes related to the circadian clock gene families and that the actual diversity of these genes has been shaped by a variety of phenomena, such as the complete deletion of ohnologs, the differential retention of genes, and lineage-specific gene duplications. From a functional perspective, the subfunctionalization of two ohnolog genes (PER1a and PER1b) in zebrafish highlights the power of whole-genome duplications to generate biological diversity.

Increased rate of hair keratin gene loss in the cetacean lineage.

BACKGROUND: Hair represents an evolutionary innovation that appeared early on mammalian evolutionary history, and presumably contributed significantly to the rapid radiation of the group. An interesting event in hair evolution has been its secondary loss in some mammalian groups, such as cetaceans, whose hairless phenotype appears to be an adaptive response to better meet the environmental conditions. To determine whether different repertoire of keratin genes among mammals can potentially explain the phenotypic hair features of different lineages, we characterized the type I and II clusters of alpha keratins from eight mammalian species, including the hairless dolphin and minke whale representing the order Cetacea. RESULTS: We combined the available genomic information with phylogenetic analysis to conduct a comprehensive analysis of the evolutionary patterns of keratin gene clusters. We found that both type I and II gene clusters are fairly conserved among the terrestrial mammals included in this study, with lineage specific gene duplication and gene loss. Nevertheless, there is also evidence for an increased rate of pseudogenization in the cetacean lineage when compared to their terrestrial relatives, especially among the hair type keratins. CONCLUSIONS: Here we present a comprehensive characterization of alpha-keratin genes among mammals and elucidate the mechanisms involved in the evolution of this gene family. We identified lineage-specific gene duplications and gene loss among the Laurasiatherian and Euarchontoglires species included in the study. Interestingly, cetaceans present an increased loss of hair-type keratin genes when compared to other terrestrial mammals. As suggested by the 'less-is-more' hypothesis, we do not rule out the possibility that the gene loss of hair-type keratin genes in these species might be associated to the hairless phenotype and could have been adaptive in response to new selective pressures imposed by the colonization of a new habitat. Our study provides support for the idea that pseudogenes are not simply 'genomic fossils' but instead have adaptive roles during the evolutionary process.

Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton.

Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.

Accelerated evolutionary rate of the myoglobin gene in long-diving whales.

Cetaceans, early in their evolutionary history, had developed many physiological adaptations to secondarily return to the sea. Among these adaptations, changes in molecules that transport oxygen and that ultimately support large periods of acute tissue hypoxia probably represent one big step toward the conquest of aquatic environments. Myoglobin contributes to intracellular oxygen storage and transcellular diffusion of oxygen in muscle, and plays an important role in supplying oxygen in hypoxic or ischemic conditions. Here we looked for evidence of adaptive molecular evolution of myoglobin in the cetacean lineage, relative to their terrestrial counterparts. We performed a comparative analysis to examine the variation of the parameter ω (d N/d S) and infer past period of adaptive evolution during the cetacean transition from the terrestrial to the aquatic environment. We also analyzed the changes in amino acid properties. At the nucleotide level, the results showed significant differences in selective pressure between cetacean and non-cetacean myoglobin (ω value three times higher in cetaceans when compared to terrestrial mammals), and also among cetacean lineages according to their diving capacities. Interestingly, both families with long duration diving cetaceans present two parallel substitutions (on sites 4 and 12). Regarding the amino acid properties, our analysis identified four significant physicochemical amino acid changes among residues in myoglobin protein under positive destabilizing selection.

Gene duplication and positive selection explains unusual physiological roles of the relaxin gene in the European rabbit.

The relaxin gene family is a group of genes involved in different physiological roles, most of them related to reproduction. In vertebrates the genes in this family are located in three separate chromosomal locations, and have been called relaxin family locus (RFL) A, B, and C. Among mammals the RFLA and RFLC are the most conserved as no gene copy-number variation has been observed thus far. The RFLB locus is also conserved on most mammals other than primates, where there are several gene gains and losses. Interestingly, the relaxin gene found on the RFLB locus in the European rabbit has acquired a novel role. In addition to the classical reproductive roles, this gene is expressed in tracheobronchial epithelial cells and its expression has been linked to squamous differentiation. We reconstructed the evolutionary history of the European rabbit RFLB locus using the tools of comparative genomics and molecular evolution. We found that the European rabbit possess a RFLB locus which is unique among mammals in that there are five tandemly arranged relaxin gene copies, which contrast with the single relaxin copy gene found in most mammals. In addition we also found that the ancestral pre-duplication gene was subject to the action of positive selection, and several amino acid sites were identified under the action of natural selection including the sites B12 and B13 which are part of the receptor recognition and binding site.

INSL4 pseudogenes help define the relaxin family repertoire in the common ancestor of placental mammals.

The relaxin/insulin-like (RLN/INSL) gene family comprises a group of signaling molecules that perform physiological roles related mostly to reproduction and neuroendocrine regulation. They are found on three different locations in the mammalian genome, which have been called relaxin family locus (RFL) A, B, and C. Early in placental mammalian evolution, the ancestral proto-RLN gene at the RFLB locus underwent successive rounds of small-scale duplications resulting in variable number of paralogous genes in different placental lineages. Most placental mammals harbor copies of the RLN2 and INSL6 paralogs in the RFLB. However, the origin of an additional paralog, INSL4 (also known as placentin), has been controversial as its phyletic distribution does not converge with its phylogenetic position. In principle, by searching for INSL4 genes in representative species of all major groups of mammals we can gain insights into when the gene originated and better reconstruct its evolutionary history. Here we identified INSL4 pseudogenes in two laurasiatherian, (alpaca and dolphin) and one xenarthran (armadillo) species. Phylogenetic and synteny analyses confirmed that the identified pseudogenes are orthologs of INSL4. According to these results, the proto-RLN gene in the RFLB underwent two successive tandem duplications which gave rise the INSL6 and INSL4 paralogs in the last common ancestor of placental mammals. The INSL4 gene was subsequently inactivated or lost from the genome in all placentals other than catarrhine primates, where its product became functionally relevant. Our results highlight the contribution of relatively old gene duplicates to the gene complement of extant species.

Gene turnover and differential retention in the relaxin/insulin-like gene family in primates.

The relaxin/insulin-like gene family is related to the insulin gene family, and includes two separate types of peptides: relaxins (RLNs) and insulin-like peptides (INSLs) that perform a variety of physiological roles including testicular descent, growth and differentiation of the mammary glands, trophoblast development, and cell differentiation. In vertebrates, these genes are found on three separate genomic loci, and in mammals, variation in the number and nature of genes in this family is mostly restricted to the Relaxin Family Locus B. For example, this locus contains a single copy of RLN in platypus and opossum, whereas it contains copies of the INSL6, INSL4, RLN2 and RLN1 genes in human and chimp. The main objective of this research is to characterize changes in the size and membership composition of the RLN/INSL gene family in primates, reconstruct the history of the RLN/INSL genes of primates, and test competing evolutionary scenarios regarding the origin of INSL4 and of the duplicated copies of the RLN gene of apes. Our results show that the relaxin/INSL-like gene family of primates has had a more dynamic evolutionary history than previously thought, including several examples of gene duplications and losses which are consistent with the predictions of the birth-and-death model of gene family evolution. In particular, we found that the differential retention of relatively old paralogs played a key role in shaping the gene complement of this family in primates. Two examples of this phenomenon are the origin of the INSL4 gene of catarrhines (the group that includes Old World monkeys and apes), and of the duplicate RLN1 and RLN2 paralogs of apes. In the case of INSL4, comparative genomics and phylogenetic analyses indicate that the origin of this gene, which was thought to represent a catarrhine-specific evolutionary innovation, is as old as the split between carnivores and primates, which took place approximately 97 million years ago. In addition, in the case of the RLN1 and RLN2 genes of apes our phylogenetic trees and topology tests indicate that the duplication that gave rise to these two genes maps to the last common ancestor of anthropoid primates. All these genomic changes in gene complement, which are particularly prevalent among anthropoid primates, might be linked to the many physiological and anatomical changes found in this group. Given the various roles of members of the RLN/INSL-like gene family in reproductive biology, it might be that changes in this gene family are associated to changes in reproductive traits.

Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 °N.

Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.

Gene fusion of heterophyletic gamma-globin genes in platyrrhine primates.

We performed phylogenetic analyses of HBG genes to assess its origin and interspecific variation among primates. Our analyses showed variation in HBG genes copy number ranging from one to three, some of them pseudogenes. For platyrrhines HBG genes, phylogenetic reconstructions of flanking regions recovered orthologous clades with distinct topologies for 5' and 3' flanking regions. The 5' region originated in the common ancestor of platyrrhines but the 3' region had an anthropoid origin. We hypothesize that the platyrrhine HBG genes of 5' and 3' heterophyletic origins arose from subsequent fusions of the (earlier) platyrrhine 5' portion and the (later) anthropoid 3' portion.

Evolution of the relaxin/insulin-like gene family in anthropoid primates.

The relaxin/insulin-like gene family includes signaling molecules that perform a variety of physiological roles mostly related to reproduction and neuroendocrine regulation. Several previous studies have focused on the evolutionary history of relaxin genes in anthropoid primates, with particular attention on resolving the duplication history of RLN1 and RLN2 genes, which are found as duplicates only in apes. These studies have revealed that the RLN1 and RLN2 paralogs in apes have a more complex history than their phyletic distribution would suggest. In this regard, alternative scenarios have been proposed to explain the timing of duplication, and the history of gene gain and loss along the organismal tree. In this article, we revisit the question and specifically reconstruct phylogenies based on coding and noncoding sequence in anthropoid primates to readdress the timing of the duplication event giving rise to RLN1 and RLN2 in apes. Results from our phylogenetic analyses based on noncoding sequence revealed that the duplication event that gave rise to the RLN1 and RLN2 occurred in the last common ancestor of catarrhine primates, between ∼ 44.2 and 29.6 Ma, and not in the last common ancestor of apes or anthropoids, as previously suggested. Comparative analyses based on coding and noncoding sequence suggests an event of convergent evolution at the sequence level between co-ortholog genes, the single-copy RLN gene found in New World monkeys and the RLN1 gene of apes, where changes in a fraction of the convergent sites appear to be driven by positive selection.

Genomic organization and differential signature of positive selection in the alpha and beta globin gene clusters in two cetacean species.

The hemoglobin of jawed vertebrates is a heterotetramer protein that contains two α- and two ß-chains, which are encoded by members of α- and ß-globin gene families. Given the hemoglobin role in mediating an adaptive response to chronic hypoxia, it is likely that this molecule may have experienced a selective pressure during the evolution of cetaceans, which have to deal with hypoxia tolerance during prolonged diving. This selective pressure could have generated a complex history of gene turnover in these clusters and/or changes in protein structure themselves. Accordingly, we aimed to characterize the genomic organization of α- and ß-globin gene clusters in two cetacean species and to detect a possible role of positive selection on them using a phylogenetic framework. Maximum likelihood and Bayesian phylogeny reconstructions revealed that both cetacean species had retained a similar complement of putatively functional genes. For the α-globin gene cluster, the killer whale presents a complement of genes composed of HBZ, HBK, and two functional copies of HBA and HBQ genes, whereas the dolphin possesses HBZ, HBK, HBA and HBQ genes, and one HBA pseudogene. For the ß-globin gene cluster, both species retained a complement of four genes, two early expressed genes-HBE and HBH-and two adult expressed genes-HBD and HBB. Our natural selection analysis detected two positively selected sites in the HBB gene (56 and 62) and four in HBA (15, 21, 49, 120). Interestingly, only the genes that are expressed during the adulthood showed the signature of positive selection.