Genome-wide signatures of convergent evolution in echolocating mammals

Evolution is typically thought to proceed through divergence of genes, proteins, and ultimately phenotypes(1-3). However, similar traits might also evolve convergently in unrelated taxa due to similar selection pressures(4,5). Adaptive phenotypic convergence is widespread in nature, and recent results from a handful of genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level(6-9). Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution(9,10) although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show for the first time that convergence is not a rare process restricted to a handful of loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four new bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Surprisingly we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognised

Un pequeño Oso de las Cavernas (Ursus rossicus) del Sur de Siberia, Rusia BARYSHNIKOV, G.

[Abstract] The skull, mandibles and cheek teeth of U. Rossicus from four localities of the South Siberia are examined. This species inhabited the steppe regions in early Middle and Late Pleistocene. By odontological characters it is more close to U. r. Rossicus from Krasnodar, than to U. Rossicus uralensis from Kizel Cave in Ural. Discriminant analysis, based on measurements of lower cheek teeth of the cave bears from seven sites of Europe and Siberia, demonstrated that U. Rossicus most resembles morphometrically U. Savini . As a result of cladistic analysis employed 17 characters of skull, limb bones, and dentition, the phylogenetic tree has been obtained for 7 species of the genus U r s u s . A four species of the cave bears are included in the subgenus Spelearctos: U. savini, U. rossicus, U. deningeri and U. spelaeu

Unravelling the hybrid vigor in domestic equids: the effect of hybridization on bone shape variation and covariation

Hybridization has been widely practiced in plant and animal breeding as a means to enhance the quality and fitness of the organisms. In domestic equids, this hybrid vigor takes the form of improved physical and physiological characteristics, notably for strength or endurance. Because the offspring of horse and donkey is generally sterile, this widely recognized vigor is expressed in the first generation (F1). However, in the absence of recombination between the two parental genomes, F1 hybrids can be expected to be phenotypically intermediate between their parents which could potentially restrict the possibilities of an increase in overall fitness. In this study, we examine the morphology of the main limb bones of domestic horses, donkeys and their hybrids to investigate the phenotypic impact of hybridization on the locomotor system. We explore bone shape variation and covariation to gain insights into the morphological and functional expressions of the hybrid vigor commonly described in domestic equids

The Archaeology of Local Human Response to an Environmental Transformation

abstract: This research addresses human adaptive decisions made at the Pleistocene-Holocene transition - the transition from the Last Glacial Maximum (LGM) to the climate regime in which humankind now lives - in the Mediterranean region of southeast Spain. Although on a geological time scale the Pleistocene-Holocene transition is the latest in a series of widespread environmental transformations due to glacial-interglacial cycles, it is the only one for which we have a record of the response by modern humans. Mediterranean Spain lay outside the refugium areas of late Pleistocene Europe, in which advancing ice sheets limited the land available for subsistence and caused relative demographic packing of hunter-gatherers. Therefore, the archaeological records of Mediterranean Spain contain more generally applicable states of the Pleistocene-Holocene transition, making it a natural laboratory for research on human adaptation to an environmental transformation. Foragers in Mediterranean Spain appear to have primarily adapted to macroclimatic change by extending their social networks to access new subsistence resources and by changing the mix of traditional relationships. Comparing faunal records from two cave sites near the Mediterranean coast with Geographic Information System (GIS) reconstructions of the coastal littoral plain from the LGM to the Holocene indicates the loss of the large ungulate species (mainly Bos primigenius and Equus) at one site coincided with the associated littoral disappearing due to sea level rise in the late Upper Paleolithic. Farther north, where portions of the associated littoral remained due to a larger initial mass and a more favorable topography, the species represented in the faunal record were constant through time. Social boundary defense definitions of territory require arranging social relationships in order to access even this lightly populated new hunting area on the interior plain. That the values of the least-cost-paths fit the parameters of two models equating varying degrees of social alliance with direct travel distances also helps support the hypothesis that foragers in Mediterranean Spain adapted to the consequences of macroclimatic change by extending their social networks to gain access to new subsistence resources Keeping these relationships stable and reliable was a mitigating factor in the mobility patterns of foragers during this period from direct travel to more distant down-the-line exchange. Information about changing conditions and new circumstances flowed along these same networks of social relationships. The consequences of climate-induced environmental changes are already a concern in the world, and human decisions in regard to future conditions are built upon past precedents. As the response to environmental risk centers on increasing the resilience of vulnerable smallholders, archaeology has an opportunity to apply its long-term perspective in the search for answersDissertation/ThesisPh.D. Anthropology 201

Triiodothyronine (T3) levels fluctuate in response to ambient temperature rather than nutritional status in a wild tropical ungulate

Animals can employ a range of physiological mechanisms in response to unpredictable changes within their environment, such as changes in food availability and human disturbances. For example, impala exhibit higher faecal glucocorticoid metabolite (FGM) levels—indicative of physiological stress—in response to low food quality and higher human disturbance. In this study, we measured faecal triiodothyronine (T3) metabolite (FTM) levels in 446 wild impala from 2016 to 2018 to test the hypothesis that environmental and human disturbances would affect their physiological status. We also validated a faecal thyroid hormone assay. T3 levels mainly regulate metabolic rate and drive thermoregulation—increasing with colder temperatures. We predicted that individuals would have lower FTM levels, indicative of poor physiological status, (i) when food quality was poor, (ii) when ambient temperature (Ta) was high, (iii) in areas of high human disturbance (due to food competition with livestock) and (iv) when FGM levels were high. Interestingly, we found that Ta was the most important predictor of FTM—FTM levels decreased by 70% from lowest to highest Ta—and food quality and human disturbance only influenced FTM levels when Ta was accounted for. FTM levels also tended to increase with increasing FGM levels, opposite our predictions. Our results suggest that food quality and availabilitymay only partially influence FTM levels and that fluctuations in Ta are a significant driver of FTM levels in a wild tropical ungulate. Given that thyroid hormones are primarily responsible for regulating metabolic rate, they may be better indicators of how wild animals metabolically and energetically respond to environmental factors and only indicate poor nutritional status in extreme cases. glucocorticoid, impala, Serengeti, stress, thyroid hormones, validationpublishedVersio

Selection On Different Genes With Equivalent Functions: The Convergence Story Told By Hox Genes Along The Evolution Of Aquatic Mammalian Lineages

Background: Convergent evolution has been a challenging topic for decades, being cetaceans, pinnipeds and sirenians textbook examples of three independent origins of equivalent phenotypes. These mammalian lineages acquired similar anatomical features correlated to an aquatic life, and remarkably differ from their terrestrial counterparts. Whether their molecular evolutionary history also involved similar genetic mechanisms underlying such morphological convergence nevertheless remained unknown. To test for the existence of convergent molecular signatures, we studied the molecular evolution of Hox genes in these three aquatic mammalian lineages, comparing their patterns to terrestrial mammals. Hox genes are transcription factors that play a pivotal role in specifying embryonic regional identity of nearly any bilateral animal, and are recognized major agents for diversification of body plans. Results: We detected few signatures of positive selection on Hox genes across the three aquatic mammalian lineages and verified that purifying selection prevails in these sequences, as expected for pleiotropic genes. Genes found as being positively selected differ across the aquatic mammalian lineages, but we identified a substantial overlap of their developmental functions. Such pattern likely resides on the duplication history of Hox genes, which probably provided different possible evolutionary routes for achieving the same phenotypic solution. Conclusions: Our results indicate that convergence occurred at a functional level of Hox genes along three independent origins of aquatic mammals. This conclusion reinforces the idea that different changes in developmental genes may lead to similar phenotypes, probably due to the redundancy provided by the participation of Hox paralogous genes in several developmental functions. © 2016 Nery et al.1

Selection On Different Genes With Equivalent Functions: The Convergence Story Told By Hox Genes Along The Evolution Of Aquatic Mammalian Lineages

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Convergent evolution has been a challenging topic for decades, being cetaceans, pinnipeds and sirenians textbook examples of three independent origins of equivalent phenotypes. These mammalian lineages acquired similar anatomical features correlated to an aquatic life, and remarkably differ from their terrestrial counterparts. Whether their molecular evolutionary history also involved similar genetic mechanisms underlying such morphological convergence nevertheless remained unknown. To test for the existence of convergent molecular signatures, we studied the molecular evolution of Hox genes in these three aquatic mammalian lineages, comparing their patterns to terrestrial mammals. Hox genes are transcription factors that play a pivotal role in specifying embryonic regional identity of nearly any bilateral animal, and are recognized major agents for diversification of body plans. Results: We detected few signatures of positive selection on Hox genes across the three aquatic mammalian lineages and verified that purifying selection prevails in these sequences, as expected for pleiotropic genes. Genes found as being positively selected differ across the aquatic mammalian lineages, but we identified a substantial overlap of their developmental functions. Such pattern likely resides on the duplication history of Hox genes, which probably provided different possible evolutionary routes for achieving the same phenotypic solution. Conclusions: Our results indicate that convergence occurred at a functional level of Hox genes along three independent origins of aquatic mammals. This conclusion reinforces the idea that different changes in developmental genes may lead to similar phenotypes, probably due to the redundancy provided by the participation of Hox paralogous genes in several developmental functions.16Ciencia sem Fronteiras - Atracao de Jovens Talentos CAPES [054/2012]FAPESP-Brazil [2010/52316-3]CNPq-Brazil [563232/2010-2]Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq