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Michael R Mcgowen - One of the best experts on this subject based on the ideXlab platform.
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phylogenomic resolution of the Cetacean tree of life using target sequence capture
Systematic Biology, 2020Co-Authors: Paul Jepson, Michael R Mcgowen, Georgia Tsagkogeorga, Sandra Alvarezcarretero, Mario Dos Reis, Monika Struebig, Robert Deaville, Simon N Jarman, Andrea M PolanowskiAbstract:The evolution of Cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among Cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for $\sim $3200 protein-coding genes for 68 Cetacean species and their close relatives including the pygmy hippopotamus. By combining data from $>$38,000 exons with existing sequences from 11 Cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for Cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.].
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the evolutionary history of Cetacean brain and body size
Evolution, 2013Co-Authors: Stephen H Montgomery, Michael R Mcgowen, Lori Marino, Jonathan H Geisler, Charlotte Fox, John GatesyAbstract:Cetaceans rival primates in brain size relative to body size and include species with the largest brains and biggest bodies to have ever evolved. Cetaceans are remarkably diverse, varying in both phenotypes by several orders of magnitude, with notable differences between the two extant suborders, Mysticeti and Odontoceti. We analyzed the evolutionary history of brain and body mass, and relative brain size measured by the encephalization quotient (EQ), using a data set of extinct and extant taxa to capture temporal variation in the mode and direction of evolution. Our results suggest that Cetacean brain and body mass evolved under strong directional trends to increase through time, but decreases in EQ were widespread. Mysticetes have significantly lower EQs than odontocetes due to a shift in brain:body allometry following the divergence of the suborders, caused by rapid increases in body mass in Mysticeti and a period of body mass reduction in Odontoceti. The pattern in Cetacea contrasts with that in primates, which experienced strong trends to increase brain mass and relative brain size, but not body mass. We discuss what these analyses reveal about the convergent evolution of large brains, and highlight that until recently the most encephalized mammals were odontocetes, not primates.
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a phylogenetic blueprint for a modern whale
Molecular Phylogenetics and Evolution, 2013Co-Authors: John Gatesy, Robert W Meredith, Mark S Springer, Jonathan H Geisler, Joseph Chang, Carl Buell, Annalisa Berta, Michael R McgowenAbstract:The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti – toothed whales), and others that batch feed using racks of baleen (Mysticeti – baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant Cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological + paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life.
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phylogeny and adaptive evolution of the brain development gene microcephalin mcph1 in Cetaceans
BMC Evolutionary Biology, 2011Co-Authors: Stephen H Montgomery, Michael R Mcgowen, Clay Clark, John GatesyAbstract:Representatives of Cetacea have the greatest absolute brain size among animals, and the largest relative brain size aside from humans. Despite this, genes implicated in the evolution of large brain size in primates have yet to be surveyed in Cetaceans. We sequenced ~1240 basepairs of the brain development gene microcephalin (MCPH1) in 38 Cetacean species. Alignments of these data and a published complete sequence from Tursiops truncatus with primate MCPH1 were utilized in phylogenetic analyses and to estimate ω (rate of nonsynonymous substitution/rate of synonymous substitution) using site and branch models of molecular evolution. We also tested the hypothesis that selection on MCPH1 was correlated with brain size in Cetaceans using a continuous regression analysis that accounted for phylogenetic history. Our analyses revealed widespread signals of adaptive evolution in the MCPH1 of Cetacea and in other subclades of Mammalia, however, there was not a significant positive association between ω and brain size within Cetacea. In conjunction with a recent study of Primates, we find no evidence to support an association between MCPH1 evolution and the evolution of brain size in highly encephalized mammalian species. Our finding of significant positive selection in MCPH1 may be linked to other functions of the gene.
John Gatesy - One of the best experts on this subject based on the ideXlab platform.
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Inactivation of the olfactory marker protein (OMP) gene in river dolphins and other odontocete Cetaceans
Molecular phylogenetics and evolution, 2017Co-Authors: Mark S Springer, John GatesyAbstract:Various toothed whales (Odontoceti) are unique among mammals in lacking olfactory bulbs as adults and are thought to be anosmic (lacking the olfactory sense). At the molecular level, toothed whales have high percentages of pseudogenic olfactory receptor genes, but species that have been investigated to date retain an intact copy of the olfactory marker protein gene (OMP), which is highly expressed in olfactory receptor neurons and may regulate the temporal resolution of olfactory responses. One hypothesis for the retention of intact OMP in diverse odontocete lineages is that this gene is pleiotropic with additional functions that are unrelated to olfaction. Recent expression studies provide some support for this hypothesis. Here, we report OMP sequences for representatives of all extant Cetacean families and provide the first molecular evidence for inactivation of this gene in vertebrates. Specifically, OMP exhibits independent inactivating mutations in six different odontocete lineages: four river dolphin genera (Platanista, Lipotes, Pontoporia, Inia), sperm whale (Physeter), and harbor porpoise (Phocoena). These results suggest that the only essential role of OMP that is maintained by natural selection is in olfaction, although a non-olfactory role for OMP cannot be ruled out for lineages that retain an intact copy of this gene. Available genome sequences from Cetaceans and close outgroups provide evidence of inactivating mutations in two additional genes (CNGA2, CNGA4), which imply further pseudogenization events in the olfactory cascade of odontocetes. Selection analyses demonstrate that evolutionary constraints on all three genes (OMP, CNGA2, CNGA4) have been greatly reduced in Odontoceti, but retain a signature of purifying selection on the stem Cetacea branch and in Mysticeti (baleen whales). This pattern is compatible with the 'echolocation-priority' hypothesis for the evolution of OMP, which posits that negative selection was maintained in the common ancestor of Cetacea and was not relaxed significantly until the evolution of echolocation in Odontoceti.
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the evolutionary history of Cetacean brain and body size
Evolution, 2013Co-Authors: Stephen H Montgomery, Michael R Mcgowen, Lori Marino, Jonathan H Geisler, Charlotte Fox, John GatesyAbstract:Cetaceans rival primates in brain size relative to body size and include species with the largest brains and biggest bodies to have ever evolved. Cetaceans are remarkably diverse, varying in both phenotypes by several orders of magnitude, with notable differences between the two extant suborders, Mysticeti and Odontoceti. We analyzed the evolutionary history of brain and body mass, and relative brain size measured by the encephalization quotient (EQ), using a data set of extinct and extant taxa to capture temporal variation in the mode and direction of evolution. Our results suggest that Cetacean brain and body mass evolved under strong directional trends to increase through time, but decreases in EQ were widespread. Mysticetes have significantly lower EQs than odontocetes due to a shift in brain:body allometry following the divergence of the suborders, caused by rapid increases in body mass in Mysticeti and a period of body mass reduction in Odontoceti. The pattern in Cetacea contrasts with that in primates, which experienced strong trends to increase brain mass and relative brain size, but not body mass. We discuss what these analyses reveal about the convergent evolution of large brains, and highlight that until recently the most encephalized mammals were odontocetes, not primates.
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rod monochromacy and the coevolution of Cetacean retinal opsins
PLOS Genetics, 2013Co-Authors: Christopher A Emerling, Robert W Meredith, Vincent York, John Gatesy, Mark S SpringerAbstract:Cetaceans have a long history of commitment to a fully aquatic lifestyle that extends back to the Eocene. Extant species have evolved a spectacular array of adaptations in conjunction with their deployment into a diverse array of aquatic habitats. Sensory systems are among those that have experienced radical transformations in the evolutionary history of this clade. In the case of vision, previous studies have demonstrated important changes in the genes encoding rod opsin (RH1), short-wavelength sensitive opsin 1 (SWS1), and long-wavelength sensitive opsin (LWS) in selected Cetaceans, but have not examined the full complement of opsin genes across the complete range of Cetacean families. Here, we report protein-coding sequences for RH1 and both color opsin genes (SWS1, LWS) from representatives of all extant Cetacean families. We examine competing hypotheses pertaining to the timing of blue shifts in RH1 relative to SWS1 inactivation in the early history of Cetacea, and we test the hypothesis that some Cetaceans are rod monochomats. Molecular evolutionary analyses contradict the “coastal” hypothesis, wherein SWS1 was pseudogenized in the common ancestor of Cetacea, and instead suggest that RH1 was blue-shifted in the common ancestor of Cetacea before SWS1 was independently knocked out in baleen whales (Mysticeti) and in toothed whales (Odontoceti). Further, molecular evidence implies that LWS was inactivated convergently on at least five occasions in Cetacea: (1) Balaenidae (bowhead and right whales), (2) Balaenopteroidea (rorquals plus gray whale), (3) Mesoplodon bidens (Sowerby's beaked whale), (4) Physeter macrocephalus (giant sperm whale), and (5) Kogia breviceps (pygmy sperm whale). All of these Cetaceans are known to dive to depths of at least 100 m where the underwater light field is dim and dominated by blue light. The knockout of both SWS1 and LWS in multiple Cetacean lineages renders these taxa rod monochromats, a condition previously unknown among mammalian species.
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a phylogenetic blueprint for a modern whale
Molecular Phylogenetics and Evolution, 2013Co-Authors: John Gatesy, Robert W Meredith, Mark S Springer, Jonathan H Geisler, Joseph Chang, Carl Buell, Annalisa Berta, Michael R McgowenAbstract:The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti – toothed whales), and others that batch feed using racks of baleen (Mysticeti – baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant Cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological + paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life.
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phylogeny and adaptive evolution of the brain development gene microcephalin mcph1 in Cetaceans
BMC Evolutionary Biology, 2011Co-Authors: Stephen H Montgomery, Michael R Mcgowen, Clay Clark, John GatesyAbstract:Representatives of Cetacea have the greatest absolute brain size among animals, and the largest relative brain size aside from humans. Despite this, genes implicated in the evolution of large brain size in primates have yet to be surveyed in Cetaceans. We sequenced ~1240 basepairs of the brain development gene microcephalin (MCPH1) in 38 Cetacean species. Alignments of these data and a published complete sequence from Tursiops truncatus with primate MCPH1 were utilized in phylogenetic analyses and to estimate ω (rate of nonsynonymous substitution/rate of synonymous substitution) using site and branch models of molecular evolution. We also tested the hypothesis that selection on MCPH1 was correlated with brain size in Cetaceans using a continuous regression analysis that accounted for phylogenetic history. Our analyses revealed widespread signals of adaptive evolution in the MCPH1 of Cetacea and in other subclades of Mammalia, however, there was not a significant positive association between ω and brain size within Cetacea. In conjunction with a recent study of Primates, we find no evidence to support an association between MCPH1 evolution and the evolution of brain size in highly encephalized mammalian species. Our finding of significant positive selection in MCPH1 may be linked to other functions of the gene.
Ulfur Arnason - One of the best experts on this subject based on the ideXlab platform.
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mitogenomic analyses provide new insights into Cetacean origin and evolution
Gene, 2004Co-Authors: Ulfur Arnason, Anette Gullberg, Axel JankeAbstract:The evolution of the order Cetacea (whales, dolphins, porpoises) has, for a long time, attracted the attention of evolutionary biologists. Here we examine Cetacean phylogenetic relationships on the basis of analyses of complete mitochondrial genomes that represent all extant Cetacean families. The results suggest that the ancestors of recent Cetaceans had an explosive evolutionary radiation 30-35 million years before present. During this period, extant Cetaceans divided into the two primary groups, Mysticeti (baleen whales) and Odontoceti (toothed whales). Soon after this basal split, the Odontoceti diverged into the four extant lineages, sperm whales, beaked whales, Indian river dolphins and delphinoids (iniid river dolphins, narwhals/belugas, porpoises and true dolphins). The current data set has allowed test of two recent morphological hypotheses on Cetacean origin. One of these hypotheses posits that Artiodactyla and Cetacea originated from the extinct group Mesonychia, and the other that Mesonychia/Cetacea constitutes a sister group to Artiodactyla. The current results are inconsistent with both these hypotheses. The findings suggest that the claimed morphological similarities between Mesonychia and Cetacea are the result of evolutionary convergence rather than common ancestry.
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Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade
Proceedings. Biological sciences, 1998Co-Authors: Björn M. Ursing, Ulfur ArnasonAbstract:Although the sister-group relationship between Cetacea and Artiodactyla is widely accepted, the actual artiodactyl group which is closest to Cetacea has not been conclusively identified. In the present study, we have sequenced the complete mitochondrial genome of the hippopotamus, Hippopotamus amphibius, and included it in phylogenetic analyses together with 15 other placental mammals. These analyses separated the hippopotamus from the other suiform included, the pig, and identified the hippopotamus as the artiodactyl sister group of the Cetaceans, thereby making both. Artiodactyla and the suborder. Suiformes paraphyletic. The divergence between the hippopotamid and Cetacean lineages was calculated using this molecular data and was estimated at ca. 54 Ma BP.
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the complete mitochondrial dna sequence of the greater indian rhinoceros rhinoceros unicornis and the phylogenetic relationship among carnivora perissodactyla and artiodactyla Cetacea
Molecular Biology and Evolution, 1996Co-Authors: Xiufeng Xu, Axel Janke, Ulfur ArnasonAbstract:The sequence (16,829 nt) of the complete mitochondrial genome of the greater Indian rhinoceros, Rhinoceros unicornis, was determined. Like other perissodactyls studied (horse and donkey) the rhinoceros demonstrates length variation (heteroplasmy) associated with different numbers of repetitive motifs in the control region. The 16,829-nt variety of the molecule includes 36 identical control region motifs. The evolution of individual peptide-coding genes was examined by comparison with a distantly related perissodactyl, the horse, and the relationships among the orders Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea) were examined on the basis of concatenated sequences of 12 mitochondrial peptide-coding genes. The phylogenetic analyses grouped Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea) into a superordinal clade and within this clade a sister group relationship was recognized between Carnivora and Perissodactyla to the exclusion of Artiodactyla (+ Cetacea). On the basis of the molecular difference between the rhinoceros and the horse and by applying as a reference the Artiodactyl/Cetacean divergence set at 60 million years ago (MYA), the evolutionary divergence between the families Rhinocerotidae and Equidae was dated to approximate to 50 MYA. (Less)
Olivier Lambert - One of the best experts on this subject based on the ideXlab platform.
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extensive diversity and disparity of the early miocene platanistoids Cetacea odontoceti in the southeastern pacific chilcatay formation peru
Life, 2020Co-Authors: Giovanni Bianucci, Christian De Muizon, Mario Urbina, Olivier LambertAbstract:Several aspects of the fascinating evolutionary history of toothed and baleen whales (Cetacea) are still to be clarified due to the fragmentation and discontinuity (in space and time) of the fossil record. Here we open a window on the past, describing a part of the extraordinary Cetacean fossil assemblage deposited in a restricted interval of time (19–18 Ma) in the Chilcatay Formation (Peru). All the fossils here examined belong to the Platanistoidea clade as here redefined, a toothed whale group nowadays represented only by the Asian river dolphin Platanista gangetica. Two new genera and species, the hyper-longirostrine Ensidelphis riveroi and the squalodelphinid Furcacetus flexirostrum, are described together with new material referred to the squalodelphinid Notocetus vanbenedeni and fragmentary remains showing affinities with the platanistid Araeodelphis. Our cladistic analysis defines the new clade Platanidelphidi, sister-group to Allodelphinidae and including E. riveroi and the clade Squalodelphinidae + Platanistidae. The fossils here examined further confirm the high diversity and disparity of platanistoids during the early Miocene. Finally, morphofunctional considerations on the entire platanistoid assemblage of the Chilcatay Formation suggest a high trophic partitioning of this peculiar Cetacean paleocommunity.
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a new early pliocene species of mesoplodon a calibration mark for the radiation of this species rich beaked whale genus
Journal of Vertebrate Paleontology, 2016Co-Authors: Olivier Lambert, Stephen LouwyeAbstract:ABSTRACTIncluding at least 15 extant species, the beaked whale genus Mesoplodon (Cetacea, Odontoceti, Ziphiidae) is by far the most species-rich Cetacean genus. Such a high diversity reflects one or several pulses of radiation, most likely involving a sexual selection mechanism affecting shape, size, and position of mandibular tusks. However, the tempo of this diversification is currently poorly constrained due to the scarce fossil record. Based on the reassessment of five partial skulls discovered in Antwerp (north of Belgium), a new fossil species of the genus Mesoplodon, M. posti, sp. nov., is described. Only the second fossil species of the genus currently recognized, it is characterized (among other features) by: transverse sections of the rostrum higher than wide (a feature proposed to correspond to the presence of lower tusks more posterior than the apex of the mandibles); the presence of a basirostral groove at the rostrum base; pentagonal joined nasals; the posterior projection of the premaxilla ...
Xiufeng Xu - One of the best experts on this subject based on the ideXlab platform.
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the complete mitochondrial dna sequence of the greater indian rhinoceros rhinoceros unicornis and the phylogenetic relationship among carnivora perissodactyla and artiodactyla Cetacea
Molecular Biology and Evolution, 1996Co-Authors: Xiufeng Xu, Axel Janke, Ulfur ArnasonAbstract:The sequence (16,829 nt) of the complete mitochondrial genome of the greater Indian rhinoceros, Rhinoceros unicornis, was determined. Like other perissodactyls studied (horse and donkey) the rhinoceros demonstrates length variation (heteroplasmy) associated with different numbers of repetitive motifs in the control region. The 16,829-nt variety of the molecule includes 36 identical control region motifs. The evolution of individual peptide-coding genes was examined by comparison with a distantly related perissodactyl, the horse, and the relationships among the orders Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea) were examined on the basis of concatenated sequences of 12 mitochondrial peptide-coding genes. The phylogenetic analyses grouped Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea) into a superordinal clade and within this clade a sister group relationship was recognized between Carnivora and Perissodactyla to the exclusion of Artiodactyla (+ Cetacea). On the basis of the molecular difference between the rhinoceros and the horse and by applying as a reference the Artiodactyl/Cetacean divergence set at 60 million years ago (MYA), the evolutionary divergence between the families Rhinocerotidae and Equidae was dated to approximate to 50 MYA. (Less)
