Cetartiodactyla: Updating a time-calibrated molecular phylogeny

Zurano, Juan Pablo; Magalhães, Felipe de Medeiros; Asato, Ana Elizabeth Bonato; Silva, Gabriel; Bidau, Claudio J.; Mesquita, Daniel Oliveira; Costa, Gabriel C.

doi:10.1016/j.ympev.2018.12.015

Cited by 92 publications

(104 citation statements)

References 39 publications

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“…The species tree inferred from all gene trees (Fig 1) was consistent with published cetacean and artiodactylan phylogenies (Zurano et al, 2019). Alignment-wide ω estimates from the PAML null models were <1 for all but one gene (median: 0.08; mean: 0.12), consistent with a baseline of strong purifying selection on protein function across all taxa and all codons (Fig 2A).…”

Section: Resultssupporting

confidence: 83%

Adaptations of energy metabolism in cetaceans have consequences for their response to foraging disruption

Derous

Sahu

Douglas

et al. 2019

Preprint

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Cetaceans have varied their anatomical structure, physiology and metabolism to adapt to the challenges of aquatic life. Key to this change is the deposition of blubber. This adipose tissue plays a significant regulatory and signaling role in mammalian metabolism. As foraging disruption by human activities is emerging as a key conservation threat for cetaceans, we need to understand how selection for aquatic life might have altered key nutrient sensing pathways associated with adipose signaling. We compared selection pressure on those energy metabolism biological pathways by contrasting the rate of substitution observed in genes associated with them in cetacean and artiodactyl genomes. We then estimated the likely consequence of these selection pressures for pathway functions. Here we show that genes involved in the insulin, mTOR, SIRT and NF-κB pathways were under significant positive selection in cetaceans compared to their terrestrial sister taxon. Our results suggest these genes may have been positively selected to adapt to a glucose-poor diet and it is unlikely that fat depots signaling function in the same manner as in terrestrial mammals. Secondary adaptation to life in water significantly affected functions in nutrient sensing pathways in cetaceans. Insulin is not likely to play the same role in energy balance as it does in terrestrial mammals and adiposity is not likely to have the deleterious health consequences it has in terrestrial mammals. The physiological ecology of cetacean fat deposition, and therefore its value as a condition index, needs to be interpreted in this evolutionary context.

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Section: Resultssupporting

confidence: 83%

Adaptations of energy metabolism in cetaceans have consequences for their response to foraging disruption

Derous

Sahu

Douglas

et al. 2019

Preprint

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“…The same was found in the combined molecular and TE analyses. This is also confirmed in recent studies using mtDNA (Marcot, 2007;Hassanin et al, 2012;Heckeberg et al, 2016;Zurano et al, 2019).…”

Section: Cervussupporting

confidence: 85%

“…In the analyses here, Dama dama and Dama mesopotamica were always sister taxa to each other and in most cases placed as the sister taxon to a clade consisting of Cervus, Rusa, Elaphurus davidianus, and Rucervus eldii. In previous studies, both Dama species were also sister taxa to each other (Randi et al, 2001;Lister et al, 2005;Hughes et al, 2006;Hassanin et al, 2012;Heckeberg et al, 2016;Zurano et al, 2019).…”

Section: Damamentioning

confidence: 74%

“…However, recent molecular studies relatively consistently showed that the clade consisting of Moschidae plus Bovidae was the sister taxon to Cervidae, which was the sister taxon to Giraffidae, then Antilocapridae; Tragulidae was the sister taxon to all of them (Kuznetsova, Kholodova & Danilkin, 2005;Marcot, 2007;Agnarsson & May-Collado, 2008;Hassanin et al, 2012;Bibi, 2014;Zurano et al, 2019). The most recent study on ruminant genomics supports a sister taxon relationship of Antilocapridae & Giraffidae .…”

Section: Cervid Systematics In Context Of Ruminant Familiesmentioning

confidence: 98%

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The systematics of the Cervidae: a total evidence approach

Heckeberg

2020

PeerJ

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Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub) classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervids. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervids. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio-and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.

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“…To that end we obtained paired-end Illumina whole-genome sequencing (WGS) reads from the European Nucleotide Archive (Leinonen et al 2011) for three well-supported mammal clades: catarrhine primates, murid rodents, and members of the infraorder Pecora. Each dataset included ten focal taxa as well as two outgroup taxa, all with well-supported evolutionary relationships ( Figure 1) (Reis et al 2018;Zurano et al 2019;Steppan and Schenk 2017) . To enable downstream ortholog annotation, each focal dataset contained one species with a well-assembled and well-annotated reference genome (Primates: Homo sapiens , Rodents: Mus musculus , Pecora: Bos taurus ).…”

Section: Raw Data Processingmentioning

confidence: 99%

Genome-scale profiling reveals higher proportions of phylogenetic signal in non-coding data

Literman

Schwartz

2019

Preprint

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Accurate estimates of species relationships are integral to our understanding of the evolution of traits and lineages, yet many relationships remain controversial despite whole genome sequence data. These controversies are due, at least in part, to complex patterns of phylogenetic and non-phylogenetic signal coming from regions of the genome experiencing different evolutionary forces. Here we profile the phylogenetic informativeness of loci from across mammalian genomes. We identified orthologous sequences from primates, rodents, and pecora, and annotated millions of sites as one or more of nine locus types (e.g. coding, intronic, intergenic) and profiled the informativeness of different locus types across the evolutionary timescales of each clade. In all cases, non-coding loci provided more overall signal and a higher proportion of phylogenetic signal compared to coding loci. Most locus types provide relatively consistent phylogenetic information across timescales, although we find evidence that coding and intronic regions may inform disproportionately about older and younger splits, respectively, to a limited degree. We also validated the SISRS pipeline as an annotation-free ortholog discovery pipeline that identifies millions of phylogenetically informative sites directly from whole-genome sequencing reads.

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Cetartiodactyla: Updating a time-calibrated molecular phylogeny

Cited by 92 publications

References 39 publications

Adaptations of energy metabolism in cetaceans have consequences for their response to foraging disruption

Adaptations of energy metabolism in cetaceans have consequences for their response to foraging disruption

The systematics of the Cervidae: a total evidence approach

Genome-scale profiling reveals higher proportions of phylogenetic signal in non-coding data

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