Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

PLoS Biology, Год журнала: 2019, Номер 17(12), С. e3000494 - e3000494

Опубликована: Дек. 4, 2019

Big, time-scaled phylogenies are fundamental to connecting evolutionary processes modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility comparative biologists. To establish a robust timescale all approximately 6,000 living mammals, we developed credible sets capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach tree building applies newly assembled 31-gene supermatrix two levels Bayesian inference: (1) backbone relationships ages among major lineages, using fossil node or tip dating, (2) species-level "patch" with nonoverlapping in-groups each correspond one representative lineage the backbone. Species unsampled DNA either excluded ("DNA-only" trees) imputed within taxonomic constraints branch lengths drawn from local birth–death models ("completed" trees). Joining patches backbones results extant Mammalia branches estimated under same modeling framework, thereby facilitating rate comparisons lineages as disparate marsupials placentals. We compare our previous estimates mammal-wide phylogeny times, finding broadly concordant studies, recent (tip-level) rates speciation more accurately study than "supertree" approaches, which unresolved nodes led branch-length artifacts. Credible mammalian history now available download at http://vertlife.org/phylosubsets, enabling investigations long-standing questions biology.

Язык: Английский

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SARS-CoV-2 infection, neuropathogenesis and transmission among deer mice: Implications for spillback to New World rodents

PLoS Pathogens, Год журнала: 2021, Номер 17(5), С. e1009585 - e1009585

Опубликована: Май 19, 2021

Coronavirus disease-19 (COVID-19) emerged in late 2019 China and rapidly became pandemic. As with other coronaviruses, a preponderance of evidence suggests the virus originated horseshoe bats ( Rhinolophus spp.) may have infected an intermediate host prior to spillover into humans. A significant concern is that SARS-CoV-2 could become established secondary reservoir hosts outside Asia. To assess this potential, we challenged deer mice Peromyscus maniculatus ) found robust replication upper respiratory tract, lungs intestines, detectable viral RNA for up 21 days oral swabs 6 lungs. Virus entry brain also occurred, likely via gustatory-olfactory-trigeminal pathway eventual compromise blood-brain barrier. Despite this, no conspicuous signs disease were observed, succumbed infection. Expression several innate immune response genes elevated lungs, including IFNα, IFNβ, Cxcl10, Oas2, Tbk1 Pycard. Elevated CD4 CD8β expression was concomitant Tbx21, IFNγ IL-21 expression, suggesting type I inflammatory response. Contact transmission occurred from naive through two passages, showing sustained natural localization olfactory bulb, recapitulating human neuropathology. In second mouse passage, insertion 4 amino acids fixation N-terminal domain spike protein predicted form solvent-accessible loop. Subsequent examination source BEI Resources determined mutation present at very low levels, demonstrating potent purifying selection insert during vivo passage. Collectively, work has are suitable animal model study neuropathogenesis, they potential serve as North America.

Язык: Английский

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Motor cortical control of vocal interaction in neotropical singing mice

Science, Год журнала: 2019, Номер 363(6430), С. 983 - 988

Опубликована: Март 1, 2019

Turn-taking in singing mice The ability to take turns is a hallmark of social interaction among animals. It occurs many different species, from dueting birds frogs, and notable part human speech. Such rapid response requires complex cascade sensory motor actions that has been difficult characterize. Okobi et al. examined turn-taking tropical mice, which males interrupt, alter, each other's songs (see the Perspective by Hage). They describe an orofacial cortex mediates transition vocal apparatus facilitates interactions. Science , this issue p. 983 see also 926

Язык: Английский

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Rodent systematics in an age of discovery: recent advances and prospects

Journal of Mammalogy, Год журнала: 2018, Номер 100(3), С. 852 - 871

Опубликована: Дек. 22, 2018

With almost 2,600 species, Rodentia is the most diverse order of mammals. Here, we provide an overview changes in our understanding systematics living rodents, including species recognition and delimitation, phylogenetics, classification, with emphasis on last three decades. Roughly, this corresponds to DNA sequencing era rodent systematics, but field undergoing a transition into genomic era. At least 248 were newly described period 2000–2017, novelties such as first member Diatomyidae murid without molars (Paucidentomys vermidax), thus highlighting fact that diversity going through age discovery. Mito-nuclear discordance (including resulting from mitochondrial introgression) has been detected some few taxonomic studies have assessed variation two or more unlinked loci. As incorporate loci, incomplete lineage sorting introgression are likely gain widespread phenomena near future. Molecular phylogenetics had major impact phylogeny allowed identification clades, here recognized suborders: 1) Hystricomorpha (sometimes referred Ctenohystrica) infraorders, Hystricognathi Ctenodactylomorphi; 2) Sciuromorpha; 3) Supramyomorpha, new suborder comprises infraorders Castorimorphi, Anomalurimorphi, Myomorphi. In spite greater ensuing stability gained during decades, several areas tree remain unresolved poorly supported. We expect analysis genomic-scale data will help resolve those radiation still understood.

Язык: Английский

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The evolution of centriole degradation in mouse sperm

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 2, 2024

Abstract Centrioles are subcellular organelles found at the cilia base with an evolutionarily conserved structure and a shock absorber-like function. In sperm, centrioles flagellum essential for embryo development in basal animals. Yet, sperm have evolved diverse forms, sometimes acting like transmission system, as cattle, becoming dispensable, house mice. How centriole to become dispensable some organisms is unclear. Here, we test hypothesis that this transition occurred through cascade of evolutionary changes proteins, structure, function was possibly driven by competition. We final steps associated change primary centriolar inner scaffold protein FAM161A rodents. This information provides first insight into molecular mechanisms adaptive evolution underlying major within internal mammalian neck.

Язык: Английский

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Mitogenomic Analysis of Glirids (Gliridae) and Squirrels (Sciuridae) From Türkiye: Evolutionary and Taxonomic Implications Within the Suborder Sciuromorpha

Ecology and Evolution, Год журнала: 2025, Номер 15(2)

Опубликована: Фев. 1, 2025

ABSTRACT Gliridae and Sciuridae, the most impressive mammalian radiations within suborder Sciuromorpha, encompass a total of 327 extant species. This study aimed to: (i) characterize mitogenomes three sciurid ( Spermophilus citellus , taurensis xanthoprymnus ) glirid Glis glis Dryomys nitedula laniger species from Türkiye; (ii) elucidate phylogeographic relationships D. using both mitochondrial cytochrome b CYTB sequences; (iii) reconstruct phylogenetic among members Sciuromorpha. Sixteen new were sequenced Turkish samples, containing 37 genes (2 ribosomal RNA s, 13 protein‐coding genes, 22 transfer s), exhibiting similarity to those other Sciuridae Based on mitogenomic data, Bayesian Inference Maximum Likelihood analyses revealed two major phylogroups corresponding families, which monophyletic. Analyses sequences at least lineages (i: Anatolia ii: Lesser Caucasus Alborz) in Anatolian region Türkiye. The data indicated that exhibited (Eastern Western), whereas comprised multiple sublineages. mean genetic distance between was 7.69%. Eastern Western 7%, distances ranged 6% 13%. Major might be considered distinct throughout species' range. demonstrates complete for reconstructing phylogeny provides important information revealing relationships.

Язык: Английский

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Fossils know it best: Using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Muridae)

Molecular Phylogenetics and Evolution, Год журнала: 2018, Номер 128, С. 98 - 111

Опубликована: Июль 18, 2018

Язык: Английский

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Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

Systematic Biology, Год журнала: 2019, Номер 69(3), С. 431 - 444

Опубликована: Июнь 14, 2019

The estimation of robust and accurate measures branch support has proven challenging in the era phylogenomics. In data sets potentially millions sites, bootstrap for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation may particularly problematic rapid radiations, where phylogenetic signal is low incomplete lineage sorting severe. Here, we explore this issue by comparing various estimates under both concatenated coalescent frameworks, recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence from 1245 independent loci several phylogenomic inference methods, unequivocally resolve majority genus-level within Hydromyini. However, at four nodes recover inconsistency among approaches. most cases, likelihood approaches using standard fast algorithms did not detect any uncertainty these nodes, regardless partitioning strategy. found could overcome with two-stage resampling, that is, across genes sites (using -bsam GENESITE IQ-TREE). addition, confidence recalcitrant was recovered UFBoot2, a revision to protocol IQ-TREE, but depended on Summary also failed some circumstances. For each an equivalent (or close equivalent) number were strong ($>$ 75% bootstrap) primary least one alternative topological hypothesis, suggesting notable conflict detected metrics. Recent debate focused appropriateness versus multigenealogical resolving species relationships, less so accurately estimating large sets. Our results demonstrate importance employing multiple when assessing highlight need greater attention development

Язык: Английский

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A helminth-derived suppressor of ST2 blocks allergic responses

eLife, Год журнала: 2020, Номер 9

Опубликована: Май 18, 2020

The IL-33-ST2 pathway is an important initiator of type 2 immune responses. We previously characterised the HpARI protein secreted by model intestinal nematode Heligmosomoides polygyrus, which binds and blocks IL-33. Here, we identify H. polygyrus Binds Alarmin Receptor Inhibits (HpBARI) HpBARI_Hom2, both consist complement control (CCP) domains, similarly to immunomodulatory Hp-TGM proteins. HpBARI murine ST2, inhibiting cell surface detection preventing interactions, IL-33 responses in vitro vivo mouse asthma. In infection, ST2 abrogated peritoneal cavity lung, consistent with systemic effects HpBARI. HpBARI_Hom2 also human high affinity, effectively PBMC Thus, show that via cytokine, receptor.

Язык: Английский

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SARS-CoV-2 infection, neuropathogenesis and transmission among deer mice: Implications for reverse zoonosis to New World rodents

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2020, Номер unknown

Опубликована: Авг. 7, 2020

Abstract Coronavirus disease-19 (COVID-19) emerged in November, 2019 China and rapidly became pandemic. As with other coronaviruses, a preponderance of evidence suggests the virus originated horseshoe bats ( Rhinolophus spp.) likely underwent recombination event an intermediate host prior to entry into human populations. A significant concern is that SARS-CoV-2 could become established secondary reservoir hosts outside Asia. To assess this potential, we challenged deer mice Peromyscus maniculatus ) found robust replication upper respiratory tract, lungs intestines, detectable viral RNA for up 21 days oral swabs 14 lungs. Virus brain also occurred, via gustatory-olfactory-trigeminal pathway eventual compromise blood barrier. Despite this, no conspicuous signs disease were observed succumbed infection. Expression several innate immune response genes elevated lungs, notably IFNα, Cxcl10, Oas2, Tbk1 Pycard. Elevated CD4 CD8β expression was concomitant Tbx21, IFNγ IL-21 expression, suggesting type I inflammatory response. Contact transmission occurred from infected naive through two passages, showing sustained natural transmission. In second mouse passage, insertion 4 amino acids fixation N-terminal domain spike protein predicted form solvent-accessible loop. Subsequent examination source BEI Resources indicated mutation present at very low levels, demonstrating potent purifying selection insert during vivo passage. Collectively, work has determined are suitable animal model study pathogenesis, they have potential serve as lead periodic outbreaks COVID-19 North America.

Язык: Английский

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