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

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(12), P. e3000494 - e3000494

Published: Dec. 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.

Language: Английский

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A global reptile assessment highlights shared conservation needs of tetrapods

Nature, Journal Year: 2022, Volume and Issue: 605(7909), P. 285 - 290

Published: April 27, 2022

Comprehensive assessments of species' extinction risks have documented the crisis1 and underpinned strategies for reducing those risks2. Global reveal that, among tetrapods, 40.7% amphibians, 25.4% mammals 13.6% birds are threatened with extinction3. Because global been lacking, reptiles omitted from conservation-prioritization analyses that encompass other tetrapods4-7. Reptiles unusually diverse in arid regions, suggesting they may different conservation needs6. Here we provide a comprehensive extinction-risk assessment show at least 1,829 out 10,196 species (21.1%) threatened-confirming previous extrapolation8 representing 15.6 billion years phylogenetic diversity. by same major factors threaten tetrapods-agriculture, logging, urban development invasive species-although threat posed climate change remains uncertain. inhabiting forests, where these threats strongest, more than habitats, contrary to our prediction. Birds, amphibians unexpectedly good surrogates reptiles, although smallest ranges tend be isolated tetrapods. Although some reptiles-including most crocodiles turtles-require urgent, targeted action prevent extinctions, efforts protect such as habitat preservation control trade species, will probably also benefit many reptiles.

Language: Английский

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The Angiosperm Terrestrial Revolution and the origins of modern biodiversity

New Phytologist, Journal Year: 2021, Volume and Issue: 233(5), P. 2017 - 2035

Published: Oct. 26, 2021

Summary Biodiversity today has the unusual property that 85% of plant and animal species live on land rather than in sea, half these tropical rainforests. An explosive boost to terrestrial diversity occurred from c . 100–50 million years ago, Late Cretaceous early Palaeogene. During this interval, Earth‐life system was reset, biosphere expanded a new level productivity, enhancing capacity environments. This biodiversity coincided with innovations flowering biology evolutionary ecology, including their flowers efficiencies reproduction; coevolution animals, especially pollinators herbivores; photosynthetic capacities; adaptability; ability modify habitats. The rise angiosperms triggered macroecological revolution drove modern secular, prolonged shift new, high levels, series processes we name here Angiosperm Terrestrial Revolution.

Language: Английский

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Cancer risk across mammals

Nature, Journal Year: 2021, Volume and Issue: 601(7892), P. 263 - 267

Published: Dec. 22, 2021

Abstract Cancer is a ubiquitous disease of metazoans, predicted to disproportionately affect larger, long-lived organisms owing their greater number cell divisions, and thus increased probability somatic mutations 1,2 . While elevated cancer risk with larger body size and/or longevity has been documented within species 3–5 , Peto’s paradox indicates the apparent lack such an association among taxa 6 Yet, unequivocal empirical evidence for lacking, stemming from difficulty estimating in non-model species. Here we build analyse database on cancer-related mortality using data adult zoo mammals (110,148 individuals, 191 species) map age-controlled mammalian tree life. We demonstrate universality high frequency oncogenic phenomena reveal substantial differences across major orders. show that phylogenetic distribution associated diet, carnivorous (especially mammal-consuming ones) facing highest mortality. Moreover, provide components by showing largely independent both mass life expectancy These results highlight key role life-history evolution shaping resistance advancements quest natural anticancer defences.

Language: Английский

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A species-level timeline of mammal evolution integrating phylogenomic data

Nature, Journal Year: 2021, Volume and Issue: 602(7896), P. 263 - 267

Published: Dec. 22, 2021

Language: Английский

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Shortfalls and opportunities in terrestrial vertebrate species discovery

Nature Ecology & Evolution, Journal Year: 2021, Volume and Issue: 5(5), P. 631 - 639

Published: March 22, 2021

Language: Английский

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Recent Changes in Patterns of Mammal Infection with Highly Pathogenic Avian Influenza A(H5N1) Virus Worldwide

Emerging infectious diseases, Journal Year: 2024, Volume and Issue: 30(3)

Published: Feb. 23, 2024

We reviewed information about mammals naturally infected by highly pathogenic avian influenza A virus subtype H5N1 during 2 periods: the current panzootic (2020-2023) and previous waves of infection (2003-2019). In panzootic, 26 countries have reported >48 mammal species virus; in some cases, has affected thousands individual animals. The geographic area number event are considerably larger than infection. most plausible source both periods appears to be close contact with birds, including their ingestion. Some studies, especially suggest that mammal-to-mammal transmission might responsible for infections; mutations found could help this pathogen replicate mammals. may changing adapting infect Continuous surveillance is essential mitigate risk a global pandemic.

Language: Английский

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Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: March 14, 2022

Northern Hemisphere forests changed drastically in the early Eocene with diversification of oak family (Fagaceae). Cooling climates over next 20 million years fostered spread temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses nuclear plastid genomes to investigate timing pattern major macroevolutionary events ancient genome-wide signatures hybridization across Fagaceae. Innovation related seed dispersal is implicated triggering waves continental radiations beginning rapid lineages resulting unparalleled transformation forest dynamics within 15 following K-Pg extinction. We detect introgression at multiple time scales, including predating origination genus-level diversity. As moved into newly available habitats Miocene, secondary contact between previously isolated species occurred. This resulted adaptive introgression, which may have further amplified white Eurasia.

Language: Английский

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U.PhyloMaker: An R package that can generate large phylogenetic trees for plants and animals

Plant Diversity, Journal Year: 2022, Volume and Issue: 45(3), P. 347 - 352

Published: Dec. 24, 2022

The previously released packages of the PhyloMaker series (i.e. S.PhyloMaker, V.PhyloMaker, and V.PhyloMaker2) have been broadly used to generate phylogenetic trees for ecological biogeographical studies. Although these can be any groups plants animals which megatrees are available, they focus on generating based provided by packages. How use other is not straightforward. Here, we present a new tool, called 'U.PhyloMaker', simple R script that easily large both at relatively fast speed.

Language: Английский

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A genomic timescale for placental mammal evolution

Science, Journal Year: 2023, Volume and Issue: 380(6643)

Published: April 27, 2023

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal relationships exhibit relatively low rates conflict diverse datasets analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades radiated during the Cenozoic. Genomic time trees reveal accumulation cladogenic before immediately after Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance K-Pg extinction in radiation.

Language: Английский

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