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1.
Nat Commun ; 11(1): 4048, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873779

RESUMO

Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures.


Assuntos
Mudança Climática , Especiação Genética , Genoma Mitocondrial , Mastodontes/genética , Animais , DNA Antigo/análise , DNA Antigo/isolamento & purificação , DNA Mitocondrial/genética , DNA Mitocondrial/isolamento & purificação , Feminino , Fósseis , Masculino , Filogeografia
2.
Mem Inst Oswaldo Cruz ; 115: e200310, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32997001

RESUMO

A new coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] is currently causing a life-threatening pandemic. In this study, we report the complete genome sequencing and genetic characterisation of a SARS-CoV-2 detected in Manaus, Amazonas, Brazil, and the protocol we designed to generate high-quality SARS-CoV-2 full genome data. The isolate was obtained from an asymptomatic carrier returning from Madrid, Spain. Nucleotide sequence analysis showed a total of nine mutations in comparison with the original human case in Wuhan, China, and support this case as belonging to the recently proposed lineage A.2. Phylogeographic analysis further confirmed the likely European origin of this case. To our knowledge, this is the first SARS-CoV-2 genome obtained from the North Brazilian Region. We believe that the information generated in this study may contribute to the ongoing efforts toward the SARS-CoV-2 emergence.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/virologia , Filogenia , Pneumonia Viral/virologia , Infecções Assintomáticas , Brasil , Genoma Viral , Genômica , Humanos , Mutação , Pandemias , Filogeografia , Espanha
3.
Nature ; 585(7823): 74-78, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32879498

RESUMO

Introductions of species by humans are causing the homogenization of species composition across biogeographic barriers1-3. The ecological and evolutionary consequences of introduced species derive from their effects on networks of species interactions4,5, but we lack a quantitative understanding of the impacts of introduced species on ecological networks and their biogeographic patterns globally. Here we address this data gap by analysing mutualistic seed-dispersal interactions from 410 local networks, encompassing 24,455 unique pairwise interactions between 1,631 animal and 3,208 plant species. We show that species introductions reduce biogeographic compartmentalization of the global meta-network, in which nodes are species and links are interactions observed within any local network. This homogenizing effect extends across spatial scales, decreasing beta diversity among local networks and modularity within networks. The prevalence of introduced interactions is directly related to human environmental modifications and is accelerating, having increased sevenfold over the past 75 years. These dynamics alter the coevolutionary environments that mutualists experience6, and we find that introduced species disproportionately interact with other introduced species. These processes are likely to amplify biotic homogenization in future ecosystems7 and may reduce the resilience of ecosystems by allowing perturbations to propagate more quickly and exposing disparate ecosystems to similar drivers. Our results highlight the importance of managing the increasing homogenization of ecological complexity.


Assuntos
Ecossistema , Espécies Introduzidas , Filogeografia , Plantas , Simbiose , Animais , Biodiversidade , Atividades Humanas , Dispersão de Sementes , Análise Espaço-Temporal
4.
Genome Res ; 30(10): 1434-1448, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32878977

RESUMO

The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the twenty-first century. We analyzed more than 4700 SARS-CoV-2 genomes and associated metadata retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus genome. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and more than 160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a rather uniform mutation occurrence along branches that could have implications for diagnostics and the design of future vaccines. Identification of the root of SARS-CoV-2 genomes is not without problems, owing to conflicting interpretations derived from either using the bat coronavirus genomes as an outgroup or relying on the sampling chronology of the SARS-CoV-2 genomes and TMRCA estimates; however, the overall scenario favors haplogroup A as the ancestral node. Phylogenetic analysis indicates a TMRCA for SARS-CoV-2 genomes dating to November 12, 2019, thus matching epidemiological records. Sub-haplogroup A2 most likely originated in Europe from an Asian ancestor and gave rise to subclade A2a, which represents the major non-Asian outbreak, especially in Africa and Europe. Multiple founder effect episodes, most likely associated with super-spreader hosts, might explain COVID-19 pandemic to a large extent.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Genoma Viral/genética , Pneumonia Viral/epidemiologia , Animais , Ásia/epidemiologia , Sequência de Bases/genética , Quirópteros/virologia , Mapeamento Cromossômico , Europa (Continente)/epidemiologia , Evolução Molecular , Variação Genética/genética , Humanos , Pandemias , Filogenia , Filogeografia , Homologia de Sequência do Ácido Nucleico
5.
Nat Commun ; 11(1): 4739, 2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32958756

RESUMO

More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.


Assuntos
Búfalos/genética , Bovinos/genética , Domesticação , Genoma/genética , Animais , Cruzamento , Búfalos/classificação , Bovinos/classificação , Evolução Molecular , Loci Gênicos/genética , Variação Genética , Fenótipo , Filogeografia , Seleção Genética
6.
PLoS One ; 15(8): e0236759, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32745105

RESUMO

The fall armyworm (Spodoptera frugiperda) is a moth pest native to the Western Hemisphere that has recently become a global problem, invading Africa, Asia, and Australia. The species has a broad host range, long-distance migration capability, and a propensity for the generation of pesticide resistance traits that make it a formidable invasive threat and a difficult pest to control. While fall armyworm migration has been extensively studied in North America, where annual migrations of thousands of kilometers are the norm, migration patterns in South America are less understood. As a first step to address this issue we have been genetically characterizing fall armyworm populations in Ecuador, a country in the northern portion of South America that has not been extensively surveyed for this pest. These studies confirm and extend past findings indicating similarities in the fall armyworm populations from Ecuador, Trinidad-Tobago, Peru, and Bolivia that suggest substantial migratory interactions. Specifically, we found that populations throughout Ecuador are genetically homogeneous, indicating that the Andes mountain range is not a long-term barrier to fall armyworm migration. Quantification of genetic variation in an intron sequence describe patterns of similarity between fall armyworm from different locations in South America with implications for how migration might be occurring. In addition, we unexpectedly found these observations only apply to one subset of fall armyworm (the C-strain), as the other group (R-strain) was not present in Ecuador. The results suggest differences in migration behavior between fall armyworm groups in South America that appear to be related to differences in host plant preferences.


Assuntos
Haplótipos/genética , Spodoptera/genética , Migração Animal , Animais , Equador , Complexo IV da Cadeia de Transporte de Elétrons/genética , Marcadores Genéticos , Íntrons/genética , Controle de Pragas , Filogenia , Filogeografia , América do Sul
7.
Euro Surveill ; 25(32)2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32794443

RESUMO

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Coronavirus/genética , Genoma Viral/genética , Pandemias , Pneumonia Viral/epidemiologia , RNA Replicase/genética , RNA Viral/análise , Sequência de Bases , Betacoronavirus/patogenicidade , Coronavirus/isolamento & purificação , Infecções por Coronavirus/virologia , Europa (Continente)/epidemiologia , Humanos , Filogeografia , Pneumonia Viral/virologia , RNA Viral/genética , Síndrome Respiratória Aguda Grave , Análise Espaço-Temporal , Organização Mundial da Saúde
8.
PLoS One ; 15(8): e0238049, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32834019

RESUMO

Genetics of pigs has been well studied in Europe and Asia, but most of previous studies of molecular phylogeny of Sus scrofa have been based on sequences of both wild and domestic forms. In this study we analysed genetic traits of Sus scrofa from 13 regions in Asia (including previously undisclosed Eastern Caucasus and Trans-Baikal regions) using purely wild boar samples. Mitochondrial control region and Y-chromosome genes (AMELY & USP9Y) were employed to resolve phylogeographic relationships. We discussed spatio-temporal dynamics of wild boar distribution and compared molecular data to morphological and cytogenetic data on wild boar variability and taxonomy. A total of 51 haplotypes were detected in mtDNA control region and five haplotypes were found in combined sequences of Y-chromosome genes. The phylogeography of Asia-wide wild boars supported a hypothesis of migration from South-East Asia to South Asia, followed by migration to East and West Asia. We present a hypothesis about independent dispersal of wild boars into West Asia from South and North-East Asia. Mitochondrial DNA phylogeny generally fits the morphologically based intraspecies taxonomy. Distribution of chromosomal variants of wild boar presently does not show clear correlation with mtDNA clades.


Assuntos
DNA Mitocondrial/genética , Filogeografia , Sus scrofa/genética , Cromossomo Y/genética , Animais , Ásia , Variação Genética
9.
Nat Commun ; 11(1): 4235, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32843626

RESUMO

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.


Assuntos
Quirópteros/virologia , Infecções por Coronavirus/veterinária , Coronavirus/genética , Evolução Molecular , Zoonoses/transmissão , Animais , Teorema de Bayes , Betacoronavirus/classificação , Betacoronavirus/genética , Biodiversidade , China , Quirópteros/classificação , Coronavirus/classificação , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Humanos , Pandemias , Filogenia , Filogeografia , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , Zoonoses/virologia
10.
PLoS Pathog ; 16(8): e1008699, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32764827

RESUMO

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.


Assuntos
Genoma Viral , Doenças dos Primatas/virologia , Febre Amarela/veterinária , Febre Amarela/virologia , Vírus da Febre Amarela/genética , Zoonoses/virologia , Animais , Brasil/epidemiologia , Surtos de Doenças , Genômica , Humanos , Filogenia , Filogeografia , Doenças dos Primatas/epidemiologia , Doenças dos Primatas/transmissão , Primatas/virologia , Febre Amarela/epidemiologia , Febre Amarela/transmissão , Vírus da Febre Amarela/classificação , Vírus da Febre Amarela/isolamento & purificação , Zoonoses/epidemiologia , Zoonoses/transmissão
11.
PLoS One ; 15(8): e0237079, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32790769

RESUMO

The phyllosphere microbiome is increasingly recognised as an influential component of plant physiology, yet it remains unclear whether stable host-microbe associations generally exist in the phyllosphere. Leptospermum scoparium (manuka) is a tea tree indigenous to New Zealand, and honey derived from manuka is widely known to possess unique antimicrobial properties. However, the host physiological traits associated with these antimicrobial properties vary widely, and the specific cause of such variation has eluded scientists despite decades of research. Notably, the manuka phyllosphere microbiome remains uncharacterised, and its potential role in mediating host physiology has not been considered. Working within the prevailing core microbiome conceptual framework, we hypothesise that the phyllosphere microbiome of manuka exhibits specific host association patterns congruent with those of a microbial community under host selective pressure (null hypothesis: the manuka phyllosphere microbiome is recruited stochastically from the surrounding environment). To examine our hypothesis, we characterised the phyllosphere and associated soil microbiomes of five distinct and geographically distant manuka populations across the North Island of New Zealand. We identified a habitat-specific and relatively abundant core microbiome in the manuka phyllosphere, which was persistent across all samples. In contrast, non-core phyllosphere microorganisms exhibited significant variation across individual host trees and populations that was strongly driven by environmental and spatial factors. Our results demonstrate the existence of a dominant and ubiquitous core microbiome in the phyllosphere of manuka, supporting our hypothesis that phyllosphere microorganisms of manuka exhibit specific host association and potentially mediate physiological traits of this nationally and culturally treasured indigenous plant. In addition, our results illustrate biogeographical patterns in manuka phyllosphere microbiomes and offer insight into factors contributing to phyllosphere microbiome assembly.


Assuntos
Leptospermum/microbiologia , Microbiota , Interações Hospedeiro-Patógeno , Leptospermum/classificação , Nova Zelândia , Filogeografia
12.
PLoS One ; 15(6): e0234385, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32603327

RESUMO

Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.


Assuntos
Genoma Mitocondrial , Viverridae/genética , Animais , Ásia Sudeste , DNA Mitocondrial/genética , DNA Mitocondrial/história , Bases de Dados de Ácidos Nucleicos , Evolução Molecular , Extinção Biológica , Fósseis/história , Especiação Genética , História Antiga , Filogenia , Filogeografia , Alinhamento de Sequência , Análise de Sequência de DNA , Especificidade da Espécie , Viverridae/classificação
13.
PLoS One ; 15(7): e0235430, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32722672

RESUMO

Phylogeographic relationships among global collections of the mosquito Aedes aegypti were evaluated using the mitochondrial Cytochrome C Oxidase 1 (CO1) and NADH dehydrogenase subunit 4 (ND4) genes including new sequences from Sri Lanka. Phylogeographic analysis estimated that Ae. aegypti arose as a species ~614 thousand years ago (kya) in the late Pleistocene. At 545 kya an "early" East African clade arose that continued to differentiate in East Africa, and eventually gave rise to three lineages one of which is distributed throughout all tropical and subtropical regions, a second that contains Southeast Asian/Sri Lankan mosquitoes and a third that contains mostly New World mosquitoes. West African collections were not represented in this early clade. The late clade continued to differentiate throughout Africa and gave rise to a lineage that spread globally. The most recent branches of the late clade are represented by South-East Asia and India/Pakistan collections. Analysis of migration rates suggests abundant gene flow between India/Pakistan and the rest of the world with the exception of Africa.


Assuntos
Aedes/genética , DNA Mitocondrial/genética , Mitocôndrias/genética , Filogeografia , Aedes/classificação , África , África Oriental , Animais , Complexo IV da Cadeia de Transporte de Elétrons/genética , Fluxo Gênico , Genes Mitocondriais/genética , Haplótipos , Índia , Mitocôndrias/metabolismo , Paquistão , Filogenia , Sri Lanka
14.
Emerg Infect Dis ; 26(10): 2411-2415, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32614767

RESUMO

We established rapid local viral sequencing to document the genomic diversity of severe acute respiratory syndrome coronavirus 2 entering Uganda. Virus lineages closely followed the travel origins of infected persons. Our sequence data provide an important baseline for tracking any further transmission of the virus throughout the country and region.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Pandemias/prevenção & controle , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Viagem Aérea , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/prevenção & controle , Variação Genética , Genoma , Política de Saúde , Humanos , Programas de Rastreamento , Veículos Automotores , Filogeografia , Pneumonia Viral/diagnóstico , Pneumonia Viral/prevenção & controle , Quarentena , Uganda/epidemiologia
15.
PLoS One ; 15(7): e0235949, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32687493

RESUMO

Areas of endemism (AoE) are the main study units in analytical biogeographic methods, and are often defined as an area with two or more endemic species living in them, presenting substantial congruence among their range limits. We explored the distribution of land planarians (Geoplanidae, Platyhelminthes) across the southern region of the Brazilian Atlantic forest (from the state of Rio de Janeiro, to the state of Rio Grande do Sul) utilizing DaSilva's et al. (2015) protocol. We used two methods, Endemicity Analysis (EA), and Geographical Interpolation of Endemism (GIE). We identified nine AoE of terrestrial flatworms in the Southern Atlantic forest. Performance of the methodologies is discussed. These AoE of land planarians can be explained through vicariance events combined with their physiological and ecological own limitations. Interestingly, these AoE are congruent with fine-scale approaches such as that with harvestmen. Most land planarians have revealed to present a very small distributional range evidencing their potential as a good model for fine-scale studies of AoE.


Assuntos
Biodiversidade , Evolução Biológica , Conservação dos Recursos Naturais , Monitoramento Ambiental , Filogeografia , Planárias/fisiologia , Animais , Brasil , Florestas , Dinâmica Populacional
16.
PLoS One ; 15(7): e0235989, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32726356

RESUMO

Despite the important roles of freshwater gastropods in aquatic ecosystems, the taxonomic status of many taxa is unclear, which is compounded by a lack of information on species population genetic structuring, distribution, and dispersal patterns. The objective of this study was to address the biogeography of the freshwater snail Planorbella trivolvis (Gastropoda: Planorbidae) in the western United States. We amplified two genetic markers (16S, COI) from individuals belonging to western USA populations and downloaded genetic data from GenBank. We utilized minimum spanning networks to assess the genetic patterns and performed Analysis of Molecular Variance and linear regression analyses to determine how geographic distance and watershed identity contributed to the observed genetic structuring. For both markers, we found that the majority of genetic variation was associated within and among populations, rather than among watersheds. Correspondingly, there was no significant effect of geographic distance on genetic distance, suggesting that long-distance dispersal was promoting gene flow between populations. The genetic similarity could reflect avian-mediated dispersal of snails along the Pacific Flyway, a major waterfowl migratory corridor. Further analysis of the population structuring across North America revealed East-West genetic structuring, suggesting that across longitudinal gradients P. trivolvis experiences significant genetic isolation.


Assuntos
DNA Mitocondrial/genética , Ecossistema , Gastrópodes/genética , Fluxo Gênico , Variação Genética , Filogeografia , Animais , América do Norte , Análise de Sequência de DNA
17.
BMC Evol Biol ; 20(1): 82, 2020 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-32652951

RESUMO

BACKGROUND: Quaternary climate fluctuations are an engine of biotic diversification. Global cooling cycles, such as the Last Glacial Maximum (LGM), are known to have fragmented the ranges of higher-latitude fauna and flora into smaller refugia, dramatically reducing species ranges. However, relatively less is known about the effects of cooling cycles on tropical biota. RESULTS: We analyzed thousands of genome-wide DNA markers across an assemblage of three closely related understorey-inhabiting scrubwrens (Sericornis and Aethomyias; Aves) from montane forest along an elevational gradient on Mt. Wilhelm, the highest mountain of Papua New Guinea. Despite species-specific differences in elevational preference, we found limited differentiation within each scrubwren species, but detected a strong genomic signature of simultaneous population expansions at 27-29 ka, coinciding with the onset of the LGM. CONCLUSION: The remarkable synchronous timing of population expansions of all three species demonstrates the importance of global cooling cycles in expanding highland habitat. Global cooling cycles have likely had strongly different impacts on tropical montane areas versus boreal and temperate latitudes, leading to population expansions in the former and serious fragmentation in the latter.


Assuntos
Evolução Biológica , Ecossistema , Camada de Gelo , Aves Canoras/crescimento & desenvolvimento , Altitude , Animais , Sequência de Bases , Simulação por Computador , Bases de Dados como Assunto , Genética Populacional , Geografia , Papua Nova Guiné , Filogenia , Filogeografia , Polimorfismo de Nucleotídeo Único/genética , Probabilidade , Especificidade da Espécie
18.
BMC Evol Biol ; 20(1): 83, 2020 07 13.
Artigo em Inglês | MEDLINE | ID: mdl-32660486

RESUMO

BACKGROUND: We have described the diversity of complete mtDNA sequences from 'relic' groups of the Russian Far East, primarily the Nivkhi (who speak a language isolate with no clear relatedness to any others) and Oroki of Sakhalin, as well as the sedentary Koryak from Kamchatka and the Udegey of Primorye. Previous studies have shown that most of their traditional territory was dramatically reshaped by the expansion of Tungusic-speaking groups. RESULTS: Overall, 285 complete mitochondrial sequences were selected for phylogenetic analyses of published, revised and new mitogenomes. To highlight the likely role of Neolithic expansions in shaping the phylogeographical landscape of the Russian Far East, we focus on the major East Eurasian maternal lineages (Y1a, G1b, D4m2, D4e5, M7a2, and N9b) that are restricted to the coastal area. To obtain more insight into autochthonous populations, we removed from the phylogeographic analysis the G2a, G3a2, M8a1, M9a1, and C4b1 lineages, also found within our samples, likely resulting from admixture between the expanding proto-Tungus and the indigenous Paleoasiatic groups with whom they assimilated. Phylogenetic analysis reveals that unlike the relatively diverse lineage spectrum observed in the Amur estuary and northwestern Sakhalin, the present-day subpopulation on the northeastern coast of the island is relatively homogenous: a sole Y1a sublineage, conspicuous for its nodal mutation at m.16189 T > C!, includes different haplotypes. Sharing of the Y1a-m.16189 T > C! sublineages and haplotypes among the Nivkhi, Ulchi and sedentary Koryak is also evident. Aside from Y1a, the entire tree approach expands our understanding of the evolutionary history of haplogroups G1, D4m, N9b, and M7a2. Specifically, we identified the novel haplogroup N9b1 in Primorye, which implies a link between a component of the Udegey ancestry and the Hokkaido Jomon. CONCLUSIONS: Through a comprehensive dataset of mitochondrial genomes retained in autochthonous populations along the coast between Primorye and the Bering Strait, we considerably extended the sequence diversity of these populations to provide new features based on the number and timing of founding lineages. We emphasize the value of integrating genealogical information with genetic data for reconstructing the population history of indigenous groups dramatically impacted by twentieth century resettlement and social upheavals.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Extinção Biológica , Genoma Mitocondrial , Grupos Populacionais/genética , Envelhecimento/genética , DNA Mitocondrial/genética , Genética Populacional , Geografia , Haplótipos/genética , Humanos , Ilhas , Filogenia , Filogeografia , Federação Russa
19.
Science ; 369(6508): 1255-1260, 2020 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-32703910

RESUMO

Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , Número Básico de Reprodução , Teorema de Bayes , Betacoronavirus/classificação , Brasil/epidemiologia , Cidades/epidemiologia , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/prevenção & controle , Infecções por Coronavirus/virologia , Europa (Continente) , Evolução Molecular , Genoma Viral , Humanos , Modelos Genéticos , Modelos Estatísticos , Pandemias/prevenção & controle , Filogenia , Filogeografia , Pneumonia Viral/prevenção & controle , Pneumonia Viral/virologia , Análise Espaço-Temporal , Viagem , População Urbana
20.
Proc Biol Sci ; 287(1931): 20200867, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-32693717

RESUMO

Knowledge of the relative importance of genetic versus environmental determinants of major developmental transitions is pertinent to understanding phenotypic evolution. In salmonid fishes, a major developmental transition enables a risky seaward migration that provides access to feed resources. In Atlantic salmon, initiation of the migrant phenotype, and thus age of migrants, is presumably controlled via thresholds of a quantitative liability, approximated by body size expressed long before the migration. However, how well size approximates liability, both genetically and environmentally, remains uncertain. We studied 32 Atlantic salmon families in two temperatures and feeding regimes (fully fed, temporarily restricted) to completion of migration status at age 1 year. We detected a lower migrant probability in the cold (0.42) than the warm environment (0.76), but no effects of male maturation status or feed restriction. By contrast, body length in late summer predicted migrant probability and its control reduced migrant probability heritability by 50-70%. Furthermore, migrant probability and length showed high heritabilities and between-environment genetic correlations, and were phenotypically highly correlated with stronger genetic than environmental contributions. Altogether, quantitative estimates for the genetic and environmental effects predicting the migrant phenotype indicate, for a given temperature, a larger importance of genetic than environmental size effects.


Assuntos
Tamanho Corporal/genética , Salmo salar/anatomia & histologia , Animais , Fenótipo , Filogeografia
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