Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 7.348
Filtrar
1.
BMC Plant Biol ; 21(1): 325, 2021 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-34229602

RESUMO

BACKGROUND: Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. RESULTS: The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties' ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). CONCLUSIONS: Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.


Assuntos
Actinidia/classificação , Actinidia/citologia , Cloroplastos/classificação , Filogeografia , Teorema de Bayes , China , DNA de Cloroplastos/genética , Ecossistema , Variação Genética , Genética Populacional , Haplótipos/genética , Método de Monte Carlo , Ploidias
2.
Mem Inst Oswaldo Cruz ; 116: e200441, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34259736

RESUMO

BACKGROUND: A previous phylogeographic study revealed two Aedes aegypti African-related mitochondrial lineages distributed in Colombian's cities with different eco-epidemiologic characteristics with regard to dengue virus (DENV). It has been proposed these lineages might indicate independent invasion sources. OBJECTIVES: Assessing to Colombian population structure and to support evidence of its probable source origin. METHODS: We analysed a total of 267 individuals from cities of Bello, Riohacha and Villavicencio, which 241 were related to the West and East African mitochondrial lineages (termed here as WAL and EAL, respectively). Eight polymorphic microsatellite loci were analysed aiming population structure. FINDINGS: Results indicate substantial gene flow among distant and low-connected cities composing a panmictic population with incipient local differentiation of Ae. aegypti is placed in Colombia. Likewise, genetic evidence indicates no significant differences among individuals related to WAL and EAL is placed. MAIN CONCLUSIONS: Minimal genetic differentiation in low-connected Ae. aegypti populations of Colombia, and lack concordance between mitochondrial and nuclear genealogies suggest that Colombian Ae. aegypti shared a common demographic history. Under this scenario, we suggest current Ae. aegypti population structure reflects a single origin instead of contemporary migration, which founding populations have a single source from a mitochondrial polymorphic African ancient.


Assuntos
Aedes , Dengue , Aedes/genética , Animais , Colômbia , Variação Genética/genética , Humanos , Filogeografia
3.
Viruses ; 13(5)2021 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-34067745

RESUMO

The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the 'GH' clade, whereas the southern part reported the 'GR', with a few exceptions. These sequences also revealed the presence of single independent mutations-E484Q and N440K-from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January-August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation.


Assuntos
COVID-19/epidemiologia , Filogeografia/métodos , SARS-CoV-2/genética , Adulto , COVID-19/genética , Feminino , Genoma Viral/genética , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Índia/epidemiologia , Masculino , Pessoa de Meia-Idade , Mutação/genética , Filogenia , SARS-CoV-2/patogenicidade
5.
Microb Genom ; 7(6)2021 06.
Artigo em Inglês | MEDLINE | ID: covidwho-1280188

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the COVID-19 pandemic, continues to cause a significant public-health burden and disruption globally. Genomic epidemiology approaches point to most countries in the world having experienced many independent introductions of SARS-CoV-2 during the early stages of the pandemic. However, this situation may change with local lockdown policies and restrictions on travel, leading to the emergence of more geographically structured viral populations and lineages transmitting locally. Here, we report the first SARS-CoV-2 genomes from Palestine sampled from early March 2020, when the first cases were observed, through to August of 2020. SARS-CoV-2 genomes from Palestine fall across the diversity of the global phylogeny, consistent with at least nine independent introductions into the region. We identify one locally predominant lineage in circulation represented by 50 Palestinian SARS-CoV-2, grouping with genomes generated from Israel and the UK. We estimate the age of introduction of this lineage to 05/02/2020 (16/01/2020-19/02/2020), suggesting SARS-CoV-2 was already in circulation in Palestine predating its first detection in Bethlehem in early March. Our work highlights the value of ongoing genomic surveillance and monitoring to reconstruct the epidemiology of COVID-19 at both local and global scales.


Assuntos
Árabes , COVID-19/epidemiologia , SARS-CoV-2/classificação , Análise de Sequência de RNA/métodos , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Israel , Oriente Médio/epidemiologia , Pandemias , Filogenia , Filogeografia , SARS-CoV-2/genética , Reino Unido
7.
Viruses ; 13(5)2021 05 17.
Artigo em Inglês | MEDLINE | ID: covidwho-1234829

RESUMO

The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the 'GH' clade, whereas the southern part reported the 'GR', with a few exceptions. These sequences also revealed the presence of single independent mutations-E484Q and N440K-from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January-August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation.


Assuntos
COVID-19/epidemiologia , Filogeografia/métodos , SARS-CoV-2/genética , Adulto , COVID-19/genética , Feminino , Genoma Viral/genética , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Índia/epidemiologia , Masculino , Pessoa de Meia-Idade , Mutação/genética , Filogenia , SARS-CoV-2/patogenicidade
8.
Arch Virol ; 166(8): 2273-2278, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34059971

RESUMO

Feline panleukopenia virus (FPV) is a highly contagious infectious pathogen of cats globally. However, there is no information on the molecular identification and characterization of FPV in Bangladesh. Here, 8.16% (8/98) and 18.37% (18/98) of diarrheic cats tested positive for FPV by an immunochromatography (IC) test and PCR, respectively. The IC test showed 44.44% sensitivity and 100% specificity in comparison with PCR. Our newly sequenced Bangladeshi FPV strain (MN826076) showed the highest (99.71%) sequence identity to strains from the United Arab Emirates (UAE). Strain MN826076 contained two characteristic amino acid variations in VP2 identifying it as an FPV strain: valine at position 103 and aspartic acid at position 323. Phylogenetically, the VP2 of strain MN826076 was found to be closely related to 19 FPV strains, sharing the same clade.


Assuntos
Diarreia/veterinária , Diarreia/virologia , Vírus da Panleucopenia Felina/classificação , Panleucopenia Felina/diagnóstico , Substituição de Aminoácidos , Animais , Bangladesh , Proteínas do Capsídeo/genética , Gatos , China , Cromatografia de Afinidade , Vírus da Panleucopenia Felina/genética , Vírus da Panleucopenia Felina/isolamento & purificação , Filogenia , Filogeografia , Portugal , Sensibilidade e Especificidade , Tailândia , Emirados Árabes Unidos
9.
Arch Virol ; 166(8): 2209-2216, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34086143

RESUMO

Enterovirus A71 (EV-A71) can cause hand, foot, and mouth disease (HFMD) in children and may be associated with severe neurological complications. There have been numerous reports of increased incidence of EV-A71 subgenogroup C1 (EV-A71 C1) infections associated with neurological diseases since the first occurrence in Germany in 2015. Here, we describe 11 full-length genome sequences of 2019 EV-A71 C1 strains isolated from HFMD patients in Thailand from 2019 to early 2020. The genetic evolution of 2019 EV-A71 C1 was traced in the outbreaks, and the emergence of multiple lineages was detected. Our results demonstrated that 2019 EV-A71 C1 from Thailand emerged through recombination between its nonstructural protein gene and those of other EV-A genotypes. Bayesian-based phylogenetic analysis showed that the 2019 EV-A71 C1 Thai strains share a common ancestor with variants in Europe (Denmark and France). The substitution rate for the 2019 EV-A71 C1 genome was estimated to be 4.38 × 10-3 substitutions/(site∙year-1) (95% highest posterior density interval: 3.84-4.94 × 10-3 substitutions/[site∙year-1]), approximating that observed between previous EV-A71 C1 outbreaks. These data are essential for understanding the evolution of EV-A C1 during the ongoing HFMD outbreak and may be relevant to disease outcomes in children worldwide.


Assuntos
Enterovirus Humano A/classificação , Variação Genética , Doença de Mão, Pé e Boca/virologia , Sequenciamento Completo do Genoma/métodos , Criança , Pré-Escolar , Dinamarca , Enterovirus Humano A/genética , Enterovirus Humano A/isolamento & purificação , Evolução Molecular , Feminino , França , Genoma Viral , Alemanha , Humanos , Lactente , Masculino , Filogenia , Filogeografia , Tailândia
10.
Arch Virol ; 166(8): 2337-2341, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34091784

RESUMO

Anemone mosaic virus (AnMV) and ranunculus mild mosaic virus (RanMMV) infect anemone plants, which exhibit characteristic mosaic patterns on their leaves. Employing next-generation sequencing of plant material imported from the Netherlands, the complete genome sequences of these two viruses were determined for the first time. AnMV and RanMMV have 9698 and 9537 nucleotides (nt), respectively, excluding the poly(A) tail. They share 80.0%/82.0% and 98.0%/97.0% nt/amino acid (aa) sequence identity, which is above the species demarcation value, in the previously reported AnMV and RanMMV coat protein sequences, but they share 69.0%/70.0% nt/aa sequence identity or less with other potyviruses in all 10 mature protein coding regions of the genome. Additionally, phylogenetic analysis confirmed the relationship of the AnMV and RanMMV genome sequences to previously reported partial sequences and placed them within the genus Potyvirus. These results show that these two viruses represent separate species within the genus Potyvirus.


Assuntos
Anemone/virologia , Potyvirus/classificação , Sequenciamento Completo do Genoma/métodos , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Japão , Países Baixos , Fases de Leitura Aberta , Filogenia , Filogeografia , Potyvirus/genética , Potyvirus/isolamento & purificação , Homologia de Sequência de Aminoácidos
11.
Microb Genom ; 7(6)2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34156923

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the COVID-19 pandemic, continues to cause a significant public-health burden and disruption globally. Genomic epidemiology approaches point to most countries in the world having experienced many independent introductions of SARS-CoV-2 during the early stages of the pandemic. However, this situation may change with local lockdown policies and restrictions on travel, leading to the emergence of more geographically structured viral populations and lineages transmitting locally. Here, we report the first SARS-CoV-2 genomes from Palestine sampled from early March 2020, when the first cases were observed, through to August of 2020. SARS-CoV-2 genomes from Palestine fall across the diversity of the global phylogeny, consistent with at least nine independent introductions into the region. We identify one locally predominant lineage in circulation represented by 50 Palestinian SARS-CoV-2, grouping with genomes generated from Israel and the UK. We estimate the age of introduction of this lineage to 05/02/2020 (16/01/2020-19/02/2020), suggesting SARS-CoV-2 was already in circulation in Palestine predating its first detection in Bethlehem in early March. Our work highlights the value of ongoing genomic surveillance and monitoring to reconstruct the epidemiology of COVID-19 at both local and global scales.


Assuntos
Árabes , COVID-19/epidemiologia , SARS-CoV-2/classificação , Análise de Sequência de RNA/métodos , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Israel , Oriente Médio/epidemiologia , Pandemias , Filogenia , Filogeografia , SARS-CoV-2/genética , Reino Unido
12.
Zool Res ; 42(4): 428-432, 2021 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-34114756

RESUMO

Accurate information on name-bearing types, including corresponding type localities, is essential for proper taxonomy. However, such geographic information is often missing or unreliable. The localities of type specimens collected 100-200 years ago can be difficult to trace due to changes in local names or simple inaccuracies. Such a case can be found for the gray-backed sportive lemur (Lepilemur dorsalis), with its type locality imprecisely fixed as Northwest Madagascar. In recent years, eight species have been newly described for the Inter-River-Systems (IRSs) of this region, however the designation of L. dorsalis remains controversial due to a lack of a precise type locality. Here, we sequenced the complete mitochondrial genomes (mitogenomes) of type specimens of L. dorsalis and L. grandidieri, which is currently recognized as a synonym of L. dorsalis and compared their sequences with those of samples of known provenance from different IRSs. Results showed that the two type specimens of L. dorsalis and L. grandidieri had identical mitogenome sequences and clustered closely with samples collected in IRS V, indicating that the type locality could be fixed to IRS V. Consequently, L. dorsalis occurs in IRS V, and L. grandidieri and L. mittermeieri are junior synonyms of L. dorsalis. This finding demonstrates the value of type specimens for clarifying phylogeographic and taxonomic questions and clarifies the taxonomy of sportive lemurs in Northwest Madagascar.


Assuntos
Distribuição Animal , Genoma Mitocondrial , Strepsirhini/genética , Animais , DNA Mitocondrial , Madagáscar , Filogenia , Filogeografia , Especificidade da Espécie , Strepsirhini/classificação , Strepsirhini/fisiologia
13.
Food Chem ; 360: 130033, 2021 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-34023716

RESUMO

Some black teas demand high market prices. Black tea samples (306) collected from 10 geographic origins, including China (Guxi, Likou, Jinzipai, Guichi, Dongzhi, Changning, Wuyishan, Shaowu), India (Darjeeling), and Sri Lanka (Kandy), were analyzed using headspace volatilization followed by GC/MS (HS-GC/MS). Forty-eight volatile compounds were identified. The aroma compounds were mainly identified as alcohols, aldehydes, ketones, and esters. Analysis of either full-spectrum data or 22 tea compounds shared among the samples with k-Nearest Neighbor (k-NN) and Random Forest (RF) models discriminated all origins at 100% using KNN and 95% with RF using either data set. The discrimination rates using 2 key aroma compounds (linalool and geraniol) by k-NN were 100% for nine origins, with the rate for Guxi area at 89%, because 3 samples were classified to Jinzipai. The findings support the use of HS-GC/MS combined with chemometrics as a tool to identify the origin of black tea.


Assuntos
Cromatografia Gasosa-Espectrometria de Massas/métodos , Filogeografia , Chá/química , Monoterpenos Acíclicos/análise , Aldeídos/análise , China , Ésteres/análise , Índia , Odorantes/análise , Microextração em Fase Sólida , Sri Lanka , Compostos Orgânicos Voláteis/análise , Volatilização
14.
Res Vet Sci ; 137: 217-225, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34023545

RESUMO

HoBi-like pestivirus, an emerging species within the Pestivirus genus, is an important pathogen associated with a variety of clinical manifestations of ruminants, especially cattle. HoBi-like pestiviruses were identified in several countries and from different hosts, and raised concerns with regard to their acute and persistent infections, which is implicated in economic losses for cattle farmers. However, the transmission path, codon usage bias, and host adaptation of the virus has not been studied. Hence, we performed the analysis the spatio-temporal transmission based on the available 5'-UTR sequences of HoBi-like pestivirus, and then conducted codon analysis of the complete coding sequence of the virus. The results show the virus appeared in 1952 (95% HPD: 1905-1985) and may have originated in India. In addition, Italy is the hub for the spread of the virus. Moreover, six potential recombination events and two complex recombination events were discovered. Analysis of codon usage patterns revealed that the effective number of codon (ENC) values with an average of 50.85, and the codon usage bias is greatly affected by natural selection, which is different from the previous BVDV-1, 2. Finally, codon adaptation index (CAI) analysis shows that pigs may be the potential origin species of the HoBi-like pestivirus. These findings will contribute to more effective control of the spread of the virus, extend the knowledge about the genetic and evolutionary features of HoBi-like viruses and provide some information for vaccine research.


Assuntos
Doenças Transmissíveis Emergentes/virologia , Evolução Molecular , Pestivirus/genética , Regiões 5' não Traduzidas , Animais , Uso do Códon , Conjuntos de Dados como Assunto , Vírus da Diarreia Viral Bovina Tipo 1/genética , Interações entre Hospedeiro e Microrganismos , Índia , Itália , Fases de Leitura Aberta , Filogenia , Filogeografia , Recombinação Genética
15.
PLoS Pathog ; 17(5): e1009571, 2021 05.
Artigo em Inglês | MEDLINE | ID: covidwho-1236598

RESUMO

During the first phase of the COVID-19 epidemic, New York City rapidly became the epicenter of the pandemic in the United States. While molecular phylogenetic analyses have previously highlighted multiple introductions and a period of cryptic community transmission within New York City, little is known about the circulation of SARS-CoV-2 within and among its boroughs. We here perform phylogeographic investigations to gain insights into the circulation of viral lineages during the first months of the New York City outbreak. Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas. In line with the high prevalence recorded in this area, our results highlight the relatively important role of the borough of Queens as a transmission hub associated with higher local circulation and dispersal of viral lineages toward the surrounding boroughs.


Assuntos
COVID-19/epidemiologia , COVID-19/transmissão , SARS-CoV-2/genética , Genoma Viral/genética , Humanos , Cidade de Nova Iorque/epidemiologia , Filogenia , Filogeografia , Prevalência , SARS-CoV-2/classificação , SARS-CoV-2/isolamento & purificação
16.
Arch Virol ; 166(8): 2279-2283, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34057610

RESUMO

Lumpy skin disease was first reported in the western provinces of Iran in 2014, and this was followed by several outbreaks throughout the country. In this study, 10 Iranian lumpy skin disease virus (LSDV) samples collected during the period of 2014-2018 were characterized by sequence analysis of the GPCR, LSDV142, and IL10LP genes. Sequence comparison of the respective genes revealed a close relationship between Iranian LSDV isolates and viruses from Asia and Europe. Interestingly, some nucleotide sequence diversity was also observed in the IL10LP genes of the Iranian field isolates.


Assuntos
Doença Nodular Cutânea/virologia , Vírus da Doença Nodular Cutânea/classificação , Análise de Sequência de DNA/métodos , Proteínas Virais/genética , Animais , Ásia , Bovinos , Europa (Continente) , Irã (Geográfico) , Vírus da Doença Nodular Cutânea/genética , Vírus da Doença Nodular Cutânea/isolamento & purificação , Filogenia , Filogeografia
17.
Nat Commun ; 12(1): 3160, 2021 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-34039976

RESUMO

Despite the high burden of Plasmodium vivax malaria in South Asian countries, the genetic diversity of circulating parasite populations is not well described. Determinants of antimalarial drug susceptibility for P. vivax in the region have not been characterised. Our genomic analysis of global P. vivax (n = 558) establishes South Asian isolates (n = 92) as a distinct subpopulation, which shares ancestry with some East African and South East Asian parasites. Signals of positive selection are linked to drug resistance-associated loci including pvkelch10, pvmrp1, pvdhfr and pvdhps, and two loci linked to P. vivax invasion of reticulocytes, pvrbp1a and pvrbp1b. Significant identity-by-descent was found in extended chromosome regions common to P. vivax from India and Ethiopia, including the pvdbp gene associated with Duffy blood group binding. Our investigation provides new understanding of global P. vivax population structure and genomic diversity, and genetic evidence of recent directional selection in this important human pathogen.


Assuntos
Genes de Protozoários , Malária Vivax/parasitologia , Plasmodium vivax/genética , Seleção Genética , África Oriental , Antimaláricos/farmacologia , Antimaláricos/uso terapêutico , Ásia , Resistência a Medicamentos/genética , Sistema do Grupo Sanguíneo Duffy , Loci Gênicos , Humanos , Malária Vivax/sangue , Malária Vivax/tratamento farmacológico , Filogenia , Filogeografia , Plasmodium vivax/efeitos dos fármacos , Plasmodium vivax/patogenicidade , Polimorfismo de Nucleotídeo Único , Proteínas de Protozoários/genética , Reticulócitos/parasitologia
18.
PLoS Pathog ; 17(5): e1009571, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-34015049

RESUMO

During the first phase of the COVID-19 epidemic, New York City rapidly became the epicenter of the pandemic in the United States. While molecular phylogenetic analyses have previously highlighted multiple introductions and a period of cryptic community transmission within New York City, little is known about the circulation of SARS-CoV-2 within and among its boroughs. We here perform phylogeographic investigations to gain insights into the circulation of viral lineages during the first months of the New York City outbreak. Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas. In line with the high prevalence recorded in this area, our results highlight the relatively important role of the borough of Queens as a transmission hub associated with higher local circulation and dispersal of viral lineages toward the surrounding boroughs.


Assuntos
COVID-19/epidemiologia , COVID-19/transmissão , SARS-CoV-2/genética , Genoma Viral/genética , Humanos , Cidade de Nova Iorque/epidemiologia , Filogenia , Filogeografia , Prevalência , SARS-CoV-2/classificação , SARS-CoV-2/isolamento & purificação
19.
BMC Ecol Evol ; 21(1): 88, 2021 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-34006219

RESUMO

BACKGROUND: Accurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for inferring recent historical events due to their high mutation rates. However, most programs analyzing microsatellite data assume a strict stepwise mutation model (SMM), which could cause false detection of population shrinkage when microsatellite mutation does not follow SMM. RESULTS: This study aims to reconstruct the recent demographic histories of five cool-temperate tree species in Eastern Asia, Quercus mongolica, Q. liaotungensis, Juglans cathayensis, J. mandshurica and J. ailantifolia, by using 19 microsatellite markers with two methods considering generalized stepwise mutation model (GSM) (MIGRAINE and VarEff). Both programs revealed that all the five species experienced expansions after the Last Glacial Maximum (LGM). Within butternuts, J. cathayensis experienced a more serious bottleneck than the other species, and within oaks, Q. mongolica showed a moderate increase in population size and remained stable after the expansion. In addition, the point estimates of the multistep mutation proportion in the GSM model (pGSM) for all five species were between 0.50 and 0.65, indicating that when inferring population demographic history of the cool-temperate forest species using microsatellite markers, it is better to assume a GSM rather than a SMM. CONCLUSIONS: This study provides the first direct evidence that five cool-temperate tree species in East Asia have experienced expansions after the LGM with microsatellite data. Considering the mutation model of microsatellite has a vital influence on demographic inference, combining multiple programs such as MIGRAINE and VarEff can effectively reduce errors caused by inappropriate model selection and prior setting.


Assuntos
Repetições de Microssatélites , Árvores , DNA de Plantas , Extremo Oriente , Repetições de Microssatélites/genética , Filogeografia , Árvores/genética
20.
Nat Commun ; 12(1): 2945, 2021 05 19.
Artigo em Inglês | MEDLINE | ID: mdl-34011982

RESUMO

Estimates of evolutionary diversification rates - speciation and extinction - have been used extensively to explain global biodiversity patterns. Many studies have analyzed diversification rates derived from just two pieces of information: a clade's age and its extant species richness. This "age-richness rate" (ARR) estimator provides a convenient shortcut for comparative studies, but makes strong assumptions about the dynamics of species richness through time. Here we demonstrate that use of the ARR estimator in comparative studies is problematic on both theoretical and empirical grounds. We prove mathematically that ARR estimates are non-identifiable: there is no information in the data for a single clade that can distinguish a process with positive net diversification from one where net diversification is zero. Using paleontological time series, we demonstrate that the ARR estimator has no predictive ability for real datasets. These pathologies arise because the ARR inference procedure yields "point estimates" that have been computed under a saturated statistical model with zero degrees of freedom. Although ARR estimates remain useful in some contexts, they should be avoided for comparative studies of diversification and species richness.


Assuntos
Biodiversidade , Evolução Biológica , Ecossistema , Modelos Biológicos , Animais , Interpretação Estatística de Dados , Extinção Biológica , Fósseis , Especiação Genética , Conceitos Matemáticos , Paleontologia/métodos , Paleontologia/estatística & dados numéricos , Filogenia , Filogeografia , Fatores de Tempo
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...