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1.
Syst Biol ; 69(1): 184-193, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31180508

RESUMO

Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.


Assuntos
Classificação/métodos , Filogeografia , Animais , Filogenia , Serpentes/classificação , Serpentes/genética
2.
BMC Ecol ; 19(1): 53, 2019 12 20.
Artigo em Inglês | MEDLINE | ID: mdl-31861996

RESUMO

BACKGROUND: Pleistocene glaciations have had an important impact on the species distribution and community composition of the North American biota. Species survived these glacial cycles south of the ice sheets and/or in other refugia, such as Beringia. In this study, we assessed, using mitochondrial DNA from three Diptera species, whether flies currently found in Beringian grasslands (1) survived glaciation as disjunct populations in Beringia and in the southern refugium; (2) dispersed northward postglacially from the southern refugium; or (3) arose by a combination of the two. Samples were collected in grasslands in western Canada: Prairies in Alberta and Manitoba; the Peace River region (Alberta); and the southern Yukon Territory. We sequenced two gene regions (658 bp of cytochrome c oxidase subunit I, 510 bp of cytochrome b) from three species of higher Diptera: one with a continuous distribution across grassland regions, and two with disjunct populations between the regions. We used a Bayesian approach to determine population groupings without a priori assumptions and performed analysis of molecular variance (AMOVA) and exact tests of population differentiation (ETPD) to examine their validity. Molecular dating was used to establish divergence times. RESULTS: Two geographically structured populations were found for all species: a southern Prairie and Peace River population, and a Yukon population. Although AMOVA did not show significant differentiation between populations, ETPD did. Divergence time between Yukon and southern populations predated the Holocene for two species; the species with an ambiguous divergence time had high haplotype diversity, which could suggest survival in a Beringian refugium. CONCLUSIONS: Populations of Diptera in Yukon grasslands could have persisted in steppe habitats in Beringia through Pleistocene glaciations. Current populations in the region appear to be a mix of Beringian relict populations and, to a lesser extent, postglacial dispersal northward from southern prairie grasslands.


Assuntos
Dípteros , Alberta , Animais , Teorema de Bayes , DNA Mitocondrial , Variação Genética , Haplótipos , Manitoba , América do Norte , Filogenia , Filogeografia
3.
Zootaxa ; 4671(4): zootaxa.4671.4.4, 2019 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-31716032

RESUMO

Knowledge on the hydrological evolution of the Neotropical region was used along with the current distribution of the anablepid species to investigate the historical biogeography of this family. Areas of endemism were delimited by endemicity analysis resulting in seven individual areas of endemism and three consensus areas located in northwestern Argentina, southern Brazil, and northern South America. These areas were discussed in the context of anablepid species diversification, especially for the genus Anableps and the subgenera Jenynsia and Plesiojenynsia. The existence of areas of endemism for the family analyzed reveals an intimate association with historical events that occurred in the geological evolution of South America, which can be associated with the main diversification patterns and historical hypotheses in the context of Neotropical freshwater fishes biogeography.


Assuntos
Ciprinodontiformes , Animais , Argentina , Brasil , Água Doce , América do Norte , Filogenia , Filogeografia , América do Sul
4.
Zootaxa ; 4624(4): zootaxa.4624.4.1, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31716195

RESUMO

Several species of Glaucomastix lizards have been described over the past decade, most of these inhabit inland Brazil. Glaucomastix abaetensis is a threatened whiptail endemic to Brazilian coastal "restinga" (sandy habitats) from Bahia State to Sergipe, with a distribution limited by riverine barriers. In order to investigate the differentiation and relationships in G. abaetensis, we integrated phylogeographic analysis, Bayesian species delimitation and morphological data to detect geographical patterns and historical events responsible for its present distribution. We recovered two highly divergent clades along its range, one of them unnamed. Glaucomastix itabaianensis sp. nov. has a a yellowish green tail, 13-16 scales in the lateral flank, 22-33 scales around tail, 28-35 femoral pores and usually four supraocular scales with the smaller one disposed posteriorly. Our results retrieved the monophyly of Glaucomastix, with G. venetacauda and G. cyanurus being sister species to a clade formed by G. littoralis and G. abaetensis. Divergence between Glaucomastix abaetensis and the new species occurred roughly 2.39 Myr ago; posterior shallow genetic divergences occurred mainly in Pleistocene. Finally, we present data on the conservation of this clade of whiptail lizards.


Assuntos
Lagartos , Animais , Teorema de Bayes , Brasil , Ecossistema , Filogenia , Filogeografia
5.
Zootaxa ; 4609(3): zootaxa.4609.3.8, 2019 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-31717098

RESUMO

Mountain chains and rivers are often found to represent barriers promoting vicariant differentiation in terrestrial vertebrates. Previous studies have supported the idea that the Cordillera de Mérida (CM), the easternmost branch of the Northern Andes, represents a geographic barrier for vertebrates, including frogs. Previous studies have also suggested that the Orinoco River (OR), the biggest river in Venezuela, also represents a geographic barrier for terrestrial vertebrates. Boana pugnax and B. xerophylla are two Neotropical hylids, members of the B. faber species group, that are distributed on either side of the CM, and whose ranges extend up to 605 and 2450 m in elevation, respectively. In addition, B. xerophylla occurs on either side of the OR. Herein, we assess the genetic, acoustic, and morphological differentiation within B. pugnax and within B. xerophylla across the CM and within B. xerophylla across the OR, and test if genetic differentiation is correlated with geographic distance. We also evaluated the acoustic differentiation between the recently recognized B. xerophylla and its sister species, B. crepitans, and found marked differences between advertisement calls, corroborating their status as distinct species. Genetic and morphometric analyses of populations from opposite sides of the CM revealed differentiation in B. pugnax but not in B. xerophylla. Within the latter species, we found molecular, acoustic, and morphometric differentiation among samples of B. xerophylla from western Venezuela versus the Guiana Shield. Genetic variation within B. pugnax and within B. xerophylla was not explained by geographic distance. Thus, our data show conspecific population structure across the CM in B. pugnax, plus the possible existence of two species within what today is considered B. xerophylla, yet the CM apparently is not involved in this divergence. These results suggest that even for closely related species with shared ecology and distribution, genetic and phenotypic differentiation respond differently to common ecological or historical factors.


Assuntos
Anuros , Deriva Genética , Acústica , Animais , DNA Mitocondrial , Variação Genética , Filogenia , Filogeografia , Rios , Venezuela
6.
Mem Inst Oswaldo Cruz ; 114: e190184, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31576903

RESUMO

American visceral leishmaniasis (AVL) has two main scenarios of transmission as follows: scattered cases in rural areas and urban outbreaks. Urban AVL is in active dispersion from the northeastern border of Argentina-Paraguay-Brazil to the South. The presence of Lutzomyia longipalpis was initially reported in urban environments in the northwestern border of the country. The presence of Lu. longipalpis, environmental variables associated with its distribution, and its genetic diversity were assessed in Salvador Mazza, Argentina, on the border with Bolivia. The genetic analysis showed high haplotype diversity, low nucleotide diversity, and low nucleotide polymorphism index. We discuss the hypothesis of an expanding urban population with introgressive hybridisation of older haplogroups found in their path in natural forest or rural environments, acquiring a new adaptability to urban environments, and the possibility of changes in vector capacity.


Assuntos
Distribuição Animal , Variação Genética/genética , Insetos Vetores/genética , Psychodidae/genética , Animais , Argentina , Bolívia , Brasil , DNA Mitocondrial/genética , Genes de Insetos/genética , Haplótipos , Insetos Vetores/classificação , Leishmaniose Cutânea/transmissão , Masculino , Filogeografia , Psychodidae/classificação
7.
Nat Commun ; 10(1): 3406, 2019 09 10.
Artigo em Inglês | MEDLINE | ID: mdl-31506422

RESUMO

The origin of Homo sapiens remains a matter of debate. The extent and geographic patterning of morphological diversity among Late Middle Pleistocene (LMP) African hominins is largely unknown, thus precluding the definition of boundaries of variability in early H. sapiens and the interpretation of individual fossils. Here we use a phylogenetic modelling method to predict possible morphologies of a last common ancestor of all modern humans, which we compare to LMP African fossils (KNM-ES 11693, Florisbad, Irhoud 1, Omo II, and LH18). Our results support a complex process for the evolution of H. sapiens, with the recognition of different, geographically localised, populations and lineages in Africa - not all of which contributed to our species' origin. Based on the available fossils, H. sapiens appears to have originated from the coalescence of South and, possibly, East-African source populations, while North-African fossils may represent a population which introgressed into Neandertals during the LMP.


Assuntos
Biodiversidade , Hominidae/fisiologia , Modelos Biológicos , Filogenia , África , Animais , Fósseis/anatomia & histologia , Hominidae/anatomia & histologia , Humanos , Filogeografia , Crânio/anatomia & histologia
8.
Int. microbiol ; 22(3): 337-342, sept. 2019.
Artigo em Inglês | IBECS | ID: ibc-184840

RESUMO

Malaria is one of the most important human diseases throughout tropical and sub-tropical regions of the world. Global distribution and ample host range have contributed to the genetic diversity of the etiological agent, Plasmodium. Phylogeographical analyses demonstrated that Plasmodium falciparum and Plasmodium vivax follow an Out of Africa (OOA) expansion, having a higher genetic diversity in African populations and a low genetic diversity in South American populations. Modeling the evolutionary rate of conserved genes for both P. falciparum and P. vivax determined the approximate arrival of human malaria in South America. Bayesian computational methods suggest that P. falciparum originated in Africa and arrived in South America through multiple independent introductions by the transatlantic African slave trade; however, in South America, P. vivax could have been introduced through an alternate migratory route. Alignments of P. vivax mitogenomes have revealed low genetic variation between the South American and Southeast Asian populations suggesting introduction through either pre-Columbian human migration or post-colonization events. To confirm the findings of these phylogeographical analyses, molecular methods were used to diagnose malaria infection in archeological remains of pre-Columbian ethnic groups. Immunohistochemistry tests were used and identified P. vivax but not P. falciparum in histologically prepared tissues from pre-Columbian Peruvian mummies, whereas shotgun metagenomics sequencing of DNA isolated from pre-Columbian Caribbean coprolites revealed Plasmodium-homologous reads; current evidence suggests that only P. vivax might have been present in pre-Columbian South America


No disponible


Assuntos
Humanos , Malária Vivax/parasitologia , Epidemiologia Molecular , Filogeografia , Plasmodium vivax/classificação , Plasmodium vivax/genética , Região do Caribe/epidemiologia , América do Sul/epidemiologia
9.
BMC Evol Biol ; 19(1): 164, 2019 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-31382876

RESUMO

BACKGROUND: Hybridogenesis can represent the first stage towards hybrid speciation where the hybrid taxon eventually weans off its parental species. In hybridogenetic water frogs, the hybrid Pelophylax kl. esculentus (genomes RL) usually eliminates one genome from its germline and relies on its parental species P. lessonae (genomes LL) or P. ridibundus (genomes RR) to perpetuate in so-called L-E and R-E systems. But not exclusively: some all-hybrid populations (E-E system) bypass the need for their parental species and fulfill their sexual cycle via triploid hybrid frogs. Genetic surveys are essential to understand the great diversity of these hybridogenetic dynamics and their evolution. Here we conducted such study using RAD-sequencing on Pelophylax from southern Switzerland (Ticino), a geographically-isolated region featuring different assemblages of parental P. lessonae and hybrid P. kl. esculentus. RESULTS: We found two types of hybridogenetic systems in Ticino: an L-E system in northern populations and a presumably all-hybrid E-E system in the closely-related southern populations, where P. lessonae was not detected. In the latter, we did not find evidence for triploid individuals from the population genomic data, but identified a few P. ridibundus (RR) as offspring from interhybrid crosses (LR × LR). CONCLUSIONS: Assuming P. lessonae is truly absent from southern Ticino, the putative maintenance of all-hybrid populations without triploid individuals would require an unusual lability of genome elimination, namely that P. kl. esculentus from both sexes are capable of producing gametes with either L or R genomes. This could be achieved by the co-existence of L- and R- eliminating lineages or by "hybrid amphigamy", i. e. males and females producing sperm and eggs among which both genomes are represented. These hypotheses imply that polyploidy is not the exclusive evolutionary pathway for hybrids to become reproductively independent, and challenge the classical view that hybridogenetic taxa are necessarily sexual parasites.


Assuntos
Hibridização Genética , Ranidae/genética , Animais , Feminino , Especiação Genética , Genoma , Células Germinativas , Heterozigoto , Masculino , Filogeografia , Ranidae/classificação , Reprodução , Isolamento Reprodutivo , Suíça , Triploidia
10.
Rev Bras Parasitol Vet ; 28(3): 451-457, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31390434

RESUMO

The msp4 gene of A. marginale is unicodon, stable and mostly homogeneous, being considered as a useful marker for phylogeographic characterization of this bacterium. The objective of this work was to analyze the phylogeography of A. marginale based on the msp4 gene in beef cattle from the Brazilian Pantanal, compared to those found in other regions worldwide. The blood samples investigated were collected from 400 animals (200 cows and 200 calves) reared in five extensive breeding farms in this region. The results indicated that of the evaluated samples, 56.75% (227/400) were positive for A. marginale based on the msp1ß gene by quantitatitve PCR (qPCR), while 8.37% (19/227) were positive for the msp4 gene in the conventional PCR. In the Network distance analysis, 14 sequences from the Brazilian Pantanal were grouped into a single group with those from Thailand, India, Spain, Colombia, Parana (Brazil), Mexico, Portugal, Argentina, China, Venezuela, Australia, Italy and Minas Gerais (Brazil). Among 68 sequences from Brazil and the world, 15 genotypes were present while genotype number one (#1) was the most distributed worldwide. Both Splitstree and network analyses showed that the A. marginale msp4 sequences detected in beef cattle from the Brazilian Pantanal showed low polymorphism, with the formation of one genogroup phylogenetically related to those found in ruminants from South and Central America, Europe, and Asia.


Assuntos
Anaplasma marginale/genética , Proteínas de Bactérias/genética , Bovinos/microbiologia , Proteínas de Membrana/genética , Filogeografia/métodos , Américas , Sequência de Aminoácidos , Anaplasma marginale/isolamento & purificação , Animais , Ásia , Brasil , DNA Bacteriano/genética , Europa (Continente) , Feminino , Genótipo , Masculino , Dados de Sequência Molecular , Reação em Cadeia da Polimerase
11.
BMC Evol Biol ; 19(1): 161, 2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31370783

RESUMO

BACKGROUND: Geological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded responding to environmental changes with the uplift of the Qinghai-Tibet Plateau (QTP) and glacial cycles during Pleistocene. In this study, we analysed the population structure of Godlewski's Bunting, Emberiza godlewskii, to determine the effects of major historical events, geographic barriers and past climatic changes on phylogenetic divergence and historical demographic dynamics of this species. RESULTS: A phylogeny based on concatenated mitochondrial and nuclear DNA datasets show two (northern and southern) clades approximately diverged 3.26 million years ago (Ma). The West Qinling Mountains serve as a dividing line between the two lineages. Both lineages experienced a recent demographic expansion during interglacial periods (marine isotope stages (MISs) 2-6). Bayesian skyline plots and the results of ecological niche modelling suggested a more intensive expansion of the northern lineage during the late Pleistocene, whereas the southern lineage was comparatively mild in population growth. CONCLUSIONS: Our results provide insights into the distribution patterns of avian taxa and the possible mechanisms for a south and north divergence model in China. The deep divergence may have been shaped by the uplift of the QTP. Habitat preferences might have facilitated the lineage divergence for E. godlewskii. Moreover, the West Qinling Mountains act as a dividing line between the two lineages, indicating a novel phylogeographic pattern of organisms in China. The difference in population expansion mode between two lineages resulted from different effects caused by the climate of the LGM and the subsequent habitat changes accompanying the arrival of a colder climate in northern and southern regions of China.


Assuntos
Ecossistema , Variação Genética , Passeriformes/genética , Animais , Teorema de Bayes , China , DNA Mitocondrial/genética , Evolução Molecular , Genes Mitocondriais , Deriva Genética , Funções Verossimilhança , Filogenia , Filogeografia , Especificidade da Espécie , Tibet
12.
Mol Genet Genomics ; 294(6): 1547-1559, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31372716

RESUMO

Distinctive peculiarities of Armenians such as their millennia-long genetic isolation and strong national identity attract a keen interest while studying the demographic history of the West Asia. Here, to examine their fine-scale matrilineal genetic structure, ancestry and relationships with neighboring populations, we analyzed 536 complete mitogenomes (141 of which are novel) from 8 geographically different Armenian populations, covering the whole stretch of historical Armenia. The observed patterns highlight a remarkable degree of matrilineal genetic heterogeneity and weak population structuring of Armenians. Moreover, our phylogeographic analysis reveals common ancestries for some mtDNA lineages shared by West Asians, Transcaucasians, Europeans, Central Asians and Armenians. About third of the mtDNA subhaplogroups found in Armenian gene pool might be considered as Armenian-specific, as these are virtually absent elsewhere in Europe, West Asia and Transcaucasia. Coalescence ages of most of these lineages do not exceed 3.1 kya and coincide well with the population size growth started around 1.8-2.8 kya detectable only in the Bayesian Skyline Plots based on the Armenian-specific mtDNA haplotypes.


Assuntos
Genoma Mitocondrial , Armênia , Ásia Central , Ásia Ocidental , DNA Mitocondrial/química , Europa (Continente) , Variação Genética , Haplótipos , Humanos , Filogenia , Filogeografia
13.
BMC Evol Biol ; 19(1): 163, 2019 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-31375065

RESUMO

BACKGROUND: Ancestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology, and ecology. Despite the existence of powerful methods and software in ancestral character state inference, difficulties may arise when interpreting the outputs of such inferences. The growing complexity of data (trees, annotations), the diversity of optimization criteria for computing trees and ancestral character states, the combinatorial explosion of potential evolutionary scenarios if some ancestral characters states do not stand out clearly from others, requires the design of new methods to explore associations of phylogenetic trees with extrinsic traits, to ease the visualization and interpretation of evolutionary scenarios. RESULT: We developed PastView, a user-friendly interface that includes numerical and graphical features to help users to import and/or compute ancestral character states from discrete variables and extract ancestral scenarios as sets of successive transitions of character states from the tree root to its leaves. PastView provides summarized views such as transition maps and integrates comparative tools to highlight agreements or discrepancies between methods of ancestral annotations inference. CONCLUSION: The main contribution of PastView is to assemble known numerical and graphical methods into a multi-maps graphical user interface dedicated to the computing, searching and viewing of evolutionary scenarios based on phylogenetic trees and ancestral character states. PastView is available publicly as a standalone software on www.pastview.org .


Assuntos
Filogenia , Software , Interface Usuário-Computador , Albânia/epidemiologia , Dengue/epidemiologia , Vírus da Dengue/genética , Infecções por HIV/epidemiologia , HIV-1/genética , Humanos , Fenótipo , Filogeografia
14.
An Acad Bras Cienc ; 91(suppl 3): e20190218, 2019 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-31411243

RESUMO

Amazonia has been a focus of interest since the early days of biogeography as an intrinsically complex and extremely diverse region. This region comprises an intricate mosaic that includes diverse types of forest formations, flooded environments and open vegetation. Increased knowledge about the distribution of species in Amazonia has led to the recognition of complex biogeographic patterns. The confrontation of these biogeographic patterns with information on the geological and climatic history of the region has generated several hypotheses dedicated to explain the origin of the biological diversity. Genomic information, coupled with knowledge of Earth's history, especially the evolution of the Amazonian landscape, presents fascinating possibilities for understanding the mechanisms that govern the origin and maintenance of diversity patterns in one of the most diverse regions of the world. For this we will increasingly need more intense and coordinated interactions between researchers studying biotic diversification and the evolution of landscapes. From the interaction between these two fields of knowledge that are in full development, an increasingly detailed understanding of the historical mechanisms related to the origin of the species will surely arise.


Assuntos
Biodiversidade , Evolução Biológica , Aves/classificação , Filogeografia , Animais , Brasil , Ecossistema
15.
BMC Evol Biol ; 19(1): 159, 2019 07 31.
Artigo em Inglês | MEDLINE | ID: mdl-31366328

RESUMO

BACKGROUND: Flathead fishes of the genus Platycephalus are economically important demersal fishes that widely inhabit the continental shelves of tropical and temperate sea waters. This genus has a long history of taxonomic revision, and recently four Platycephalus species (Platycephalus sp. 1, Platycephalus sp. 2, P. indicus, and P. cultellatus) in the northwestern Pacific Ocean (NWP) have been recognized and redescribed. However, many aspects of their systematics and evolutionary history are unclear. RESULTS: A total of 411 individuals were sampled from 22 different sites across their distributions in the NWP. Three mitochondrial loci were sequenced to clarify the phylogeny and phylogeographic history of the fishes. The results showed significant differentiation of four Platycephalus species in the NWP with well-supported clades in which Platycephalus sp. 1 and Platycephalus sp. 2 were the closest, clustered with P. cultellatus, while their genetic relationship with P. indicus was the furthest. There were significant genealogical branches corresponding to P. indicus but not to other Platycephalus lineages. We further examined the phylogeographic patterns of 16 Platycephalus sp. 1 populations along the coastlines of China and Japan. A total of 69 haplotypes were obtained, with 23 shared among populations. One dominant haplotypic group, with a modest lineage structure and low levels of haplotype diversity and nucleotide diversity, was observed among Platycephalus sp. 1 populations. The demographic history reconstruction suggested a Platycephalus sp. 1 population expansion event dating back to the late Pleistocene. CONCLUSIONS: Distributional rang variations may be the crucial factors shaping the genetic relationships of the genus Platycephalus. Reproductive schooling and potential egg/larval dispersal ability, coupled with the effects of ocean currents, are responsible for the present phylogeographic pattern of Platycephalus sp. 1.


Assuntos
DNA Mitocondrial/genética , Perciformes/classificação , Perciformes/genética , Filogeografia , Animais , Sequência de Bases , Teorema de Bayes , China , Variação Genética , Japão , Oceano Pacífico , Filogenia , Água do Mar
16.
BMC Evol Biol ; 19(1): 151, 2019 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-31340765

RESUMO

BACKGROUND: Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced genetic differentiation across the region by investigating phylogeographic patterns in the Pitta sordida species complex. RESULTS: We generated a de novo genome and compared population genomics of 29 individuals of Pitta sordida from the entire distributional range and we reconstructed phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset and single nucleotide polymorphisms (SNPs). We found deep divergence between an eastern and a western group of taxa across Indo-Australasia. Within both groups we have identified major lineages that are geographically separated into Philippines, Borneo, western Sundaland, and New Guinea, respectively. Although these lineages are genetically well-differentiated, suggesting a long-term isolation, there are signatures of extensive gene flow within each lineage throughout the Pleistocene, despite the wide geographic range occupied by some of them. We found little evidence of hybridization or introgression among the studied taxa, but forsteni from Sulawesi makes an exception. This individual, belonging to the eastern clade, is genetically admixed between the western and eastern clades. Geographically this makes sense as Sulawesi is not far from Borneo that houses a population of hooded pittas that belongs to the western clade. CONCLUSIONS: We found that geological vicariance events cannot explain the current genetic differentiation in the Pitta sordida species complex. Instead, the glacial-interglacial cycles may have played a major role therein. During glacials the sea level could be up to 120 m lower than today and land bridges formed within both the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and faunal elements. The geographic distribution of hooded pittas shows the importance of overwater, "stepping-stone" dispersals not only to deep-sea islands, but also from one shelf to the other. The most parsimonious hypothesis is an Asian ancestral home of the Pitta sordida species complex and a colonization from west to east, probably via Wallacea.


Assuntos
Genoma , Ilhas , Passeriformes/genética , Animais , Austrália , Fluxo Gênico , Variação Genética , Índia , Filogenia , Filogeografia , Dinâmica Populacional , Análise de Componente Principal , Fatores de Tempo
17.
Arch Virol ; 164(10): 2613-2616, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31321586

RESUMO

A new virus with a circular double-stranded DNA genome was discovered in green Sichuan pepper with vein clearing symptoms. Its complete genome of 8,014 bp contains three open reading frames (ORF) on the plus strand, which is typical of members of the genus Badnavirus in the family Caulimoviridae. Sequence comparisons revealed that the new virus has the highest nucleotide sequence identity with grapevine vein-clearing virus (GVCV). In particular, the identity of the two viruses in the ORF3 RT-RNase H region is 71.9%, which is below the species demarcation cutoff of 80% for badnaviruses. Phylogenetic analysis also placed the new virus with GVCV in a cluster. The virus was tentatively named "green Sichuan pepper vein clearing-associated virus" (GSPVCaV). The geographical distribution and genetic diversity of GSPVCaV were studied. Another isolate was found to be highly divergent.


Assuntos
Badnavirus/classificação , Badnavirus/isolamento & purificação , DNA Viral/genética , Filogeografia , Doenças das Plantas/virologia , Zanthoxylum/virologia , DNA/química , DNA/genética , DNA Circular/química , DNA Circular/genética , DNA Viral/química , Genoma Viral , Fases de Leitura Aberta , Análise de Sequência de DNA , Homologia de Sequência
18.
Ann Hum Biol ; 46(2): 140-144, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31267777

RESUMO

Two key moments shaped the extant South Asian gene pool within the last 10 thousand years (ka): the Neolithic period, with the advent of agriculture and the rise of the Harappan/Indus Valley Civilisation; and Late Bronze Age events that witnessed the abrupt fall of the Harappan Civilisation and the arrival of Indo-European speakers. This study focuses on the phylogeographic patterns of mitochondrial haplogroups H2 and H13 in the Indian Subcontinent and incorporates evidence from recently released ancient genomes from Central and South Asia. It found signals of Neolithic arrivals from Iran and later movements in the Bronze Age from Central Asia that derived ultimately from the Steppe. This study shows how a detailed mtDNA phylogeographic approach, combining both modern and ancient variation, can provide evidence of population movements, even in a scenario of strong male bias such as in the case of the Bronze Age Steppe dispersals.


Assuntos
DNA Antigo/análise , DNA Mitocondrial/análise , Migração Humana/história , Arqueologia , Ásia , Grupo com Ancestrais do Continente Asiático/genética , DNA Mitocondrial/genética , Pool Gênico , Haplótipos , História Antiga , Humanos , Irã (Geográfico) , Filogeografia
19.
Arch Virol ; 164(10): 2459-2467, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31286220

RESUMO

Tobacco vein banding mosaic virus (TVBMV) is of increasing importance in tobacco production. Knowledge of the genetic structure and variability of the virus population is vital for developing sustainable management. In this study, 24 new TVBMV isolates from Sichuan Province together with 46 previous isolates were studied based on their coat protein sequences. Two distinguishable clades were supported by phylogenetic analysis. The summary statistics PS, AI and MC showed a strong TVBMV-geography association between the isolates from Southwest China (SW) and Mainland China (MC). Further analysis indicated that the spatial genetic structure of TVBMV populations is likely to have been caused by natural selection. Phylogeographic analysis provided strong support for spatial diffusion pathways between the Southwest and Northwest tobacco-producing regions. The TVBMV CP gene was found to be under negative selection, and no significant positive selection of amino acids was detected in the SW group; however, the isolates of the MC group experienced significant positive selection pressure at the first and third amino acid sites of CP. This study suggests that natural selection and habitat heterogeneity are important evolutionary mechanisms affecting the genetic structure of the TVBMV population.


Assuntos
Variação Genética , Doenças das Plantas/virologia , Potyvirus/classificação , Potyvirus/genética , Tabaco/virologia , Proteínas do Capsídeo/genética , China , Filogeografia , Potyvirus/isolamento & purificação , Seleção Genética , Análise de Sequência de DNA
20.
Parasit Vectors ; 12(1): 327, 2019 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-31253176

RESUMO

BACKGROUND: Microsporidians are obligate endoparasites infecting taxonomically diverse hosts. Both vertical (from mother to eggs) and horizontal (between conspecifics or between species) transmission routes are known. While the former may promote co-speciation and host-specificity, the latter may promote shifts between host species. Among aquatic arthropods, freshwater amphipod crustaceans are hosts for many microsporidian species. However, despite numerous studies, no general pattern emerged about host specificity and co-diversification. In south-eastern Europe, the gammarid Gammarus roeselii is composed of 13 cryptic lineages of Miocene to Pleistocene age but few genotypes of one lineage have spread postglacially throughout north-western Europe. Based on nearly 100 sampling sites covering its entire range, we aim to: (i) explore the microsporidian diversity present in G. roeselii and their phylogenetic relationships, especially in relation to the parasites infecting other Gammaridae; (ii) test if the host phylogeographical history might have impacted host-parasite association (e.g. co-diversifications or recent host shifts from local fauna). METHODS: We used part of the small subunit rRNA gene as source of sequences to identify and determine the phylogenetic position of the microsporidian taxa infecting G. roeselii. RESULTS: Microsporidian diversity was high in G. roeselii with 24 detected haplogroups, clustered into 18 species-level taxa. Ten microsporidian species were rare, infecting a few individual hosts in a few populations, and were mostly phylogenetically related to parasites from other amphipods or various crustaceans. Other microsporidians were represented by widespread genera with high prevalence: Nosema, Cucumispora and Dictyocoela. Two contrasting host association patterns could be observed. First, two vertically transmitted microsporidian species, Nosema granulosis and Dictyocoela roeselum, share the pattern of infecting G. roeselii over most of its range and are specific to this host suggesting the co-diversification scenario. This pattern contrasted with that of Dictyocoela muelleri, the three species of Cucumispora, and the rare parasites, present only in the recently colonised region by the host. These patterns suggest recent acquisitions from local host species, after the recent spread of G. roeselii. CONCLUSIONS: Microsporidians infecting G. roeselii revealed two scenarios of host-parasite associations: (i) ancient associations with vertically transmitted parasites that probably co-diversified with their hosts, and (ii) host shifts from local host species, after the postglacial spread of G. roeselii.


Assuntos
Anfípodes/parasitologia , Interações Hospedeiro-Parasita , Microsporídios/fisiologia , Anfípodes/fisiologia , Animais , Feminino , Genes de RNAr , Variação Genética , Masculino , Microsporídios/genética , Microsporidiose , Filogenia , Filogeografia , Especificidade da Espécie
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