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1.
Sci Rep ; 10(1): 6872, 2020 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-32327716

RESUMO

People in the Solomon Islands today are considered to have derived from Asian- and Papuan-related ancestors. Papuan-related ancestors colonized Near Oceania about 47,000 years ago, and Asian-related ancestors were Austronesian (AN)-speaking population, called Lapita, who migrated from Southeast Asia about 3,500 years ago. These two ancestral populations admixed in Near Oceania before the expansion of Lapita people into Remote Oceania. To understand the impact of the admixture on the adaptation of AN-speaking Melanesians in Near Oceania, we performed the genome-wide single nucleotide polymorphism (SNP) analysis of 21 individuals from Munda, the main town of the New Georgia Islands in the western Solomon Islands. Population samples from Munda were genetically similar to other Solomon Island population samples. The analysis of genetic contribution from the two different ancestries to the Munda genome revealed significantly higher proportions of Asian- and Papuan-related ancestries in the region containing the annexin A1 (ANXA1) gene (Asian component > 82.6%) and in the human leukocyte antigen (HLA) class II region (Papuan component > 85.4%), respectively. These regions were suspected to have undergone natural selection since the time of admixture. Our results suggest that admixture had affected adaptation of AN-speaking Melanesians in the Solomon Islands.


Assuntos
Pool Gênico , Genoma Humano , Grupo com Ancestrais Oceânicos/genética , Seleção Genética , Cromossomos Humanos Par 6/genética , Simulação por Computador , Humanos , Imunidade , Melanesia , Papua Nova Guiné , Filogenia , Análise de Componente Principal
2.
Mol Microbiol ; 113(3): 672-681, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32185830

RESUMO

Bottlenecks reduce the size of the gene pool within populations of all life forms with implications for their subsequent survival. Here, we examine the effects of bottlenecks on bacterial commensal-pathogens during transmission between, and dissemination within, hosts. By reducing genetic diversity, bottlenecks may alter individual or population-wide adaptive potential. A diverse range of hypermutable mechanisms have evolved in infectious agents that allow for rapid generation of genetic diversity in specific genomic loci as opposed to the variability arising from increased genome-wide mutation rates. These localised hypermutable mechanisms include multi-gene phase variation (PV) of outer membrane components, multi-allele PV of restriction systems and recombination-driven antigenic variation. We review selected experimental and theoretical (mathematical) models pertaining to the hypothesis that localised hypermutation (LH) compensates for fitness losses caused by bottlenecks and discuss whether bottlenecks have driven the evolution of hypermutable loci.


Assuntos
Bactérias/genética , Variação Genética/genética , Interações Hospedeiro-Patógeno/genética , Variação Antigênica , Evolução Biológica , Evolução Molecular , Pool Gênico , Modelos Genéticos , Mutação , Recombinação Genética/genética , Seleção Genética/genética
3.
Sci Rep ; 10(1): 2111, 2020 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-32034221

RESUMO

This study provides insights in patterns of distribution of abiotic and biotic stress resilience across Vigna gene pools to enhance the use and conservation of these genetic resources for legume breeding. Vigna is a pantropical genus with more than 88 taxa including important crops such as V. radiata (mung bean) and V. unguiculata (cowpea). Our results show that sources of pest and disease resistance occur in at least 75 percent of the Vigna taxa, which were part of screening assessments, while sources of abiotic stress resilience occur in less than 30 percent of screened taxa. This difference in levels of resilience suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses because of short growing seasons or with taxa, which tolerate salinity. We recommend prioritizing these rare Vigna taxa for conservation and screening for combined abiotic and biotic stress resilience resulting from stacked or multifunctional traits. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that will suffer from salinization under global climate change.


Assuntos
Vigna/crescimento & desenvolvimento , Conservação dos Recursos Naturais , Resistência à Doença/genética , Pool Gênico , Filogeografia , Melhoramento Vegetal , Estresse Fisiológico/genética , Vigna/genética
4.
Theor Appl Genet ; 133(3): 1039-1054, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31974666

RESUMO

KEY MESSAGE: Glycine soja germplasm can be used to successfully introduce new alleles with the potential to add valuable new genetic diversity to the current elite soybean gene pool. Given the demonstrated narrow genetic base of the US soybean production, it is essential to identify beneficial alleles from exotic germplasm, such as wild soybean, to enhance genetic gain for favorable traits. Nested association mapping (NAM) is an approach to population development that permits the comparison of allelic effects of the same QTL in multiple parents. Seed yield, plant maturity, plant height and plant lodging were evaluated in a NAM panel consisting of 392 recombinant inbred lines derived from three biparental interspecific soybean populations in eight environments during 2016 and 2017. Nested association mapping, combined with linkage mapping, identified three major QTL for plant maturity in chromosomes 6, 11 and 12 associated with alleles from wild soybean resulting in significant increases in days to maturity. A significant QTL for plant height was identified on chromosome 13 with the allele increasing plant height derived from wild soybean. A significant grain yield QTL was detected on chromosome 17, and the allele from Glycine soja had a positive effect of 166 kg ha-1; RIL's with the wild soybean allele yielded on average 6% more than the lines carrying the Glycine max allele. These findings demonstrate the usefulness and potential of alleles from wild soybean germplasm to enhance important agronomic traits in a soybean breeding program.


Assuntos
Mapeamento Cromossômico , Locos de Características Quantitativas , Soja/genética , Alelos , Cruzamentos Genéticos , Fabaceae/genética , Pool Gênico , Genótipo , Desequilíbrio de Ligação , Fenótipo , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único , Soja/crescimento & desenvolvimento
5.
Vopr Virusol ; 65(5): 243-258, 2020 11 14.
Artigo em Russo | MEDLINE | ID: mdl-33533208

RESUMO

The possible formation of population gene pools of zoonotic viruses with a respiratory route of transmission and a possibility of a pandemic at different stages of biosphere evolution is analyzed. Forming of Poxviruses  (Entomopoxvirinae) gene pool could be the beginning of transformation from Plants to Arthropoda (Carbon - 375 million years ago) with further evolution connected with Rodentia (Pliocene - 75-70 million years ago) and further separation of genera (500-300 thousand years ago), and respiratory transmission (epidemics) between humans (10-2 thousand years BC). Smallpox comeback would be possible. Orthomyxoviruses relicts (genus Isavirus) were possibly connected with Ichthya (Silurian - 500-410 million years ago), and then close interaction with Aves (the Cretaceous, 125-110 million years ago) with the division of genera and respiratory transmission (epidemics) between humans (10-2 thousand BC). Next pandemic of influenza A could be catastrophic in terms of the number of victims and economic damage.Coronaviruses formed a gene pool by interaction with Amphibia (subfamily Letovirinae) and then with Chiroptera in Tertiary (110-75 million years ago) with transformation to Artiodactyla (Eocene - 70-60 million years ago), and only 10-2 thousand years BC acquired the ability to a respiratory transmission and became Alphaviruses, a seasonal infection of humans. A similar situation is possible in the near future with SARS-CoV-2. Pandemics associated with zoonoses even more serious than COVID-19 are likely. Constant monitoring of  populational gene pools of zoonotic viruses is necessary.


Assuntos
/genética , Reservatórios de Doenças/virologia , Evolução Molecular , Pool Gênico , Zoonoses/genética , Anfíbios/virologia , Animais , /transmissão , Quirópteros/virologia , Humanos , Zoonoses/epidemiologia , Zoonoses/transmissão , Zoonoses/virologia
6.
PLoS One ; 14(12): e0223680, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31830054

RESUMO

Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological importance and medical relevance, MGEs from the gut microbiome have not been systematically characterized. Here, we present a comprehensive analysis of chromosomal MGEs in the gut microbiome using a method that enables the identification of the mobilizable unit of MGEs. We curated a database of 5,219 putative MGEs encompassing seven MGE classes called ImmeDB. We observed that many MGEs carry genes that could confer an adaptive advantage to the gut environment including gene families involved in antibiotic resistance, bile salt detoxification, mucus degradation, capsular polysaccharide biosynthesis, polysaccharide utilization, and sporulation. We find that antibiotic resistance genes are more likely to be spread by conjugation via integrative conjugative elements or integrative mobilizable elements than transduction via prophages. Horizontal transfer of MGEs is extensive within phyla but rare across phyla, supporting phylum level niche-adaptive gene pools in the gut microbiome. ImmeDB will be a valuable resource for future studies on the gut microbiome and MGE communities.


Assuntos
Bactérias/classificação , Bactérias/genética , Farmacorresistência Bacteriana/genética , Microbioma Gastrointestinal/genética , Trato Gastrointestinal/microbiologia , Pool Gênico , Sequências Repetitivas Dispersas , Antibacterianos/farmacologia , Bactérias/efeitos dos fármacos , Evolução Molecular , Genoma Bacteriano , Humanos , Filogenia
7.
Am J Hum Genet ; 105(6): 1254-1261, 2019 12 05.
Artigo em Inglês | MEDLINE | ID: mdl-31809748

RESUMO

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.


Assuntos
Grupo com Ancestrais do Continente Africano/genética , Fósseis , Genética Populacional , Genoma Humano , Hominidae/genética , Homem de Neandertal/genética , Animais , Pool Gênico , Humanos
8.
Curr Biol ; 29(22): 3953-3959.e4, 2019 11 18.
Artigo em Inglês | MEDLINE | ID: mdl-31679935

RESUMO

North Africa is located at the crossroads of the Mediterranean Sea, the Middle East, and the Sahara Desert. Extensive migrations and gene flow in the region have shaped many different cultures and ancestral genetic components through time [1-6]. DNA data from ancient Moroccan sites [7, 8] has recently shed some light to the population continuity-versus-replacement debate, i.e., the question of whether current North African populations descend from Palaeolithic groups or, on the contrary, subsequent migrations swept away all pre-existing genetic signal in the region. In the present study, we analyze 21 complete North African genomes and compare them with extant and ancient genome data in order to address the demographic continuity-versus-replacement debate, to assess whether these demographic events were homogeneous (including Berber and Arabic-speaking groups), and to explore the effect of Neolithization and posterior migration waves. The North African genetic pool is defined as a melting pot of genetic components, including an endemic North African Epipalaeolithic component at low frequency that forms a declining gradient from Western to Eastern North Africa. This scenario is consistent with Neolithization having shaped most of the current genetic variation in the region when compared to posterior back-to-North-Africa migration waves such as the Arabization. A common and distinct genetic history of the region is shown, with internal different proportions of genetic components owing to differential admixture with surrounding groups as well as to genetic drift due to isolation and endogamy in certain populations.


Assuntos
Grupo com Ancestrais do Continente Africano/genética , Fluxo Gênico/genética , África ao Sul do Saara , África do Norte , Grupo com Ancestrais do Continente Europeu/genética , Fósseis , Pool Gênico , Variação Genética , Genética Populacional/métodos , Genoma/genética , Haplótipos , História Antiga , Migração Humana/história , Humanos , Polimorfismo de Nucleotídeo Único
9.
J Genet ; 982019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31767820

RESUMO

Rattans, the spiny climbing palms of Arecaceae (Palmae) family exhibit high endemism to the biodiversity hot spots in India. Of the five rattan genera, Calamus is the only genus found in peninsular India with 15 of 21 species, endemic to the Western Ghats. The extensive utilization of rattans owing to their strength, durability and huge demand has resulted in depletion of their natural resources. Of the 15 endemic species, C. nagbettai is the most affected species on account of endemism, low population size and restricted distribution with fragmented populations. The present study revealed high amount of genetic diversity in the surviving scattered populations of the species using microsatellite markers. High gene flow (Nm = 1.498) observed across the populations resulted in low genetic differentiation (14%). A clear genetic admixture could be seen in Kerala as well as one of the Karnataka's populations while the remaining two populations were genetically distinct. UPGMA, PCoA and STRUCTURE analyses showed significantly different genetic composition in Kerala population compared to other populations. Kerala and Karnataka populations of C. nagbettai were also unique in their genetic structure and allelic composition. Therefore, effective management and conservation strategies have to be implemented to preserve the rarealleles with adaptive potential to protect this economically valuable Calamus species from endangerment. Over exploitation, low seed set and poor regeneration, as well as habitat fragmentation can further threaten the survival of this endemic, narrowly distributed dioecious rattan species in the Western Ghats region.


Assuntos
Calamus/genética , Pool Gênico , Calamus/classificação , Conservação dos Recursos Naturais , Ecossistema , Variação Genética , Genética Populacional , Índia , Repetições de Microssatélites , Filogenia
10.
BMC Plant Biol ; 19(1): 442, 2019 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-31646962

RESUMO

BACKGROUND: Common bean (Phaseolus vulgaris L.) is the most important food legume for direct human consumption around the world, as it represents a valuable source of components with nutritional and health benefits. RESULTS: We conducted a study to define and explain the genetic relatedness and diversification level of common bean (Phaseolus vulgaris L.) germplasm from Portugal to Ukraine, along a western-to-eastern line of southern European countries, including Poland. This was based on the P. vulgaris genetic structure, and was designed to better describe its distribution and domestication pathways in Europe. Using the multi-crop passport descriptors that include geographic origin and different phaseolin types (corresponding to the Mesoamerican and Andean gene pools), 782 accessions were obtained from nine gene banks and 12 geographic origins. We selected 33 genome/ gene-related/ gene-pool-related nuclear simple sequence repeat markers that covered the genetic diversity across the P. vulgaris genome. The overall polymorphic information content was 0.800. Without specifying geographic origin, global structure cluster analysis generated 10 genetic clusters. Among the PvSHP1 markers, the most informative for gene pool assignment of the European P. vulgaris germplasm was PvSHP1-B. Results of AMOVA show that 89% of the molecular variability is shared within the 782 accessions, with 4% molecular variability among the different geographic origins along this western-to-eastern line of southern Europe (including Poland). CONCLUSIONS: This study shows that the diversification line of the European P. vulgaris germplasm followed from the western areas of southern Europe (Portugal, Spain, Italy, Slovenia) to the more eastern areas of southern Europe. This progression defines three geographically separated subgroups, as the northern (Poland, Ukraine, Romania), southern (Albania, Bulgaria), and central (Bosnia and Herzegovina, Serbia, Hungary) areas of eastern Europe.


Assuntos
Pool Gênico , Variação Genética , Phaseolus/genética , Análise por Conglomerados , Europa (Continente) , Genótipo , Geografia , Repetições de Microssatélites/genética
11.
Proc Natl Acad Sci U S A ; 116(42): 21302-21311, 2019 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-31570572

RESUMO

Mexico is recognized as the center of origin and domestication of maize. Introduction of modern maize varieties (MVs) into Mexico raised concerns regarding the possible effects of gene flow from MVs into maize landraces (LRs) and their wild relatives (WRs), teosintes. However, after more than 60 y from the release of the first MVs, the impact of the sympatry with LRs and their WRs has not been explored with genetic data. In this work, we assessed changes in the genomes of 7 maize LRs and 2 WR subspecies from collections spanning over 70 y. We compared the genotypes obtained by genotyping by sequencing (GBS) for LRs and WRs before and after the adoption of MVs, and observed introgression from sympatric MVs into LRs and into the WR Zea mays ssp. mexicana sampled after the year 2000. We also found a decrease in the paired divergence index (F ST ) between MV-LR and MV-WR over the same time frame. Moreover, we determined that LR genetic diversity increased after 2000, probably as a result of gene flow from MVs introduced in the 1990s. Our findings allowed us to identify ongoing changes in the domesticated and wild maize genetic pools, and concur with previous works that have evaluated short-term gene flow from MVs into LRs in other crops. Our approach represents a useful tool for tracking evolutionary change in wild and domesticated genetic resources, as well as for developing strategies for their conservation.


Assuntos
Fluxo Gênico/genética , Genoma de Planta/genética , Zea mays/genética , Produtos Agrícolas/genética , Domesticação , Pool Gênico , Variação Genética/genética , Genótipo , México , Simpatria/genética
12.
Appl Environ Microbiol ; 85(24)2019 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-31562174

RESUMO

We studied symbiotic performance of factorial combinations of diverse rhizobial genotypes (GR) and East African common bean varieties (GL) that comprise Andean and Mesoamerican genetic groups. An initial wide screening in modified Leonard jars (LJ) was followed by evaluation of a subset of strains and genotypes in pots (contained the same, sterile medium) in which fixed nitrogen was also quantified. An additive main effect and multiplicative interaction (AMMI) model was used to identify the contribution of individual strains and plant genotypes to the GL × GR interaction. Strong and highly significant GL × GR interaction was found in the LJ experiment but with little evidence of a relation to genetic background or growth habits. The interaction was much weaker in the pot experiment, with all bean genotypes and Rhizobium strains having relatively stable performance. We found that R. etli strain CFN42 and R. tropici strains CIAT899 and NAK91 were effective across bean genotypes but with the latter showing evidence of positive interaction with two specific bean genotypes. This suggests that selection of bean varieties based on their response to inoculation is possible. On the other hand, we show that symbiotic performance is not predicted by any a priori grouping, limiting the scope for more general recommendations. The fact that the strength and pattern of GL × GR depended on growing conditions provides an important cautionary message for future studies.IMPORTANCE The existence of genotype-by-strain (GL × GR) interaction has implications for the expected stability of performance of legume inoculants and could represent both challenges and opportunities for improvement of nitrogen fixation. We find that significant genotype-by-strain interaction exists in common bean (Phaseolus vulgaris L.) but that the strength and direction of this interaction depends on the growing environment used to evaluate biomass. Strong genotype and strain main effects, combined with a lack of predictable patterns in GL × GR, suggests that at best individual bean genotypes and strains can be selected for superior additive performance. The observation that the screening environment may affect experimental outcome of GL × GR means that identified patterns should be corroborated under more realistic conditions.


Assuntos
Genótipo , Phaseolus/genética , Phaseolus/microbiologia , Rhizobium tropici/genética , Pool Gênico , Nitrogênio , Fixação de Nitrogênio , Phaseolus/crescimento & desenvolvimento , Filogenia , Nodulação , Rhizobium/classificação , Rhizobium/genética , Rhizobium/metabolismo , Rhizobium tropici/classificação , Rhizobium tropici/metabolismo , Simbiose/genética
13.
PLoS One ; 14(8): e0221471, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31449539

RESUMO

In many beef and some dairy production systems, crossbreeding is used to take advantage of breed complementarity and heterosis. Admixed animals are frequently identified by their coat color and body conformation phenotypes, however, without pedigree information it is not possible to identify the expected breed composition of an admixed animal and in the presence of selection, the actual composition may differ from expectation. As the roles of DNA and genotype data become more pervasive in animal agriculture, a systematic method for estimating the breed composition (the proportions of an animal's genome originating from ancestral pure breeds) has utility for a variety of downstream analyses including the estimation of genomic breeding values for crossbred animals, the estimation of quantitative trait locus effects, and heterosis and heterosis retention in advanced generation composite animals. Currently, there is no automated or semi-automated ancestry estimation platform for cattle and the objective of this study was to evaluate the utility of extant public software for ancestry estimation and determine the effects of reference population size and composition and number of utilized single nucleotide polymorphism loci on ancestry estimation. We also sought to develop an analysis pipeline that would simplify this process for members of the livestock genomics research community. We developed and tested a tool, "CRUMBLER", to estimate the global ancestry of cattle using ADMIXTURE and SNPweights based on a defined reference panel. CRUMBLER, was developed and evaluated in cattle, but is a species agnostic pipeline that facilitates the streamlined estimation of breed composition for individuals with potentially complex ancestries using publicly available global ancestry software and a specified reference population SNP dataset. We developed the reference panel from a large cattle genotype data set and breed association pedigree information using iterative analyses to identify purebred individuals that were representative of each breed. We also evaluated the numbers of markers necessary for breed composition estimation and simulated genotypes for advanced generation composite animals to evaluate the precision of the developed tool. The developed CRUMBLER pipeline extracts a specified subset of genotypes that is common to all current commercially available genotyping platforms, processes these into the file formats required for the analysis software, and predicts admixture proportions using the specified reference population allele frequencies.


Assuntos
Bovinos/genética , Filogenia , Software , Animais , Cruzamento , Pool Gênico , Marcadores Genéticos , Genótipo , Hibridização Genética , Linhagem , Polimorfismo de Nucleotídeo Único/genética , Padrões de Referência , Reprodutibilidade dos Testes , Tamanho da Amostra
14.
Environ Microbiol ; 21(12): 4597-4613, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31385413

RESUMO

The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food-borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spread of AMR among source and sink populations. In particular, questions remain about how Campylobacter resistomes interact between species and hosts, and the potential role of sewage as a conduit for the spread of AMR. Here, we investigate the genomic variation associated with AMR in 168 C. jejuni and 92 C. coli strains isolated from humans, livestock and urban effluents in Spain. AMR was tested in vitro and isolate genomes were sequenced and screened for putative AMR genes and alleles. Genes associated with resistance to multiple drug classes were observed in both species and were commonly present in multidrug-resistant genomic islands (GIs), often located on plasmids or mobile elements. In many cases, these loci had alleles that were shared among C. jejuni and C. coli consistent with horizontal transfer. Our results suggest that specific antibiotic resistance genes have spread among Campylobacter isolated from humans, animals and the environment.


Assuntos
Campylobacter coli/genética , Campylobacter jejuni/genética , Farmacorresistência Bacteriana Múltipla/genética , Pool Gênico , Transferência Genética Horizontal , Gado/microbiologia , Esgotos/microbiologia , Animais , Antibacterianos/farmacologia , Infecções por Campylobacter/microbiologia , Campylobacter coli/efeitos dos fármacos , Humanos , Testes de Sensibilidade Microbiana , Aves Domésticas/microbiologia , Espanha
15.
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
16.
Mol Ecol ; 28(17): 4077-4096, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31342583

RESUMO

The mating system is a central parameter of plant biology because it shapes their ecological and evolutionary properties. Therefore, determining ecological variables that influence the mating system is important for a deeper understanding of the functioning of plant populations. Here, using old concepts and recent statistical developments, we propose a new statistical tool to make inferences about ecological determinants of outcrossing in natural plant populations. The method requires codominant genotypes of seeds collected from maternal plants within different locations. Using extensive computer simulations, we demonstrated that the method is robust to the issues expected for real-world data, including the Wahlund effect, inbreeding and genotyping errors such as allele dropout and allele misclassification. Furthermore, we showed that the estimates of ecological effects and outcrossing rates can be severely biased if genotyping errors and genetic differentiation are not treated explicitly. Application of the new method to the case study of a dioecious tree (Taxus baccata) allowed revealing that female trees that grow in lower local densities have a greater tendency towards mating with relatives. Moreover, we also demonstrated that biparental inbreeding is higher in populations that are characterized by a longer mean distance between trees and a smaller mean trunk perimeter. We found these results to agree with both the theoretical predictions and the history of English yew.


Assuntos
Simulação por Computador , Cruzamentos Genéticos , Ecossistema , Endogamia , Taxus/genética , Algoritmos , Teorema de Bayes , Pool Gênico , Loci Gênicos , Análise de Regressão
17.
Nature ; 570(7760): 182-188, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31168093

RESUMO

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.


Assuntos
Genoma Humano/genética , Migração Humana/história , Ásia/etnologia , DNA Antigo/análise , Europa (Continente)/etnologia , Pool Gênico , Haplótipos , História do Século XV , História Antiga , História Medieval , Humanos , Índios Norte-Americanos , Masculino , Sibéria/etnologia
18.
Theor Appl Genet ; 132(9): 2553-2565, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31214741

RESUMO

KEY MESSAGE: We have mapped a new downy mildew resistance gene, Pl35, derived from wild Helianthus argophyllus to sunflower linkage group 1. New germplasms incorporating the Pl35 gene were developed for both oilseed and confection sunflower Sunflower downy mildew (DM), caused by the oomycete pathogen Plasmopara halstedii, is an economically important and widespread sunflower disease worldwide. Non-race-specific resistance is not available in sunflower, and breeding for DM resistance relies on race-specific resistance to control this disease. The discovery of the novel DM resistance genes is a long-term task due to the highly virulent and aggressive nature of the P. halstedii pathogen, which reduces the effectiveness of resistance genes. The objectives of this study were to: (1) transfer DM resistance from a wild sunflower species Helianthus argophyllus (PI 494576) into cultivated sunflowers; (2) map the resistance gene; and (3) develop diagnostic single-nucleotide polymorphism (SNP) markers for efficient targeting of the gene in breeding programs. The H. argophyllus accession PI 494576 previously identified with resistance to the most virulent P. halstedii race 777 was crossed with oilseed and confection sunflower in 2012. Molecular mapping using the BC2F2 and BC2F3 populations derived from the cross CONFSCLB1/PI 494576 located a new resistance gene Pl35 on linkage group 1 of the sunflower genome. The new gene Pl35 was successfully transferred from PI 494576 into cultivated sunflowers. SNP markers flanking Pl35 were surveyed in a validation panel of 548 diversified sunflower lines collected globally. Eleven SNP markers were found to be diagnostic for Pl35 SNP alleles, with four co-segregating with Pl35. The developed oilseed and confection germplasms with diagnostic SNP markers for Pl35 will be very useful resources for breeding of DM resistance in sunflower.


Assuntos
Cromossomos de Plantas/genética , Resistência à Doença/genética , Helianthus/genética , Doenças das Plantas/genética , Proteínas de Plantas/genética , Polimorfismo de Nucleotídeo Único , Óleo de Girassol/química , Mapeamento Cromossômico , Pool Gênico , Genótipo , Helianthus/microbiologia , Fenótipo , Doenças das Plantas/microbiologia
19.
Sci Rep ; 9(1): 7786, 2019 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-31127140

RESUMO

Hungarians who live in Central Europe today are one of the westernmost Uralic speakers. Despite of the proposed Volga-Ural/West Siberian roots of the Hungarian language, the present-day Hungarian gene pool is highly similar to that of the surrounding Indo-European speaking populations. However, a limited portion of specific Y-chromosomal lineages from haplogroup N, sometimes associated with the spread of Uralic languages, link modern Hungarians with populations living close to the Ural Mountain range on the border of Europe and Asia. Here we investigate the paternal genetic connection between these spatially separated populations. We reconstruct the phylogeny of N3a4-Z1936 clade by using 33 high-coverage Y-chromosomal sequences and estimate the coalescent times of its sub-clades. We genotype close to 5000 samples from 46 Eurasian populations to show the presence of N3a4-B539 lineages among Hungarians and in the populations from Ural Mountain region, including Ob-Ugric-speakers from West Siberia who are geographically distant but linguistically closest to Hungarians. This sub-clade splits from its sister-branch N3a4-B535, frequent today among Northeast European Uralic speakers, 4000-5000 ya, which is in the time-frame of the proposed divergence of Ugric languages.


Assuntos
Cromossomos Humanos Y , Grupo com Ancestrais do Continente Europeu/genética , Pool Gênico , Genética Populacional , Haplótipos , Humanos , Hungria , Idioma , Filogenia , Filogeografia , Sibéria
20.
Theor Appl Genet ; 132(8): 2285-2294, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31049633

RESUMO

KEY MESSAGE: Introgressing one-eighth of synthetic hexaploid wheat genome through a double top-cross plus a two-phase selection is an effective strategy to develop high-yielding wheat varieties. The continued expansion of the world population and the likely onset of climate change combine to form a major crop breeding challenge. Genetic advances in most crop species to date have largely relied on recombination and reassortment within a relatively narrow gene pool. Here, we demonstrate an efficient wheat breeding strategy for improving yield potentials by introgression of multiple genomic regions of de novo synthesized wheat. The method relies on an initial double top-cross (DTC), in which one parent is synthetic hexaploid wheat (SHW), followed by a two-phase selection procedure. A genotypic analysis of three varieties (Shumai 580, Shumai 969 and Shumai 830) released from this program showed that each harbors a unique set of genomic regions inherited from the SHW parent. The first two varieties were generated from very small populations, whereas the third used a more conventional scale of selection since one of bread wheat parents was a pre-breeding material. The three varieties had remarkably enhanced yield potential compared to those developed by conventional breeding. A widely accepted consensus among crop breeders holds that introducing unadapted germplasm, such as landraces, as parents into a breeding program is a risky proposition, since the size of the breeding population required to overcome linkage drag becomes too daunting. However, the success of the proposed DTC strategy has demonstrated that novel variation harbored by SHWs can be accessed in a straightforward, effective manner. The strategy is in principle generalizable to any allopolyploid crop species where the identity of the progenitor species is known.


Assuntos
Pão , Pool Gênico , Melhoramento Vegetal , Poliploidia , Triticum/genética , Alelos , Cruzamentos Genéticos , Genes de Plantas , Genótipo , Modelos Genéticos , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética
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