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1.
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
2.
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
3.
Ann Hum Biol ; 46(2): 160-168, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30939942

RESUMO

Background: Aurès is a vast territory in the east of Algeria, characterised by its traditional Berber settlement which has preserved its language and its rich history; its name goes back to antiquity and before the Roman conquest it was part of the territory of ancient Numidia. The Chaoui people in this region are one of Algeria's largest Berber groups. Aim: The aims were to investigate the level of genetic diversity of the Berbers of Aurès through the analysis of the paternal gene pool and to estimate the percentage of genetic variation among different geographical regions and linguistic groups from Algeria. Subjects and methods: Twenty-three Y-STRs were genotyped in a sample of 218 unrelated males of the Berbers of Aurès. Algorithms were used to estimate the Y-chromosome haplogroups. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between sample groups. Results: The paternal lineage of this sample of the Aurès region did not exhibit strong signals of differentiation with other samples from North-central, Northwest, and South Algeria. However, significant differences were found within this sample, demonstrating a high degree of heterogeneity. Conclusion: The results demonstrate that Aurès people are isolated and closed, but nevertheless have quite different genetic profiles.


Assuntos
Pool Gênico , Variação Genética , Herança Paterna/genética , Argélia , Humanos , Masculino
4.
Mol Genet Genomics ; 294(4): 919-930, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30929049

RESUMO

According to genetic studies, the Hungarian Y-chromosomal gene pool significantly differs from other Uralic-speaking populations. Hungarians possess a significant frequency of haplogroup R1a-Z280 and a low frequency of haplogroup N-Tat, which is common among other Uralic-speaking populations. Based on this evidence, we further worked to define the links between the linguistically related Hungarian, Mansi and Bashkirian Mari populations. Samples were collected from 45 Bashkirian Mari and 36 Southern Mansi males in the Ural region. We analyzed male-specific markers including 23 STRs and 36 SNPs, which reflect past and recent paternal genetic history. We found that the haplogroup distribution of the two population samples showed high genetic similarity to each other except for the N-Tat* and R1a-Z93 haplogroups in the Bashkirian Mari males. On the MDS plots constructed from Fst- and Rst-genetic distances, the Bashkirian Mari and Southern Mansi population groups showed close genetic affinities with the Khanty, Northern Mansi, Mari, and Estonian populations. For phylogenetic studies, networks were constructed for the most frequent haplogroups in both populations together with other Eurasian populations. Both populations shared common haplotypes within haplogroups R1a-Z280 or N-L1034 with Hungarian speakers, suggesting a common paternal genetic footprint that arose in prehistoric or historic times. Overall, the Hungarian, Mansi, and Bashkirian Mari populations have a much more complex genetic history than the traditional linguistic model or history would suggest. Further studies are needed to clarify the common genetic profiles may have been acquired directly or indirectly during the more or less known their history.


Assuntos
Cromossomos Humanos Y/genética , Grupos Étnicos/genética , Repetições de Microssatélites , Polimorfismo de Nucleotídeo Único , Pool Gênico , Genética Populacional , Haplótipos , Humanos , Hungria/etnologia , Masculino , Filogenia
6.
PLoS One ; 14(2): e0211315, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30753199

RESUMO

Nine wild Iberian provenances of Castanea sativa Mill. grouped in two gene pools, North Iberian Peninsula and Mediterranean, were evaluated for several adaptive traits in two provenance-progeny trials with the aim of evaluating the role of natural selection in shaping adaptive variation and increasing our understanding of the genetic structure of this species, as well as reporting complete information on the genetic variation among and within the studied populations. An annual growth rhythm experiment was evaluated during the first 3 years after establishment for phenology, growth, stem form and survival, and a periodic drought-stress experiment was evaluated for dry weight, growth, survival and other related drought traits in both well-watered and drought-stress treatments. The high genetic variability reported in both trials is largely due to the genetic variation among populations. The significant differences reported between quantitative genetic and neutral marker differentiation indicated the local adaptation of these populations through directional selection, mainly for phenology, growth and biomass allocation. A clinal variation among populations was determined through correlations of phenology with latitude and xerothermic index of the provenances, showing that central and southern Mediterranean populations had earlier phenology than northern populations and that drought played a relevant role in this differentiation. The significant correlation between phenological traits and the ancestry values in the Mediterranean gene pool supported the different pattern of behavior between both gene pools and also indicated the existence of two ecotypes: xeric and mesophytic ecotypes, corresponding to Mediterranean and North Iberian gene pools, respectively. The results obtained in the drought-stress experiment confirmed that, in general terms, xeric populations showed a greater adaptability to drought, with more developed root systems and higher survival than northern populations. Moreover, the genetic variability observed within populations indicated the potential response capacity of Iberian C. sativa populations to undergo fast adaptive evolution.


Assuntos
Fagaceae/genética , Variação Genética , Adaptação Fisiológica , Evolução Biológica , Biomassa , Secas , Ecótipo , Fagaceae/crescimento & desenvolvimento , Pool Gênico , Região do Mediterrâneo , Folhas de Planta/crescimento & desenvolvimento , Seleção Genética , Espanha
7.
Mol Phylogenet Evol ; 134: 172-185, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30769098

RESUMO

Zelkova species, trees of the elm family (Ulmaceae), are part of the Cenozoic relict flora. In western Eurasia, the genus comprises three species that are restricted to disjunct areas (Z. sicula on Sicily, Z. abelicea on Crete and Z. carpinifolia in Transcaucasia). The situation is different in East Asia, where three species (Z. serrata, Z. schneideriana and Z. sinica) have at least partly overlapping distributions. The phylogenetic and phylogeographic status of these East Asian species is still not well understood, mainly since all previous studies used almost exclusively plant material collected in botanical gardens and were based on very small numbers of individuals. Our study is the first based on 33 natural populations covering all important areas with Zelkova species in the Sino-Japanese Floristic Region. Chloroplast and microsatellite markers were used, and Bayesian analyses were run for both types of markers. East Asian Zelkova species cluster into two groups that partially overlap when comparing the two types of markers. For chloroplast markers, the two groups coincide with all Japanese, some Korean and northern Chinese Z. serrata in one group and all other individuals in the other group, regardless of whether they are attributed to Z. serrata, Z. sinica or Z. schneideriana from Korea, mainland China and Taiwan. At the nuclear level, however, the clustering clearly groups all the Z. serrata individuals together, regardless of whether they are from Japan, Korea or China, and the two other species in a second group. This complex genetic pattern in East Asian Zelkova species is most likely due to a combination of ancient diversification and speciation events and more recent hybridization during the last glacial/interglacial retractions and recolonizations. One of the surprising results of our study concerns the populations from Taiwan, which are genetically similar to Z. schneideriana. Thus, their assignation to a separate taxon (Z. tarokoensis) or to a variety of Z. serrata (Z. serrata var. tarokoensis), as currently reported in all local and national floras, might be in need of revision. Furthermore, our results indicate that the East Asian species are more closely related to Z. carpinifolia than to any other Western European species. Haplotypes of Z. sicula and Z. abelicea (Mediterranean region) as well as those of Z. sinica and Z. schneideriana (East Asia) seem to have diversified more recently. The most ancient haplotypes are found among the western Eurasian Z. carpinifolia and the East Asian Z. serrata. This result is in agreement with the carpinifolia and serrata-like morphotypes commonly found in the fossil record.


Assuntos
Pool Gênico , Variação Genética , Ulmaceae/classificação , Teorema de Bayes , Núcleo Celular/genética , Cloroplastos/genética , Haplótipos/genética , Repetições de Microssatélites/genética , Filogenia , Filogeografia , Especificidade da Espécie
8.
BMC Bioinformatics ; 20(Suppl 1): 35, 2019 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-30717677

RESUMO

BACKGROUND: The utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species. Biogeographical analyses can yield detailed understanding of their population biology and facilitate the geo-localization of individuals to promote their efficacious management, particularly when bred in captivity. The Geographic Population Structure (GPS) algorithm is an admixture based tool for inference of biogeographical affinities and has been employed for the geo-localization of various human populations worldwide. Here, we applied the GPS tool for biogeographical analyses and localization of the ancestral origins of wild and captive gorilla genomes, of unknown geographic source, available in the Great Ape Genome Project (GAGP), employing Gorillas with known ancestral origin as the reference data. RESULTS: Our findings suggest that GPS was successful in recapitulating the population history and estimating the geographic origins of all gorilla genomes queried and localized the wild gorillas with unknown geographical origin < 150 km of National Parks/Wildlife Reserves within the political boundaries of countries, considered as prominent modern-day abode for gorillas in the wild. Further, the GPS localization of most captive-born gorillas was congruent with their previously presumed ancestral homes. CONCLUSIONS: Currently there is limited knowledge of the ancestral origins of most North American captive gorillas, and our study highlights the usefulness of GPS for inferring ancestry of captive gorillas. Determination of the native geographical source of captive gorillas can provide valuable information to guide breeding programs and ensure their appropriate management at the population level. Finally, our findings shine light on the broader applicability of GPS for protecting the genetic integrity of other endangered non-human species, where controlled breeding is a vital component of their conservation.


Assuntos
Algoritmos , Gorilla gorilla/classificação , Filogeografia , Dinâmica Populacional , Animais , Análise por Conglomerados , Pool Gênico , Genética Populacional , Genoma , Gorilla gorilla/genética , Análise de Componente Principal
9.
PLoS One ; 13(12): e0207519, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30517116

RESUMO

History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries-a time of agricultural intensification well before the Inka and Spanish conquests-and then between the 13th century and today-a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories.


Assuntos
Chenopodium quinoa/genética , Técnicas de Genotipagem/métodos , Alelos , Argentina , Biodiversidade , DNA Antigo/análise , Pool Gênico , Variação Genética/genética , Genótipo , Técnicas de Genotipagem/história , História do Século XVIII , Sementes
10.
PLoS One ; 13(12): e0207459, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30521562

RESUMO

The compilation of archaeological and genetic data for ancient European human groups has provided persuasive evidence for a complex series of migrations, population replacements and admixture until the Bronze Age. If the Bronze-to-Iron Age transition has been well documented archaeologically, ancient DNA (aDNA) remains rare for the latter period and does not precisely reflect the genetic diversity of European Celtic groups. In order to document the evolution of European communities, we analysed 45 individuals from the Late Iron Age (La Tène) Urville-Nacqueville necropolis in northwestern France, a region recognized as a major cultural contact zone between groups from both sides of the Channel. The characterization of 37 HVS-I mitochondrial sequences and 40 haplogroups provided the largest maternal gene pool yet recovered for the European Iron Age. First, descriptive analyses allowed us to demonstrate the presence of substantial amounts of steppe-related mitochondrial ancestry in the community, which is consistent with the expansion of Bell Beaker groups bearing an important steppe legacy in northwestern Europe at approximately 2500 BC. Second, maternal genetic affinities highlighted with Bronze Age groups from Great Britain and the Iberian Peninsula regions tends to support the idea that the continuous cultural exchanges documented archaeologically across the Channel and along the Atlantic coast (during and after the Bronze Age period) were accompanied by significant gene flow. Lastly, our results suggest a maternal genetic continuity between Bronze Age and Iron Age groups that would argue in favour of a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. The palaeogenetic data gathered for the Urville-Nacqueville group constitute an important step in the biological characterization of European Iron age groups. Clearly, more numerous and diachronic aDNA data are needed to fully understand the complex relationship between the cultural and biological evolution of groups from the period.


Assuntos
DNA Mitocondrial/genética , Grupo com Ancestrais do Continente Europeu/genética , Arqueologia/métodos , DNA Antigo/análise , DNA Mitocondrial/análise , Europa (Continente)/etnologia , França/etnologia , Pool Gênico , Variação Genética/genética , Genética Populacional/métodos , Genótipo , Haplótipos , História Antiga , Humanos , Reino Unido
11.
Eur J Cancer ; 103: 205-213, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30268921

RESUMO

PURPOSE: Patients with left-sided colon tumours have better survival and respond differently to biologics compared with patients with right-sided tumours. Left-sided colon tumours and rectal cancers are often grouped together. Herein, we examined the clinicopathological differences and outcomes between left-sided colon and rectal cancers. PATIENTS AND METHODS: Data from 2879 metastatic colorectal cancer patients enrolled on six first-line clinical trials during 2004-2010 were pooled. Patients were included if the primary tumour origin was clearly defined. Progression-free survival (PFS) and overall survival (OS) were compared in the two groups after adjusting for patient and tumour characteristics, metastatic sites and the first-line regimen. RESULTS: In total, 1374 patients with metastatic left-sided colon cancer and 1505 patients with metastatic rectal cancers were evaluated. Left-sided colon cancer patients were more likely to be female (40.1% versus 32.6%; P < 0.0001) and older (31.0% ≥ 70 years versus 25.8%; P = 0.0033) compared with rectal cancers patients. Patients with left-sided colon cancer had higher rates of liver metastases (80.9% versus 72.3%, P < 0.0001) but lower rates of lung metastases (34.2% versus 53.8%, P < 0.0001). KRAS mutations were slightly less frequent among left-sided tumours (34.8% versus 40.5%; P = 0.0103). Patients with left-sided tumours had approximately similar PFS (median 7.4 versus 6.9 months; hazard ratio [HR] 0.92, 95% confidence interval [CI] 0.87-1.03; P = 0.1998) and OS (median 17.4 versus 16.6 months; HR 0.99, 95% CI 0.91-1.07; P = 0.7597) compared with rectal cancer patients. CONCLUSION: The site of tumour origin within the left side was not prognostic of outcomes. Moreover, neither bevacizumab nor cetuximab impacted, differently, the findings of the comparisons in outcomes between patients with left-sided colon tumours or rectal cancers.


Assuntos
Neoplasias do Colo/terapia , Neoplasias Retais/terapia , Neoplasias do Colo/patologia , Feminino , Pool Gênico , Humanos , Masculino , Pessoa de Meia-Idade , Neoplasias Retais/patologia
12.
BMC Plant Biol ; 18(1): 246, 2018 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-30340523

RESUMO

BACKGROUND: Crop landraces embody a source of beneficial genes potentially providing endurance to environmental stress and other agronomic qualities including yield. Our study included 88 snake melon accessions (Cucumis melo var. flexuosus) collected from 9 districts in the Palestinian West-Bank. These accessions represent four landraces of Palestinian snake melon: Green, and White Baladi, and Green, and White Sahouri. RESULTS: This is the first report on successful application of genotyping by sequencing in snake melon. Nine thousand seven hundred fifty single-nucleotide polymorphism (SNP) and 7400 DArTseq genetic markers were employed to evaluate genetic biodiversity and population structure of Palestinian snake melon germplasm collection. Clustering based on neighbor-joining-analysis, principle coordinate and Bayesian model implemented in Structure showed that patterns of genetic diversity of snake melon landraces depends on their geographical source and unraveled the presence of two major local landraces (Sahouri, and Baladi) with accessions from each group clustering together. A significant correlation was observed between both types of markers in Mantel correlation test. A significant association between genetic and geographic matrices (P < 0.0001) was also detected. AMOVA indicated that majority of variation (90%) was due to the difference within accessions. CONCLUSION: The Palestinian landraces seem to have unique genes that may allow the enhancement of the global snake melon gene pool and developments of the plant production worldwide. Our subsequent objective is to detect genotypes with promising qualities and to conduct association mapping studies concentrating on Fusarium-wilt resistance, yield, and environmental stresses.


Assuntos
Cucumis melo/genética , Variação Genética , Polimorfismo de Nucleotídeo Único/genética , Teorema de Bayes , Pool Gênico , Marcadores Genéticos , Genótipo , Geografia , Análise de Sequência de DNA
13.
PLoS One ; 13(10): e0205363, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30308006

RESUMO

Turkey presents a great diversity of common bean landraces in farmers' fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2-3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.


Assuntos
Pool Gênico , Phaseolus/anatomia & histologia , Sequenciamento Completo do Genoma/métodos , Genes de Plantas , Variação Genética , Phaseolus/genética , Fenótipo , Filogenia , Melhoramento Vegetal , Turquia
14.
PLoS One ; 13(10): e0205920, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30335830

RESUMO

It has been widely accepted that the Finno-Ugric Hungarian language, originated from proto Uralic people, was brought into the Carpathian Basin by the conquering Hungarians. From the middle of the 19th century this view prevailed against the deep-rooted Hungarian Hun tradition, maintained in folk memory as well as in Hungarian and foreign written medieval sources, which claimed that Hungarians were kinsfolk of the Huns. In order to shed light on the genetic origin of the Conquerors we sequenced 102 mitogenomes from early Conqueror cemeteries and compared them to sequences of all available databases. We applied novel population genetic algorithms, named Shared Haplogroup Distance and MITOMIX, to reveal past admixture of maternal lineages. Our results show that the Conquerors assembled from various nomadic groups of the Eurasian steppe. Population genetic results indicate that they had closest connection to the Onogur-Bulgar ancestors of Volga Tatars. Phylogenetic results reveal that more than one third of the Conqueror maternal lineages were derived from Central-Inner Asia and their most probable ultimate sources were the Asian Scythians and Asian Huns, giving support to the Hungarian Hun tradition. The rest of the lineages most likely originated from the Bronze Age Potapovka-Poltavka-Srubnaya cultures of the Pontic-Caspian steppe. Available data imply that the Conquerors did not have a major contribution to the gene pool of the Carpathian Basin.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Genoma Mitocondrial , Filogenia , Cemitérios , Pool Gênico , Genética Populacional , Geografia , Migração Humana , Humanos , Hungria , Crânio/anatomia & histologia
15.
Sci Rep ; 8(1): 11422, 2018 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-30061702

RESUMO

Cuba is the most populated country in the Caribbean and has a rich and heterogeneous genetic heritage. Here, we take advantage of dense genomic data from 860 Cuban individuals to reconstruct the genetic structure and ancestral origins of this population. We found distinct admixture patterns between and within the Cuban provinces. Eastern provinces have higher African and Native American ancestry contributions (average 26% and 10%, respectively) than the rest of the Cuban provinces (average 17% and 5%, respectively). Furthermore, in the Eastern Cuban region, we identified more intense sex-specific admixture patterns, strongly biased towards European male and African/Native American female ancestries. Our subcontinental ancestry analyses in Cuba highlight the Iberian population as the best proxy European source population, South American and Mesoamerican populations as the closest Native American ancestral component, and populations from West Central and Central Africa as the best proxy sources of the African ancestral component. Finally, we found complex admixture processes involving two migration pulses from both Native American and African sources. Most of the inferred Native American admixture events happened early during the Cuban colonial period, whereas the African admixture took place during the slave trade and more recently as a probable result of large-scale migrations from Haiti.


Assuntos
Demografia , Genética Populacional , Cuba , Feminino , Pool Gênico , Variação Genética , Hispano-Americanos/genética , Migração Humana , Humanos , Masculino , Fatores de Tempo
16.
Proc Natl Acad Sci U S A ; 115(30): 7771-7776, 2018 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-29987016

RESUMO

New Zealand's geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans 750 y ago, its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and timing of past extinctions. The exact temporal and spatial dynamics of New Zealand's extinct fauna, however, can be difficult to interpret, as only a small proportion of animals are preserved as morphologically identifiable fossils. Here, we conduct a large-scale genetic survey of subfossil bone assemblages to elucidate the impact of humans on the environment in New Zealand. By genetically identifying more than 5,000 nondiagnostic bone fragments from archaeological and paleontological sites, we reconstruct a rich faunal record of 110 species of birds, fish, reptiles, amphibians, and marine mammals. We report evidence of five whale species rarely reported from New Zealand archaeological middens and characterize extinct lineages of leiopelmatid frog (Leiopelma sp.) and kakapo (Strigops habroptilus) haplotypes lost from the gene pool. Taken together, this molecular audit of New Zealand's subfossil record not only contributes to our understanding of past biodiversity and precontact Maori subsistence practices but also provides a more nuanced snapshot of anthropogenic impacts on native fauna after first human arrival.


Assuntos
Biodiversidade , Osso e Ossos , DNA/genética , Fósseis , Pool Gênico , Animais , DNA/química , DNA/isolamento & purificação , Nova Zelândia
17.
Environ Microbiol ; 20(12): 4401-4414, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30033663

RESUMO

Bulk soil and rhizosphere are soil compartments selecting different microbial communities. However, it is unknown whether this selection also can change the genome content of specific bacterial taxa, splitting a population in distinct ecotypes. To answer this question we compared the genome sequences of 53 isolates obtained from sugarcane rhizosphere (28) and bulk soil (25). These isolates were previously classified in the Pseudomonas koreensis subgroup of the P. fluorescens complex. Phylogenomics showed a trend of separation between bulk soil and rhizosphere isolates. Discriminant analysis of principal components (DAPC) identified differences in the accessory genome of rhizosphere and bulk soil sub-populations. We found significant changes in gene frequencies distinguishing rhizosphere from bulk soil ecotypes, for example, enrichment of phosphatases and xylose utilization (xut) genes, respectively. Phenotypic assays and deletion of xutA gene indicated that accumulation of xut genes in the bulk soil sub-population provided a higher growth capacity in a d-xylose medium, supporting the corresponding genomic differences. Despite the clear differences distinguishing the two ecotypes, all 53 isolates were classified in a single 16S rRNA gene OTU. Collectively, our results revealed that the gene pool and ecological behavior of a bacterial population can be different for ecotypes living in neighbouring soil habitats.


Assuntos
Variação Genética , Pseudomonas/genética , Rizosfera , Microbiologia do Solo , Ecótipo , Pool Gênico , Microbiota , Raízes de Plantas/microbiologia , RNA Ribossômico 16S/genética , Solo
18.
Plant Genome ; 11(2)2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-30025015

RESUMO

Genomic selection (GS) has revolutionized breeding for quantitative traits in plants, offering potential to optimize resource allocation in breeding programs and increase genetic gain per unit of time. Modern high-density single nucleotide polymorphism (SNP) arrays comprising up to several hundred thousand markers provide a user-friendly technology to characterize the genetic constitution of whole populations and for implementing GS in breeding programs. However, GS does not build upon detailed genotype profiling facilitated by maximum marker density. With extensive genome-wide linkage disequilibrium (LD) being a common characteristic of breeding pools, fewer representative markers from available high-density genotyping platforms could be sufficient to capture the association between a genomic region and a phenotypic trait. To examine the effects of reduced marker density on genomic prediction accuracy, we collected data on three traits across 2 yr in a panel of 203 homozygous Chinese semiwinter rapeseed ( L.) inbred lines, broadly encompassing allelic variability in the Asian genepool. We investigated two approaches to selecting subsets of markers: a trait-dependent strategy based on genome-wide association study (GWAS) significance thresholds and a trait-independent method to detect representative tag SNPs. Prediction accuracies were evaluated using cross-validation with ridge-regression best linear unbiased predictions (rrBLUP). With semiwinter rapeseed as a model species, we demonstrate that low-density marker sets comprising a few hundred to a few thousand markers enable high prediction accuracies in breeding populations with strong LD comparable to those achieved with high-density arrays. Our results are valuable for facilitating routine application of cost-efficient GS in breeding programs.


Assuntos
Brassica napus/genética , Marcadores Genéticos , Melhoramento Vegetal/métodos , China , Pool Gênico , Genoma de Planta , Estudo de Associação Genômica Ampla , Fenótipo , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
19.
Plant Genome ; 11(2)2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-30025029

RESUMO

Common bean ( L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to , (A. Gray), and L. were sequenced by whole-genome sequencing, identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between and the two other domesticated species, but also within , affecting hundreds of protein-coding genomic regions. A large number of inter-gene pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed single nucleotide polymorphism markers within previously discovered quantitative trait loci for common bacterial blight and angular leaf spot provides improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.


Assuntos
Pool Gênico , Variação Genética , Phaseolus/genética , Variações do Número de Cópias de DNA , DNA de Plantas , Resistência à Doença/genética , Genoma de Planta , Sequenciamento de Nucleotídeos em Larga Escala , Melhoramento Vegetal , Doenças das Plantas/genética , Polimorfismo de Nucleotídeo Único
20.
Science ; 360(6392): 1028-1032, 2018 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-29853688

RESUMO

Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.


Assuntos
Evolução Biológica , Deriva Genética , Genoma Humano , População/genética , DNA Antigo , Feminino , Efeito Fundador , Pool Gênico , Genótipo , Humanos , Islândia , Masculino , Fenótipo
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