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1.
J Hum Evol ; 173: 103268, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36288639

RESUMO

Recent studies have shown that global variation in body proportions is more complex than previously thought as some traits formerly associated with climate adaptation are better explained by geographic proximity and neutral evolutionary forces. While the recent incorporation of quantitative genetic methodologies has improved understanding of patterns related to climate in Africa, Europe, and the Americas, Asia remains underrepresented in recent and historic studies of body form. As ecogeographic studies tend to focus on male morphology, potential sex differences in features influenced by climate remain largely unexplored. Skeletal measurements encompassing the dimensions of the skull, pelvis, limbs, hands, and feet were collected from male (n = 459) and female (n = 442) remains curated in 13 collections across seven countries in East Asia (n = 901). Osteological data were analyzed with sex and minimum temperature as covariates adjusted by autosomal single-nucleotide polymorphism population genetic distance using univariate Bayesian linear mixed models, and credible intervals were calculated for each trait. Analysis supports a relationship between specific traits and climate as well as providing the magnitude of response in both sexes. After accounting for genetic distance between populations, greater association between climate and morphology was found in postcranial traits, with the relationship between climate and the skull limited primarily to breadth measurements. Larger body size is associated with colder climates with most measurements increasing with decreased temperature. The same traits were not always associated with climate for males and females nor correlated with the same intensity for both sexes. The varied directional association with climate for different regions of the skeleton and between the sexes underscores the necessity of future ecogeographic research to holistically evaluate body form and to look for sex-specific patterns to better understand population responses to environmental stresses.


Assuntos
Clima , Crânio , Feminino , Masculino , Humanos , Teorema de Bayes , Crânio/anatomia & histologia , Deriva Genética , Clima Frio
2.
Cell ; 185(11): 1842-1859.e18, 2022 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-35561686

RESUMO

The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.


Assuntos
Fazendeiros , Genoma , Agricultura , DNA Mitocondrial/genética , Europa (Continente) , Deriva Genética , Genômica , História Antiga , Migração Humana , Humanos
3.
Sci Rep ; 11(1): 17985, 2021 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-34504229

RESUMO

This study clarifies the role of refugia and landscape permeability in the formation of the current genetic structure of peoples of the Caucasus. We report novel genome-wide data for modern individuals from the Caucasus, and analyze them together with available Paleolithic and Mesolithic individuals from Eurasia and Africa in order (1) to link the current and ancient genetic structures via landscape permeability, and (2) thus to identify movement paths between the ancient refugial populations and the Caucasus. The ancient genetic ancestry is best explained by landscape permeability implying that human movement is impeded by terrain ruggedness, swamps, glaciers and desert. Major refugial source populations for the modern Caucasus are those of the Caucasus, Anatolia, the Balkans and Siberia. In Rugged areas new genetic signatures take a long time to form, but once they do so, they remain for a long time. These areas act as time capsules harboring genetic signatures of ancient source populations and making it possible to help reconstruct human history based on patterns of variation today.


Assuntos
Genoma Humano , Genômica/métodos , Genótipo , Migração Humana/história , População Branca/genética , Cromossomos Humanos Y/genética , DNA/genética , DNA/isolamento & purificação , Bases de Dados Genéticas , Deriva Genética , Variação Genética , República da Geórgia , História do Século XXI , História Antiga , Humanos , Masculino , Linhagem , Refugiados/história , Federação Russa , Turquia
4.
Proc Natl Acad Sci U S A ; 118(17)2021 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-33875589

RESUMO

Wind disperses the pollen and seeds of many plants, but little is known about whether and how it shapes large-scale landscape genetic patterns. We address this question by a synthesis and reanalysis of genetic data from more than 1,900 populations of 97 tree and shrub species around the world, using a newly developed framework for modeling long-term landscape connectivity by wind currents. We show that wind shapes three independent aspects of landscape genetics in plants with wind pollination or seed dispersal: populations linked by stronger winds are more genetically similar, populations linked by directionally imbalanced winds exhibit asymmetric gene flow ratios, and downwind populations have higher genetic diversity. For each of these distinct hypotheses, partial correlations between the respective wind and genetic metrics (controlling for distance and climate) are positive for a significant majority of wind-dispersed or wind-pollinated genetic data sets and increase significantly across functional groups expected to be increasingly influenced by wind. Together, these results indicate that the geography of both wind strength and wind direction play important roles in shaping large-scale genetic patterns across the world's forests. These findings have implications for various aspects of basic plant ecology and evolution, as well as the response of biodiversity to future global change.


Assuntos
Fluxo Gênico/genética , Variação Genética/genética , Árvores/genética , Biodiversidade , Ecossistema , Florestas , Deriva Genética , Genética Populacional , Repetições de Microssatélites/genética , Pólen/genética , Polinização/genética , Dispersão de Sementes/fisiologia , Sementes/genética , Árvores/crescimento & desenvolvimento , Vento
5.
Proc Natl Acad Sci U S A ; 118(13)2021 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-33753512

RESUMO

Island Southeast Asia has recently produced several surprises regarding human history, but the region's complex demography remains poorly understood. Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least ∼8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines ∼2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive "out-of-Taiwan" model of farming-language-people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting ∼1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.


Assuntos
Migração Humana/história , Grupos Populacionais/história , Agricultura , Sudeste Asiático/etnologia , Austrália/etnologia , Feminino , Deriva Genética , Genômica , História Antiga , Humanos , Masculino , Oryza , Filipinas , Grupos Populacionais/genética , Taiwan/etnologia
6.
Sci Rep ; 11(1): 3045, 2021 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-33542324

RESUMO

Calabrian Greeks are an enigmatic population that have preserved and evolved a unique variety of language, Greco, survived in the isolated Aspromonte mountain area of Southern Italy. To understand their genetic ancestry and explore possible effects of geographic and cultural isolation, we genome-wide genotyped a large set of South Italian samples including both communities that still speak Greco nowadays and those that lost the use of this language earlier in time. Comparisons with modern and ancient populations highlighted ancient, long-lasting genetic links with Eastern Mediterranean and Caucasian/Near-Eastern groups as ancestral sources of Southern Italians. Our results suggest that the Aspromonte communities might be interpreted as genetically drifted remnants that departed from such ancient genetic background as a consequence of long-term isolation. Specific patterns of population structuring and higher levels of genetic drift were indeed observed in these populations, reflecting geographic isolation amplified by cultural differences in the groups that still conserve the Greco language. Isolation and drift also affected the current genetic differentiation at specific gene pathways, prompting for future genome-wide association studies aimed at exploring trait-related loci that have drifted up in frequency in these isolated groups.


Assuntos
Cromossomos Humanos Y/genética , DNA Mitocondrial/genética , Genética Populacional , Genoma Humano/genética , DNA Antigo/análise , Deriva Genética , Genótipo , Grécia , Haplótipos/genética , História Antiga , Humanos , Itália , Idioma , População Branca/genética
7.
C R Biol ; 343(1): 63-72, 2020 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-32720489

RESUMO

Xanthium italicum is an aggressive weed found worldwide. Despite several ecological, morphological, and physiological research on its invasion mechanism, the mechanism of its successful invasion has not been revealed from the viewpoint of population genetics. Thus, we aimed to evaluate the genetic variation within and among populations of the alien invasive weed X. italicum in China, and to provide a theoretical basis for its invasion mechanism. For that, we employed inter-simple sequence repeat (ISSR) markers to explore the genetic diversity and genetic differentiation of 185 individuals sampled from 10 populations. Eight selected primers yielded a total of 76 bright and discernible bands. X. italicum showed an intermediate genetic diversity at the population level (percentage of polymorphic loci (PPL) = 60.26%, Nei's genetic diversity (H) = 0.2098, Shannon's information index (I) = 0.3129). However, the genetic diversity at the species level was significantly high (PPL = 100%; H = 0.3673; I = 0.5425). The coefficient of gene differentiation (GST, 41.4%) and analysis of molecular variance showed that genetic differentiation mainly occurred within populations. The estimated gene flow (Nm, 0.7085) and Mantel test indicated that genetic differentiation in the populations may primarily come from genetic drift and anthropogenic activities. Our results revealed the high genetic diversity of X. italicum, which may help explain its invasion success in China. This knowledge may contribute to the efforts for decreasing and eventually stopping X. italicum invasion in China.


Xanthium italicum est une plante envahissante trouvée dans le monde entier. En dépit de quelques recherches écologiques, morphologiques et physiologiques à propos de son mécanisme d'invasion, le mécanisme de son invasion réussie n'a pas encore été révélé du point de vue de la génétique démographique. Donc, nous avons visé à évaluer la variation génétique au sein de et parmi les populations de plante exotique envahissante X. italicum en Chine, et à offrir une base théorique à son mécanisme d'invasion. À cet effet, nous avons employé des marqueurs des répétitions de séquences inter-simples (ISSR) afin d'explorer la diversité génétique et la différenciation génétique de 185 individus échantillonnés à partir de 10 populations. Huit amorces sélectionnées ont donné un total de 76 bandes brillantes et perceptibles. X. italicum a montré une diversité génétique intermédiaire au niveau de la population (pourcentage de loci polymorphe (PPL) = 60.26%, la diversité génétique de Nei (H) = 0.2098, l'indice d'information de Shannon (I) = 0.3129). Toutefois, la diversité génétique était considérablement élevée au niveau des espèces (PPL = 100% ; H = 0.3673 ; I = 0.5425). Tant le coefficient de différenciation génétique (GST, 41.4%) que l'analyse de la variance moléculaire ont reflété que la différenciation génétique se produisait principalement au sein des populations. En fonction du flux génétique estimé (Nm, 0.7085) et du test Mantel, la différenciation génétique au sein des populations pourrait provenir principalement de la dérive génétique et des activités anthropiques. Nos résultats ont révélé la haute diversité génétique de X. italicum, cela peut aider à expliquer son succès d'invasion en Chine. Ces connaissances pourraient contribuer à la réduction et à l'arrêt éventuel de l'invasion de X. italicum en Chine.


Assuntos
Variação Genética , Plantas Daninhas/genética , Xanthium/genética , China , Primers do DNA , Deriva Genética , Genética Populacional , Humanos , Repetições de Microssatélites , Filogenia
8.
Sci Adv ; 5(9): eaaw3492, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31517044

RESUMO

European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.


Assuntos
DNA Antigo , Bases de Dados Genéticas , Deriva Genética , Genoma Humano , População Branca/genética , Animais , Estudo de Associação Genômica Ampla , História Antiga , Genética Humana , Humanos , Itália , Homem de Neandertal/genética
9.
Curr Biol ; 29(14): 2430-2441.e10, 2019 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-31303491

RESUMO

The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.


Assuntos
DNA Antigo/análise , DNA Mitocondrial/análise , Deriva Genética , Migração Humana , Arqueologia , Etnicidade/genética , Genoma Humano , História Antiga , Humanos , Masculino , Ucrânia
10.
Sci Rep ; 9(1): 1202, 2019 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-30718743

RESUMO

The tea green leafhopper, Empoasca (Matsumurasca) onukii Matsuda, is one of the dominant pests in major tea production regions of East Asia. Recent morphological studies have revealed variation in the male genitalic structures within and among populations. However, the genetic structure of this pest remains poorly understood. This study explores the genetic diversity and population structure of this pest in nineteen populations from the four main Chinese tea production areas using microsatellite markers, with one Japanese population also examined. The results show low to moderate levels of genetic differentiation with populations grouped into four clusters, i.e. the Jiangbei group, the Southwest group 1, the Southwest group 2 and the South China group. Populations from China have a close phylogenetic relationship but show significant isolation by distance. Lower genetic diversity and genetic differentiation of E. (M.) onukii were found in the Kagoshima population of Japan. Evidence for genetic bottlenecks was detected in the South China and Jiangnan populations. Population expansion was found in the Southwest, Jiangbei and Kagoshima populations. This is the most extensive study of the population genetics of this species and contributes to our understanding of its origin and evolutionary history.


Assuntos
Genética Populacional/métodos , Hemípteros/genética , Hemípteros/metabolismo , Animais , China , Deriva Genética , Variação Genética , Repetições de Microssatélites/genética , Filogenia , Chá
11.
Sci Adv ; 4(10): eaat4457, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30417088

RESUMO

For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.


Assuntos
Genoma Humano/genética , Migração Humana/história , Ásia , Cromossomos Humanos Y , DNA Mitocondrial , Europa (Continente) , Ásia Oriental , Deriva Genética , Genética Populacional , Haplótipos , História Antiga , Humanos , Masculino , População Branca/genética
12.
Sci Rep ; 8(1): 14879, 2018 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-30291256

RESUMO

Ancient DNA genome-wide analyses of Neolithic individuals from central and southern Europe indicate an overall population turnover pattern in which migrating farmers from Anatolia and the Near East largely replaced autochthonous Mesolithic hunter-gatherers. However, the genetic history of the Neolithic transition in areas lying north of the European Neolithic core region involved different levels of admixture with hunter-gatherers. Here we analyse genome-wide data of 17 individuals spanning from the Middle Neolithic to the Early Bronze Age (4300-1900 BCE) in order to assess the Neolithic transition in north-central Poland, and the local impacts of hunter-farmer contacts and Late Neolithic steppe migrations. We evaluate the influence of these on local populations and assess if and how they change through time, reporting evidence of recurrent hunter-farmer admixture over three millennia, and the co-existence of unadmixed hunter-gatherers as late as 4300 BCE. During the Late Neolithic we report the appearance of steppe ancestry, but on a lesser scale than previously described for other central European regions, with evidence of stronger affinities to hunter-gatherers than to steppe pastoralists. These results help understand the Neolithic palaeogenomics of another central European area, Kuyavia, and highlight the complexity of population interactions during those times.


Assuntos
Migração Humana , Agricultura/história , Arqueologia , Cromossomos Humanos Y/genética , DNA Antigo/análise , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Europa (Continente) , Fazendeiros , Deriva Genética , Genética Populacional , Genoma Humano , Estudo de Associação Genômica Ampla , Genômica , História Antiga , Humanos , Oriente Médio , Polônia
13.
Vaccine ; 36(43): 6383-6392, 2018 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-30224200

RESUMO

Influenza virus hemagglutinin (HA) and neuraminidase (NA) proteins elicit protective antibody responses and therefore, are used as targets for vaccination, especially the HA protein. However, these proteins are subject to antigenic drift, decreasing vaccine efficacy, and few to no studies have analyzed antigenic variability of these proteins by growing the viruses under immune pressure provided by human sera. In this work, we show that after growing different influenza virus strains under immune pressure, the selection of amino acid changes in the NA protein is much more limited than the selection in the HA protein, suggesting that the NA protein could remain more conserved under immune pressure. Interestingly, all the mutations in the HA and NA proteins affected protein antigenicity, and many of the selected amino acid changes were located at the same positions found in viruses circulating. These studies could help to inform HA and NA protein residues targeted by antibody responses after virus infection in humans and are very relevant to update the strains used for influenza virus vaccination each year and to improve the currently available vaccines.


Assuntos
Aminoácidos/genética , Variação Antigênica/genética , Deriva Genética , Glicoproteínas de Hemaglutininação de Vírus da Influenza/genética , Neuraminidase/genética , Anticorpos Antivirais/sangue , Monitoramento Epidemiológico , Células HEK293 , Glicoproteínas de Hemaglutininação de Vírus da Influenza/imunologia , Humanos , Vírus da Influenza A Subtipo H1N1 , Vírus da Influenza A Subtipo H3N2 , Vacinas contra Influenza/imunologia , Influenza Humana/prevenção & controle , Neuraminidase/imunologia , Seleção Genética
14.
Plant Dis ; 102(11): 2074-2082, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30156961

RESUMO

Annual epidemics of Cercospora leaf spot (CLS), caused by the fungus Cercospora beticola, can result in substantial defoliation in table beet fields in New York. High allelic and genotypic diversity have been described within C. beticola populations; however, information on the temporal stability of populations is lacking. C. beticola isolates were obtained from symptomatic leaves in three table beet fields in successive years. Two of the fields were organic mixed-cropping farms and the third was managed conventionally in a broad-acre cropping system. C. beticola isolates (n = 304) were genotyped using 12 microsatellite markers. Genotypic diversity (Simpson's complement index = 0.178 to 0.990), allele frequencies, and indices of differentiation between years varied. Pairwise index of differentiation values ranged from 0.02 to 0.25 for clone-corrected data, and indicated significant genetic differentiation at Farm 2. No multilocus genotype was shared between years. The shift in multilocus genotypes between years questions the role of clonally reproducing primary inoculum. Collectively, these results suggest that a dominant inoculum source for initiating annual CLS epidemics is external to the field of interest. These findings have implications for CLS disease management in conventional and organic table beet production.


Assuntos
Ascomicetos/genética , Beta vulgaris/microbiologia , Variação Genética , Genética Populacional , Doenças das Plantas/microbiologia , Ascomicetos/isolamento & purificação , Ascomicetos/fisiologia , Frequência do Gene , Genes Fúngicos Tipo Acasalamento/genética , Deriva Genética , Genótipo , Técnicas de Genotipagem , Repetições de Microssatélites/genética , Tipagem de Sequências Multilocus , Técnicas de Tipagem Micológica , New York , Folhas de Planta/microbiologia
15.
Science ; 360(6396)2018 06 29.
Artigo em Inglês | MEDLINE | ID: mdl-29743352

RESUMO

The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.


Assuntos
Povo Asiático/genética , Domesticação , Deriva Genética , Genoma Humano , Cavalos , Migração Humana/história , Animais , Ásia , Cromossomos Humanos Y/genética , DNA Antigo , DNA Mitocondrial/genética , Europa (Continente) , Pradaria , História Antiga , Humanos , Idioma , Sequenciamento Completo do Genoma
16.
J Virol ; 91(16)2017 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-28592544

RESUMO

RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid).IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes.


Assuntos
Evolução Molecular , Deriva Genética , Genética Populacional , Potyvirus/classificação , Potyvirus/crescimento & desenvolvimento , Solanum tuberosum/virologia , Resistência à Doença , Interações Hospedeiro-Patógeno , Polimorfismo de Nucleotídeo Único , Potyvirus/genética , Solanum tuberosum/imunologia , Fatores de Tempo
17.
J Hered ; 108(4): 415-423, 2017 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-28369406

RESUMO

Varronia curassavica is an important medicinal species associated with the restinga, one of the most threatened coastal ecosystems of the Atlantic Forest. These circumstances call for studies aimed at estimating effective population size and gene flow to improve conservation efforts. Hence, the present study aimed to characterize the genetic diversity, ploidy level, and population structure of this species in different areas of restinga using microsatellites. Varronia curassavica was characterized as an autotetraploid, with high genetic variability, low divergence, and no significant fixation indices, indicating the absence of, or reduced, inbreeding and genetic drift in the study area. About 44% of the alleles occurred at low frequency in adults of all populations and 41% in the progenies evaluated. Gene flow was high, consistent with outcrossing species with high dispersal capacity (Nm = 4.87). The results showed no tendency toward isolation by distance. The estimated effective size indicates that the populations studied have the potential to ensure conservation of the species in the long term. The genetic variability and population structure of V. curassavica, as determined in this study, could form the foundation for activities directed toward the sustainable use of this resource and its conservation. Even though the restinga ecosystem has suffered dramatic reductions in area, this study provides evidence that this species is resilient to anthropogenic threats to its genetic integrity, since it is a polyploid with self-incompatibility mechanisms that contribute to maintaining high genetic diversity in an panmictic meta-population along the coast of Santa Catarina.


Assuntos
Florestas , Variação Genética , Genética Populacional , Magnoliopsida/genética , Poliploidia , Alelos , Brasil , Fluxo Gênico , Frequência do Gene , Deriva Genética , Endogamia , Repetições de Microssatélites , Plantas Medicinais/genética , Densidade Demográfica
18.
Infect Genet Evol ; 47: 1-8, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27847329

RESUMO

For thousands of years human beings have resisted life-threatening pathogens. This ongoing battle is considered to be the major force shaping our gene pool as every micro-evolutionary process provokes specific shifts in the genome, both that of the host and the pathogen. Past populations were more susceptible to changes in allele frequencies not only due to selection pressure, but also as a result of genetic drift, migration and inbreeding. In the present study we have investigated the frequency of five polymorphisms within innate immune-response genes (SLC11A1 D543N, MBL2 G161A, P2RX7 A1513C, IL10 A-1082G, TLR2 -196 to -174 ins/del) related to susceptibility to infections in humans. The DNA of individuals from two early Roman-Period populations of Linowo and Rogowo was analysed. The distribution of three mutations varied significantly when compared to the modern Polish population. The TAFT analysis suggests that the decreased frequency of SLC11A1 D543N in modern Poles as compared to 2nd century Linowo samples is the result of non-stochastic mechanisms, such as purifying or balancing selection. The disparity in frequency of other mutations is most likely the result of genetic drift, an evolutionary force which is remarkably amplified in low-size groups. Together with the FST analysis, mtDNA haplotypes' distribution and deviation from the Hardy-Weinberg equilibrium, we suggest that the two populations were not interbreeding (despite the close proximity between them), but rather inbreeding, the results of which are particularly pronounced among Rogowo habitants.


Assuntos
Doenças Transmissíveis/genética , DNA Antigo/análise , Predisposição Genética para Doença/genética , Proteínas de Transporte de Cátions/genética , Deriva Genética , História Antiga , Humanos , Imunidade Inata/genética , Polônia , Polimorfismo de Nucleotídeo Único/genética , Mundo Romano
19.
Genet Mol Res ; 15(2)2016 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-27323174

RESUMO

Sinopodophyllum hexandrum is an important medicinal plant that has been listed as an endangered species, making the conservation of its genetic diversity a priority. Therefore, the genetic diversity and population structure of S. hexandrum was investigated through inter-simple sequence repeat analysis of eight natural populations. Eleven selected primers generated 141 discernible fragments. The percentage of polymorphic bands was 37.59% at the species level, and 7.66-24.32% at the population level. Genetic diversity of S. hexandrum was low within populations (average HE = 0.0366), but higher at the species level (HE = 0.0963). Clear structure and high genetic differentiation were detected between populations using unweighted pair groups mean arithmetic and principle coordinate analysis. Clustering approaches clustered the eight sampled populations into three major groups, and AMOVA confirmed there to be significant variation between populations (63.27%). Genetic differentiation may have arisen through limited gene flow (Nm = 0.3317) in this species. Isolation by distance among populations was determined by comparing genetic distance versus geographical distance using the Mantel test. The results revealed no correlation between spatial pattern and geographic location. Given the low within-population genetic diversity, high differentiation among populations, and the increasing anthropogenic pressure on this species, in situ conservation measures, in addition to sampling and ex situ preservation, are recommended to preserve S. hexandrum populations and to retain their genetic diversity.


Assuntos
Berberidaceae/genética , Variação Genética , Repetições de Microssatélites/genética , Filogeografia , Berberidaceae/crescimento & desenvolvimento , Conservação dos Recursos Naturais , Espécies em Perigo de Extinção , Deriva Genética , Genética Populacional
20.
Genet Mol Res ; 15(2)2016 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-27173347

RESUMO

Mixed linear models have been used for the analysis of the genetic diversity and provided further accurate results in crops such as eucalyptus, castor, and sugarcane. However, to date, research that combined this analysis with Ward-MLM procedure has not been reported. Therefore, the aim of the present study was to identify divergent coffee genotypes by Ward-MLM procedure, in association with the mixed-decision models. The experiment was initiated in February 2007, in the northwestern Rio de Janeiro State. The 25 evaluated genotypes were grown with a spacing of 2.5 x 0.8 m, in a randomized block design, with 5 replications, containing 8 plants each. The following agronomic traits were evaluated: plant height, stem diameter, plagiotropic branch number, and productivity. Four measurements were performed for each character from 2009 to 2012, between May and July. Data were analyzed using REML/BLUP analysis and Ward- MLM procedure. The Ward-MLM procedure in association with mixed linear models demonstrated the genetic variability among the studied coffee genotypes. We identified two groups of most divergent coffee genotypes, which can be combined by crossings and selections in order to obtain genotypes with high productivity and variability.


Assuntos
Café/genética , Modelos Genéticos , Produtos Agrícolas/genética , Deriva Genética , Variação Genética , Genótipo , Fenótipo , Melhoramento Vegetal , Característica Quantitativa Herdável
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