共查询到20条相似文献,搜索用时 0 毫秒
1.
2.
Marcelo Bertellotti José A. Donázar Guillermo Blanco Manuela G. Forero 《Biodiversity and Conservation》2003,12(4):743-747
Guanay cormorants Phalacrocorax bougainvilli aredistributed mostly on the Pacific coast of Peru and northern Chile. A smallpopulation of around 50 pairs was described on the Patagonian Atlantic coast inthe late 1960s. Further records have revealed a progressive decrease of thispopulation. During 1999 we looked for guanay cormorants at those Atlanticcolonies where the species was recorded in the past. Only four individuals weredetected in one colony (Punta Lobería), and all of them were mated withking cormorants P. albiventer. In addition, we recordedhybrids between guanay and king cormorants mated with pure king and imperialcormorants P. atriceps. Causes of the population declineare unknown. Since guanay cormorants inhabiting the Atlantic coast could be agenetically differentiated population, we emphasize the need for molecularstudies. If genetic polymorphism is detected, the capture of remnant individualsin order to constitute a genetic stock should be considered. 相似文献
3.
4.
5.
Naama M. Kopelman Jonathan Mayzel Mattias Jakobsson Noah A. Rosenberg Itay Mayrose 《Molecular ecology resources》2015,15(5):1179-1191
The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population‐genetic data analysis. Application of model‐based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model‐based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp . Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak , available at http://clumpak.tau.ac.il , simplifies the use of model‐based analyses of population structure in population genetics and molecular ecology. 相似文献
6.
Seldin MF Tian C Shigeta R Scherbarth HR Silva G Belmont JW Kittles R Gamron S Allevi A Palatnik SA Alvarellos A Paira S Caprarulo C Guillerón C Catoggio LJ Prigione C Berbotto GA García MA Perandones CE Pons-Estel BA Alarcon-Riquelme ME 《American journal of physical anthropology》2007,132(3):455-462
Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. 相似文献
7.
8.
9.
Bonilla C Gutiérrez G Parra EJ Kline C Shriver MD 《American journal of physical anthropology》2005,128(4):861-869
We studied 156 individuals of Native American descent from the city of Tlapa in the state of Guerrero in western Mexico. Most individuals' ethnicity was either Nahua, Mixtec, or Tlapanec, but self-identified Mestizos and individuals of mixed ethnicities were also included in the sample. We typed 24 autosomal, one Y-chromosome, and four mitochondrial ancestry-informative markers (AIMs) to estimate group and individual admixture proportions, and determine whether the admixture process involved directional gene flow between parental groups. When genetically defined (GD) Mestizos were excluded from the analysis, Native American ancestry represented approximately 98% of the population's gene pool, while European and West African ancestry represented approximately 1% each. Maternally inherited markers also showed an exceptionally high Native American contribution (98.5%), as did the paternally inherited marker, DYS199 (90.7%). We did not detect genetic structure in this population using these AIMs, which appears consistent with the homogeneity of the sample in terms of admixture proportions. The addition of GD Mestizos to the sample did not produce a considerable change in admixture estimates, but it had a major effect on population structure. These results show that the population of Tlapa in Guerrero, Mexico, has experienced little admixture with Europeans and/or West Africans. They also show that the impact of a small number of admixed individuals on an otherwise homogeneous population might have profound implications on subsequent ancestry/phenotype analysis and mapping strategies. We suggest that heterogeneity is a major characteristic of Mexican populations and, as a consequence, should not be disregarded when designing epidemiological studies of Mexican and Mexican American populations. 相似文献
10.
11.
Katherine S Elliott Marc Haber Hinda Daggag George B Busby Rizwan Sarwar Derek Kennet Michael Petraglia Lawrence J Petherbridge Parisa Yavari Frauke U Heard-Bey Bindu Shobi Tariq Ghulam Dalia Haj Alia Al Tikriti Alshafi Mohammad Suma Antony Maitha Alyileili Shatha Alaydaroos Evelyn Lau Mark Butler Arash Yavari Julian C Knight Houman Ashrafian Maha T Barakat 《Molecular biology and evolution》2022,39(3)
The indigenous population of the United Arab Emirates (UAE) has a unique demographic and cultural history. Its tradition of endogamy and consanguinity is expected to produce genetic homogeneity and partitioning of gene pools while population movements and intercontinental trade are likely to have contributed to genetic diversity. Emiratis and neighboring populations of the Middle East have been underrepresented in the population genetics literature with few studies covering the broader genetic history of the Arabian Peninsula. Here, we genotyped 1,198 individuals from the seven Emirates using 1.7 million markers and by employing haplotype-based algorithms and admixture analyses, we reveal the fine-scale genetic structure of the Emirati population. Shared ancestry and gene flow with neighboring populations display their unique geographic position while increased intra- versus inter-Emirati kinship and sharing of uniparental haplogroups, reflect the endogamous and consanguineous cultural traditions of the Emirates and their tribes. 相似文献
12.
Due to pervasive gene flow and admixture, simple bifurcating trees often do not provide an accurate representation of relationships among diverging lineages, but limited resolution in the available genomic data and the spatial distribution of samples has hindered detailed insights regarding the evolutionary and demographic history of many species and populations. In this issue of Molecular Ecology, Foote et al. (2019) combine a powerful sampling design with novel analytical methods adopted from human genetics to describe previously unrecognized patterns of recurrent vicariance and admixture among lineages in the globally distributed killer whale (Orcinus orca). Based on sequence data from modern samples alone, they discover clear signatures of ancient admixture with a now extinct “ghost” lineage, providing one of the first accounts of archaic introgression in a nonhominid species. Coupling a cost‐effective sequencing strategy with novel analytical approaches, their paper provides a roadmap for advancing inference of evolutionary history in other nonmodel species, promising exciting times ahead for our field. 相似文献
13.
Jada Benn Torres Anne C. Stone Rick Kittles 《American journal of physical anthropology》2013,151(1):135-143
Variable socio‐cultural influences developed in the colonial Caribbean as a result of competing European hegemonic rule. In this study, we examine how colonial regulations regarding social hierarchies and mate choice worked to influence the genetic landscape of contemporary African Caribbean populations. To this end, 420 individuals from Dominica, Grenada, St. Kitts, St. Lucia, St. Thomas, St. Vincent, Jamaica, and Trinidad were genotyped for 105 autosomal ancestry informative markers. Based on these data, population substructure and admixture were assessed using an exact test, a model‐based clustering method, and principal components analysis. On average, individual admixture estimates of the pooled African Caribbean sample were 77% (SD ± 18%) West African, 15% (SD ± 15%) European, and 7.7% (SD ± 8%) Native American. In general, ancestry estimates were significantly different between Dominica and all other islands. Genetic structure analyses indicated subdivision into two subpopulations on most islands. Finally, unlike all of the other Caribbean populations that clustered adjacent to African populations, the Dominican population was more intermediate between the three parental groups in the principal components plot. As a result of the significant French influence throughout Dominican history, Dominica did not have the same cultural influences that typified other Anglophone colonies. Consequently, there were different social hierarchies and resulting mate choices on Dominica compared with the other considered islands. This study highlights the complex socio‐cultural history of a broad region of the Caribbean and attests to the interplay between social and biological factors in shaping the genetic diversity present in present‐day communities. Am J Phys Anthropol 151:135–143, 2013. © 2013 Wiley Periodicals, Inc. 相似文献
14.
Kip D. Zimmerman Theodore G. Schurr Wei-Min Chen Uma Nayak Josyf C. Mychaleckyj Queen Quet Lee H. Moultrie Jasmin Divers Keith L. Keene Diane L. Kamen Gary S. Gilkeson Kelly J. Hunt Ida J. Spruill Jyotika K. Fernandes Melinda C. Aldrich David Reich W. Timothy Garvey Carl D. Langefeld Michèle M. Sale Paula S. Ramos 《American journal of physical anthropology》2021,175(4):905-919
15.
Miguel Delgado Luis Miguel Ramírez Kaustubh Adhikari Macarena Fuentes-Guajardo Clément Zanolli Rolando Gonzalez-José Samuel Canizales Maria-Catira Bortolini Giovanni Poletti Carla Gallo Francisco Rothhammer Gabriel Bedoya Andres Ruiz-Linares 《American journal of physical anthropology》2019,168(3):438-447
16.
Noah A. Rosenberg 《Molecular ecology resources》2004,4(1):137-138
In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as structure . distruct provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups. distruct , available at http://www.cmb.usc.edu/~noahr/distruct.html , can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group. 相似文献
17.
It has become clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference methods. Due to the diverse effects of admixture, this interest is shared across disparate fields, from human genetics to research in ecology and evolutionary biology. However, local ancestry inference methods are sensitive to a range of biological and technical parameters which can impact accuracy. Here we present paired simulation and ancestry inference pipelines, mixnmatch and ancestryinfer, to help researchers plan and execute local ancestry inference studies. mixnmatch can simulate arbitrarily complex demographic histories in the parental and hybrid populations, selection on hybrids, and technical variables such as coverage and contamination. ancestryinfer takes as input sequencing reads from simulated or real individuals, and implements an efficient local ancestry inference pipeline. We perform a series of simulations with mixnmatch to pinpoint factors that influence accuracy in local ancestry inference and highlight useful features of the two pipelines. mixnmatch is a powerful tool for simulations of hybridization while ancestryinfer facilitates local ancestry inference on real or simulated data. 相似文献
18.
19.
Admixture is a common biological phenomenon among populations of the same or different species. Identifying admixed tracts within individual genomes can provide valuable information to date admixture events, reconstruct ancestry-specific demographic histories, or detect adaptive introgression, genetic incompatibilities, as well as regions of the genomes affected by (associative-) overdominance. Although many local ancestry inference (LAI) methods have been developed in the last decade, their performance was accessed using large reference panels, which are rarely available for non-model organisms or ancient samples. Moreover, the demographic conditions for which LAI becomes unreliable have not been explicitly outlined. Here, we identify the demographic conditions for which local ancestries can be best estimated using very small reference panels. Furthermore, we compare the performance of two LAI methods (RFMix and MOSAIC) with the performance of a newly developed approach (simpLAI) that can be used even when reference populations consist of single individuals. Based on simulations of various demographic models, we also determine the limits of these LAI tools and propose post-painting filtering steps to reduce false-positive rates and improve the precision and accuracy of the inferred admixed tracts. Besides providing a guide for using LAI, our work shows that reasonable inferences can be obtained from a single diploid genome per reference under demographic conditions that are not uncommon among past human groups and non-model organisms. 相似文献
20.