Clustering patterns mirror the geographical distribution and genetic history of Lemnos and Lesvos sheep populations

Elucidating the genetic variation and structure of Lemnos and Lesvos sheep is critical for maintaining local genetic diversity, ecosystem integrity and resilience of local food production of the two North Aegean islands. In the present study, we explored genetic diversity and differentiation as well as population structure of the Lemnos and Lesvos sheep. Furthermore, we sought to identify a small panel of markers with the highest discriminatory power to assign animals across islands. A total number of n = 424 (n = 307, Lemnos and n = 117, Lesvos) ewes, sampled from n = 24 herds dispersed at different geographic regions on the two islands, were genotyped with the 50K SNP array. Mean observed heterozygosity was higher (but not statistically significantly different) in Lesvos than in Lemnos population (0.384 vs. 0.377) while inbreeding levels were higher in Lemnos than Lesvos herds (0.065 vs. 0.031). Results of principal components along with that of admixture analysis and estimated genetic distances revealed genetic clusters corresponding to Lesvos and Lemnos origin and the existence of infrastructure within islands that were associated with geographical isolation and genetic history of the studied populations. In particular, genetic analyses highlighted three geographically isolated herds in Lemnos that are located at mountainous areas of the island and are characterized as representatives of the local sheep by historic data and reports. Admixture analysis also showed a shared genetic background between Lemnos and Lesvos sheep attributable to past gene flow. Little overall genetic differentiation was detected between the two island sheep populations, while 150 discriminatory SNPs could accurately assign animals to their origin. Present results are comparable with those reported in the worldwide sheep breeds, suggesting geography related genetic patterns across and within islands and the existence of the local Lemnos sheep.

Download Full-text

The paternal and maternal genetic history of Vietnamese populations

European Journal of Human Genetics ◽

10.1038/s41431-019-0557-4 ◽

2019 ◽

Vol 28 (5) ◽

pp. 636-645 ◽

Cited By ~ 3

Author(s):

Enrico Macholdt ◽

Leonardo Arias ◽

Nguyen Thuy Duong ◽

Nguyen Dang Ton ◽

Nguyen Van Phong ◽

...

Keyword(s):

Genetic Diversity ◽

Linguistic Diversity ◽

Genetic History ◽

Majority Group ◽

History Of ◽

Low Levels ◽

Potential Impact ◽

The Many ◽

Male Specific ◽

Complete Mtdna

AbstractVietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and ~2.3 Mb sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.

Download Full-text

The paternal and maternal genetic history of Vietnamese populations

10.1101/719831 ◽

2019 ◽

Cited By ~ 1

Author(s):

Enrico Macholdt ◽

Leonardo Arias ◽

Nguyen Thuy Duong ◽

Nguyen Dang Ton ◽

Nguyen Van Phong ◽

...

Keyword(s):

Genetic Diversity ◽

Linguistic Diversity ◽

Genetic History ◽

Majority Group ◽

History Of ◽

Low Levels ◽

Potential Impact ◽

The Many ◽

Male Specific ◽

Complete Mtdna

AbstractVietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and 2.34 mB sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with some limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.

Download Full-text

Origin and dispersion pathways of guava in the Galapagos Islands inferred through genetics and historical records

10.22541/au.161745825.56117059/v1 ◽

2021 ◽

Author(s):

Diego Urquia ◽

Bernardo Gutierrez ◽

Gabriela Pozo ◽

Maria Pozo ◽

Maria Torres

Keyword(s):

Genetic Diversity ◽

Psidium Guajava ◽

Galapagos Islands ◽

Genetic Distances ◽

Galápagos Islands ◽

Santa Cruz ◽

Historical Sources ◽

Introduction History ◽

Galapagos Archipelago ◽

History Of

Guava (Psidium guajava) is one of the most aggressive invasive plants in the Galapagos Islands. Determining its provenance and genetic diversity could provide valuable information for its control. With this purpose, we analyzed 11 SSR markers in guava individuals collected from Isabela, Santa Cruz, San Cristobal and Floreana islands in the Galapagos, as well as from mainland Ecuador. The mainland guava population appeared genetically differentiated from the Galapagos populations, with higher genetic diversity levels found in the former. By using different approaches for data analysis, we consistently found that the Central Highlands region of mainland Ecuador is one of the most likely origins of the Galapagos populations. Moreover, the guavas from Isabela and Floreana show a potential genetic input from southern mainland Ecuador, while the population from San Cristobal would be linked to the coastal mainland regions. Interestingly, the proposed origins for the Galapagos guava coincide with the first human settlings of the archipelago. By employing Approximate Bayesian Computation, we propose a model where San Cristobal was the first island to be colonized by guava from the mainland, from which it would have spread to Floreana and finally to Santa Cruz; Isabela would have been seeded from Floreana. An independent trajectory could also have contributed in the invasion of Floreana and Isabela. The pathway shown in our model agrees with the human colonization history of the different islands in the Galapagos. Our model, in conjunction with the clustering patterns of the guava individuals (based on genetic distances), suggests that guava introduction history in the Galapagos archipelago was driven predominantly by a single event (or events in rapid succession) instead of several independent introductions. We thus show that genetic analyses supported by historical sources can be used to answer questions on the variability and history of guava in the Galapagos Islands.

Download Full-text

Genetic past, present, and future of the honey bee (Apis mellifera) in the United States of America

Apidologie ◽

10.1007/s13592-020-00836-4 ◽

2021 ◽

Author(s):

Madeline H. Carpenter ◽

Brock A. Harpur

Keyword(s):

United States ◽

Honey Bee ◽

United States Of America ◽

Honey Bees ◽

Management Practices ◽

The United States ◽

Primary Sources ◽

Genetic History ◽

History Of ◽

Historic Data

AbstractHumans have domesticated hundreds of animal and plant species for thousands of years. Artwork, archeological finds, recorded accounts, and other primary sources can provide glimpses into the historic management practices used over the course of a given species’ domestication history. Pairing historic data with newly available genomic data can allow us to identify where and how species were moved out of their native ranges, how gene flow may have occurred between distantly related populations, and quantify how selection and drift each contributed to levels of genetic diversity. Intersecting these approaches has greatly improved our understanding of many managed species; however, there has yet to be a thorough review in a managed insect. Here, we review the archival and genetic history of honey bees introduced to the mainland United States to reconstruct a comprehensive importation history. We find that since 1622, at least nine honey bee subspecies were imported from four of the five honey bee lineages and distributed en masse across the country. Many imported genotypes have genetic evidence of persisting today and may segregate non-randomly across the country. However, honey bee population genetic comparisons on the nationwide scale are not yet feasible because of gaps in genetic and archival records. We conclude by suggesting future avenues of research in both fields.

Download Full-text

Worldwide phylogeography and history of wheat genetic diversity

10.1101/477455 ◽

2018 ◽

Author(s):

François Balfourier ◽

Sophie Bouchet ◽

Sandra Robert ◽

Romain De Oliveira ◽

Hélène Rimbert ◽

...

Keyword(s):

Genetic Diversity ◽

Snp Array ◽

Wild Relatives ◽

Human Migration ◽

Structural Variations ◽

Breeding Programs ◽

Allele Distribution ◽

Fertile Crescent ◽

History Of ◽

New Alleles

AbstractSince its domestication in the Fertile Crescent ~8,000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4,506 landraces and cultivars originating from 105 different countries genotyped with a high-density SNP array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the apparition of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.One Sentence SummaryA phylogeographical study reveals the complex history of wheat genetic diversity through time and space.

Download Full-text

A genetic history of migration, diversification, and admixture in Asia

10.47248/hpgg2202010001 ◽

2022 ◽

pp. 1-32

Author(s):

Melinda A. Yang

Keyword(s):

Large Scale ◽

Sequence Data ◽

Evolutionary Genetics ◽

Genetic Distances ◽

Chromosome 21 ◽

Late 20Th Century ◽

Genetic History ◽

Asian Populations ◽

Human Dispersal ◽

History Of

L.L. Cavalli-Sforza spearheaded early efforts to study the genetic history of humans, recognizing the importance of sampling diverse populations worldwide. He supported research on human evolutionary genetics in Asia, with research on human dispersal into Asia and genetic distances between present-day East Asians in the late 20th century. Since then, great strides have been made in understanding the genetic history of humans in Asia, through large-scale genomic sequencing of present-day humans and targeted sequencing of DNA from ancient humans. In this review, I survey the genetic prehistory of humans in Asia, based on research using sequence data from humans who lived in Asia as early as 45,000 years ago. Genetic studies comparing present-day Australasians and Asians show that they likely derived from a single dispersal out of Africa, rapidly differentiating into three main lineages: one that persists partially in South Asia, one that is primarily found today in Australasia, and one that is widely represented across Siberia, East Asia, and Southeast Asia. Studies of ancient DNA from human remains in Asia dating from as far back as 45,000 years has greatly increased our understanding of the population dynamics leading to the current Asian populations. Based on "Jin L, Underhill PA, Doctor V, Davis RW, Shen P, Cavalli-Sforza LL, Oefner PJ. Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations. Proc Natl Acad Sci U S A. 1999;96(7):3796-3800”.

Download Full-text

Faculty Opinions recommendation of Reconstructing the genetic history of late Neanderthals.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.732875435.793548688 ◽

2018 ◽

Author(s):

Nicola Mulder

Keyword(s):

Genetic History ◽

History Of

Download Full-text

Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

Sustainability ◽

10.3390/su13126830 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6830

Author(s):

Murat Guney ◽

Salih Kafkas ◽

Hakan Keles ◽

Mozhgan Zarifikhosroshahi ◽

Muhammet Ali Gundesli ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Genetic Resources ◽

Juglans Regia ◽

Genetic Distances ◽

Mean Value ◽

Central Anatolia ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

Download Full-text

The evolution of hard tick-borne relapsing fever borreliae is correlated with vector species rather than geographical distance

BMC Ecology and Evolution ◽

10.1186/s12862-021-01838-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ranna Nakao ◽

Kentaro Kasama ◽

Bazartseren Boldbaatar ◽

Yoshitoshi Ogura ◽

Hiroki Kawabata ◽

...

Keyword(s):

Core Gene ◽

Genetic Distances ◽

Hard Tick ◽

Vector Species ◽

Relapsing Fever ◽

Strain Isolation ◽

Ecological Features ◽

Geographical Distances ◽

History Of ◽

Hokkaido Island

Abstract Background Relapsing fever (RF) borreliae are arthropod-borne spirochetes and some of them cause human diseases, which are characterized by relapsing or recurring episodes of fever. Recently, it has been classified into two groups: soft tick-borne RF (STRF) borreliae and hard tick-borne RF (HTRF) borreliae. STRF borreliae include classical RF agents and HTRF borreliae, the latter of which include B. miyamotoi, a human pathogen recently identified in Eurasia and North America. Results In this study, we determined the genome sequences of 16 HTRF borreliae strains: 15 B. miyamotoi strains (9 from Hokkaido Island, Japan, 3 from Honshu Island, Japan, and 3 from Mongolia) and a Borrelia sp. tHM16w. Chromosomal gene synteny was highly conserved among the HTRF strains sequenced in this study, even though they were isolated from different geographic regions and different tick species. Phylogenetic analysis based on core gene sequences revealed that HTRF and STRF borreliae are clearly distinguishable, with each forming a monophyletic group in the RF borreliae lineage. Moreover, the evolutionary relationships of RF borreliae are consistent with the biological and ecological features of each RF borreliae sublineage and can explain the unique characteristics of Borrelia anserina. In addition, the pairwise genetic distances between HTRF borreliae strains were well correlated with those of vector species rather than with the geographical distances between strain isolation sites. This result suggests that the genetic diversification of HTRF borreliae is attributed to the speciation of vector ticks and that this relationship might be required for efficient transmission of HTRF borreliae within vector ticks. Conclusions The results of the present study, together with those from previous investigations, support the hypothesis that the common ancestor of borreliae was transmitted by hard-bodied ticks and that only STRF borreliae switched to using soft-bodied ticks as a vector, which was followed by the emergence of Borrelia recurrentis, lice-borne RF borreliae. Our study clarifies the phylogenetic relationships between RF borreliae, and the data obtained will contribute to a better understanding of the evolutionary history of RF borreliae.

Download Full-text

Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽

10.3390/v13050737 ◽

2021 ◽

Vol 13 (5) ◽

pp. 737

Author(s):

Issiaka Bagayoko ◽

Marcos Giovanni Celli ◽

Gustavo Romay ◽

Nils Poulicard ◽

Agnès Pinel-Galzi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Sierra Leone ◽

Evolutionary History ◽

Molecular Diversity ◽

Genomic Data ◽

Gene Recombination ◽

Necrosis Virus ◽

History Of ◽

Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

Download Full-text