Insights into reproductive isolation within the pelagic copepod Pleuromamma abdominalis with high genetic diversity using genome-wide SNP data

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

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Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

PLoS ONE ◽

10.1371/journal.pone.0054997 ◽

2013 ◽

Vol 8 (1) ◽

pp. e54997 ◽

Cited By ~ 121

Author(s):

Jessica L. Petersen ◽

James R. Mickelson ◽

E. Gus Cothran ◽

Lisa S. Andersson ◽

Jeanette Axelsson ◽

...

Keyword(s):

Genetic Diversity ◽

Snp Data ◽

Genome Wide

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Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data

PLoS ONE ◽

10.1371/journal.pone.0154353 ◽

2016 ◽

Vol 11 (5) ◽

pp. e0154353 ◽

Cited By ~ 34

Author(s):

Carina Visser ◽

Simon F. Lashmar ◽

Este Van Marle-Köster ◽

Mario A. Poli ◽

Daniel Allain

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

South African ◽

Snp Data ◽

Genome Wide ◽

Angora Goats

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Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep

Archives Animal Breeding ◽

10.5194/aab-62-143-2019 ◽

2019 ◽

Vol 62 (1) ◽

pp. 143-151 ◽

Cited By ~ 6

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Nahid Parna ◽

Pourya Davoudi ◽

Majid Khansefid

Keyword(s):

Genetic Diversity ◽

Linkage Disequilibrium ◽

Association Studies ◽

Genome Wide Association Studies ◽

Effective Population ◽

High Genetic Diversity ◽

Single Nucleotide ◽

Genome Wide ◽

Snp Panel ◽

Zandi Sheep

Abstract. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), and runs of homozygosity (ROHs) in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped with Illumina Ovine SNP50 BeadChip. The amount of LD (r2) for single-nucleotide polymorphism (SNP) pairs in short distances (10–20 kb) was 0.21±0.25 but rapidly decreased to 0.10±0.16 by increasing the distance between SNP pairs (40–60 kb). The Ne of Zandi sheep in past (approximately 3500 generations ago) and recent (five generations ago) populations was estimated to be 6475 and 122, respectively. The ROH-based inbreeding was 0.023. We found 558 ROH regions, of which 37 % were relatively long (> 10 Mb). Compared with the rate of LD reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced more rapidly by increasing the distance between SNP pairs. According to the LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic selection and genome-wide association studies in this breed.

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Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations

10.1101/2021.10.08.463677 ◽

2021 ◽

Author(s):

Kyle D Gustafson ◽

Roderick B Gagne ◽

Michael R Buchalski ◽

T Winston Vickers ◽

Seth PD Riley ◽

...

Keyword(s):

Genetic Diversity ◽

Linkage Disequilibrium ◽

Puma Concolor ◽

Genomic Diversity ◽

Strong Linkage Disequilibrium ◽

Fine Scale ◽

High Genetic Diversity ◽

Population Genomic ◽

Genome Wide ◽

Genetic Clusters

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.

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Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome‐wide SNP data

Animal Genetics ◽

10.1111/age.12819 ◽

2019 ◽

Vol 50 (5) ◽

pp. 449-459 ◽

Cited By ~ 4

Author(s):

T. Tozaki ◽

M. Kikuchi ◽

H. Kakoi ◽

K. Hirota ◽

S. Nagata ◽

...

Keyword(s):

Genetic Diversity ◽

Snp Data ◽

Genome Wide

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Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star Protoreaster nodosus

Royal Society Open Science ◽

10.1098/rsos.160253 ◽

2016 ◽

Vol 3 (8) ◽

pp. 160253 ◽

Cited By ~ 13

Author(s):

Y. C. Tay ◽

M. W. P. Chng ◽

W. W. G. Sew ◽

F. E. Rheindt ◽

K. P. P. Tun ◽

...

Keyword(s):

Genetic Diversity ◽

Marine Invertebrates ◽

Small Population ◽

Population Connectivity ◽

Marine Biodiversity ◽

Coral Triangle ◽

Sea Star ◽

High Genetic Diversity ◽

Broadcast Spawning ◽

Genome Wide

The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained despite decades of continued anthropogenic disturbance. We postulate that it is probably due to broadcast spawning which is likely to maintain high levels of population connectivity. To test this, we analysed 6140 genome-wide single nucleotide polymorphism (SNP) loci for Singapore's populations and demonstrate a pattern of near panmixia. We here document a second case of high genetic diversity and low genetic structure for a broadcast spawner in Singapore, which suggests that such species have high resilience against anthropogenic disturbances. The study demonstrates the feasibility and power of using genome-wide SNPs for connectivity studies of marine invertebrates without a sequenced genome.

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Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

10.1101/016493 ◽

2015 ◽

Author(s):

Emiliano Trucchi ◽

Benoit Facon ◽

Paolo Gratton ◽

Emiliano Mori ◽

Nils Chr. Stenseth ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary Dynamics ◽

Leading Edge ◽

High Genetic Diversity ◽

Hystrix Cristata ◽

The North ◽

Fundamental Information ◽

Genome Wide ◽

Crested Porcupine ◽

Species Specific

AbstractStudying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from Sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.

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Post-Genotyping Optimization of Dataset Formation Could Affect Genetic Diversity Parameters: An Example of Analyses with Alpine Goat Breeds

10.21203/rs.3.rs-133590/v1 ◽

2020 ◽

Author(s):

Neža Pogorevc ◽

Mojca Simčič ◽

Negar Khayatzadeh ◽

Johann Soelkner ◽

Beate Berger ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Genetic Distances ◽

Phylogenetic Study ◽

European Alps ◽

Global Context ◽

Outlier Test ◽

Snp Data ◽

Genome Wide ◽

A Genome

Abstract BackgroundLocal breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. One objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters.ResultsDistinct genetic origin of the Drežnica goat was demonstrated having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning.ConclusionsGenetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of the breeding and management programs and therefore important for preserving genetic variability and uniqueness of local rare breeds.

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