scholarly journals Inferring Effective Population Size and Divergence Time in the Lithuanian Population According to High-Density Genotyping Data

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 293
Author(s):  
Alina Urnikytė ◽  
Alma Molytė ◽  
Erinija Pranckevičienė ◽  
Zita Aušrelė Kučinskienė ◽  
Vaidutis Kučinskas
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Substantial Reduction ◽  
Divergence Time ◽  
High Density ◽  
Effective Population ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Partial Isolation ◽  
Object Of Study

The prehistory of the Lithuanian population and genetic relationship to other populations are poorly studied. Thus, the Lithuanian population, as an object of study, is interesting due to its partial isolation with genetic distinctiveness within the European context and with preserved ancient genetic composition. The main objects of this study was to infer demographic parameters, effective population size (Ne), and divergence time using high-density single nucleotide polymorphism (SNP) genotyping data generated with the Illumina HumanOmmiExpress-12v1.1 array in 295 individuals from the Lithuanian population and to compare our data with other populations from the Human Genome Cell Line Diversity Panel (HGDP-CEPH). We also aimed to reconstruct past events between the main ethnolinguistic regions—Aukštaitija and Žemaitija of Lithuania. Historically, these regions probably developed as two independent Baltic tribes. Our results of Ne in the Lithuanian population through time demonstrated a substantial reduction of Ne over the 150,000–25,000 years before present (YBP). The estimated long-term Ne of the Lithuanian population is quite low—it equals 5404, which likely is a consequence of the bottlenecks associated with the last glacial period of 25,000–12,000 YBP in Europe. The obtained divergence time estimates between the study populations are in agreement with recent studies. The reconstructed past events in Aukštaitija and Žemaitija showed significant differences between these two regions of Lithuania.

scholarly journals PSX-18 High-density genomic description of Russian native sheep breed of the Republic of Tyva

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 453-454
Author(s):  
Tatiana Evgenievna Deniskova ◽  
Alexandra Abdelmanova ◽  
Arsen V Dotsev ◽  
Chechena Sambu-Khoo ◽  
Henry Reyer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
High Density ◽  
Sheep Breed ◽  
Current Status ◽  
Effective Population ◽  
Sheep Breeds ◽  
Native Sheep ◽  
The Republic

Abstract Tuva breed is the oldest native sheep breed in Russia with more than 2000 year-history and comes in third place by population size among coarse wool sheep. Tuva sheep produce high-quality meat as well as coarse wool to make traditional clothing in the Republic of Tyva. In present study, we aimed to evaluate genetic diversity and to establish genetic links of the Tuva breed with the other Russian coarse wool sheep to understand the origin and current status of this valuable livestock species. Twenty samples of Tuva were genotyped using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). SNP-data were processed in PLINKv1.9, R package ‘diveRsity’ and SneP software. High-density SNP-genotypes of 10 coarse wool sheep breeds were used as comparison groups. Observed heterozygosity (Ho) and allelic richness (Ar) in Tuva breed were 0.336 and 1.884, respectively, and were practically equal to mean values estimated across all analyzed sheep breeds (Ho=0.335, Ar=1.884). All coarse wool breeds showed moderate heterozygote excess which was the highest in Tuva breed (1.6%). Effective population sizes estimated for three and five generations ago for Tuva breed (Ne3 =118 and Ne5 =179) were less than those in other breeds (Ne3 = 314 and Ne5 = 441 for Edilbai or Ne3 = 300 and Ne5 = 450 for Kalmyk) but not the lowest (Ne3 = 49 and Ne5 = 72 for Buubei). Values of historical effective population size estimated for 60 generations ago for Tuva breed was 1457 that was compatible with those obtained for other breeds (Ne60 from 586 for Buubei to 2634 for Kalmyk). Despite the obvious decrease in effective population size, levels of genetic diversity are not critical that would allow to develop programs to ensure preservation and sustainable development of Tuva breed. The study was funded by RSF No. 19-16-00070.

scholarly journals Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocome and Eudyptes moseleyi)

2019 ◽  
Author(s):  
Herman L Mays ◽  
David A Oehler ◽  
Kyle W Morrison ◽  
Ariadna E Morales ◽  
Alyssa Lycans ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Species Delimitation ◽  
Diversity Index ◽  
Divergence Time ◽  
Distinct Species ◽  
Effective Population ◽  
Heuristic Approaches

Abstract Rockhopper penguins are delimited as 2 species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (Eudyptes chrysocome), with the latter comprising 2 subspecies, the western rockhopper (Eudyptes chrysocome chrysocome) and the eastern rockhopper (Eudyptes chrysocome filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow, and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or 2 lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.

scholarly journals Myotis rufoniger Genome Sequence and Analyses: M. rufoniger’s Genomic Feature and the Decreasing Effective Population Size of Myotis Bats

2017 ◽  
Author(s):  
Youngjune Bhak ◽  
Yeonsu Jeon ◽  
Sungwon Jeon ◽  
Oksung Chung ◽  
Sungwoong Jho ◽  
...  
Keyword(s):  
Amino Acid ◽  
Population Size ◽  
Effective Population Size ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Demographic History ◽  
Divergence Time ◽  
Functional Enrichment ◽  
Genomic Feature ◽  
Effective Population

AbstractMyotis rufoniger is a vesper bat in the genus Myotis. Here we report the whole genome sequence and analyses of the M. rufoniger. We generated 124 Gb of short-read DNA sequences with an estimated genome size of 1.88 Gb at a sequencing depth of 66× fold. The sequences were aligned to M. brandtii bat reference genome at a mapping rate of 96.50% covering 95.71% coding sequence region at 10× coverage. The divergence time of Myotis bat family is estimated to be 11.5 million years, and the divergence time between M. rufoniger and its closest species M. davidii is estimated to be 10.4 million years. We found 1,239 function-altering M. rufoniger specific amino acid sequences from 929 genes compared to other Myotis bat and mammalian genomes. The functional enrichment test of the 929 genes detected amino acid changes in melanin associated DCT, SLC45A2, TYRP1, and OCA2 genes possibly responsible for the M. rufoniger’s red fur color and a general coloration in Myotis. N6AMT1 gene, associated with arsenic resistance, showed a high degree of function alteration in M. rufoniger. We further confirmed that M. rufoniger also has bat-specific sequences within FSHB, GHR, IGF1R, TP53, MDM2, SLC45A2, RGS7BP, RHO, OPN1SW, and CNGB3 genes that have already been published to be related to bat’s reproduction, lifespan, flight, low vision, and echolocation. Additionally, our demographic history analysis found that the effective population size of Myotis clade has been consistently decreasing since ∼30k years ago. M. rufoniger’s effective population size was the lowest in Myotis bats, confirming its relatively low genetic diversity.

Sign in / Sign up

Export Citation Format

Share Document