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opencc-zeroOct 2023View details →

Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake

Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation reflecting long-term impacts of genetic drift, yet this widely used approach has been questioned in the genomics era. Here we leverage a chromosome-level assembly and whole genome resequencing data (N=110 individuals) from an endangered rattlesnake (Sistrurus catenatus) to evaluate the relationship between genome-wide neutral and functional diversity over long- and short-term timescales. As predicted for populations at long-term equilibrium, we found a positive correlation between population-level estimates of neutral genetic diversity (π) and the mean number of highly detrimental loss-of-function mutations, and a negative relationship between neutral genetic diversity and an estimate of genetic load. In contrast, we found only a weak, non-significant positive correlation between levels of neutral and adaptive variation. Additional analyses using estimates of drift at more recent time scales (> 100 generations) show expected correlations between both measures of genetic load, but a lack of a significant correlation with levels of adaptive variation. Individual-based demographic metrics that capture drift impacts over recent time scales confirm these results. Broadly, our results confirm that estimates of diversity and demography based on neutral genetic variation provide an accurate measure of a key component of genetic erosion – genetic load – in populations of a threatened vertebrate. Our findings also provide nuance to the neutral-functional diversity controversy by demonstrating that neutral genetic diversity is useful in predicting some, but not all, components of functional genetic diversity.

opencc-zeroOct 2023View details →

A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants

Underrepresentation of non-European populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72K subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East-Asian-specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell-type-specific effects. We suggest this data set will add to the potential value of Asian precision medicine.

publicOct 2023View details →

A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants

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publicOct 2023View details →

Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake

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opencc-zeroDec 2014View details →

Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus

Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.

opencc-zeroDec 2017View details →

Data from: Complete blood count reference intervals from a healthy adult urban population in Kenya

Background: There are racial, ethnic and geographical differences in complete blood count (CBC) reference intervals (RIs) and therefore it is necessary to establish RIs that are population specific. Several studies have been carried out in Africa to derive CBC RIs but many were not conducted with the rigor recommended for RI studies hence limiting the adoption and generalizability of the results. Method: By use of a Beckman Coulter ACT 5 DIFF CP analyser, we measured CBC parameters in samples collected from 528 healthy black African volunteers in a largely urban population. The latent abnormal values exclusion (LAVE) method was used for secondary exclusion of individuals who may have had sub-clinical diseases. The RIs were derived by both parametric and non-parametric methods with and without LAVE for comparative purposes. Results: Haemoglobin (Hb) levels were lower while platelet counts were higher in females across the 4 age stratifications. The lower limits for Hb and red blood cell parameters significantly increased after applying the LAVE method which eliminated individuals with latent anemia and inflammation. We adopted RIs by parametric method because 90% confidence intervals of the RI limits were invariably narrower than those by the non-parametric method. The male and female RIs for Hb after applying the LAVE method were 14.5−18.7 g/dL and 12.0−16.5 g/dL respectively while the platelet count RIs were 133−356 and 152−443 x103 per µL respectively. Conclusion: Consistent with other studies from Sub-Saharan Africa, Hb and neutrophil counts were lower than Caucasian values. Our finding of higher Hb and lower eosinophil counts compared to other studies conducted in rural Kenya most likely reflects the strict recruitment criteria and healthier reference population after secondary exclusion of individuals with possible sub-clinical diseases.

opencc-zeroDec 2013View details →

Data from: Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats

Background: The non-migratory killifish Fundulus heteroclitus inhabits clean and polluted environments interspersed throughout its range along the Atlantic coast of North America. Several populations of this species have successfully adapted to environments contaminated with toxic aromatic hydrocarbon pollutants such as polychlorinated biphenyls (PCBs). Previous studies suggest that the mechanism of resistance to these and other "dioxin-like compounds" (DLCs) may involve reduced signaling through the aryl hydrocarbon receptor (AHR) pathway. Here we investigated gene diversity and evidence for positive selection at three AHR-related loci (AHR1, AHR2, AHRR) in F. heteroclitus by comparing alleles from seven locations ranging over 600 km along the northeastern US, including extremely polluted and reference estuaries, with a focus on New Bedford Harbor (MA, USA), a PCB Superfund site, and nearby reference sites. Results: We identified 98 single nucleotide polymorphisms within three AHR-related loci among all populations, including synonymous and nonsynonymous substitutions. Haplotype distributions were spatially segregated and F-statistics suggested strong population genetic structure at these loci, consistent with previous studies showing strong population genetic structure at other F. heteroclitus loci. Genetic diversity at these three loci was not significantly different in contaminated sites as compared to reference sites. However, for AHR2 the New Bedford Harbor population had significant FST values in comparison to the nearest reference populations. Tests for positive selection revealed ten nonsynonymous polymorphisms in AHR1 and four in AHR2. Four nonsynonymous SNPs in AHR1 and three in AHR2 showed large differences in base frequency between New Bedford Harbor and its reference site. Tests for isolation-by-distance revealed evidence for non-neutral change at the AHR2 locus. Conclusion: Together, these data suggest that F. heteroclitus populations in reference and polluted sites have similar genetic diversity, providing no evidence for strong genetic bottlenecks for populations in polluted locations. However, the data provide evidence for genetic differentiation among sites, selection at specific nucleotides in AHR1 and AHR2, and specific AHR2 SNPs and haplotypes that are associated with the PCB-resistant phenotype in the New Bedford Harbor population. The results suggest that AHRs, and especially AHR2, may be important, recurring targets for selection in local adaptation to dioxin-like aromatic hydrocarbon contaminants.

opennotspecifiedOct 2019View details →

Artibeus gnomus is placed in Dermanura by some authors, but itis reassigned to Artibeus (subgenus Dermanura) after reinterpretation of molecular results. Before its description, some populations were referred to as A. pumilio, although that name is now associated with A. glaucus. Monotypic. Distribution. South America, E of Andes, including E Venezuela, the Guianas, E Colombia, E Ecuador, E Peru, Bolivia, and Brazil. in Phyllostomidae

Artibeus gnomus is placed in Dermanura by some authors, but itis reassigned to Artibeus (subgenus Dermanura) after reinterpretation of molecular results. Before its description, some populations were referred to as A. pumilio, although that name is now associated with A. glaucus. Monotypic. Distribution. South America, E of Andes, including E Venezuela, the Guianas, E Colombia, E Ecuador, E Peru, Bolivia, and Brazil.

opencc-by-4.0Nov 2021View details →

Addiitional Files: The diagrams of population structure, highly divergent regions, GC content and Nanopore reads depth, SNP number and Nanopore reads depth, and analyses of co-linearity against Nipponbare reference genome in 251 accessions.

Additional Files for " A Super Pan-Genomic Landscape of Rice". Addtional File1:  Supplementary File1.Population structure of 251 rice accessions inferred by ADMIXTURE from K=6 to K=15. Additional File2: Supplementary File2.The diagram of co-linearity for assembled genome against Nipponbare refercne genome in 251 rice accessions. Additional File3: Supplementary File3. Highly divergent regions based on SV. Additional File4: Supplementary File4. The diagram of SNP number and Nanopore reads depth per 100kb windows in 251 rice accessions. Additonal File5:Supplementary File5. The diagram of GC content and the Nanopore reads depth per 10kb windows in 251 rice accessions.

opennotspecifiedJun 2015View details →

Distribution. New Guinea, including Yapen, Mios Num, and Roon Is in Cenderawasih (= Geelvink) Bay, Karkar and Walis Is off the N coast, Raja Ampat Is of Salawati, Sorong, and Misool, SE Papua New Guinea Is of Samarai (= Dinner) and Dufaure (= Dufour), and Aru Is. It is present on many islands of C & S Moluccas (Seram, Ambon, Pulau Pandjang, Buru, and the Tayandu and Kai archipelagos). It has been introduced to Selayar I between Sulawesi and Flores (W occurrence of the species), and there are vague records from Flores and Sulawesi, which may also refer to the Selayar population. This species was also apparently introduced to Mussau (St. Matthias Group, NE Bismarck Archipelago) in prehistoric times and to New Ireland I (Bismarck Archipelago) in the 20™ century. in Phalangeridae

Distribution. New Guinea, including Yapen, Mios Num, and Roon Is in Cenderawasih (= Geelvink) Bay, Karkar and Walis Is off the N coast, Raja Ampat Is of Salawati, Sorong, and Misool, SE Papua New Guinea Is of Samarai (= Dinner) and Dufaure (= Dufour), and Aru Is. It is present on many islands of C & S Moluccas (Seram, Ambon, Pulau Pandjang, Buru, and the Tayandu and Kai archipelagos). It has been introduced to Selayar I between Sulawesi and Flores (W occurrence of the species), and there are vague records from Flores and Sulawesi, which may also refer to the Selayar population. This species was also apparently introduced to Mussau (St. Matthias Group, NE Bismarck Archipelago) in prehistoric times and to New Ireland I (Bismarck Archipelago) in the 20™ century.

opencc-zeroDec 2011View details →

Data from: Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear.

In species with large geographic ranges, genetic diversity of different populations may be well studied, but differences in loci and sample sizes can make the results of different studies difficult to compare. Yet, such comparisons are important for assessing the status of populations of conservation concern. We propose a simple approach of using a single well-studied reference population as a "yardstick" to calibrate results of different studies to the same scale, enabling comparisons. We use a well-studied large carnivore, the brown bear (Ursus arctos), as a case study to demonstrate the approach. As a reference population, we genotyped 513 brown bears from Slovenia using 20 polymorphic microsatellite loci. We used this dataset to calibrate and compare heterozygosity and allelic richness for 30 brown bear populations from 10 different studies across the global distribution of the species. The simplicity of the reference population approach makes it useful for other species, enabling comparisons of genetic diversity estimates between previously incompatible studies and improving our understanding of how genetic diversity is distributed along a species range.