DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors
TLDR
A new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (θ, GST) and population differentiation statistics (DJost, GST ' , χ2 test for population heterogeneity), among others.Abstract:
Summary
We present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (θ, GST) and population differentiation statistics (DJost, GST ', χ2 test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective.
diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F-statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co-dominant marker types (e.g. allozymes, SNPs).
Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity. Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis.read more
Citations
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Reproductive characteristics, population genetics, and pairwise kinship inform strategic recovery of a plant species in a fragmented landscape
Chantelle A. T. Doyle,Jia-Yee S. Yap,Jason G. Bragg,Maurizio Rossetto,Andrew Orme,Mark K. J. Ooi +5 more
TL;DR: This article examined the mating system and used molecular genetics to measure pairwise kinship and the potential for inbreeding in Hibbertia spanantha, a critically endangered long-lived shrub endemic to the Sydney Basin, Australia.
Journal ArticleDOI
Population Genetics and Phylogeography of Galapagos Fur Seals
Jaime A. Chaves,Fernando Ricardo Vieira Lopes,Daniela Martinez,Darío F. Cueva,Gabriela Gavilanes,Sandro L. Bonatto,Larissa Rosa de Oliveira,Diego Páez-Rosas +7 more
TL;DR: The genetic consequences of the geographic distribution of rookeries in Galapagos fur seals (GFS) are reported, suggesting that the marked structuring of populations recovered in GFS is likely related to an interplay between long-term site fidelity and long-distance migration in both male and female individuals.
Journal ArticleDOI
Time is running out: Microsatellite data predict the imminent extinction of the boreal lynx (Lynx lynx) in France
TL;DR: In this paper , the authors used 23 microsatellite markers and 78 DNA samples, collected between 2008 and 2020, to establish the genetic state of the French Jura Mountain lynx population, showing extremely low genetic diversity with an observed heterozygosity (Ho) of 0.36 and an effective population size (Ne) of 38.2.
Journal ArticleDOI
Heterozygosity as a factor of increasing the meat productivity of kalmyk steers
Elena Yurievna Anisimova,Marina Slozhenkina,Ivan Fiodorovich Gorlov,Dmitry Nikolaev,Natalia Ivanovna Mosolova,D.A. Mosolova +5 more
TL;DR: In this paper , the authors carried out full-genome SNP genotyping of 16-month-old Kalmyk steers to study their productive characteristics and beef quality indicators in the leading farms of the Republic of Konymykia.
Journal ArticleDOI
Long-term Monitoring of a Brown Trout (Salmo Trutta) Population Reveals Kin-associated Migration Patterns and Contributions by Resident Trout to the Anadromous Run
Eloïse Duval,Eloïse Duval,Øystein Skaala,María Quintela,Geir Dahle,Aurélien Delaval,Vidar Wennevik,Kevin A. Glover,Michael Møller Hansen +8 more
TL;DR: The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners and suggest that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size.
References
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