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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Journal ArticleDOI
Population genetic structure and adaptation of malaria parasites on the edge of endemic distribution.
Craig W. Duffy,Hampate Ba,Samuel Assefa,Ambroise D. Ahouidi,Yacine Boubou Deh,Abderahmane Tandia,Freja C. M. Kirsebom,Dominic P. Kwiatkowski,David J. Conway +8 more
TL;DR: Whether the major human malaria parasite Plasmodium falciparum exhibits fragmented population structure or local adaptation at the northern limit of its African distribution where the dry Sahel zone meets the Sahara, samples were collected from diverse locations within Mauritania.
Journal ArticleDOI
Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents
Marlene Jahnke,Martin Gullström,Josefine Larsson,Maria E. Asplund,Maria E. Asplund,Said S. Mgeleka,Mathew Ogalo Silas,Arielle I. Hoamby,Jamal Angelot Mahafina,Lina Mtwana Nordlund,Lina Mtwana Nordlund +10 more
TL;DR: This study suggests that the three regionally predominant ocean current systems rather than distance determine genetic connectivity and structure of T. hemprichii within the WIO, and conservation planning and implementation of marine protection should be considered at the regional scale—across national borders.
Journal ArticleDOI
Patterns and mechanisms of dispersal in a keystone seagrass species
Marlene Jahnke,Asbjørn Christensen,Dragos Micu,N. A. Mil'chakova,Murat Sezgin,Valentina Todorova,Stefan Strungaru,Gabriele Procaccini +7 more
TL;DR: This work assesses dispersal of the seagrass Zostera noltei, an important foundation species of the coastal zone, and investigates whether small scale seed dispersal and long-distance propagule dispersal do play a role for meta-population dynamics.
Journal ArticleDOI
Genetic conservation of a threatened Neotropical palm through community-management of fruits in agroforests and second-growth forests
Mariana Novello,João Paulo Gomes Viana,Alessandro Alves-Pereira,Ellida de Aguiar Silvestre,Hendrie Ferreira Nunes,José Baldin Pinheiro,Pedro H. S. Brancalion,Maria Imaculada Zucchi +7 more
TL;DR: Evaluated the value of community-managed agroforests and secondary forests for conserving genetic structure and diversity of Euterpe edulis, an endemic palm explored for fruit and palm heart production and investigated the genetic diversity of seeds extracted during pulp removal, proving the potential of using these seeds to recover overexploited populations.
Journal ArticleDOI
Intraspecific genetic lineages of a marine mussel show behavioural divergence and spatial segregation over a tropical/subtropical biogeographic transition
Gerardo I. Zardi,Katy R. Nicastro,Christopher D. McQuaid,Rita Castilho,Joana Costa,Joana Costa,Ester A. Serrão,Gareth A. Pearson +7 more
TL;DR: The functional role of diversity below the species level in evolutionary trends is highlighted and the need to understand this when predicting biodiversity responses to environmental change is understood.
References
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