On the Trail of Spatial Patterns of Genetic Variation

José A Peña,Miguel A Alfonso-Sánchez,Luis Gómez-Pérez

doi:10.1007/s11692-021-09552-y

José A Peña, Miguel A Alfonso-Sánchez + Show 1 more

Open Access

https://doi.org/10.1007/s11692-021-09552-y

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Journal: Evolutionary Biology	Publication Date: Oct 7, 2021
Citations: 1	License type: open-access

Affiliation: University of the Basque Country

Abstract

The accurate determination of the spatial trends on the variability of a species’ gene pool is essential to elucidate the underlying demographic-evolutionary events, thus helping to unravel the microevolutionary history of the population under study. Herein we present a new software called GenoCline, mainly addressed to detect genetic clines from allele, haplotype, and genome-wide data. This program package allows identifying the geographic orientation of clinal genetic variation through a system of iterative rotation of a virtual coordinate axis. Besides, GenoCline can perform complementary analyses to explore the potential origin of the genetic clines observed, including spatial autocorrelation, isolation by distance, centroid method, multidimensional scaling and Sammon projection. Among the advantages of this software is the ease in data entry and potential interconnection with other programs. Genetic and geographic data can be entered in spreadsheet table formatting (.xls), whereas genome-wide data can be imported in Eigensoft format. Genetic frequencies can also be exported in a format compatible with other programs dealing with population genetic and evolutionary biology analyses. All illustrations of results are saved in.svg format so that there will be high quality and easily editable vectorial graphs available for the researcher. Being implemented in Java, GenoCline is highly portable, thus working in different operating systems.

Highlights

The genetic variability of a species is not uniform all over its distribution range
A small average migration distance compared to the species' distribution range may lead to a sort of seclusion called "isolation by distance" (Wright, 1943), even lacking physical barriers
The phenomenon of isolation by distance can lead to a clear pattern of genetic differentiation over space

Summary

Introduction

The genetic variability of a species is not uniform all over its distribution range. When a species expands over a broad region, it most likely split into subpopulations so that mating probabilities between individuals from distinct subpopulations tend to decrease over distance (Kimura & Weiss, 1964). Genetic clines are often defined as the gradual variation in the frequency of a given genetic marker regarding latitude, longitude, altitude (Roy et al, 2018) or the distance up to an origin (Pérez-Losada & Fort, 2018). In this way, thorough studies of the spatial orientation of clinal genetic variation stand helpful to assist in the interpretation of potential evolutionary forces shaping the gene pool of a species (Kyriacou et al, 2008; Maes & Volckaert, 2002; Razgour, 2015). GenoCline has been already used, for example, to determine the geographic direction of a frequency gradient for the human MAPT*H2 haplotype in western Eurasia (Alfonso-Sánchez et al, 2018) or to study the movements of a small migratory falcon, the lesser kestrel (Falco naumanni), to unravel the origin of birds converging to premigratory sites (Bounas et al, 2018)

Methods

Findings

Centroid Method