PleistoDist: A toolbox for visualising and quantifying the effects of Pleistocene sea‐level change on island archipelagos

Abstract

Pleistocene sea‐level change played a significant role in the evolution and assembly of island biotas. The formation of land bridges between islands during Quaternary glacial maxima, when sea levels were more than 120 metres below present‐day sea levels, often facilitated historical dispersal and gene flow between islands that are today geographically disconnected. Despite the importance of Pleistocene sea‐level change, few software packages exist that model the effects of this phenomenon in a standardised and generalised manner. Here, we present PleistoDist, an R package that allows users to visualise and quantify the effects of Pleistocene sea‐level change on islands over time, and test multiple temporally explicit hypotheses of inter‐island dispersal and community assembly. Re‐analysing published datasets, we demonstrate how using PleistoDist to account for historical sea‐level change can provide greater explanatory power when analysing extant island communities, and show how population genetic simulations can be used to generate spatiotemporally explicit neutral expectations of population genetic structure across island archipelagos.

Phylogeography of Solomon Islands blossom bats reflects oceanic divides and Pleistocene connections

“…We calculated among‐individual genetic distances (Nei's genetic distance) using the R package ‘StAMPP’ (Pembleton et al, 2013) and used distance‐based redundancy analyses (dbRDA) (which account for spatial autocorrelation) to test for correlations between genetic distance and our four interisland metrics (Tan et al, 2022). Permutational ANOVAs implemented in the R package ‘vegan’ (Oksanen et al, 2008) were used to identify significant correlations and stepwise model selection implemented in ‘vegan’ was used to identify which metric best fit genetic distance data.…”

“…We used the R package ‘PleistoDist’ (Tan et al, 2022) to further assess the influences of Pleistocene sea level changes on genetic divergence patterns of Nesonycteris . The package enables users to test multiple temporally explicit hypotheses of inter‐island dispersal and the influences of sea level change on the genetic structure of island biotas.…”

“…Least-cost distances were calculated using a rasterised archipelago shapefile whereby areas above sea level are assigned a resistance value of 1, and areas underwater are assigned a resistance value of 999,999. The least cost distance should minimize the amount of overwater movement between sampling points (Tan et al, 2022). Centroid-to-centroid distances were measured from island centroids, and least shore-to-shore calculated the shortest shore-to-shore distances between islands.…”

“…We calculated among-individual genetic distances (Nei's genetic distance) using the R package 'StAMPP' (Pembleton et al, 2013) and used distance-based redundancy analyses (dbRDA) (which account for spatial autocorrelation) to test for correlations between genetic distance and our four interisland metrics (Tan et al, 2022).…”

Waves of Colonization and Gene Flow in a Great Speciator

“…For example, the higher number of migrants originating from larger islands and continents can mean that smaller islands adjacent to larger ones are especially prone to the formation of hybrid populations (see MacArthur & Wilson 1963, 1967Gyllenhaal et al 2020). Additionally, glacial cycles can cause cyclical connectivity of islands and thereby increase rates of gene flow between island populations (Brown et al 2013, Tan et al 2022. This phenomenon of glacial eustasy could promote the formation of island hybrid zones, but as such cycles have occurred for millennia, present-day insular hybrid zones likely represent a deviation from longer-term isolation.…”