Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

Abstract

Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus. To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.

Is genomic diversity a useful proxy for census population size? Evidence from a species‐rich community of desert lizards

“…Our study reveals that a species‐rich community of related taxa displays the same positive diversity–abundance association found by other studies at both narrower and broader phylogenetic and geographical scales. The proportion of variance in genetic diversity that was explained by local‐scale abundance in the present study is similar to that explained by museum occurrence records (a proxy for global population size) in a recent study of genetic diversity in the lizard genus Ctenotus , a member of the Sphenomorphine clade that is represented in the current data set (Singhal, Huang et al, ). Similarly, Pearson correlations between abundance and diversity recovered from broader phylogenetic sampling and meta‐analyses in other taxa are also comparable to the correlation recovered here ( r = 0.4; Leimu et al, ; McCusker & Bentzen, ).…”

“…Previous studies have found positive relationships between heterozygosity and proxies for species abundance, including population size estimated from calculations of density and acreage (Patton & Yang, ), extrapolations calculated from active social groups (Stangel, Lennartz, & Smith, ), categorical estimates (“large,” “small”) of population size (Godt, Johnson, & Hamrick, ; Hague & Routman, ) and museum occurrence records (Singhal, Huang, et al, ). Studies that more directly compare intraspecific genetic diversity and abundance have reported positive associations, but these studies have generally focused on single species or paired species comparisons (Devillard, Santin‐Janin, Say, & Pontier, ; Lozier, ; Ortego, Aparicio, Cordero, & Calabuig, ; Sun, ), or on many species sampled at a broad geographical scale (Bazin, Glémin, & Galtier, ; Leimu, Mutikainen, Koricheva, & Fischer, ; McCusker & Bentzen, ; Pinsky & Palumbi, ).…”

“…Genome‐wide data increase our power to recover associations between genetic diversity, ecological correlates, and evolutionary processes acting over shorter time periods (Faircloth et al, ; Harvey, Aleixo, Ribas, & Brumfield, ). Recent studies have found strong relationships between ecological traits and genetic diversity at broad phylogenetic scales (e.g., across phyla; Romiguier et al, ); whether such patterns are also exhibited by more closely related species with similar life history traits remains equivocal (Ellegren & Galtier, ; Romiguier et al, ; Singhal, Huang, et al, ). Additionally, there is some evidence that microhabitat preference can limit dispersal and reduce within‐population genetic diversity (Brouat, Chevallier, Meusnier, Noblecourt, & Rasplus, ; Brouat, Sennedot, Audiot, Leblois, & Rasplus, ; Dalongeville et al, ; Khimoun et al, ; Pianka, ; Rabosky, Cowan, Talaba, & Lovette, ), but studies combining genome‐wide diversity estimates with ecological traits at the community level are rare.…”

“…"small") of population size (Godt, Johnson, & Hamrick, 1996;Hague & Routman, 2016) and museum occurrence records (Singhal, Huang, et al, 2017). Studies that more directly compare intraspecific genetic diversity and abundance have reported positive associations, but these studies have generally focused on single species or paired species comparisons (Devillard, Santin-Janin, Say, & Pontier, 2011;Lozier, 2014;Ortego, Aparicio, Cordero, & Calabuig, 2008;Sun, 1996), or on many species sampled at a broad geographical scale (Bazin, Glémin, & Galtier, 2006;Leimu, Mutikainen, Koricheva, & Fischer, 2006;McCusker & Bentzen, 2010;Pinsky & Palumbi, 2014).…”

“…Genome-wide data increase our power to recover associations between genetic diversity, ecological correlates, and evolutionary processes acting over shorter time periods (Faircloth et al, 2012;Harvey, Aleixo, Ribas, & Brumfield, 2017). Recent studies have found strong relationships between ecological traits and genetic diversity at broad phylogenetic scales (e.g., across phyla; Romiguier et al, 2014); whether such patterns are also exhibited by more closely related species with similar life history traits remains equivocal (Ellegren & Galtier, 2016;Romiguier et al, 2014;Singhal, Huang, et al, 2017).…”