Abstract
Habitat loss and alteration has driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The tricolored blackbird (Agelaius tricolor) has suffered severe losses during the previous century largely due to anthropogenic impacts on their habitat. Using a dataset composed of a whole genome paired with reduced representation libraries (RAD‐Seq) from samples collected across the species’ range, we find evidence for panmixia using multiple methods, including PCA (no geographic clustering), admixture analyses (ADMIXTURE and TESS conclude K = 1), and comparisons of genetic differentiation (average FST = 0.029). Demographic modeling approaches recovered an ancient decline that had a strong impact on genetic diversity but did not detect any effect from the known recent decline. We also did not detect any evidence for selection, and hence adaptive variation, at any site, either geographic or genomic. These results indicate that species continues to have high vagility across its range despite population decline and habitat loss and should be managed as a single unit.
Highlights
Rising anthropogenic pressures over the past century have created a global biodiversity crisis (Ceballos et al, 2015)
Our primary objectives are to (a) assess gene flow and genetic diversity, both neutral and adaptive, (a) estimate current and long-term effective population sizes (Ne), and (c) provide management recommendations based upon our results
Our results illustrate the analytical power and additional information gained from reexamining a system only informed by classical genetic markers with a modern genomic approach
Summary
Given the increasing accessibility of genome-wide data, we can move toward more precise evaluations of evolutionary processes by directly assessing adaptive variation (Bay et al, 2018; Funk et al, 2012; Ruegg et al, 2018), analyzing fine-scale gene flow patterns and hierarchical genetic structure (Hendricks et al, 2017; Ruegg et al, 2014; Younger et al, 2017), and estimating recent and historical demographic trends (Beichman et al, 2018, 2019; Oh et al, 2019) One such species experiencing severe impacts in the course of anthropogenic activities is the tricolored blackbird (tricoloreds; Agelaius tricolor), a colonial songbird that is near endemic to California (Beedy et al, 2018). Our primary objectives are to (a) assess gene flow and genetic diversity, both neutral and adaptive (the latter being the product of local environmental selection), (a) estimate current and long-term effective population sizes (Ne), and (c) provide management recommendations based upon our results
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