RT Journal Article
SR Electronic
T1 Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.10.08.463677
DO 10.1101/2021.10.08.463677
A1 Kyle D. Gustafson
A1 Roderick B. Gagne
A1 Michael R. Buchalski
A1 T. Winston Vickers
A1 Seth P.D. Riley
A1 Jeff Sikich
A1 Jaime L. Rudd
A1 Justin A. Dellinger
A1 Melanie E.F. LaCava
A1 Holly B. Ernest
YR 2021
UL http://biorxiv.org/content/early/2021/10/09/2021.10.08.463677.abstract
AB Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California’s central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.Competing Interest StatementThe authors have declared no competing interest.