Shaping species with ephemeral boundaries: the distribution and genetic structure of desert tortoise (Gopherus morafkai) in the Sonoran Desert region

Abstract

Aim We examine the role biogeographical features played in the evolution of Morafka's desert tortoise (Gopherus morafkai) and test the hypothesis that G. morafkai maintains genetically distinct lineages associated with different Sonoran Desert biomes. Increased knowledge of the past and present distribution of the Sonoran Desert region's biota provides insight into the forces that drive and maintain its biodiversity.Location Sonoran Desert biogeographical region; Sonora and Sinaloa, Mexico and Arizona, USA.Methods We examined wild tortoises from Mexico (n = 155) and Arizona (n = 78), spanning their known distribution. We used mtDNA sequences to reconstruct matrilineal relationships and 25 microsatellite (STR) loci for Bayesian analyses of gene flow. We performed clinal analyses on both mtDNA and STR loci to determine the position and amount of introgression where lineages co-occur. We used GIS to assess the association of genetic structuring with ecological features. We used these data in a hypothesis-driven approach to assess different models of how genetic diversity is maintained and distributed in G. morafkai.Results Gopherus morafkai was found to comprise genetically and geographically distinct 'Sonoran' and 'Sinaloan' lineages. Both lineages occurred in a relatively narrow zone of overlap in Sinaloan thornscrub, where it transitions into Sonoran desertscrub. Limited introgression occurred at the contact zone. The best-fit model suggests that these lineages diverged in parapatry where the distribution of genotypes is environment-dependent and introgression is inhibited by exogenous selection. Main conclusionsThe historically shifting ecotone between tropical deciduous forest and Sonoran desertscrub appears to be a boundary that fostered divergence between parapatric lineages of tortoises. The sharp genetic cline between the two lineages suggests that periods of isolation in temporary refugia due to Pleistocene climatic cycling influenced divergence. Despite incomplete reproductive isolation, the Sonoran and Sinaloan lineages of G. morafkai are on separate evolutionary trajectories.

Assessing models of speciation under different biogeographic scenarios; an empirical study using multi‐locus and RNA‐seq analyses

“…Despite strong biogeographic evidence that the current contact zone between the Sonoran and Sinaloan lineages is a result of secondary contact after periods of isolation in Pleistocene refugia (Edwards et al. ) the rejection of hypothesis H‐SS gf suggests that divergence in parapatry and/or periods of secondary contact did not result in significant introgression between lineages. The best fit model for Sonoran/Sinaloan divergence (e.g.…”

“…Phylogenetic analyses employed 82 DNA samples collected from 38 sites previously used in other studies (Edwards et al. , , , ; Murphy et al. ).…”

“…We defined individuals with questionable genotypes based on their mtDNA haplotype as either Sinaloan or Sonoran based on Edwards et al. (). We used the HKY with four gamma distributed rate categories for all loci except TB07 which we applied the GTR with four gamma distributed rate categories.…”

“…; Edwards et al. , ). All three lineages appear to have experienced population expansions since the Last Glacial Maximum (LGM) based on mtDNA analysis; star phylogenies are observed at the tips of each of the long, matrilineal branches (Edwards ; Edwards et al.…”

“…All three lineages appear to have experienced population expansions since the Last Glacial Maximum (LGM) based on mtDNA analysis; star phylogenies are observed at the tips of each of the long, matrilineal branches (Edwards ; Edwards et al. ). Populations within each lineage have low estimates of genetic differentiation: F ST = 0.06 for G. agassizii ; F ST = 0.05 for G. morafkai Sonoran; and F ST = 0.09 for G. morafkai Sinaloan (Edwards and Harrison ; T. Edwards unpubl.…”