DOI: 10.5061/dryad.4hs71t6t
title: Data from: Mitochondrial DNA assessment of the phylogeography of the gopher tortoise

description: Identifying geographic barriers that define genetic structure within a
 species is crucial in formulating an effective conservation plan. The
 identification of appropriate management units is critical for the
 protection and recovery of the gopher tortoise Gopherus polyphemus, which
 have declined across their entire range. Previous molecular work at
 various spatial scales has identified distinct population assemblages of
 the gopher tortoise. The goal of this study was to assess the genetic
 structure in gopher tortoises through a more complete sampling of the
 federally listed as threatened portion of the range and evaluate the
 extent of genetic isolation imposed by several potential geographic
 barriers. We sequenced a 712–base-pair portion of a mitochondrial gene
 (NADH dehydrogenase 4) for 322 individuals from 42 sites across the range.
 We found two major assemblages of haplotypes separated by a modest
 phylogenetic break (average uncorrected p distance  =  0.015). The
 biogeographic barrier that best explained the geographic partitioning of
 genetic variation was the Apalachicola–Chattahoochee rivers and not the
 one used to delimit the federally listed as threatened portion of the
 range (Tombigbee–Mobile). However, the presence of distinct (group 1 and
 2) haplotypes on either side of Apalachicola–Chattahoochee rivers
 indicates that the two lineages experienced historical isolation and
 divergence, after which they came back into contact. If one were to define
 genetic units of conservation for gopher tortoises, then the
 Apalachicola–Chattahoochee rivers delineation would be the most
 appropriate based on the analysis of molecular variance of the
 mitochondrial sequence data. However, a model that combines the
 Apalachicola–Chattahoochee and Tombigbee–Mobile rivers as geographic
 breaks was the second-best model in this analysis, which suggests that the
 federally listed as threatened portion of the range also contains
 important geographic structure. Thus, we recommend that making management
 decisions on the basis of mitochondrial data alone is premature, and that
 prior to any status review additional work that examines finer scale
 patterns of genetic structure by using microsatellite loci is required.
description: Gopherus_ND4Nexus file used in the phylogenetic analyses.Gopherus_ND4_AMOVA_Model_01Arlequin file for AMOVA model 1 - Tombigbee/Mobile split (see Table 4)Gopherus_ND4_AMOVA_Model_02Arlequin file for AMOVA model 2 - Apalachicola/Flint split (see Table 4)Gopherus_ND4_AMOVA_Model_03Arlequin file for AMOVA model 3 - Apalachicola/Chattahoochee split (see Table 4)Gopherus_ND4_AMOVA_Model_04Arlequin file for AMOVA model 4 - Peninsular Florida split (see Table 4)Gopherus_ND4_AMOVA_Model_05Arlequin file for AMOVA model 5 - Combines models 1 & 4 (see Table 4)Gopherus_ND4_AMOVA_Model_06Arlequin file for AMOVA model 6 - combines models 1 & 3 (see Table 4)Gopherus_ND4_inputdata arpSAMOVA genetic data fileGopherus_ND4_inputdata.arpGopherus_ND4_inputdata geoSAMOVA site coordinates fileGopherus_ND4_inputdata.geo