Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum.

Abstract

Nonrandom associations of alleles or haplotypes with geographical location can arise from restricted gene flow, historical events (fragmentation, range expansion, colonization), or any mixture of these factors. In this paper, we show how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that are due to historical events. In this last case, criteria are given to discriminate among contiguous range expansion, long-distance colonization, and population fragmentation. The ability to make these discriminations depends critically upon an adequate geographical sampling design. These points are illustrated with a worked example: mitochondrial DNA haplotypes in the salamander Ambystoma tigrinum. For this example, prior information exists about restricted gene flow and likely historical events, and the nested cladistic analyses were completely concordant with this prior information. This concordance establishes the plausibility of this nested cladistic approach, but much future work will be necessary to demonstrate robustness and to explore the power and accuracy of this procedure.

Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini)

“…Geographic expansion of formerly allopatric and isolated populations may lead to their secondary contact (Avise et al, 1987); if since then gene flow has been sufficiently restricted, the lineages from the different former isolates may still have limited overlap in their distribution (Templeton et al, 1995). This is what we detected, with the presence of the two clades in the Béchar Province (Fig.…”

A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling

“…The highly structured distribution of haplotypes in the western lineage, with most haplotypes specific to populations, is consistent with persistence of the species through multiple climatic cycles. In contrast, the widespread distribution of several haplotypes with internal positions in the network in the northern, eastern and southern peripheral populations of the eastern lineage is consistent with contraction of the species from these areas during arid cycles, and expansion from a refugial area during mesic conditions (Crandall and Templeton, 1993;Templeton et al, 1995). This latter pattern can occur when populations are in equilibrium and have been in their present range for a substantial period of time (Slatkin, 1993).…”

Evidence of two lineages of the symbiont ‘Candidatus Erwinia dacicola’ in Italian populations of Bactrocera oleae (Rossi) based on 16S rRNA gene sequences

“…The NCPA first tests the null hypotheses of no association between geography and the haplotype network. Only when this null hypothesis is rejected at the 5 % level of significance is it possible to infer likely historical and geographical events (Templeton et al, 1995). Fisher's exact test was applied to observe associations between the haplotype of 'Ca.…”