Nested clade analysis and the genetic evidence for population expansion in the phylogeography of the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela)

High mitochondrial diversity within and among populations of Malagasy poison frogs

The diurnal, brightly colored, and toxic frogs of the genus Mantella are among the most prominent representatives of the endemic anuran fauna of Madagascar. Especially three closely related species, M. aurantiaca, M. crocea, and M. milotympanum, are intensively collected for the pet trade, although basic data on their natural history and genetic diversity are still lacking. Our phylogenetic analyses based on 2.8 kbp of partial 16S rRNA, 12S rRNA, cytochrome b, and rhodopsin DNA sequences confirmed that these species belong to one of the five major clades in Mantella, the M. madagascariensis group. A haplotype network constructed using 830 bp of cytochrome b in 49 individuals from seven populations revealed that M. milotympanum and M. crocea have largely similar haplotypes sharing, confirming doubts about the species validity of M. milotympanum and indicating independent evolution of bright orange pattern in M. milotympanum and M. aurantiaca. Further, clustering of four individuals of M. aurantiaca from Andranomena with M. crocea suggests incomplete lineage sorting or introgression resulting from secondary contact of refugial populations. AMOVA confirmed significant intrapopulation nucleotide diversity (>20%). These diversity patterns and our field observations indicate relatively large population sizes. Hence, overcollecting is probably a minor problem and conservation efforts should rather focus on saving some large populations from habitat destruction through logging and forest fires.

Demographic expansion of parasitic nematodes of livestock based on mitochondrial DNA regions that conflict with the infinite-sites model

Mitochondrial ND4 sequences of populations of four species of parasitic nematodes of livestock were subjected to demographic analyses. Deviation from selective neutrality was detectable using the frequency spectrum of segregating sites and highly negative neutrality statistics. However, the mitochondrial data sets do not comply with the infinite-sites model that underlies these tests, and as a consequence, it was not established whether these features are solely a result of population expansion, or whether aspects of the molecular evolution of these mitochondrial regions are also involved. Coalescent analyses based on Fu's Fs neutrality test, which incorporated estimates of rate heterogeneity, the transition-transversion ratio and nucleotide bias, as well as analyses that are fairly robust to deviations from the infinite-sites model supported population expansion. Also analyses that do not depend on the infinite-sites model suggested historical population expansion of these nematodes. The very similar time since expansion, the absence of signatures of positive selection in ND4 and the logical association with human demography imply that selective sweeps of mitochondrial variants are less probable, and that expansion is the most likely scenario for the parasitic nematodes of livestock. The methods used to characterize the expansion have different assumptions and emphasize different aspects of expansions. The resulting restrictions on the interpretation of expansions are outlined.

Population genetic structure of the toad Bufo woodhousii: an empirical assessment of the effects of haplotype extinction on nested cladistic analysis

Nested cladistic analysis (NCA) is increasingly being used to infer historical population-level processes, including population fragmentation, range expansion and long-distance colonization. However, the effects on interpretation of NCA inferences of stochastic extinction of haplotypes due to genetic drift (lineage sorting), or of haplotype loss via localized biotic or climatic influences, have not been thoroughly explored. We provide empirical evidence suggesting that NCA may misinterpret population history when haplotypes or haplotype groups from one clade are replaced by those of another clade. We do so by using NCA to analyse mitochondrial sequences from the toad Bufo woodhousii from 45 locations spanning the Great Plains and southwestern USA. Portions of this region were glaciated and/or desertified in the late Pleistocene and early Holocene, and hence uninhabitable for plains-dwelling organisms. Although NCA inferences of isolation-by-distance and gradual range expansion in B. woodhousii are compatible with expectations based on climatic data and toad biology, NCA also detected several instances of long-distance movement. Such movement seems unlikely, given the low vagility of this species. We conclude that inferences of long-distance colonization likely result from extinction of haplotypes in intervening areas. We suggest using additional methods to look for congruent inferences, and amending the NCA inference key, to help avoid misinterpretations resulting from haplotype extinction.

Dispersal of viviparity across contact zones in Iberian populations of fire salamanders (Salamandra) inferred from discordance of genetic and morphological traits

We used partial sequences of the cytochrome b mitochondrial DNA (mtDNA) gene, obtained from 76 individuals representing 45 populations of Iberian Salamandra salamandra plus 15 sequences of additional species of Salamandra and related genera, to investigate contact zones. These zones, identified by earlier allozymic and morphological analyses, are between populations of viviparous (S. s. bernardezi and S. s. fastuosa) and ovoviviparous (S. s. gallaica and S. s. terrestris) salamanders. The distribution of mtDNA and nuclear markers is mostly concordant at one contact zone (between S. s. gallaica and S. s. bernardezi), but at another (between S. s. fastuosa and S. s. terrestris) the markers are offset by about 250 km. The observed geographic variation fits a model of mtDNA capture. Among the potential mechanisms responsible for such discordance we favor a combination of range shifts due to climatic fluctuations and biased genetic admixture across moving contact zones. We apply our findings to the issue of possible homoplasy in the evolution of viviparity and conclude that viviparity likely arose only once within S. salamandra.

Population Genetics of Tor douronensis in Sarawak – A Revisit

Tor douronensis, known locally as Semah, is one of the valuable resources of Sarawak due to its high nutritional value and demand as game fish. Several molecular studies related to T. douronensis have been carried out and deposited in GenBank including the data collected from Ba Kelalan, Layar and Limbang. Although there are other studies on Tor spp., the data was not available in GenBank, thus there are not included in the analysis. One fieldtrip to Bakun Dam was carried out on June 2014 with initial aim to assess overall fish diversity. During this sampling, 11 individuals of T. douronensis were caught, which later subjected to molecular work to investigate the genetic structure and evolutionary relationship among four of T. douronensis in Sarawak using partial Cytochrome c oxidase I (COI) mtDNA gene. A fragment of 465 bp of CO1 gene of T. douronensis was successfully amplified. Based on the phylogenetic trees generated, three clade could be observed namely Central, Southern, and Northern populations; 1st clade (haplogroup I) from Bakun, 2nd clade (haplogroup II) from Layar and 3rd clade (haplogroup III) from Ba Kelalan and Ulu Limbang. Overall, there were 13 haplotypes and none was shared among populations, suggesting low level of inter-population gene flow has been observed. The small number of migrants per generation (Nm<1.0) among the population indicated that the small populations were isolated possibly due to large geographical areas. All population had undergone expansion with a large negative value and significant test of Fu’ Fs in Bakun population suggested recent expansion. In addition, result also suggested that all populations did not deviate from evolutionary neutrality.