Conservation genetics of the black rhinoceros (Diceros bicornis)

We analysed genetic variation in mitochondrial DNA (mtDNA) control region in the Diceros bicornis minor and D. b. michaelianimals at the Western Plains Zoo, which form part of an international ex-situ breeding program. Six of the nine D. b. minor animals were wild-caught from Zimbabwe during the 1990s, and our study revealed five distinct mtDNA haplotypes, and a haplotype diversity of 0.86 in the colony. Phylogenetic relationships between mtDNA haplotypes analyzed using the neighbor joining method reveal that for the small sample available, D. b. minor and D. b. michaeli are reciprocally monophyletic and represent separate ancestral lineages. Nucleotide divergence between the black and and white rhinoceros(Ceratotherium simum) was 14.0%, and nucleotide divergencebetween the D. b. minor and the D. b. michaeli subspecies was 2.6%. This suggests a divergence time for the two blackrhinoceros subspecies of between 0.93 MY and 1.3 MY.     

The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake

Although new empirical evidence shows that sympatric speciation has occurred in some species, there are few indisputable model organisms for this process of speciation. The two subspecies ( Gymnocypris eckloni eckloni and G . e . scoliostomus ) of the schizothoracine Gymnocypris fish species complex from a small glacier lake in the Tibetan Plateau, Lake Sunmcuo, fit several of the key characteristics of the sympatric speciation model. We used combined mitochondrial control region sequences and the cytochrome b gene (1894 bp) to address the phylogenetics and population genetics of 232 specimens of G . e . eckloni and G . e . scoliostomus , as well as all of its closely related sister species. We found that: (i) a total of four old lineages were uncovered in the widespread G . e . eckloni , of which only one was shown to be shared with all G . e . scoliostomus individuals and (ii) the new subspecies ( G . e . scoliostomus ) evolved in Lake Sunmcuo from the ancestral G . e . eckloni population within approximately 0.057 Ma. These two taxa of the species complex are morphologically distinct, and reproductive isolation is further suggested. Ecological disruptive selection based on morphological traits (e.g. mouth cleft characters) and food utilization may be a mechanism of incipient speciation of two sympatric populations within Lake Sunmcuo. This study provides the first genetic evidence for sympatric speciation in the schizothoracine fish.     

Mitochondrial lineages reveal intense gene flow between Iberian wild boars and South Iberian pig breeds

The phylogeography of wild boars (WB) and domestic pigs (Sus scrofa) has contributed important insights into where and when domestication occurred. The geographic distribution of two core haplotypes (E1a and E1c) of the main European phylogenetic clade suggests that Central Europe was an early domestication centre, although the complexity of the pattern does not exclude the possibility that multiple domestication events occurred in different regions. To investigate the relationships among WB and domestic pig breeds in Iberia, a fragment of the mitochondrial DNA control region from a large sample (n = 409) of WB and local pig breeds was co‐analysed with published sequences from other European populations. The Iberian sample revealed a high frequency of a sub‐cluster (E1c) of the European haplogroup E1 in 77% of total Iberian samples, 96% of WB, 90% of Alentejano (Portugal) and 87% of Iberian breed pigs (Spain; Black Hairy, Black Hairless and Red varieties). Low genetic distance (F’_ST = 0.105) was observed between Alentejano (Portugal) and Iberian breed pigs (Spain). Alentejano and Iberian breed pigs showed low genetic distances to both Iberian and Central European WB (average F’_ST = 0.345 and 0.215, respectively). This pattern suggests that early pig husbandry in the Iberian Peninsula did not solely rely on imported Central European stock, but also included the recruitment of local WB.     

Recent divergence between two morphologically differentiated subspecies of bluethroat (Aves: Muscicapidae: Luscinia svecica) inferred from mitochondrial DNA sequence variation

We assessed the mitochondrial DNA sequence divergence of a 718 bp fragment of the control region and 1007 bp of the cytochrome b gene between two allopatric morphologically different subspecies of bluethroat ( Luscinia svecica ). None of the 17 total haplotypes was shared between L. s. namnetum and L. s. svecica . However, the mean distances between subspecies were very low for both fragments (0.00168 ± 0.00001 (mean ± SE) for the control region; 0.00306 ± 0.00016 for the cytochrome b gene). Only one substitution made the two subspecies genetically differentiated, highlighting their recent divergence. Interestingly, the control region was not more variable than the cytochrome b gene.     

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

We examined the sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 286 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified, NEP), western Europe (domesticus, DOM) and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37–0.47 and 0.14–0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of the four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia and Korea, are inferred, with the possibility of several different routes.     

Comparative phylogeography of three endemic rodents from the Albertine Rift, east central Africa

The major aim of this study was to compare the phylogeographic patterns of codistributed rodents from the fragmented montane rainforests of the Albertine Rift region of east central Africa. We sampled individuals of three endemic rodent species, Hylomyscus denniae, Hybomys lunaris and Lophuromys woosnami from four localities in the Albertine Rift. We analysed mitochondrial DNA sequence variation from fragments of the cytochrome b and control region genes and found significant phylogeographic structuring for the three taxa examined. The recovered phylogenies suggest that climatic fluctuations and volcanic activity of the Virunga Volcanoes chain have caused the fragmentation of rainforest habitat during the past 2 million years. This fragmentation has played a major role in the diversification of the montane endemic rodents of the region. Estimation of the divergence times within each species suggests a separation of the major clades occurring during the mid to late Pleistocene.     

Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.