We successfully extracted DNA from a bone sample of a Neolithic skeleton (dated 3,600 +/- 60 years BP) excavated in northeastern Yakutia (east Siberia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by sequencing of the hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The STR profile, the mitochondrial haplotype, and the haplogroup determined were compared with those of modern Eurasian and Native American populations. The results showed the affinity of this ancient skeleton with both east Siberian/Asian and Native American populations.
How species respond to an increased availability of habitat, for example at the end of the last glaciation, has been well established. In contrast, little is known about the opposite process, when the amount of habitat decreases. The hypothesis of habitat tracking predicts that species should be able to track both increases and decreases in habitat availability. The alternative hypothesis is that populations outside refugia become extinct during periods of unsuitable climate. To test these hypotheses, we used ancient DNA techniques to examine genetic variation in the arctic fox (Alopex lagopus) through an expansion/contraction cycle. The results show that the arctic fox in midlatitude Europe became extinct at the end of the Pleistocene and did not track the habitat when it shifted to the north. Instead, a high genetic similarity between the extant populations in Scandinavia and Siberia suggests an eastern origin for the Scandinavian population at the end of the last glaciation. These results provide new insights into how species respond to climate change, since they suggest that populations are unable to track decreases in habitat avaliability. This implies that arctic species may be particularly vulnerable to increases in global temperatures.
Although the cultural and nutritive importance of the turkey (Meleagris gallopavo) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC-AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey (Meleagris gallopavo gallopavo) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices.
Cites: Mol Ecol. 2002 Apr;11(4):643-5711972754
Cites: Bioinformatics. 2003 Aug 12;19(12):1572-412912839
Peregrine falcon populations underwent devastating declines in the mid-20th century due to the bioaccumulation of organochlorine contaminants, becoming essentially extirpated east of the Great Plains and significantly reduced elsewhere in North America. Extensive re-introduction programs and restrictions on pesticide use in Canada and the United States have returned many populations to predecline sizes. A proper population genetic appraisal of the consequences of this decline requires an appropriate context defined by (i) meaningful demographic entities; and (ii) suitable reference populations. Here we explore the validity of currently recognized subspecies designations using data from the mitochondrial control region and 11 polymorphic microsatellite loci taken from 184 contemporary individuals from across the breeding range, and compare patterns of population genetic structure with historical patterns inferred from 95 museum specimens. Of the three North American subspecies, the west coast marine subspecies Falco peregrinus pealei is well differentiated genetically in both time periods using nuclear loci. In contrast, the partitioning of continental Falco peregrinus anatum and arctic Falco peregrinus tundrius subspecies is not substantiated, as individuals from these subspecies are historically indistinguishable genetically. Bayesian clustering analyses demonstrate that contemporary genetic differentiation between these two subspecies is mainly due to changes within F. p. anatum (specifically the southern F. p. anatum populations). Despite expectations and a variety of tests, no genetic bottleneck signature is found in the identified populations; in fact, many contemporary indices of diversity are higher than historical values. These results are rationalized by the promptness of the recovery and the possible introduction of new genetic material.
Species biogeography is a result of complex events and factors associated with climate change, ecological interactions, anthropogenic impacts, physical geography, and evolution. To understand the contemporary biogeography of a species, it is necessary to understand its history. Specimens from areas of localized extinction are important, as extirpation of species from these areas may represent the loss of unique adaptations and a distinctive evolutionary trajectory. The walrus (Odobenus rosmarus) has a discontinuous circumpolar distribution in the arctic and subarctic that once included the southeastern Canadian Maritimes region. However, exploitation of the Maritimes population during the 16th-18th centuries led to extirpation, and the species has not inhabited areas south of 55°N for ~250 years. We examined genetic and morphological characteristics of specimens from the Maritimes, Atlantic (O. r. rosmarus) and Pacific (O. r. divergens) populations to test the hypothesis that the first group was distinctive. Analysis of Atlantic and Maritimes specimens indicated that most skull and mandibular measurements were significantly different between the Maritimes and Atlantic groups and discriminant analysis of principal components confirmed them as distinctive groups, with complete isolation of skull features. The Maritimes walrus appear to have been larger animals, with larger and more robust tusks, skulls and mandibles. The mtDNA control region haplotypes identified in Maritimes specimens were unique to the region and a greater average number of nucleotide differences were found between the regions (Atlantic and Maritimes) than within either group. Levels of diversity (h and p) were lower in the Maritimes, consistent with other studies of species at range margins. Our data suggest that the Maritimes walrus was a morphologically and genetically distinctive group that was on a different evolutionary path from other walrus found in the north Atlantic.
In this study, we explore the geographic and temporal distribution of a unique variant of the O blood group allele called O1v(G542A) , which has been shown to be shared among Native Americans but is rare in other populations. O1v(G542A) was previously reported in Native American populations in Mesoamerica and South America, and has been proposed as an ancestry informative marker. We investigated whether this allele is also found in the Tlingit and Haida, two contemporary indigenous populations from Alaska, and a pre-Columbian population from California. If O1v(G542A) is present in Na-Dene speakers (i.e., Tlingits), it would indicate that Na-Dene speaking groups share close ancestry with other Native American groups and support a Beringian origin of the allele, consistent with the Beringian Incubation Model. If O1v(G542A) is found in pre-Columbian populations, it would further support a Beringian origin of the allele, rather than a more recent introduction of the allele into the Americas via gene flow from one or more populations which have admixed with Native Americans over the past five centuries. We identified this allele in one Na-Dene population at a frequency of 0.11, and one ancient California population at a frequency of 0.20. Our results support a Beringian origin of O1v(G542A) , which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus. This result is consistent with the hypothesis that Na-Dene and other Native American populations primarily derive their ancestry from a single source population.
Small, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland.
Microsatellite diversity within the subspecies (HE?=?0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (FST?=?0.107) than in maternally inherited mtDNA (FST?=?0.444), indicating a sevenfold difference in the gene flow mediated by males versus females.
Genetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.
Many East African mountains are characterized by an exceptionally high biodiversity. Here we assess the hypothesis that climatic fluctuations during the Plio-Pleistocene led to ecological fragmentation with subsequent genetic isolation and speciation in forest habitats in East Africa. Hypotheses on speciation in savannah lineages are also investigated. To do this, mitochondrial DNA sequences from a group of bush crickets consisting of both forest and savannah inhabiting taxa were analysed in relation to Plio-Pleistocene range fragmentations indicated by palaeoclimatic studies. Coalescent modelling and mismatch distributions were used to distinguish between alternative biogeographical scenarios. The results indicate two radiations: the earliest one overlaps in time with the global spread of C4 grasslands and only grassland inhabiting lineages originated in this radiation. Climatically induced retraction of forest to higher altitudes about 0.8 million years ago, promoting vicariant speciation in species inhabiting the montane zone, can explain the second radiation. Although much of the biodiversity in East Africa is presently threatened by climate change, past climatic fluctuations appear to have contributed to the species richness observed in the East African hot spots. Perceiving forests as centres of speciation reinforces the importance of conserving the remaining forest patches in the region.
The Yakuts are a Turkic-speaking population from northeastern Siberia who are believed to have originated from ancient Turkic populations in South Siberia, based on archaeological and ethnohistorical evidence. In order to better understand Yakut origins, we modeled 25 demographic scenarios and tested by coalescent simulation whether any are consistent with the patterns of mtDNA diversity observed in present-day Yakuts. The models consist of either two simulated demes that represent Yakuts and a South Siberian ancestral population, or three demes that also include a regional Northeast Siberian population that served as a source of local gene flow into the Yakut deme. The model that produced the best fit to the observed data defined a founder group with an effective female population size of only 150 individuals that migrated northwards approximately 1,000 years BP and who experienced significant admixture with neighboring populations in Northeastern Siberia. These simulation results indicate a pronounced founder effect that was primarily kin-structured and reconcile reported discrepancies between Yakut mtDNA and Y chromosome diversity levels.
A complete mitochondrial genome sequence of amphipoda Eulimnogammarus vittatus Dybowsky, 1874 from Lake Baikal was obtained using next-generation sequencing approach. Mitochondrial DNA with the length of 15,534?bp contains 13 protein-coding genes, 2 ribosomal RNA, 23 transfer RNA and non-coding sequences: a putative control region and 7 intergenic spacers. A brief comparative analysis of mitochondrial genomes of E. vittatus and its sister species Eulimnogammarus verrucosus was performed.