Mitochondrial DNA Control Region Sequences Research Articles

Inter- and intra-population genetic divergence of East Asian cattle populations: focusing on Korean cattle

In order to facilitate the on-going cattle conservation and improvement programs in Korea, we examined genetic relationships among East Asian cattle, focusing on Korean native cattle, using complete mitochondrial DNA control region sequences. In total, 67 haplotypes were discriminated by 97 variable sites in East Asian cattle. Of the variable sites, 35 represented singleton variable sites and 62 were parsimony informative sites. For Korean cattle, 30 haplotypes were discriminated by 40 variable sites. The variable sites identified in this study correspond to transition or transversion point mutations. Inter-populations genetic distance varied from 0.004 to 0.052 for East Asian cattle populations. The genetic divergence observed between Korean Brown and Jeju Black (0.004) was among the lowest. The Mongolian cattle were slightly divergent from other East Asian cattle populations studied. The network analysis uncovered that Jeju Black and Yunbian samples represented the possible ancestral Haplotype within T3 Bos taurus main lineage. Thus, we hypothesized that the Jeju and Yunbian cattle may represent one of the original native North East Asian cattle in the region.

Genetic variation and phylogenetic relationship between three serow species of the genus Capricornis based on the complete mitochondrial DNA control region sequences

The molecular evidence of phylogenetic status regarding the Formosan serow (Capricornis swinhoei) is not robust and little is known about the genetic diversity of the Sumatran serow (Capricornis sumatraensis), which partly is due to the hardness in sample collection. Here we determined the sequences of the complete mitochondrial DNA control region (1,014bp) of 19 Sumatran-serow individuals. Nine new haplotypes were defined based on 78 variable sites. Combined analysis with other 32 haplotypes downloaded from the public database, including 1 Sumatran-serow, 11 Formosan-serow and 20 Japanese-serow (Capricornis crispus) haplotypes, a relatively high level of nucleotide diversity was first observed in Sumatran serow (π=0.0249). By comparative analysis with structural consensus sequences from other mammals, we have identified central, left and right domains and depicted the putative functional structure, including extend termination associated sequences and conserve sequence blocks, in mtDNA control region. The alignment of mtDNA control region revealed that both Sumatran and Japanese serow have two tandem repeats (TRs), but three TRs in Formosan serow. Phylogenetic analyses revealed that the Formosan serow is distinct species with the Japanese serow, but a sister group with the Sumatran serow. The divergence time estimated among three serow species revealed that Pleistocene climate changes and the uplift of Qinghai-Tibetan plateau might play an important role in the genetic differentiation of the serows. These results mainly provide the convinced evidence on the genetic relationship between three serow species.

Contrasting patterns of genetic diversity between the northern and southern populations of yellow bullhead catfish, Ameiurus natalis in North America

Environmental conditions have profound influence on the life history characteristics of a species, for instance, the yellow bullhead (Ameiurus natalis) population in its southernmost native range, South Florida was previously reported to be distinguished from other A. natalis populations in the United States by growth rates and feeding habits. Utilizing mitochondrial DNA control region sequence data, the present study sought to evaluate the patterns of intraspecific diversification of this North American freshwater catfish, A. natalis. The analyses have revealed the existence of four distinct matrilineal lineages (Mississippi, Gulf coast, Southeast Atlantic, and South Florida) with strong geographic specificity. Although all the lineages showed rapid demographic expansion, the South Florida lineage is shown to have greater genetic diversity than the remaining lineages. The persistence of more favorable environmental conditions and suitable habitats during the late-Pleistocene period in southern Florida could be the possible explanation for such genetic disparities among the lineages. However, taken together with the conclusion of previous studies, the present study predicted that the recurrent density-dependent process resulting from the altercation of hydrology in South Florida may cause the reduction in genetic diversity and put this species at risk in this region.

Refugia in Patagonian fjords and the eastern Andes during the Last Glacial Maximum revealed by huemul (Hippocamelus bisulcus) phylogeographical patterns and genetic diversity

AbstractAimOur aim was to determine the combined impacts of Pleistocene climatic oscillations and glacial periods with recognized biogeographical barriers on the evolutionary history of huemul deer (Hippocamelus bisulcus).LocationSouthern Chile and Argentina's Andean forest, and Patagonian fjords.MethodsWe examined the phylogeography of huemul using 772 bp of the mitochondrial DNA control region sequence from 275 samples (29 locations) collected throughout the distributional range of the species. We grouped samples into clusters based on Bayesian genetic and spatial structure analyses and reconstructed the species' phylogeographical and demographic history.ResultsWe observed 63 haplotypes that grouped into three clusters (Central Chile, North Patagonia and South Patagonia). All but five haplotypes in North and South Patagonia were distributed locally. Bayesian skyline plots showed that population sizes remained fairly constant until an increase during and after the Last Glacial Maximum. Genetic diversity was generally low, except in three populations in the eastern Andes and on Wellington Island (Patagonian fjords).Main conclusionsOur results suggest that the biogeographical separation of huemul into phylogeographical groups has been heavily influenced by Pleistocene glacial stages, and more recently by habitat fragmentation and isolation. This provides the first evidence that the region west of the Cordilleran ice field was a refugium for at least one species of large mammal during the Pleistocene in southern South America. These results have direct implications for the conservation and management of this endangered deer species.

Mitochondrial DNA population structure of the scalloped lobster Panulirus homarus (Linnaeus 1758) from the West Indian Ocean

AbstractFarhadi, A., Farhamand, H., Nematollahi, M. A., Jeffs, A., and Lavery, S. D. 2013. Mitochondrial DNA population structure of the scalloped lobster Panulirus homarus (Linnaeus 1758) from the West Indian Ocean. – ICES Journal of Marine Science, 70: . The scalloped spiny lobster Panulirus homarus (Linnaeus, 1758) is a highly valuable species with a widespread global distribution, ranging from South Africa around the Persian Gulf, and across the Indo-Pacific as far as Japan and French Polynesia. Throughout its range, the species is an important fisheries species with global annual landings in the order of 3000 t. Mitochondrial control region DNA sequences (625 bp) were used to investigate the population genetic structure of this species in the West Indian Ocean (WIO), using 137 individuals collected from four sites, including two locations along the south coast of Iran, and sites along the coast of the Sultanate of Oman in the Arab Sea, as well as Tanzania in eastern Africa. High levels of haplotype diversity (H = 0.997) were observed in all populations, although nucleotide diversity was relatively low (pi = 0.035). The hypothesis of a single stock in this region was rejected, with highly significant genetic differentiation revealed between Tanzania and the remaining locations (overall ΦST = 0.039, p < 0.00001), as well as slight genetic structure in the Arabian Sea region. Historical population expansion was inferred from Tajima's D and Fu's F tests. The results reveal at least two distinct genetic stocks in WIO and may have major implications for fisheries management.

Phylogenetic Relationship of the Greater White-Fronted GooseAnser albifronsSubspecies Wintering in the Palaearctic Region

Greater White-fronted Goose Anser albifrons has a holarctic breeding distribution and is polymorphic. Three subspecies winter in the Palaearctic region, one of which also winters in the Nearctic region: European White-fronted Goose A. a. albifrons breeds in the far north of Europe and Asia and winters in the south and west of Europe; Pacific White-fronted Goose A. a. frontalis breeds in east Siberia and Arctic Canada and winters in East Asia and United States; and Greenland White-fronted Goose A. a. flavirostris breeds in Greenland and winters in Ireland and western Scotland. The phylogenetic relationships among these three subspecies are unclear. We determined the mitochondrial DNA control region sequences of Pacific Whitefronted Goose, using 66 shed feathers collected from wintering sites in Japan, and compared the sequences with those previously published for Greater White-fronted Goose subspecies. Phylogenetic trees and networks revealed that there are three clades within the species. The sequence divergence among the clades corresponds to divergence long before the last glacial maximum (15–25 thousand years ago), which suggests the existence of at least three ancient refugia for the species. However, all three subspecies consist of haplotypes from two of the three clades. This suggests that they originated from individuals that survived in two refugia during the last glacial period.

Genetic structure and different color morphotypes suggest the occurrence and bathymetric segregation of two incipient species of Sebastes off Argentina

Rockfishes of the genus Sebastes are extensively distributed in the Pacific and Atlantic oceans. Although the occurrence of two morphologically similar species in the Southern Hemisphere, Sebastes oculatus and Sebastes capensis, is now clearly established, the taxonomic status and phylogeographic patterns for the genus in the region have not yet been completely resolved. In this study, we provide new insights into the taxonomy and evolutionary relationships of rockfishes inhabiting the Southwestern Atlantic Ocean, off the coast of mainland Argentina, by combining mitochondrial DNA (mtDNA) control region sequences, microsatellite data, and color pattern analyses. Differences in coloration ("dark" and "light" fish) together with bathymetric segregation between color morphotypes were evident from fish collection and literature review. In addition, the mtDNA phylogenetic analysis and Bayesian clustering analysis using microsatellite data separated the fish into two distinct groups (F ST = 0.041), most likely representing incipient species. Our results suggest that speciation-by-depth in the absence of physical barriers could be a widespread mechanism of speciation in Sebastes from both the Northern and Southern Hemispheres. Nevertheless, the degree of genetic differentiation found, added to the large number of individuals displaying high levels of admixture, points to the occurrence of incomplete reproductive barriers between color morphotypes. Beyond the taxonomic and phylogeographic implications of our findings, the occurrence of distinct groups of Sebastes off the coast of Argentina being targeted by different fisheries (angling and trawling) has consequences for the design and implementation of appropriate fishery regulations to avoid overharvest of either group.

Green turtles (Chelonia mydas) of the north‐western Arabian Gulf, Kuwait: the need for conservation

Abstract This study provides the first ever baseline data on reproductive ecology and genetic identification of the endangered green turtle, Chelonia mydas, in the north‐western Arabian Gulf, Kuwait. Two offshore islands were surveyed for nesting turtles in 2004 and 2005. The findings reveal that nesting (nest numbers, nesting season, incubation period, clutch size, and hatching success) by green turtles off the Kuwait coast is comparable with that of C. mydas worldwide. At Umm Al‐Maradim Island, no turtles nested during 2005 because of excavation and dredging activities associated with the construction of a coastguard dock. Mitochondrial DNA control region sequences of 97 green turtles revealed six haplotypes, of which five have not previously been reported from rookeries in adjoining regional waters or adjacent oceans; this signifies the possibility of them being novel to the region. Prudent management approaches, represented mainly by the rehabilitation and restoration of Umm Al‐Maradim Island and the designation of both foraging and nesting habitats as marine protected areas (MPAs), should be implemented by national as well as regional policy‐makers to maintain the region's native biological diversity.Copyright © 2013 John Wiley & Sons, Ltd.

Composition of green turtle feeding aggregations along the Japanese archipelago: implications for changes in composition with current flow

In order to develop effective conservation strategies for endangered migratory species, the link between feeding and breeding grounds needs to be clarified. In this study, the genetic compositions of consecutive Japanese feeding aggregations of green turtles (Chelonia mydas) along the Kuroshio Current were examined by mixed-stock analyses of mitochondrial DNA control-region sequences. The results indicated that the southern feeding aggregation around Yaeyama (24.3°N, 124.0°E) was sourced from various Pacific rookeries in the Yaeyama, Ogasawara, Western Pacific, and Indian Oceans and Southeast Asia. Among northern feeding aggregations, the Ginoza (26.5°N, 128.0°E) aggregation was also sourced from the Western Pacific Ocean, but the Nomaike (31.4°N, 130.1°E), Muroto (33.2°N, 134.2°E), and Kanto (35.6°N, 140.5°E) aggregations were contributed mostly by the closer Ogasawara rookeries. The reduced contribution from tropical Pacific rookeries to northern feeding aggregations and the significant correlation between genetic differentiation and geographical distance matrices of feeding aggregations indicated that most hatchlings from these regions transported by the Kuroshio Current settle in upstream feeding grounds along the Japanese archipelago, implying that current flow influences the composition of feeding aggregations. Differences in the composition of relatively close neritic feeding aggregations have important conservation implications, for which both regional and multinational conservation strategies are needed.

Genetic data confirm critical status of the reintroduced Dinaric population of Eurasian lynx

Eurasian lynx (Lynx lynx) reintroduction to the Dinaric Mountains is considered one of the most successful reintroductions of a large predator. Six reintroduced ani- mals founded the population, which rapidly expanded from Slovenia, through Croatia, and all the way to Bosnia and Herzegovina. However, a decrease of the population size has been observed during the last 10-15 years. Considering that possible inbreeding depression would be additive to threats like poaching, traffic mortality and prey base depletion, another extinction of this species from the Dinaric Mountains is a real possibility. We analyzed 204 samples collected between 1979 and 2010 using twenty microsatellite loci and 900-bp mitochondrial DNA control region sequence to evaluate conservation genetics aspects of this endangered population. Both markers confirmed low genetic variability of the Dinaric lynx population, and considerable effective inbreeding (0.3) compared to the source Carpathian population. Our analysis of effective population size and microsatellite variability supported field observations of decreasing population number. As a natural recolonization is a very remote possibility, we recommend population augmentation from a large source population.

Migrations as a reason for genetic homogeneity of pacific herring (Clupea pallasii) from the Sea of Okhotsk

Using parameters of molecular variability, calculated on the basis of comparison of mitochondrial DNA (mtDNA) control region sequences, no differentiation between samples of spawning herring from different regions of Sea of Okhotsk was found (p > 0.05). The absence of differentiation can be attributed to a permanent gene flow between schools, and it is possible to establish the value of the flow of migrants (Nm) only indirectly. Analysis of total molecular variability (global AMOVA) demonstrated that, when combining all studied samples or when pairwise uniting them, the intersample component accounts for approximately 0.1–0.2% of polymorphism with a high level of significance (p > 0.1); it can be considered a consequence of the influence of intense migrations. When estimating the minimal portion of migrants, it was determined that their amount is 3.6–9.5% per year by locality.

Recent geological events and intrinsic behavior influence the population genetic structure of the chiru and tibetan gazelle on the tibetan plateau.

The extent to which a species responds to environmental changes is mediated not only by extrinsic processes such as time and space, but also by species-specific ecology. The Qinghai-Tibetan Plateau uplifted approximately 3000 m and experienced at least four major glaciations during the Pleistocene epoch in the Quaternary Period. Consequently, the area experienced concurrent changes in geomorphological structure and climate. Two species, the Tibetan antelope (Pantholops hodgsonii, chiru) and Tibetan gazelle (Procapra picticaudata), both are endemic on the Qinghai-Tibetan Plateau, where their habitats overlap, but have different migratory behaviors: the chiru is inclined to have female-biased dispersal with a breeding migration during the calving season; in contrast, Tibetan gazelles are year-round residents and never migrate distantly. By using coalescence methods we compared mitochondrial control region DNA sequences and variation at nine microsatellite loci in these two species. Coalescent simulations indicate that the chiru and Tibetan gazelle do not share concordant patterns in their genealogies. The non-migratory Tibetan gazelle, that is more vulnerable to the impact of drastic geographic changes such as the elevation of the plateau, glaciations and so on, appears to have a strong population genetic structure with complicated demographic history. Specifically, the Tibetan gazelle population appears to have experienced isolation and divergence with population fluctuations since the Middle Pleistocene (0.781 Ma). However, it showed continued decline since the Upper Pleistocene (0.126 Ma), which may be attributed to the irreversible impact of increased human activities on the plateau. In contrast, the migratory chiru appears to have simply experienced population expansion. With substantial gene flow among regional populations, this species shows no historical population isolation and divergence. Thus, this study adds to many empirical studies that show historical and contemporary extrinsic and intrinsic processes shape the recent evolutionary history and population genetic structure of species.

Microsatellite and mitochondrial DNA analysis of the genetic structure of Chinese horseshoe crab ( Tachypleus tridentatus ) in southeast China coast

Chinese horseshoe crab ( Tachypleus tridentatus ) is a Xiphosura animal of significant commercial importance and in danger of extinction in China. To better estimate how genetic structure can be used to obtain a conservation perspective of the species, genetic variation was examined in nine locations covering its distributing range in the coast of Chinese mainland using ten nuclear microsatellite DNA loci and mitochondrial DNA control region (CR) sequences. Moderate levels of genetic diversity were detected (expected heterozygosity from microsatellites was 0.635, haplotype diversity from mitochondrial DNA was 0.800) as a whole. Significant genetic differentiation was detected only by mitochondrial DNA ( F ST = 0.0693, P < 0.01), while microsatellite markers indicated nuclear genetic homogeneity of these locations. Probably, nuclear genetic homogeneity was caused by outbreeding among different groups due to artificial transporting. Very weak genetic differentiation indicates that reintroduction programs of the movement and mixing of horseshoe crab from different locations will result in minimal negative genetic effects. Upon four management units were inferred from the results of CR analysis, accordingly four or more nature reserves should be established to conserve this endangered animal along the Chinese coast. Haplotype network pattern indicated that T. tridentatus population in Chinese coast has undergone historic population expansion and very recent historic population recession. Mismatch distributions analysis also revealed existence of historic demographic expansion. Keywords : Tachypleus tridentatus , microsatellites, mitochondrial DNA, population structure, genetic diversity African Journal of Biotechnology Vol. 12(16), pp. 2088-2099

Phylogeography and population genetic structure of the Talas tuco-tuco (Ctenomys talarum): integrating demographic and habitat histories

We examined the phylogeography of the South American subterranean rodent Ctenomys talarum (Talas tucotuco) using mitochondrial DNA control region (D-loop) sequences. This species is an herbivorous rodent endemic to the province of Buenos Aires, Argentina, that lives in natural grasslands in coastal sand dune habitats and in some fragmented inland populations. In this study we assessed the genetic relationship among populations of C. talarum across its entire distributional range and analyzed how the geological history of the habitat has affected the genetic structure and demographic history of these populations. A complex network of haplotypes in conjunction with analysis of molecular variance results showed high genetic subdivision and a strong phylogeographic pattern among populations of C. talarum .P airwiseFST-values showed significant differentiation among all populations studied. The overall pattern was similar to that expected under the isolation-by-distance model, suggesting equilibrium between gene flow and local genetic drift. Major geographical barriers (e.g., rivers and unsuitable habitat) in the area, in conjunction with population isolation, appeared to be associated with strong genetic differentiation among the different geographical groups. Local mismatch distributions and tests of neutrality suggest contrasting histories for different groups of populations; although some populations appeared to be characterized by demographic stability and no significant departures from neutrality, others showed departures from strict neutrality consistent with a recent demographic expansion. Finally, a close association seems to exist between the major climatic changes that occurred during the late Pleistocene and Holocene in the central region of Argentina and the main historical demographic changes inferred from C. talarum. Current populations of C. talarum appear to be relicts of a more extended historical distribution along the Argentinean Pampas. These historical extinctions, however, have not erased the signature of long-term stability and geographical structure in this species along the coastal and inland distribution ranges.

Genetic evidence of multiple matrilineal lineages of the channel catfish, Ictalurus punctatus in North America

Using mitochondrial DNA control region (mtDNA CR) sequence data the present study evaluates the genetic status of the wild populations of channel catfish, Ictalurus punctatus, in North America. A total of 584 individuals representing 56 drainages across its distributional range in the United States were collected. There were 105 mtDNA CR haplotypes defined by 51 variable sites. Phylogenetic analyses have revealed the existence of six distinct matrilineal genetic lineages of channel catfish in the United States. Four of these lineages were restricted to southeast Gulf Coast, a region that never glaciated during the Pleistocene. While samples from the Mississippi river and its tributaries represent a single genetic lineage, samples from the southeast Atlantic coastal plain drainages formed a unique lineage. Each lineage should be regarded as an evolutionarily significant unit/management unit and therefore separate management and conservation strategies should be undertaken in order to conserve the genetic resources.

Genetic diversity and population structure of yellow catfish Pelteobagrus fulvidraco from five lakes in the middle and lower reaches of the Yangtze River, China, based on mitochondrial DNA control region

Genetic diversity and population structure of yellow catfish Pelteobagrus fulvidraco were examined by using mitochondrial DNA control region sequences in 143 specimens sampled from five lakes in the middle and lower reaches of the Yangtze River, China; 151 polymorphic sites defined 72 distinct haplotypes. Haplotype diversity indices (0.903–0.953) and nucleotide diversity indices (0.00378–0.00970) demonstrated low genetic diversity of the yellow catfish populations in the five lakes. The analysis of molecular variance and the fixation index ( = 0.0896) revealed insignificant genetic difference between samples from different lakes. In addition, neutral tests and analysis of mismatch distribution suggested that yellow catfish might have undergone a population expansion. Neighbor-joining tree indicated a correlation between these population genetic differences and geographic distance. This study revealed the extant population genetic diversity and structure of the yellow catfish and was in favor of the related fishery management issues including fishery stock identification, conservation, and artificial breeding.

Pleistocene sea level fluctuations and the phylogeography of the dugong in Australian waters

AbstractWe investigated phylogeography, demography, and population connectivity of the dugong (Dugong dugon) in Australian waters using mitochondrial control region DNA sequences from 177 Australian dugongs and 11 from elsewhere. The dugong is widespread in shallow Indo‐West Pacific waters suitable for growth of its main food, seagrass. We hypothesized that the loss of habitat and creation of a land barrier (the Torres Strait landbridge) during low sea level stands associated with Pleistocene glacial cycles have left a persisting genetic signature in the dugong. The landbridge was most recently flooded about 7,000 yr ago. Individual dugongs are capable of traveling long distances, suggesting an alternative hypothesis that there might now be little genetic differentiation across the dugong's Australian range. We demonstrated that Australian dugongs fall into two distinct maternal lineages and exhibit a phylogeographic pattern reflecting Pleistocene sea‐level fluctuations. Within each lineage, genetic structure exists, albeit at large spatial scales. We suggest that these lineages diverged following the last emergence of the Torres Strait landbridge (ca. 115 kya) and remained geographically separated until after 7 kya when passage through Torres Strait again became possible for marine animals. Evidence for population growth in the widespread lineage, especially after the last glacial maximum, was detected.

First evidence of autotriploidization in sterlet (Acipenser ruthenus)

Polyploidization has played an important role in vertebrate evolution. Acipenseridae bring clear examples of polyploidy ancestry and, also, polyploidization seems to be an ongoing process in these fishes. In the present study, the genetic origin of six triploid specimens morphologically determined as Acipenser ruthenus from commercial aquaculture was analyzed using a combination of mitochondrial and nuclear markers. A further five successive statistical analyses including median joining of mitochondrial DNA control region sequences, principal coordinate analysis (PCA), factorial correspondence analysis (FCA), STRUCTURE assignation, and NewHybrids status determination for microsatellite data were applied for the clarification of the origin of one extra chromosome set added in these triploids genomes. Although interspecific hybridization had been suggested as a source of these triploids, the statistical analyses showed that the investigated triploids originate from autotriploidization rather than from interspecific hybridization. Therefore, we conclude that a combination of molecular markers with suitable statistical analyses should be used to verify the origin of unusual ploidy level. Evidently, such an approach is critically essential in aquaculture, where interspecific hybridization is very common and usually detected by changes in ploidy levels only.

Phylogeographic structure of a protogynous hermaphrodite species, the ballan wrasse Labrus bergylta, in Ireland, Scotland, and Norway, using mitochondrial DNA sequence data

AbstractD'Arcy, J., Mirimin, L., and FitzGerald, R. Phylogeographic structure of a protogynous hermaphrodite species, the ballan wrasse Labrus bergylta, in Ireland, Scotland, and Norway, using mitochondrial DNA sequence data. – ICES Journal of Marine Science, 70: 685–693. The ballan wrasse, Labrus bergylta, is a protogynous hermaphrodite marine fish species that inhabits coastal waters of the eastern North Atlantic. Sequential hermaphrodite species tend to be characterized by a skewed sex ratio, which is thought to lead to marked population structuring due to a reduced effective number of breeders. Furthermore, due to its large body size (compared with other wrasse species) and its peculiar feeding behaviour, this species has been identified as a candidate cleaner fish to be used in parasite control of farmed finfish. In the present study, we used mitochondrial DNA (control region) sequence data to investigate the genetic diversity and population structuring of ballan wrasse in waters around the British Isles and southern Norway. Ballan wrasse in southern Norway showed lower levels of genetic diversity than around the British Isles, which appear to be the result of historical demographic events (population bottleneck followed by expansion). Analysis of mismatch distributions and the presence of two highly divergent clades unevenly represented in Atlantic and Scandinavian regions suggest distinct recolonization patterns in these two regions. These results provide a first insight on the status of wild populations of ballan wrasse in the eastern North Atlantic, with implications for conservation and management.

Genetic structure of introduced populations: 120‐year‐old DNA footprint of historic introduction in an insular small mammal population

Wildlife populations have been introduced to new areas by people for centuries, but this human-mediated movement can disrupt natural patterns of genetic structure by altering patterns of gene flow. Insular populations are particularly prone to these influences due to limited opportunities for natural dispersal onto islands. Consequently, understanding how genetic patterns develop in island populations is important, particularly given that islands are frequently havens for protected wildlife. We examined the evolutionary origins and extent of genetic structure within the introduced island population of red squirrels (Sciurus vulgaris) on the Channel Island of Jersey using mitochondrial DNA (mtDNA) control region sequence and nuclear microsatellite genotypes. Our findings reveal two different genetic origins and a genetic architecture reflective of the introductions 120 years ago. Genetic structure is marked within the maternally inherited mtDNA, indicating slow dispersal of female squirrels. However, nuclear markers detected only weak genetic structure, indicating substantially greater male dispersal. Data from both mitochondrial and nuclear markers support historic records that squirrels from England were introduced to the west of the island and those from mainland Europe to the east. Although some level of dispersal and introgression across the island between the two introductions is evident, there has not yet been sufficient gene flow to erase this historic genetic “footprint.” We also investigated if inbreeding has contributed to high observed levels of disease, but found no association. Genetic footprints of introductions can persist for considerable periods of time and beyond traditional timeframes of wildlife management.