Microsatellite analysis of genetic diversity of the Vietnamese sika deer (Cervus nippon pseudaxis).

J Hered. 2004 Jan-Feb; 95(1):11-8.


The Vietnamese sika deer (Cervus nippon pseudaxis) is an endangered subspecies of economic and traditional value in Vietnam. Most living individuals are held in traditional farms in central Vietnam, others being found in zoos around the world. Here we study the neutral genetic diversity and population structure of this subspecies using nine microsatellite loci in order to evaluate the consequences of the limited number of individuals from which this population was initiated and of the breeding practices (i.e., possible inbreeding). Two hundred individuals were sampled from several villages. Our data show both evidence for limited local inbreeding and isolation by distance with a mean F(ST) value of 0.02 between villages. This suggests that exchange of animals occurs at a local scale, at a rate such that highly inbred mating is avoided. However, the genetic diversity, with an expected heterozygosity (H(e)) of 0.60 and mean number of alleles (k) of 5.7, was not significantly larger than that estimated from zoo populations of much smaller census size (17 animals sampled; H(e) = 0.65, k = 4.11). Our results also suggest that the Vietnamese population might have experienced a slight bottleneck. However, this population is sufficiently variable to constitute a source of individuals for reintroduction in the wild in Vietnam.


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Genetic diversity analysis of captive populations : the Vietnamese sika deer (Cervus nippon pseudaxis) in zoological parks.

Zoo Biology 22:  465-475.


The Vietnamese sika deer (Cervus nippon pseudaxis) is an endangered subspecies; it has disappeared in the wild, but is being bred in zoological parks. We studied the neutral genetic diversity and population structure of herds kept in different European zoos, using nine microsatellite loci. The goal was to evaluate the consequences of founding effects and breeding practices on the level and structure of genetic variability. The level of genetic diversity within the European zoos is not lower than that of the populations kept in Vietnamese farms. Strong differences among zoological parks and between the European group and the Vietnamese population were detected. This is probably due to founding effects, genetic drift, and possibly hybridization in both Europe and Vietnam. We expected to find a much lower level of genetic diversity in Europe. The current overall level of genetic diversity is probably due to the recent introduction of Cuc Phuong individuals, and to important differences among the populations of different zoological parks, which increase the total genetic variability. Although the current level of genetic variability is not particularly low, future levels are probably threatened by the current herd sizes and structure. Based on these results, management guidelines are proposed.


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Samstag, 15 Dezember 2018 10:38


Captive breeding of squirrel monkeys, Saimiri sciureus and Saimiri boliviensis: The problem of hybrid groups.

Zoo Biology 17 (2): 95-109


The electrophoretic variability of blood proteins coding for up to 32 genetic loci was analyzed in 108 squirrel monkeys (Saimiri sciureus, Saimiri boliviensis, hybrids) from two captive colonies. Twelve polymorphic loci with 31 alleles are reported. The biallelic Ada* locus, G‐statistics and Hardy‐Weinberg genotype equilibria are useful for recognizing hybrids between S. sciureus and S. boliviensis. Backcrosses in hybrid stocks and gene flow in a natural hybrid belt, however, complicate the taxonomic diagnosis of captive specimens: S. sciureus phenotypes imported from Peru possessed the allele Ada*132, which generally characterizes S. boliviensis (or species hybrids). The complex taxonomy of Saimiri spp. Requires careful planning of captive breeding. We suggest a genetic analysis of the founder individuals before their inclusion in the European studbook population and to breed S. sciureus from Guyana separately from Peruvian imports, because the latter bear a greater risk of being taxonomically heterogeneous.


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Cryptic, Sympatric Diversity in Tegu Lizards of the Tupinambis teguixin Group (Squamata, Sauria, Teiidae) and the Description of Three New Species.

PLoS ONE 11(8): e0158542. https://doi.org/10.1371/journal.pone.0158542


Tegus of the genera Tupinambis and Salvator are the largest Neotropical lizards and the most exploited clade of Neotropical reptiles. For three decades more than 34 million tegu skins were in trade, about 1.02 million per year. The genus Tupinambis is distributed in South America east of the Andes, and currently contains four recognized species, three of which are found only in Brazil. However, the type species of the genus, T. teguixin, is known from Bolivia, Brazil, Colombia, Ecuador, French Guyana, Guyana, Peru, Suriname, Trinidad and Tobago, and Venezuela (including the Isla de Margarita). Here we present molecular and morphological evidence that this species is genetically divergent across its range and identify four distinct clades some of which are sympatric. The occurrence of cryptic sympatric species undoubtedly exacerbated the nomenclatural problems of the past. We discuss the species supported by molecular and morphological evidence and increase the number of species in the genus Tupinambis to seven. The four members of the T. teguixin group continue to be confused with Salvator merianae, despite having a distinctly different morphology and reproductive mode. All members of the genus Tupinambis are CITES Appendix II. Yet, they continue to be heavily exploited, under studied, and confused in the minds of the public, conservationists, and scientists.

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Sonntag, 23 Juli 2017 15:25

STOW, A. J. & SUNNUCKS, P. (2004)

STOW, A. J. & SUNNUCKS, P. (2004a)

High mate and site fidelity in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat.

Molecular Ecology 13 (2): 419-430. 10.1046/j.1365-294X.2003.02061.x


While habitat alteration has considerable potential to disrupt important within-population processes, such as mating and kin structure, via changed patterns of dispersal, this has rarely been tested. We are investigating the impact of anthropogenic habitat alteration on the population biology of the rock-dwelling Australian lizard Egernia cunninghami on the Central Tablelands of New South Wales, Australia, by comparing deforested and adjacent naturally vegetated areas. The novel analyses in this paper, and its companion, build on previous work by adding a new replicate site, more loci and more individuals. The additional microsatellite loci yield sufficient power for parentage analysis and the sociobiological inferences that flow from it. Genetic and capture–mark–recapture techniques were used to investigate mate and site fidelity and associated kin structure. Analyses of the mating system and philopatry using 10 microsatellite loci showed high levels of site fidelity by parents and their offspring in natural and deforested habitats. Parentage assignment revealed few individuals with multiple breeding partners within seasons and fidelity of pairs across two or more breeding seasons was typical. Despite reduced dispersal, increased group sizes and significant, dramatic increases in relatedness among individuals within rock outcrops in deforested areas, no significant differences between deforested and natural areas were evident in the degree of multiple mating or philopatry of breeding partners within and across seasons. With the exception that there was a significantly higher proportion of unmated males in the deforested area, the social and mating structure of this species has so far been surprisingly robust to substantial perturbation of dispersal and relatedness structure. Nonetheless, approximately 10-fold elevation of mean pairwise relatedness in the deforested areas has great potential to increase inbred matings, which is investigated in the companion paper.


STOW, A. J. & SUNNUCKS, P. (2004b)

Inbreeding avoidance in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat.

Molecular Ecology 13 (2): 443-447. 10.1046/j.1365-294X.2003.02060.x


Habitat fragmentation/alteration has been proposed as a distinct process threatening the viability of populations of many organisms. One expression of its impact may be the disruption of core population processes such as inbreeding avoidance. Using the experimental design outlined in our companion paper, we report on the impact of habitat alteration (deforestation) on inbreeding in the rock-dwelling Australian lizard Egernia cunninghami. Ten microsatellite loci were used to calculate relatedness coefficients of potential and actual breeding pairs, and to examine mate-choice and heterozygosity. Despite significantly less dispersal and higher within-group relatedness between potential mates in deforested than in natural habitats, this did not result in significantly more inbred matings. Average relatedness amongst breeding pairs was low, with no significant difference between natural and fragmented populations in relatedness between breeding pairs, or individual heterozygosity. Active avoidance of close kin as mates was indicated by the substantially and significantly lower relatedness in actual breeding pairs than potential ones. These facts, and heterozygote excesses in all groups of immature lizards from both habitats, show that E. cunninghami maintained outbreeding in the face of increased accumulation of relatives.

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Genomic ancestry of the American puma (Puma concolor).

Journal of Heredity 91 (3): 186-197.


Puma concolor, a large American cat species, occupies the most extensive range of any New World terrestrial mammal, spanning 100 degrees of latitude from the Canadian Yukon to the Straits of Magellan. Until the recent Holocene, pumas co-existed with a diverse array of carnivores including the American lion (Panthera atrox), the North American cheetah (Miracynonyx trumani), and the saber toothed tiger (Smilodon fatalis). Genomic DNA specimens from 315 pumas of specified geographic origin (261 contemporary and 54 museum specimens) were collected for molecular genetic and phylogenetic analyses of three mitochondrial gene sequences (16S rRNA, ATPase-8, and NADH-5) plus composite microsatellite genotypes (10 feline loci). Six phylogeographic groupings or subspecies were resolved, and the entire North American population (186 individuals from 15 previously named sub-species) was genetically homogeneous in overall variation relative to central and South American populations. The marked uniformity of mtDNA and a reduction in microsatellite allele size expansion indicates that North American pumas derive from a recent (late Pleistocene circa 10,000 years ago) replacement and recolonization by a small number of founders who themselves originated from a centrum of puma genetic diversity in eastern South America 200,000-300,000 years ago. The recolonization of North American pumas was coincident with a massive late Pleistocene extinction event that eliminated 80% of large vertebrates in North America and may have extirpated pumas from that continent as well.



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Western Zambian sable: Are they a geographic extension of the giant sable antelope?

South African Journal of Wildlife Research, 40 (1): 35-42.


Over recent years many studies have looked at the effects that translocations have on the conservation of evolutionary patterns within game species. One of the most valuable game ranch species in South Africa is the sable antelope (Hippotragus niger). Four subspecies of this species are recognised based on morphological characteristics; these include the Roosevelt (Hippotragus niger roosevelti, and Kirk's sable (Hippotragus niger kirkii) in East Africa, the southern sable (Hippotragus niger niger) found from south-western Tanzania southwards including in South Africa, and the giant sable (Hippotragus niger variani) which occurs in Angola.

One subspecies whose survival is of great concern is giant sable. Years of civil unrest in Angola, and being limited to a small area and interbreeding with its congener the roan antelope, has lead to the giant sable being listed as critically endangered by the IUCN. Originally known to occur only in the central part of Angola, sightings of antelopes that superficially resemble the giant sable antelope have been reported in the eastern areas of Western Zambia. The antelopes sighted resembled the giant sable antelope in phenotype, most notably the distinct facial markings and coat colour. These reports prompted speculation in the popular media that the distribution area of the giant sable may be larger than is reflected in the scientific literature, a view that could have a serious impact on current conservation efforts to protect the giant sable antelope.

The recent study by Jansen van Vuuren and colleagues compared the genetic profiles from representative specimens from all four subspecies (including animals from western Zambia) to determine the evolutionary placement of western Zambian sable within Hippotragus niger niger or Hippotragus niger variani based on genetic characters rather than just morphological characteristics.

Their results confirmed previous reports that indicate significant separation of genetic variation (differences at genetic level) in sable antelope subspecies across their pan-African distribution. In addition, although the western Zambian and giant sable antelope resemble one another in morphology, particularly with respect to facial markings, significant genetic differences underpin these two evolutionary lineages with the western Zambian sable falling within the southern sable subspecies (Hippotragus niger niger).

These results indicate substantial phenotypic plasticity (the ability of an organism to change its phenotype in response to changes in the environment) in the characters that are conventionally used to distinguish the giant sable antelope from other sable subspecies. Consequently, neither horn length nor facial markings of the giant sable antelope should be driving conservation concerns, but rather its unique evolutionary history. The findings from this study underscore the need for rethinking decision making in conservation efforts to ensure the survival of the giant sable in Angola.



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Donnerstag, 14 Juni 2018 07:34


The genetic consequences of ex situ breeding in the European wildcat (Felis silvestris silvestris) and the Arabian sand cat (Felis margarita harrisoni).

Dr. rer. nat. Diss
125 Seiten
Erstgutachter: PD Dr. Axel Hochkirch,
Zweitgutachter: Prof. Dr. Michael Veith
Universität Trier
In Kooperation mit mehreren deutschen und internationalen Zoos, Tier- und Wildparks

Volltext (3 der vier Kapitel können über diesen Link heruntergeladen werden, Kapitel 1 oder der Volltext kann bei Interesse als PDF durch die Autorin per Mail versendet werden.)


In den letzten Jahren ist die Anzahl bedrohter Arten, die auf ex situ-Schutzprogramme angewiesen sind, deutlich gestiegen. Bislang wurde die Effizienz von ex situ-Zuchtprogrammen allerdings selten systematisch untersucht. Ziel dieser Arbeit war es zunächst den aktuellen Wissensstand zu den Auswirkungen der ex situ-Zucht auf die genetische Vielfalt bedrohter Arten zusammen zu fassen (Kapitel 1). Hierbei sollte geklärt werden ob die selbst gesetzten Ziele des Weltverbandes der Zoos und Aquarien (WAZA) in rezenten Zoopopulationen erreicht werden. Bei dieser Auswertung publizierter Daten stellte sich heraus, dass eine Zucht in Gefangenschaft auf Dauer zu einem Verlust der genetischen Vielfalt führt (Kraaijeveld-Smit et al. 2006; Frankham et al. 2010), dass diesem Effekt allerdings durch ein sorgfältiges Management der Zuchtpopulation entgegengewirkt werden kann. Die Daten aus Kapitel 1 legen nahe, dass es Grenzwerte für die Zahl der Gründer (15) und die Größe der Zuchtpopulation (100) gibt, mit deren Erreichen Inzucht minimiert und ein vergleichsweise hohes Maß genetischer Vielfalt erhalten werden kann. Es zeigte sich aber auch, dass noch viel Forschungsbedarf in Bezug auf die genetischen Auswirkungen von ex situ-Zucht besteht. Vor allem der Vergleich zwischen der Zuchtpopulation und natürlichen Wildpopulationen ist von elementarer Bedeutung um die Effizienz und den Erfolg von Zuchtprogrammen bewerten zu können. Auch zeigte sich, dass es zusätzlichen Forschungsbedarf bezüglich genetischer Anpassungen an die Bedingungen in Gefangenschaft gibt (Frankham 2008), was die vermehrte Nutzung von nicht-neutralen genetischen Markern nahe legt. Zudem sollte verstärkt eine Übertragung der wissenschaftlichen Erkenntnisse in die praktische Anwendung im Zoo erfolgen (z. B. in Bezug auf die Artenzusammensetzung oder die Managementstrategien).

In Kapitel 2 und 3 werden Fallbeispiele für genetische Untersuchungen an ex situ-Populationen behandelt. Die Untersuchungen an der Europäischen Wildkatze (Felis silvestris silvestris) in Kapitel 2 zeigen, dass es im Laufe der Haltung in Zoos vermutlich mehrfach zu Hybridisierung mit Hauskatzen oder zur Aufnahme von Hybriden kam. Lediglich ein Drittel der Zuchtpopulation wies den mitochondrialen Haplotyp auf, der auch in wilden Populationen zu finden ist. Insgesamt kann die ex situ Population nicht für eine weitere Zucht empfohlen werden. Dies macht die Aufnahme von zusätzlichen Individuen aus den Wildpopulationen zu einer nötigen Voraussetzung zur effektiven Erhaltung der genetischen Diversität dieser Art. Von weiteren Wiederansiedelungen mit Tieren aus der ex situ Zucht ist generell abzuraten, da sich die Europäische Wildkatze inzwischen wieder auf natürlichem Wege ausbreitet. Die genetischen Daten liefern in diesem Fall einen wichtigen Grundstock für die Etablierung eines Zuchtbuches.

Eine Analyse der derzeitigen Haltungsbedingungen für diese Art zeigte, dass die Haltungsstandards die gesetzlichen Mindestanforderungen weit übertreffen (Kapitel 4). Allerdings zeigte ein Vergleich mit den Empfehlungen aus der Verhaltensforschung bei Kleinkatzen (Shepherdson et al. 1993; Mellen et al. 1998;Hartmann 2007; Hönig & Gusset 2010), dass vor allem in Bezug auf den Kontakt zu den Pflegern und der Fütterung noch Verbesserungspotenzial besteht.

Die genetischen Untersuchungen an der ex situ-Population der Arabischen Sandkatze (Felis margarita harrisoni) (Kapitel 3) zeigen, dass trotz einer stärkeren Bedrohung, weniger Gründertieren und einer kleineren Zuchtpopulation bei dieser Art ein hohes Maß an genetischer Diversität erhalten werden konnte. Die Daten legen nahe, dass die 18 Gründer für dieses Zuchtprogramm eine hohe genetische Diversität eingebracht haben und nicht näher mit einander verwandt waren. Zudem zeigt dieses Beispiel dass genetische Untersuchungen auch bei Populationen mit detaillierten Zuchtbuchdaten sehr sinnvoll sein können, da ein Fehler in den Zuchtbuchdaten nachgewiesen werden konnte. Die genetischen Daten bestätigen zudem die Ergebnisse aus Kapitel 1 zu den Grenzwerten für die Anzahl der Gründer und die Größe der Zuchtpopulation.

Insgesamt scheinen ex situ-Zuchtprogramme durchaus geeignet zu sein um die genetische Vielfalt bedrohter Arten zu erhalten. Wichtig ist eine ausreichend große Zahl genetisch variabler Gründer und ein sorgsames Zuchtmanagement. Allerdings lässt sich langfristig aufgrund der kleinen Populationsgrößen Inzucht und der Verlust genetischer Vielfalt in Zoopopulationen nicht vermeiden. Die Fallbeispiele untermalen den großen Nutzen den genetische Untersuchungen für die Kontrolle und Verbesserung von Erhaltungszuchtprogrammen haben.


Nowadays, there is an increasing number of species which depend on ex situ conservation programmes for survival. However, the efficiency of the ex situ breeding programmes has so far rarely been evaluated systematically. The aim of this thesis was to first of all review the current knowledge on the effects of captive breeding on the genetic diversity of endangered species (Chapter 1). The studies presented here also aim at evaluating whether ex situ breeding programmes can meet the goals set by the Word Association of Zoos and Aquariums (WAZA). The literature review revealed, that on the long term, captive breeding always leads to a loss of genetic diversity (e. g. Kraaijeveld-Smit et al. 2006; Frankham et al. 2010). However, the data also indicated, that this effect can be counteracted by a thorough management of the captive population. The analyses presented in Chapter 1 suggest, that there is a minimum number of founders (15) and a minimum captive population size (100), which are necessary to minimize inbreeding and to conserve a high amount of genetic diversity. However, the review also showed, that there is still a great need for further research on the genetic effects of captive breeding. In order to be able to evaluate the efficiency and success of captive breeding programmes it is of fundamental importance to compare captive populations to natural wild populations. Additionally there is a need to study the genetic adaptations to captive environments in endangered species (Frankham 2008), which indicates an increasing need for the use of non-neutral marker systems. Also, there is a need for an increase in the implementation of the knowledge gained by scientific research into the planning and management of current breeding programmes.

Chapters 2 and 3 deal with case studies for the genetic analysis of ex situ populations. Genetic data from the European wildcat (Felis silvestris silvestris) (Chapter 2) revealed, that hybrids or even domestic cats must have been integrated into the captive population. Only about one third of the analysed captive individuals possessed the mitochondrial haplotype found in wild populations. Hence, none of the captive individuals can be recommended for breeding. This leads to the necessity to acquire new founders from the wild populations to effectively conserve the genetic diversity of this species. Furthermore, it would be advisable to abstain from reintroductions using the captive population as a source, as the wild populations are already expanding naturally. The genetic data presented in this study provides valuable basic information for the establishment of a studbook. An analysis of the keeping conditions for this species (Chapter 4) revealed, that the current conditions by far exceed the minimum requirements set by law. Yet, the comparison with recommendations from behavioural studies on small felids (Shepherdson et al. 1993; Mellen et al. 1998;Hartmann 2007; Hönig & Gusset 2010) indicated, that there is a potential for optimization concerning the contact to the keepers and the feeding.

In Chapter 3 a genetic analysis of the captive population of the Arabian sand cat (Felis margarita harrisoni) is presented. Despite its smaller captive population size and the smaller number of founders, a high amount of genetic diversity is found in the captive population of this species. The results indicate, that the 18 founders of this breeding programme must have been genetically highly diverse and unrelated. This study also highlights the benefit of genetic studies in established breeding programmes with detailed pedigree, as an error could be detected in the studbook. The results of this analysis also confirm the minimum values for the number of founders and the captive population size which were determined in Chapter 1.

In general, ex situ breeding programmes seem to be suitable to retain a high amount of the genetic diversity of endangered species. However, it is crucial that the population is based on a sufficient number of genetically divers founders and is afterwards carefully managed. Nevertheless, on the long term, inbreeding and a loss of genetic diversity cannot be avoided in captive populations due to restrictions in population size. The case studies presented here highlight the great value of genetic studies for the evaluation and optimization of ex situ breeding programmes.



The genetic consequences of ex situ breeding in the European wildcat (Felis silvestris silvestris) and the Arabian sand cat (Felis margarita harrisoni)

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The importance of genetic research in zoo breeding programmes for threatened species: the African dwarf crocodiles (genus Osteolaemus ) as a case study.

International Zoo Yearbook 49: xx-xx.ISSN 0074-9664 (Print) ISSN 1748-1090 (Online).


The threatened African dwarf crocodiles (genus Osteolaemus) are distributed throughout West and Central Africa. Traditionally two subspecies were described (Osteolaemus tetraspis tetraspis and Osteolaemus tetraspis osborni), although recent molecular studies demonstrate the presence of three allopatric lineages that should be recognized as full species. These highly divergent taxa are distributed in the three major forested biogeographic zones of western Africa: Congolian (Osteolaemus osborni), Lower Guinean (Osteolaemus tetraspis) and Upper Guinean (Osteolaemus sp. nov. cf. tetraspis). Largely because of their diminutive size, dwarf crocodiles are regularly kept in zoos and aquariums worldwide. In Europe, the collection is managed by a European studbook coordinated by Leipzig Zoo, Germany, since 2006, while American zoological institutions do not yet manage these species as part of a studbook programme. To facilitate ex situ conservation efforts, it is important to identify accurately each individual to the appropriate species following the latest systematic understanding of the genus. Population aggregation analysis with mitochondrial and nuclear gene sequences was used for both species identification and detection of interspecific hybridization. The results of our study show that only European collections house all three Osteolaemus  taxa, although only a single individual O. osborni  was confirmed. The most prevelant species present in both European and North American institutions was O. tetraspis. Additionally, several O. sp. nov. cf. tetraspis were identified, likely originating from the Senegambia region, especially in the North American collections. This will represent an important resource for future conservation efforts as Osteolaemus  are highly threatened in this region of West Africa. Unfortunately, both zoo populations showed relatively high frequencies (c. 25–28%) of hybridization between O. tetraspis a nd O. sp. nov. cf. tetraspis bred in captivity. We highly recommend that zoological institutions ensure they know the species identity of the Osteolaemus they maintain and work together to transfer individuals into single-species colonies to avoid further hybridization. In the USA, this may necessitate the creation of a studbook programme. It may also prove valuable to consider a cooperative programme between the European Association of Zoos and Aquaria and the Association of Zoos & Aquariums, wherein each Association focuses its resources largely on a single Osteolaemus  species. This would, however, require trans-Atlantic transfer of individuals. The case study of dwarf crocodiles in zoological institutions reinforces the importance of genetic research in conservation-breeding programmes, highlights the potential for collaboration between European and American zoological institutions for the ex situ conservation of threatened wildlife, and foreshadows some of the regulatory challenges in managing captive populations internationally.



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Mitochondrial DNA phylogeography of red deer (Cervus elaphus).

Molecular Phylogenetics and Evolution 31 (2004) 1064–1083.



In order to understand the origin, phylogeny, and phylogeography of the species Cervus elaphus, we examined the DNA sequence variation of the mitochondrial cytochrome b gene of 51 populations of deer from the entire distribution area of Cervinae with an emphasis on Europe and Asia. Several methods, including maximum parsimony, maximum likelihood, and nested clade analysis, revealed that red deer originated from the area between Kyrgyzstan and Northern India. We found two distinct groups of red deer: a western group consisting of four subgroups and an eastern group consisting of three subgroups. Our mtDNA data do not support the traditional classification of red deer as only one species nor its division into numerous subspecies. The discrepancies between the geographical pattern of differentiation based on mtDNA cytochrome b and the existing specific and subspecific taxonomy based on morphology are discussed.



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