Sequences from complete mitochondrial control regions (mtDNA CR) were used to infer phylogenetic relationships in 25 Cervinae taxa. Cervus splits into clades that are partially discordant with current species delimitations. Nominate Cervus elaphus includes two divergent clades that must be referred to as species elaphus (European elaphoid deer) and canadensis (Eurasian and North American wapitoid deer). Cervus nippon splits into Japanese and continental plus Taiwan sika. Père David's deer is nested within Cervus, suggesting that Elaphurus should be merged with Cervus. European and Persian fallow deer are genetically divergent and distinct species. Sequence length varied due to a CR‐I insertion, tandemly repeated twice in rusa and sambar deer, sika and wapiti, and repeated up to six times in a clade of Japanese sika. Variable copy numbers of this repeat are also fixed in different sika subspecies, and could be used as a diagnostic marker for subspecies. Sequence variability at the mtDNA CR is informative for defining species and subspecies boundaries, and for locating the geographical origin of captive‐reared stocks. Natural and farmed populations of some species have been deeply affected by human management and the conservation of deer populations would be aided by the appropriate identification of the different evolutionary and taxonomic units.

Thirty bovine and eight ovine microsatellite primer pairs were tested on four tropical deer species: Eld's and Swamp deer (highly threatened) and Rusa and Vietnamese Sika deer (economically important). Thirty markers gave an amplified product in all four species (78.9%). The number of polymorphic microsatellite markers varied among the species from 14 in Eld's deer (47%) to 20 in Swamp deer (67%). Among them, 11 microsatellite loci were multiplexed in three polymerase chain reactions (PCRs) and labelled with three different fluorochromes that can be loaded in one gel-lane. To test the efficiency of the multiplex, primary genetic studies (mean number of alleles, expected heterozygosities and Fis values) were carried out on four deer populations. Parentage exclusion probability and probability of identity were computed and discussed on a Swamp deer population. These multiplexes PCRs were also tested on several other deer species and subspecies. The aim of this study is to establish a tool useful for genetic studies of population structure and diversity in four tropical deer species which with few modifications can be applied to other species of the genus Cervus.

R-banded chromosomes of Vietnamese sika (VS) deer (Cervus nippon pseudaxis, 2N = 66), a threatened subspecies of sika deer endemic to Vietnam, are presented for the first time and were compared with bovine R-banded chromosomes to define a standard karyotype. Nineteen VS deer autosomes (CNP) were identified on the basis of the banding pattern relative to bovine chromosomes (BTA), while hypotheses for the remaining thirteen were proposed from comparisons with the published deer genetic map, BTA 1, 2, 5, 6, 8 and 9 each equivalent to two separate acrocentric CNP chromosomes and BTA 26 and 28 associated in a tandem fusion. To confirm these hypotheses, probes for the twenty-nine Texas nomenclature type I markers specific for each cattle autosome, sixteen other type I and fourteen microsatellite markers were used in FISH experiments on VS deer chromosomes. CNP7 presented the most complex rearrangement as compared with cattle chromosomes. A complete correspondence between VS deer and cattle chromosomes was established and it was extended with a comparison with the human karyotype to transfer human map information to this species of scientific and economic interest. Moreover, this work anchors the deer genetic linkage map to chromosome-specific markers.

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

Among the three subspecies generally recognized within the Eld's deer (Cervus eldi)--C. e. eldi, C. e. thamin, and C. e. siamensis--C. e. siamensis is considered to be particularly endangered following its disappearance from a major portion of its original range. The only captive breeding population of this subspecies is in the zoological parks at the Paris Museum of Natural History. Taking into account its low effective population size (Ne = 7) and the increasing levels of inbreeding, the continued breeding of this "micropopulation" in isolation from closely related subspecies and in particular from C. e. thamin, which is much more common in zoos as well as in the nature, is questioned. As an initial step in determining if crosses between these subspecies could be performed without risk of outbreeding depression due, in part, to gross differences in their karyotypes, a comparative chromosome banding analysis (RBG-bands) of C. e. siamensis and C. e. thamin was undertaken. No chromosomal differences were identified between the taxa at the level of resolution obtained. The study suggests that, at least from a karyotypic perspective, no obvious differences delimit the two subspecies, and hybridization between endangered C. e. siamensis and C. e. thamin is not likely to lead to impaired fertility in hybrid animals.