Phylogeography and conservation of impala and greater kudu

The phylogeography of the bush habituated African bovid species impala (Aepyceros melampus) and greater kudu (Tragelaphus strepsiceros) is investigated using mitochondrial DNA (mtDNA) markers. Combined analysis of individual lineages, relationships and population genetics suggest a colonization process from Southern Africa toward Eastern regions in the greater kudu. Results are less clear for the impala, although remaining consistent with a similar pattern of historical dispersion. The study reveals a similar pattern, that is a marked divergence of lineages from South-western Africa relative to other regions. This pattern is opposed to previously published findings in other African bovid species. In the impala, the genetically isolated region is consistent with morphology because it is recognized as the subspecies A. m. petersi, the black-faced impala. In contrast, the similar split of South-western mitochondrial lineages was not expected in the greater kudu on the basis of morphology. Both species show a significant population genetic differentiation. Beyond their phylogeographical value, our results should raise conservation concerns about South-western populations of both species. The black-faced impala is categorized as vulnerable and our data show indications of hybridization with common impala A. m. melampus. The previously unrecognized genetic status of the South-western kudus could also imply conservation regulations.     

No suggestion of hybridization between the vulnerable black-faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha National Park, Namibia

There are two recognized subspecies of impala in sub-Saharan Africa: the common impala (Aepyceros melampus melampus) -- widespread in southern and east Africa -- and the vulnerable black-faced impala (A. m. petersi) -- found naturally in only a small enclave in southwest Africa. The Etosha National Park (NP) in Namibia harbours the largest and only protected-area population of black-faced impala, numbering some 1500 individuals. Due to translocations of the exotic common impala to commercial farms in Namibia during the past decades, the black-faced impala in Etosha is faced with the potentially serious threat of hybridization posed by secondary contact with the common impala inhabiting bordering farms. Using eight microsatellite DNA markers, we analysed 127 black-faced impala individuals from the five subpopulations in Etosha NP, to determine the degree, if any, of hybridization within the park. We found that (a) the black-faced impala were highly genetically differentiated from the common impala (pairwise theta-values ranged from 0.18 to 0.39 between subspecies; overall value = 0.27) and (b) black-faced samples showed high levels of genetic variability [average expected heterozygosity (H(E)) = 0.61 +/- 0.01 SE], although not as high as that observed in the common impala (average H(E) = 0.69 +/- 0.02 SE). (c) No hybridization between the subspecies in Etosha was suggested. A Bayesian Markov Chain Monte Carlo approach revealed clear distinction of individuals into groups according to their subspecies of origin, with a zero level of 'genetic admixture' among subspecies.     

A morphometric assessment of geographical variation and subspecies in impala

The single species of Aepyceros, Aepyceros melampus (impala), is native to central and southern Africa, from Uganda to South Africa. It inhabits open woodlands, sandy bush country and acacia savannah. This study tested the morphological and geographical variation among specimens of impala and their possible relation with described subspecies. Nineteen skull and horn measurements were taken. A multivariate analysis was used and size and shape were explored. Facial coat patterns were also coded. The results supported four out of five traditionally described subspecies: Aepyceros melampus petersi from Angola/Namibia, Aepyceros melampus melampus from South Africa, Aepyceros melampus suara from East Africa and Aepyceros melampus johnstoni from Zambia and Malawi. We consider Aepyceros melampus rendilis to be a synonym of suara . A revised synopsis is suggested, with comments on the geographical ranges of the subspecies. Skull dimensions also allowed us to estimate the geographical origin and subspecies of some individuals of unknown provenance. Coat patterns showed no clear relation with subspecies or geographic location, with the exception of A. m. petersi .     

Genetic structure of the common impala (Aepyceros melampus melampus) in South Africa: phylogeography and implications for conservation

We analysed 131 common impala (Aepyceros melampus melampus) samples from two provinces in South Africa (Limpopo and KwaZulu‐Natal) that are separated by the Drakensberg Mountain Range using sequences of the mitochondrial control region and seven polymorphic nuclear microsatellite loci. In line with earlier studies on bovid species, we found very high values of genetic diversity, particularly at the mtDNA locus with an overall nucleotide diversity of 3.6% and an overall haplotype diversity of 0.98. All statistical approaches confirmed a significant population differentiation between Limpopo and KwaZulu‐Natal, suggesting that areas of unsuitable habitat caused by the presence of the Drakensberg Range and the Indian Ocean coastal belt act as a barrier to gene flow. Only few individuals with signs of admixed origin were indicative of translocations or rare migration between the two provinces. Combination of our mtDNA data set with those of previous studies on impala from south‐western, southern and eastern Africa revealed the highest diversity in South Africa. This is in line with the hypothesis of a southern glacial refuge from which various African ungulate species spread northeast during the Holocene, although in the case of impala further analyses based on larger data sets will be necessary to definitively settle this question.     

The genetic status of naturally occurring black-nosed impala from northern South Africa

The impala (Aepyceros melampus ssp.) is a widespread antelope species occurring in sub-Saharan Africa. The two recognized subspecies have non-overlapping distribution ranges, with no known natural mixture of these subspecies until human interference. A number of common impala individuals (A. m. melampus) displaying phenotypic characteristics commonly observed in the black-faced impala (A. m. petersi), namely black facial markings, were seen on a farm in the Limpopo Province, South Africa. This farm falls outside the natural distribution range of A. m. petersi. We therefore aimed to identify the taxonomic placement of these individuals (i.e. A. m. melampus or A. m. petersi) through phylogenetic and molecular clock analyses using D-loop and cytochrome subunit b sequence data. Our results showed that these black-nosed impala from Limpopo are in fact A. m. melampus individuals. The existence of the black-nose phenotype in common impala could be more widespread than previously estimated. The occurrence of introgression between the two subspecies in this region could, however, not be fully excluded, and can only be fully assessed through the use of nuclear DNA analysis.     

Mammalian body size changes and Plio-Pleistocene environmental shifts: implications for understanding hominin evolution in eastern and southern Africa

This study examines geographic and temporal variation in three mammalian taxa co-occurring in eastern and southern Africa. The selected taxa-the spotted hyena (Crocuta crocuta), the plains zebra (Equus burchellii), and the impala (Aepyceros melampus)--are geographically widespread in modern times and are abundant in eastern and southern African Plio-Pleistocene fossil sites. Craniodental measurements of modern conspecifics from known geographic locations are compared using multivariate statistical methods to discern patterns of modern geographic variation within taxa. Modern and fossil samples are statistically compared to assess the nature and extent of inferred shifts in body size, both between modern samples and through time in each region. These results indicate that modern spotted hyenas and plains zebras exhibit mainly size variation between regions, with southern African samples possessing statistically larger craniodental metrics than eastern African samples. Comparison of fossil and modern samples reveals that the fossil assemblages do not show the same pattern of geographic variation. Significant temporal changes are more numerous between fossil and modern eastern African samples, and these changes are not mirrored by similar changes in the southern African samples. The changes experienced by taxa in eastern Africa appear to have been more extreme and wide-ranging than those in southern Africa, a presumed refugium. This result accords well with genetic studies of several large mammal species and paleoenvironmental studies suggesting that eastern African localized environments were more affected by tectonism and volcanism than were those in southern Africa. This study suggests that different evolutionary scenarios may have existed within Africa during the Plio-Pleistocene, but that both regions played unique and complementary roles in the evolution of African hominins and the broader faunal community.     

Skin papillomas in an impala (Aepyceros melampus) and a giraffe (Giraffa camelopardalis).

Viral particles, typical of the papovavirus family, were demonstrated by electronmicroscopy in small papillomas found on the feet of an impala (Aepyceros melampus) and on the face of a giraffe (Giraffa camelopardalis) in Kenya. Histologically the tissues proved to be typical papillomas. The viral particles measured 38 nm and 40 nm in diameter in all tissue sections from the impala and giraffe respectively.     

Trade-off between resource seasonality and predation risk explains reproductive chronology in impala

We investigated the variation in birth synchrony displayed by impala Aepyceros melampus populations across their distribution from southern to eastern Africa. Our analysis was based on field data from Chobe National Park in Botswana and Mala Mala Private Game Reserve in South Africa (4 and 13 years of monitoring, respectively). We compared our results with those from other studies conducted across the impala species range. Impala lambing was highly synchronized in Chobe with 90% of lambs born within 2 weeks in mid-November. Variation in rainfall in the preceding wet season explained 74% of variation in the dates of the first lamb observation in Mala Mala. In Chobe, the earliest birth peak occurred after the highest rainfall and the body condition of lambs in that cohort was also best for both males and females. No association was found between the lunar cycle and the estimated onset of the conception period, despite previous studies having found an association between the lunar cycle and the rutting behaviour in males. On a regional scale, impalas in areas with a marked dry season (several months with no rain) tend to synchronize births with the onset of the rains, when grass quality is highest. Number of months with rain explained 78% of the regional variation in birth synchrony. Neither latitude nor total rainfall contributed significantly to a stepwise multiple regression model. These data support the theory that impalas synchronize births in areas with a highly seasonal food supply, and temporally space births in less seasonal (equatorial) areas to reduce predation risks.     

Hepatic lesions associated with Cooperioides hepaticae (Nematoda: Trichostrongyloidea) infection in impala (Aepyceros melampus) of the Kruger National Park

Intrahepatic biliary lesions were observed in two of 12 lambs, seven of 12 yearlings and 10 of 25 adult impala (Aepyceros melampus) surveyed in the Kruger National Park, Republic of South Africa. Lesions were associated with the nematode Cooperioides hepaticae, a trichostrongyloid parasite that inhabits the bile ducts of impala, and ranged from a mild chronic-eosinophilic cholangitis to foci of florid hyperplastic cholangitis with duct ectasia. The latter almost always contained viable worms and, after the worms died, the lesions appeared as foreign-body granulomas. Infection was acquired early in life; severe lesions were seen most frequently in yearlings. Adults were less severely infected, which suggested an acquired immunity. Although the incidence of infection was high, cooperiiasis did not appear to be a serious herd-health problem at the time of this study.     

Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus)

Genetic analyses of bird subspecies designated as conservation units can address whether they represent units with independent evolutionary histories and provide insights into the evolutionary processes that determine the degree to which they are genetically distinct. Here we use mitochondrial DNA control region sequence and six microsatellite DNA loci to examine phylogeographical structure and genetic differentiation among five North American grasshopper sparrow (Ammodramus savannarum) populations representing three subspecies, including a population of the endangered Florida subspecies (A. s. floridanus). This federally listed taxon is of particular interest because it differs phenotypically from other subspecies in plumage and behaviour and has also undergone a drastic decline in population size over the past century. Despite this designation, we observed no phylogeographical structure among populations in either marker: mtDNA haplotypes and microsatellite genotypes from floridanus samples did not form clades that were phylogenetically distinct from variants found in other subspecies. However, there was low but significant differentiation between Florida and all other populations combined in both mtDNA (FST = 0.069) and in one measure of microsatellite differentiation (theta = 0.016), while the non-Florida populations were not different from each other. Based on analyses of mtDNA variation using a coalescent-based model, the effective sizes of these populations are large (approximately 80,000 females) and they have only recently diverged from each other (< 26,000 ybp). These populations are probably far from genetic equilibrium and therefore the lack of phylogenetic distinctiveness of the floridanus subspecies and minimal genetic differentiation is due most probably to retained ancestral polymorphism. Finally, levels of variation in Florida were similar to other populations supporting the idea that the drastic reduction in population size which has occurred within the last 100 years has not yet had an impact on levels of variation in floridanus. We argue that despite the lack of phylogenetic distinctiveness of floridanus genotypes the observed genetic differentiation and previously documented phenotypic differences justify continued designation of this subspecies as a protected population segment.     

Characterization of nine microsatellite loci in impala (Aepyceros melampus)

Nine microsatellite loci were isolated from a genomic DNA library created from impala (Aepyceros melampus). Observed and expected levels of heterozygosity were computed utilizing 25 individuals from a population in central Kenya. Tests for Hardy–Weinberg equilibria were conducted and found that three of the nine loci deviated from equilibrium in this population. These markers were developed to analyse the genetic effects of culling and isolation on a game preserve in Kenya.     

Phylogeography of three closely related African bovids (tribe Alcelaphini)

The phylogeography of three species of African bovids, the hartebeest (Alcelaphus buselaphus), the topi (Damaliscus lunatus), and the wildebeest (Connochaetes taurinus), is inferred from sequence variation of 345 sequences at the control region (d-loop) of the mtDNA. The three species are closely related (tribe Alcelaphini) and share similar habitat requirements. Moreover, their former distribution extended over Africa, as a probable result of the expansion of open grassland on the continent during the last 2.5 Myr. A combination of population genetics (diversity and structure) and intraspecific phylogeny (tree topology and relative branch length) methods is used to substantiate scenarios of the species history. Population dynamics are inferred from the distribution of sequence pairwise differences within populations. In the three species, there is a significant structuring of the populations, as shown by analysis of molecular variance (AMOVA) pairwise and hierarchical differentiation estimations. In the wildebeest, a pattern of colonization from southern Africa toward east Africa is consistent with the asymmetric topology of the gene tree, showing a paraphyletic position of southern lineages, as well as their relatively longer branch lengths, and is supported by a progressive decline in population nucleotide diversity toward east Africa. The phylogenetic pattern found in the topi and the hartebeest differs from that of the wildebeest: lineages split into monophyletic clades, and no geographical trend is detected in population diversity. We suggest a scenario where these antelopes, previously with wide pan-African distributions, became extinct except in a few refugia. The hartebeest, and probably also the topi, survived in refugia north of the equator, in the east and the west, respectively, as well as one in the south. The southern refugium furthermore seems to have been the only place where the wildebeest has survived.     

Population history,gene flow,and bottlenecks in island populations of a secondary seed disperser,the southern grey shrike (Lanius meridionalis koenigi)

Studying the population history and demography of organisms with important ecological roles can aid understanding of evolutionary processes at the community level and inform conservation. We screened genetic variation (mtDNA and microsatellite) across the populations of the southern grey shrike (Lanius meridionalis koenigi) in the Canary Islands, where it is an endemic subspecies and an important secondary seed disperser. We show that the Canarian subspecies is polyphyletic with L. meridionalis elegans from North Africa and that shrikes have colonized the Canary Islands from North Africa multiple times. Substantial differences in genetic diversity exist across islands, which are most likely the product of a combination of historical colonization events and recent bottlenecks. The Eastern Canary Islands had the highest overall levels of genetic diversity and have probably been most recently and/or frequently colonized from Africa. Recent or ongoing bottlenecks were detected in three of the islands and are consistent with anecdotal evidence of population declines due to human disturbance. These findings are troubling given the shrike's key ecological role in the Canary Islands, and further research is needed to understand the community‐level consequences of declines in shrike populations. Finally, we found moderate genetic differentiation among populations, which largely reflected the shrike's bottleneck history; however, a significant pattern of isolation‐by‐distance indicated that some gene flow occurs between islands. This study is a useful first step toward understanding how secondary seed dispersal operates over broad spatial scales.     

Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis

Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.     

The pathogenicity of bovine strains of foot and mouth disease virus for impala and wildebeest.

Impala (Aepyceros melampus) and wildebeest (Connochaetes taurinus) were infected with bovine strains of foot and mouth disease virus by intradermolingual inoculation. No clinical signs developed in the impala but mild atypical lesions developed in the tongues of the wildebeest with generalized spread to one foot in two of the eight animals exposed. All the impala but only some of the wildebeest developed viraemia. No virus could be isolated from any tissues in either species after the 7th day following virus inoculation. Immune response occurred in both species. A field survey revealed few animals of either species with significant antibody titers and no virus 'carriers' were found.     

Subspecies composition and founder contribution of the captive U.S. chimpanzee (Pan troglodytes) population

Chimpanzees are presently classified into three subspecies: Pan troglodytes verus from west Africa, P.t. troglodytes from central Africa, and P.t. schweinfurthii from east Africa. A fourth subspecies (P.t. vellerosus), from Cameroon and northern Nigeria, has been proposed. These taxonomic designations are based on geographical origins and are reflected in sequence variation in the first hypervariable region (HVR-I) of the mtDNA D-loop. Although advances have been made in our understanding of chimpanzee phylogenetics, little has been known regarding the subspecies composition of captive chimpanzees. We sequenced part of the mtDNA HVR-I region in 218 African-born population founders and performed a phylogenetic analysis with previously characterized African sequences of known provenance to infer subspecies affiliations. Most founders were P.t. verus (95.0%), distantly followed by the troglodytes schweinfurthii clade (4.6%), and a single P.t. vellerosus (0.4%). Pedigree-based estimates of genomic representation in the descendant population revealed that troglodytes schweinfurthii founder representation was reduced in captivity, vellerosus representation increased due to prolific breeding by a single male, and reproductive variance resulted in uneven representation among male P.t.verus founders. No increase in mortality was evident from between-subspecies interbreeding, indicating a lack of outbreeding depression. Knowledge of subspecies and their genomic representation can form the basis for phylogenetically informed genetic management of extant chimpanzees to preserve rare genetic variation for research, conservation, or possible future breeding.     

Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation

The roan antelope (Hippotragus equinus) is the second largest African antelope, distributed throughout the continent in sub-Saharan savannah habitat. Mitochondrial DNA (mtDNA) control region sequencing (401 bp, n = 137) and microsatellite genotyping (eight loci, n = 137) were used to quantify the genetic variability within and among 18 populations of this species. The within-population diversity was low to moderate with an average mtDNA nucleotide diversity of 1.9% and average expected heterozygosity with the microsatellites of 46%, but significant differences were found among populations with both the mtDNA and microsatellite data. Different levels of genetic resolution were found using the two marker sets, but both lent strong support for the separation of West African populations (samples from Benin, Senegal and Ghana) from the remainder of the populations studied across the African continent. Mismatch distribution analyses revealed possible past refugia for roan in the west and east of Africa. The West African populations could be recognized together as an evolutionarily significant unit (ESU), referable to the subspecies H. e. koba. Samples from the rest of the continent constituted a geographically more diverse assemblage with genetic associations not strictly corresponding to the other recognized subspecies.     

Rotavirus (reovirus-like) infection of neonatal ruminants in a zoo nursery.

An outbreak of a pneumoenteric disease occurred in neonates in a zoo nursery. Four of seven affected animals died. Rotaviruses were observed in the feces of an affected 4-day old impala (Aepyceros melampus), a Thomson's gazelle (Gazella thomsonii) and an addax (Addax nasomaculatus). Encapsulated Escherichia coli also were isolated from the feces. The recovered rotaviruses was antigenically related to bovine rotavirus. A bovine rotavirus vaccine was given orally and no adverse effects were noted.     

Genetic differentiation and limited gene flow among fragmented populations of New Zealand endemic Hector’s and Maui’s dolphins

Gene flow among small fragmented populations is critical for maintaining genetic diversity, and therefore the evolutionary potential of a species. Concern for two New Zealand endemic subspecies, the Hector’s (Cephalorhynchus hectori hectori) and Maui’s (C. h. maui) dolphins, arises from their low abundance, slow rate of reproduction, and susceptibility to fisheries-related mortality. Our work examined genetic differentiation and migration between the subspecies and among regional and local Hector’s dolphin populations using mitochondrial (mt) DNA and microsatellite genotypes from 438 samples. Results confirmed earlier reports of a single unique mtDNA control region haplotype fixed in the Maui’s dolphin, and provided new evidence of reproductive isolation from Hector’s dolphins (9-locus microsatellite F _ST?=?0.167, P?<?0.001). Independent evolutionary trajectories were also supported for Hector’s dolphin populations of the East Coast, West Coast, Te Waewae Bay and Toetoe Bay. Low asymmetrical migration rates were found among several Hector’s dolphin populations and assignment tests identified five Hector’s dolphins likely to have a migrant father from another regional population. There appears to be sufficient step-wise gene flow to maintain genetic diversity within the East and West Coasts; however, the two local South Coast populations exhibited a high degree of differentiation given their close proximity (~100?km). To maintain the evolutionary potential and long-term survival of both subspecies, genetic monitoring and conservation management must focus on maintaining corridors to preserve gene flow and prevent further population fragmentation and loss of genetic diversity, in addition to maintaining local population abundances.     

黑斑羚粪便中碳同位素揭示的食性变化

利用稳定碳同位素数据(δ13C)分析了南非克鲁格国家公园混食性黑斑羚(Aepyceros melampus)时间和空间尺度上的食性变化,验证了两个假说,即有蹄类食性变化是由生境中木本植物与草本植物的相对配比导致;降雨控制有蹄类生态。结果表明:黑斑羚的食性涵盖了精食者-粗食者采食谱系,且食性中木本与草本比例在不同月间、季节、年度和区域间存在很大变化。栖息于开放性热带稀树草原和草原中的黑斑羚通常采食比生境中更高比例的草本,但在时间尺度上并不恒定。在克鲁格北部的一个区域(Punda Maria) ,黑斑羚采食的草本比克鲁格国家公园中其它任何区域都多。与其它生境相比,在河边的黑斑羚采食草本数量更少,尤其是在食性空间变化更为明显的旱季。因此,我们的数据不支持有蹄类食性组成变化是由生境中木本与草本比例不同造成的假说,食性与降雨量间也无明显的关系。我们的结果支持草本中蛋白含量增加引起黑斑羚采食比例的增加这一模型。粪便中氮含量在时间和空间上的变化很小,揭示在可利用食物中,无论木本还是草本,黑斑羚进行选择采食以保证最好的食物质量。基于这些结果,我们认为更具体的食物选择和可利用性最适采食理论能够更好地解释这种生态学变化。