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.     

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.     

Regional genetic structuring and evolutionary history of the impala Aepyceros melampus

Samples of 162 impala antelope (Aepyceros melampus) from throughout its distribution range in sub-Saharan Africa were surveyed using eight polymorphic microsatellite loci. Furthermore, 155 previously published mitochondrial DNA (mtDNA) sequences from the same localities were reanalyzed. Two subspecies of impala are presently recognized--the isolated black-faced impala (Aepyceros melampus petersi) in southwest Africa and the common impala (Aepyceros melampus melampus) abundant in southern and east Africa. All tests performed indicated significant genetic differentiation at the subspecific level. Furthermore, individual-based analyses split the common impala subspecies into two distinct genetic groups, conforming with regional geographic affiliation to southern or east Africa. This was supported by assignment tests, genetic distance measures, pairwise theta values, and analysis of molecular variance. We suggest that the presence of such previously unknown regional structuring within the subspecies reflects a pattern of colonization from a formerly large panmictic population in southern Africa toward east Africa. This scenario was supported by a progressive decline in population diversity indices toward east Africa and a significant increase in the quantity theta/(1 - theta). Both microsatellite and mtDNA data indicated a genetic distinctiveness of the Samburu population in Kenya.     

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 network analysis between Apis mellifera subspecies based on mtDNA argues the purity of specimens from North Africa,the Levant and Saudi Arabia

ObjectivesThis study aimed to analyze the genetic relationships between honey bee subspecies using reference specimens and recently collected specimens from different parts of the world. The purity of these specimens was discussed in light of the obtained results.MethodsThe genetic networks were constructed between 21 subspecies of honey bees, Apis mellifera L.: 9 in Africa, 7 in Europe and 5 in Asia. The analysis was performed using the mtDNA of these subspecies and the Population Analysis with Reticulate Trees software. Some subspecies were represented by more than two specimens based on the available online sequences.Results and conclusionsThe subspecies A. m. sahariensis from Africa showed unique characteristics and is genetically isolated than all other studied bee subspecies. Specimens collected from Saudi Arabia showed genetic relatedness to A. m. jemenitica, A. m. lamarckii, and some European subspecies, suggesting high degree of hybridization. The close genetic relationship between the Egyptian bees, A. m. lamarckii, and the Syrian bees, A. m. syriaca, were emphasized. The overall genetic network showed the presence of three distinct branches in relation to geographical locations. The high accurateness of the used analysis was confirmed by previous phylogenetic studies as well as the genetic relationships between hybrid bees of A. m. capensis and A. m. scutellata. The genetic networks showed the presence of bee subspecies from Africa in all branches including Europe and Asia. The study suggests the impurity of some specimens mostly due to the hybridization between subspecies. Specific recommendations for future conservation efforts of bees were presented in light of this study.     

Ixodid ticks of African buffalo (<Emphasis Type="Italic">Syncerus caffer</Emphasis>), impala (<Emphasis Type="Italic">Aepyceros melampus</Emphasis>) and elephant (<Emphasis Type="Italic">Loxodonta africana</Emphasis>) in five protected park estates in the Zambezi valley,Zimbabwe

Wildlife hosts many pathogens of economic importance and is considered as a reservoir of important tick-borne diseases of livestock in southern Africa. The species composition of ticks parasitizing buffalo (Syncerus caffer), impala (Aepyceros melampus) and elephant (Loxodonta africana) was investigated in five protected parks in the Zambezi valley, Zimbabwe. A total of 1104 adult ticks was collected from 75 adult animals comprising five buffaloes, five elephants and five impalas drawn from five protected wildlife parks. Five tick species belonging to two genera were recovered, with Rhipicephalus decoloratus being the most prevalent species in all the three animal groups. Amblyomma hebraeum was only recovered from buffaloes whereas Rhipicephalus zambeziensis was recovered from buffalos and elephants. Significant differences in mean tick species distribution and concentration were observed amongst the wildlife parks and these appeared to be influenced by the number of hosts in each park. The study revealed that buffaloes are the major host of R. decoloratus in the Zambezi valley. The presence of these ixodid ticks within the Zambezi valley may have significant ecological and economic impacts on wildlife conservation, domestic animals and human health.     

Stable isotope evidence for impala Aepyceros melampus diets at Akagera National Park,Rwanda

Stable isotope analysis of tooth enamel was used to investigate the relative proportions of grass and browse in seasonal and overall diets of impala Aepyceros melampus at Akagera National Park, Rwanda. Bulk enamel samples suggest that on average, impala ate c. 86% C₄ grass year‐round, far more than in most previously studied impala populations across Africa. Intra‐tooth samples show that seasonal changes in the proportion of C₄ grass versus C₃ browse are minimal (c. 10%), the diet being dominated by C₄ grass year‐round in contrast to other impala populations that consume ≥50% browse during the dry season. Intra‐tooth oxygen isotope values track carbon isotope changes to a moderate degree, but are not patterned clearly enough to permit identification of wet versus dry seasons. As other studies have shown that impala select high‐protein diets, the foraging behaviour at Akagera is probably because of the availability of palatable grass for much of the year in the edaphic grasslands around the lacustrine environments of the eastern portions of Akagera National Park.     

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.     

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.     

Introgression of nuclear and mitochondrial DNA markers of Mus musculus musculus to aboriginal populations of wild mice from Central Asia (M. m. wagneri) and South Siberia (M. m. gansuensis)

Variability of the nucleotide sequences of the second intron of the b1-chain of hemoglobin (Hbb-b1) and complete control region of mitochondrial DNA (D-loop) was studied in aboriginal and synanthropic populations of M. m. wagneri from Central Asia and M. m. gansuensis from South Siberia. A difference in the frequency of the Hbb^w1 hemoglobin variant for natural and urban populations of mice was shown. All mice from natural habitats of studied areas have musculus type of mtDNA. Apparently, the substitution of taxon-specific mitochondrial haplotypes of wagneri, and gansuensis might occur due to the absorbing hybridization with nominate subspecies musculus, which is consistent with the results on nuclear DNA (Hbb-b1 gene) obtained in this work. Two differentiated haplogroups among aboriginal subspecies wagneri (d = 0.01), one of which included house mice from Turkmenistan, were discovered for the first time. This may indicate mtDNA introgression from synanthropic forms of Turkmenistan into natural populations of Kazakhstan mice. The type of mtDNA typical for the castaneus subspecies was detected in two individuals from the natural habitat of Kazakhstan and Turkmenistan; it had not been encountered in Central Asia before. It has been suggested that the gene flow of nuclear and mitochondrial genomes in microevolution processes in M. musculus is directed from the synanthropic forms towards wild populations.     

Geometric morphometric and phylogenetic analyses of Arizona Sky Island populations of Scaphinotus petersi Roeschke (Coleoptera: Carabidae)

Scaphinotus petersi Roeschke, 1907 (Carabidae) is a ground beetle endemic to Sky Islands in south‐eastern Arizona. Previous taxonomic studies described several subspecies with morphological differences inhabiting geographically isolated mountain ranges. We combined molecular sequence data and morphometric data, especially head and pronotum shape analyses, to examine the variation and divergence in subspecies and isolated montane populations. In this study, we employ a combination of distance morphometrics as well as geometric morphometrics to quantify the level of morphological variation, and to test the hypothesis that geographically distinct populations of S. petersi are phenotypically distinct. Results suggest that these isolated populations have diverged morphologically and genetically. Phylogenetic analyses identified two monophyletic lineages within the species that correspond generally to pronotum shape. We observed significant morphological variation among most montane populations in of S. petersi, with the pronotum shape as the clearest delimiting trait. © 2015 The Linnean Society of London     

基于细胞色素b基因的中国岩羊不同地理种群遗传差异分析

为了揭示中国岩羊不同地理种群的遗传差异,探讨岩羊亚种分化的分子机制,采用中国岩羊不同地理种群的细胞色素b(Cyt b)基因的全序列,分析了碱基变异情况、遗传距离以及核苷酸序列差异。用最大似然法和贝叶斯法构建分子系统树并对获得的拓扑结构进行分析。结果发现,西藏亚种与四川亚种Cyt b基因平均序列差异为4.2%(±0.007),处于偶蹄目亚种的序列差异范围内,支持了目前对岩羊西藏亚种的分类地位。四川亚种内部各地理种群之间的遗传距离(0.033±0.0 111)与它们分别到西藏种群的遗传距离(0.042±0.007)差异不显著(t=1.824,P=0.084),说明四川亚种内部各地理种群间已经发生较显著的遗传分化。其中,四川、甘肃和青海种群亲缘关系较近,并与四川亚种内部的其它种群已产生了显著的遗传分化。因此认为四川亚种内部各地理种群的种下分化需要深入研究。     

On the Dispersal of Bottle Gourd [<Emphasis Type="Italic">Lagenaria siceraria</Emphasis> (Mol.) Standl.] Out of Africa: a Contribution from the Analysis of Nuclear Ribosomal DNA Haplotypes,Divergent Paralogs and Variants of 5.8S Protein Sequences

Bottle gourd (Lagenaria siceraria), a multipurpose crop, is among the first domesticates of humans. This study analyses nuclear ribosomal DNA (nrDNA) of the two cultivated subspecies to improve our understanding on the African origin and the dispersal to Asia. A total of 146 nrDNA sequences representing 79 individuals from African cultivars and 67 individuals from Asian cultivars were compared; the resulting nrDNA sequences were composed of 35 and 16 haplotypes specific to Africa and Asia, respectively, and two additional haplotypes shared by both continents. When all the rDNA haplotypes were bulked, the genetic differentiation (F _ST ) was significant between the subspecies (P?<?0.001), within Africa (P?<?0.001) and within Asia (P?<?0.05), and the nucleotide diversity was 2.5-fold higher in Africa. Sorting the haplotypes by classes of paralogs revealed more classes in Africa, and in classes where African and Asian cultivars were represented, the diversity was higher in Africa, in general. The 5.8S-coding regions showed two to four amino acid differences resulting to nine protein sequence variants, one of which encompassed all the Asian cultivars. The nucleotide diversity at that shared variant was 1.43-fold higher in Africa than in Asia. Analyses of phylogenetic networks revealed major shared haplotypes containing 23.91 % of the cultivars and having founder locations. We suggest that African cultivars reached Asia. The study tags for the first time nrDNA haplotypes capable of discriminating between and within the subspecies. Thirty single nucleotide polymorphisms (SNPs) and five insertion-deletions (Indels) derived from the haplotypes and registered in GenBank are provided.     

Population Genetics of Seaside Sparrow (Ammodramus maritimus) Subspecies along the Gulf of Mexico

Seaside Sparrows (Ammodramus maritimus) along the Gulf of Mexico are currently recognized as four subspecies, including taxa in Florida (A. m. juncicola and A. m. peninsulae) and southern Texas (Ammodramus m. sennetti), plus a widespread taxon between them (A. m. fisheri). We examined population genetic structure of this “Gulf Coast” clade using microsatellite and mtDNA data. Results of Bayesian analyses (Structure, GeneLand) of microsatellite data from nine locations do not entirely align with current subspecific taxonomy. Ammodramus m. sennetti from southern Texas is significantly differentiated from all other populations, but we found evidence of an admixture zone with A. m. fisheri near Corpus Christi. The two subspecies along the northern Gulf Coast of Florida are significantly differentiated from both A. m. sennetti and A. m. fisheri, but are not distinct from each other. We found a weak signal of isolation by distance within A. m. fisheri, indicating this population is not entirely panmictic throughout its range. Although continued conservation concern is warranted for all populations along the Gulf Coast, A. m. fisheri appears to be more secure than the far smaller populations in south Texas and the northern Florida Gulf Coast. In particular, the most genetically distinct populations, those in Texas south of Corpus Christi, occupy unique habitats within a very small geographic range.     

Evaluation of the efficacy of mitochondrial ATP 6 and 8, Cyt b and 16S rDNA genes for differentiation of Iranian honeybees (Apis mellifera meda) from commercial subspecies of Apis mellifera L. and comparison with geometric morphometric method

Mitochondrial DNA sequence variations and the geometric morphometric method can be used to differentiate honeybee subspecies and evolutionary lineages. Molecular markers are powerful tools for discriminating honeybee subspecies. In this study, 19 beekeeping sites were selected to collect Iranian honeybee samples. The honeybee forewing images stored at Oberursel (the Bee Data Bank) were used to compare with those of Iranian honeybees using the geometric morphometric method. Furthermore, the abilities of DNA markers to differentiate Iranian honeybees (A. m. meda) from the most common commercial subspecies (A. m. carnica and A. m. ligustica) were assessed. In the present research, 16S rDNA (Mitochondrial 16S rDNA Region) showed greater ability in differentiating Iranian honeybees from other subspecies compared with ATP 6 and 8 and Cyt b. The phylogenetic tree derived from 16S rDNA differentiated A. m. carnica and A. m. ligustica from Iranian honeybees. Principle component analysis (PCA) discriminated C lineage and Z subgroup from A and M lineages using 16S rDNA. In addition, the phylogenetic tree of the 16S rDNA affirmed the findings of the cluster analysis derived from the geometric morphometric method in differentiating A. m. carnica and A. m. ligustica from Iranian honeybees. The cluster analysis grouped reference subspecies of A. m. meda with Iranian honeybees. Moreover, the Discriminant Function Analyses (DFA) differentiated Iranian honeybees from A. m. ligustica and A. m. carnica.     

Mammal road‐type associations in Kruger National Park,South Africa: Common mammals do not avoid tar roads more than dirt roads

The majority of Africa''s parks and conservation areas have a vast road network, facilitating motorized vehicle game viewing. These roads have an influence that is both road type‐ and species‐specific, on the surrounding ecosystem. Due to their higher traffic volumes, we hypothesized that tar roads and their immediate surrounds within the Kruger National Park, South Africa, are avoided to a greater extent by medium‐to‐large mammals than comparable dirt roads in the park. We systematically recorded the presence of medium‐to‐large mammal species from our vehicle, recording data at 401 tar and 369 dirt road stops in the Kruger National Park. In addition to species presence, we also estimated the proximity of animals to the road, as well as herd sizes. Our results indicate an equal likelihood of viewing the commonly recorded medium‐to‐large mammal species from both road types. The likelihood of observing larger herd sizes was also similar between tar and dirt roads for the three most commonly observed species, African elephant (Loxodonta africana), impala (Aepyceros melampus), and plains zebra (Equus quagga), and the likelihood of viewing impala and zebra close to the road also did not differ between tar and dirt roads. However, elephant was observed more often close to tar roads, compared to dirt roads. We interpreted this as the result of potentially increased woody cover associated with more water runoff in close proximity to tar roads compared with dirt roads. Our results not only have ecological significance, supporting the notion that many of the park''s species are habituated to human infrastructure, but also management implications, informing park officials about the influence of road traffic and road type on wildlife distributions.     

Guiding Classical Biological Control of an Invasive Mealybug Using Integrative Taxonomy

Delottococcus aberiae De Lotto (Hemiptera: Pseudococcidae) is a mealybug of Southern African origin that has recently been introduced into Eastern Spain. It causes severe distortions on young citrus fruits and represents a growing threat to Mediterranean citrus production. So far, biological control has proven unsatisfactory due to the absence of efficient natural enemies in Spain. Hence, the management of this pest currently relies only on chemical control. The introduction of natural enemies of D. aberiae from the native area of the pest represents a sustainable and economically viable alternative to reduce the risks linked to pesticide applications. Since biological control of mealybugs has been traditionally challenged by taxonomic misidentification, an intensive survey of Delottococcus spp. and their associated parasitoids in South Africa was required as a first step towards a classical biological control programme. Combining morphological and molecular characterization (integrative taxonomy) a total of nine mealybug species were identified in this study, including three species of Delottococcus. Different populations of D. aberiae were found on wild olive trees, in citrus orchards and on plants of Chrysanthemoides monilifera, showing intra-specific divergences according to their host plants. Interestingly, the invasive mealybug populations from Spanish orchards clustered together with the population on citrus from Limpopo Province (South Africa), sharing COI haplotypes. This result pointed to an optimum location to collect natural enemies against the invasive mealybug. A total of 14 parasitoid species were recovered from Delottococcus spp. and identified to genus and species level, by integrating morphological and molecular data. A parasitoid belonging to the genus Anagyrus, collected from D. aberiae in citrus orchards in Limpopo, is proposed here as a good biological control agent to be introduced into Spain.