Differences between ecological niches in northern and southern populations of Angolan black and white colobus monkeys (Colobus angolensis palliatus and Colobus angolensis sharpei) throughout Kenya and Tanzania

Ecological niche models can be useful for clarifying relationships between environmental factors and a species’ geographic distribution. In this study, we use presence‐only data and environmental layers to create an ecological niche model to better understand the distribution of the East African Angolan black and white colobus monkey, Colobus angolensis palliatus, and to assess whether the model supports considering the population as two separate subspecies, Colobus angolensis sharpei and C. a. palliatus. We found the range of the predicted distribution for suitable habitat of C. a. palliatus as currently classified to be only 12.4% of that shown in the International Union for Conservation of Nature Red List range map and to be fragmented. As C. angolensis is considered a “Least Concern” species, this difference suggests that generalized maps may lead to understating the species’ extinction risk. When presence points were divided into two previously proposed subspecies —C. a. palliatus (Kenya and Northern Tanzania) and C. a. sharpei (Southern Tanzania)—we found significant environmental differences between the distributions. The most important ecological variable for C. a. palliatus was predominantly precipitation of the driest month (69.1%) whereas for C. a. sharpei annual precipitation (44.8%) and land cover (normalized difference vegetation index, 16.4%) were the most important. When comparing suitable ranges for the separate distributions, we found only a 1.2% geographical overlap. These differences are consistent with previous subspecies delineations of C. a. palliatus and C. a. sharpei based upon morphology, pelage, and genetics. Our study suggests that extirpation of C. a. palliatus in suitable habitat areas and occurrence of this subspecies in anthropogenic environments, warrant further consideration for conservation actions.     

Mitochondrial DNA D‐loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations

The Small East African (SEA) goat are widely distributed in different agro‐ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goat populations, namely Fipa, Songwe, Tanga, Pwani, Iringa, Newala, Lindi, Gogo, Pare, Maasai, Sukuma, and Ujiji, based on the mitochondrial DNA (mtDNA) D‐loop. High haplotype (H _d = 0.9619–0.9945) and nucleotide (π = 0.0120–0.0162) diversities were observed from a total of 389 haplotypes. The majority of the haplotypes (n = 334) belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B, and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro‐ecological regions of the country.     

Genetic diversity of Diaphorina citri (Hemiptera: Liviidae) unravels phylogeographic structure and invasion history of eastern African populations

The Asian citrus psyllid (Diaphorina citri Kuwayama) is a key pest of Citrus sp. worldwide, as it acts as a vector for Candidatus Liberibacter asiaticus, the bacterial pathogen that causes citrus Huanglongbing. Diaphorina citri has been reported in Kenya, Tanzania, and more recently in Ethiopia. This study assessed the genetic diversity and phylogeographic structure of the pest to gain insights into the potential sources of its introduction into Africa. Population structure and differentiation of D. citri populations from China, Ethiopia, Kenya, Tanzania, and the USA were assessed using 10 microsatellite loci. Additionally, five new complete mitogenomes of D. citri collected in China, Ethiopia, Kenya, Tanzania, and the USA were analyzed in the context of publicly available sequences. Genotype data grouped the D. citri populations from Kenya and Tanzania in one cluster, and those from Ethiopia formed a separate cluster. The two genetic clusters inferred from genotype data were congruent with mitochondrial sequence data. The mitogenomes from Kenya/Tanzania/China had 99.0% similarity, and the Ethiopia/USA had 99.9% similarity. In conclusion, D. citri populations in eastern Africa have different sources, as the Kenyan and Tanzanian populations probably originated from southeastern Asia, while the Ethiopian population most probably originated from the Americas.     

Three new species of Callulina (Amphibia: Anura: Brevicipitidae) highlight local endemism and conservation plight of Africa's Eastern Arc forests

Material ascribed to the genus Callulina from north‐east Tanzania and south‐east Kenya is assessed. Three new species of Callulina are described from the North ( Callulina laphami sp. nov. ) and South ( Callulina shengena sp. nov. and Callulina stanleyi sp. nov. ) Pare Mountains in Tanzania. The species are diagnosed based on morphological, acoustic, and molecular data. A new key to the species of Callulina is provided. Based on an interpretation of the International Union for Conservation of Nature (IUCN) red list, we suggest that the three species will qualify as critically endangered, because of their small distributions and the ongoing threat to their habitat. We reveal the high local endemism of Callulina in the northern part of the Eastern Arc Mountains, with each species restricted to no more than one mountain (fragment) block. This high local endemism in Callulina is probably widespread across the Eastern Arc, raising further conservation concern for this group of amphibians. Based on new molecular phylogenetic data for Callulina, we discuss biogeographical relationships among north‐east Tanzanian mountains, and evolutionary patterns in Eastern Arc breviciptids. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 496–514.     

A previously undescribed mangabey from Southern Tanzania

A new form ofCercocebus galeritus is described. The new mangabey was discovered recently in the Uzungwe Mountains of Tanzania. It inhabits a restricted area of lowland and transitional rain forest on the steep, dissected, southeast-facing scarp slopes. In general appearance (size, shape, hair patterns, posture, gait), it closely resembles other forms of this species:C. g. galeritus from the Tana River gallery forests in Kenya andC. g. agilis from Gabon and Zaire. The pelage is intermediate in color between these two subspecies. Areas of bare skin differ markedly from the otherC. galeritus, particularly the almost cream-colored face. Vocalizations are typical forC. galeritus. Preliminary field observations indicate that these mangabeys form multimale groups with a tendency to move as dissociated subparties, as is the case forC. g. galeritus. Although no formal classification is proposed, the evidence suggests that the new mangabey should joinC. g. galeritus,C. g. agilis andC. g. chrysogaster as a fourth distinct form within the polytypic speciesC. galeritus.     

Genetic and morphological differentiation of the mangrove crab Perisesarma guttatum (Brachyura: Sesarmidae) along an East African latitudinal gradient

The genetic structure and morphometric differentiation of mangrove crab Perisesarma guttatum populations were examined among shelf connected locations along a latitudinal gradient on the East African coast. Over 2200 specimens were sampled from 23 mangrove sites for geometric morphometrics analysis. Population genetic analyses of mitochondrial cytochrome c oxidase subunit I (COI) DNA sequences were used to evaluate connectivity among populations. A total of 73 haplotypes were detected, and almost no haplotypes were found in common between two highly supported phylogeographic clades: southern Mozambique (Inhaca Island and Maputo Bay) and a northern clade that included north Mozambique, Tanzania and Kenya. These two clades were identified based on the species' populations pairwise genetic differentiation and geographical location. Φ_ST values were considerably high between the two clades, indicating the presence of significant population genetic structure between Kenya and South Mozambique. However, each clade was composed of genetically similar populations along the latitudinal gradient, and no significant population structure was found within each clade because the Φ_st values were not significant. The morphometric analysis corroborated the division into two clades (i.e. Inhaca Island/Maputo Bay and northern populations) and also detected less shape variation among populations that were few kilometres apart. The significant spatial genetic structuring between the southern and the northern populations of P. guttatum along the geographic gradient under study, combined with morphological differences, suggests that these populations may be considered as cryptic species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 28–46.     

The forest batis, Batis mixta, is two species: description of a new, narrowly distributed Batis species in the Eastern Arc biodiversity hotspot

The forest batis, Batis mixta, is a common bird of the forests of the Eastern Arc Mountains of Tanzania and in some adjacent montane and coastal forests. Through new collecting efforts in most of this range we documented a well-marked change in morphology in the middle of the range. Supplementary genetic studies of the historical population structure suggest connectivity among the south-western and northern/coastal populations, but not between these parapatric groups. It is concluded that two species are involved, and a new name B. crypta is proposed for the south-western populations. A marked genetic break also exists towards B. capensis sola in northern Malawi. The morphologically distinctive form reichenowi in south-eastern Tanzania is genetically nested within B. mixta, and for now we keep it as a subspecies of B. mixta.     

Evidence that Kenyan House Sparrows Passer domesticus invaded from multiple sites

Here we characterize genetic patterns across the range of House Sparrows in Kenya using six microsatellite markers. We screened House Sparrows from two remote locations in northern Kenya, Marsabit (n = 24) and Wajir (n = 27), which are separated from other colonized areas in Kenya by minimally developed, arid habitat, and then compared these birds with House Sparrows in 10 more central and longer established Kenyan cities (n = 233) in this range. House Sparrows from Marsabit and Wajir originated from a separate source, probably Somalia and/or Ethiopia, from other Kenyan House Sparrows, probably Mombasa. Furthermore, the genetic characteristics of northern and southern populations indicate that they have not yet mixed, supporting a hypothesis that the large, minimally (human) developed, arid landscape spanning nearly all of northern Kenya, including the 100 000 km² Chalbi Desert, is a barrier to dispersal for House Sparrows.     

Genetic diversity,genetic structure and phylogeography of the Iberian endemic Gypsophila struthium (Caryophyllaceae) as revealed by AFLP and plastid DNA sequences: connecting habitat fragmentation and diversification

Iberian gypsum outcrops are highly fragmented and ecologically challenging environments for plant colonization. As gypsophytes occur exclusively in such habitats, they are ideal models for the study of both the effects of habitat fragmentation and selection on population genetic diversity and structure. In this study, we used amplified fragment length polymorphism (AFLP) and plastid DNA sequences to investigate the phylogeographical history of the Iberian plant Gypsophila struthium (Caryophyllaceae), a widespread endemic restricted to Iberian gypsum outcrops. Gypsophila struthium consists of two subspecies that differ in the architecture of their inflorescence and have mostly allopatric ranges. Gypsophila struthium subsp. struthium occurs in central, eastern and south‐eastern Iberia, whereas G. struthium subsp. hispanica occurs in northern and eastern areas. AFLPs revealed low but significant genetic differentiation between the subspecies, probably as a result of a recent diversification during the Pliocene–Pleistocene. In the geographical contact zone between the taxa, the Bayesian analyses revealed populations with mixed ancestries and genetic clusters predominantly of one or the other subspecies, indicating incomplete reproductive barriers between them. Plastid DNA haplotypes revealed strong geographical structure and testified to processes of isolation by distance and continuous range expansion for some haplotype clades. The Bayesian analyses of the population structure of AFLP data and nested clade phylogeographical analysis (NCPA) of plastid haplotypes revealed that the putative ancestral range corresponded to central and eastern populations of G. struthium subsp. struthium, with those lineages contributing through more recent expansion to increased genetic diversity and structure of the south‐eastern and eastern ranges of this subspecies and to the diversification of G. struthium subsp. hispanica in northern and eastern gypsum outcrops. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 654–675.     

Genetic diversity and population structure of selected lacustrine and riverine populations of African catfish,Clarias gariepinus (Burchell, 1822), in Kenya

Determining the genetic characteristics of natural fish stocks is useful for conservation and aquaculture programs. For African catfish, Clarias gariepinus, genetic characterization could help identify populations suitable as brood stock for culture, and those in need of conservation. This study determined the genetic diversity, population structure, and demographic history of C. gariepinus from Lakes Victoria (LV), Kenyatta (LKE), Kamnarok (LKA), and Rivers Nyando (NR), Tana (TR) and Sosiani (SR) in Kenya. Using 128 DNA sequences of D-loop control region, 34 haplotypes were recovered, of which 79.4% were singletons. Only 7 haplotypes were shared between sites, implying little gene flow between sites. Number of haplotypes was highest in LKE and NR populations and lowest in SR. Haplotype diversity was highest in LV, and lowest in SR, while, nucleotide diversity was highest in LKA and lowest in LV. Phylogenetic analyses revealed five clusters: Lakes Victoria, Kamnarok and Kenyatta, and Rivers Tana and Nyando, from both maximum likelihood tree and minimum spanning network. This, together with significant F _ST values among the sites imply population differentiation. Mismatch distributions were multi-modal in LKA, LKE, NR and TR, signifying demographic equilibria. Neutrality tests Tajima`s D values for the sampled populations were negative and significantly different, suggesting stable populations. These results show the existence of genetically distinct populations of C. gariepinus that require spatially explicit management actions such as reducing fishing pressure, pollution, minimizing habitat destruction and fragmentation for sustainable utilisation of stocks.     

Intraspecific molecular phylogeny and phylogeography of the Meriones meridianus (Rodentia: Cricetidae) complex in northern China reflect the processes of desertification and the Tianshan Mountains uplift

The phylogeographical patterns and demographic history of mitochondrial DNA (cytochrome b, N = 327; D‐loop, N = 252) and nuclear DNA (IRBP gene, N = 235) haplotypes were studied for the Meriones meridianus complex in northern China, a desert‐dwelling gerbil species complex. The phylogenetic analyses, which were performed on the separate and combined (mitochondrial + nuclear) datasets, revealed two divergent clades (Clade A and Clade B) corresponding to distinct geographical regions. Clade A contained the haplotypes found mostly in individuals from the Tianshan Mountains area. Clade B contained haplotypes from populations located in other deserts in northern China. The divergence times indicated that the history of the M. meridianus complex was influenced by the uplift of the Tianshan Mountains and climate‐induced habitat fluctuations. In the Pleistocene, the expansion of forests and grasslands during interglacial period led to the isolation of the M. meridianus complex, which preferred to inhabit deserts. Hence, long geological isolation and the M. meridianus complex adaptation to local ecological conditions led to its genetic divergence. Clade A had long‐lasting demographic stability, most likely because the populations of this clade remained in a stable desert environment for a long time. However, the extension of other deserts and disappearance of palaeolakes during the last glacial period resulted in demographic expansion of Clade B. Furthermore, our genetic data indicated that two subspecies may exist within the M. meridianus complex. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 362–383.     

Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of Africa

Background  

The Eastern Arc Mountains of Africa have become one of the focal systems with which to explore the patterns and mechanisms of diversification among montane species and populations. One unresolved question is the extent to which populations inhabiting montane forest interact with those of adjacent lowland forest abutting the coast of eastern Africa. The Tiny Greenbul (Phyllastephus debilis) represents the only described bird species within the Eastern Arc/coastal forest mosaic, which is polytypic across an altitudinal gradient: the subspecies albigula (green head) is distributed in the montane Usambara and Nguru Mountains whereas the subspecies rabai (grey head) is found in Tanzanian lowland and foothill forest. Using a combination of morphological and genetic data, we aim to establish if the pattern of morphological differentiation in the Tiny Greenbul (Phyllastrephus debilis) is the result of disruptive selection along an altitudinal gradient or a consequence of secondary contact following population expansion of two differentiated lineages.     

Some developmental markers in yellow baboon infants of Mikumi National Park,Tanzania

Infants of known birthdates were sampled from a population of yellow baboons (Papio cynocephalus) in Mikumi National Park, Tanzania, to ascertain the reliability of several maturational changes which could be used to age infants whose birthdates are unknown. The transition from the infant's black natal coat to the uniform yellow or tan adult pelage proved extremely variable, with completion varying from 7 to 19 months. The transition from the pink skin of the newborn to the completely grey adult pigmentation was much less variable. Skin on the hands and feet and on the paracallosal area was completely grey in all individuals by 8 months, while skin on the face and ears changed more gradually and was entirely grey by 12 months. These data are in substantial agreement with maturational markers established for yellow baboon infants in Amboseli National Park, Kenya, despite differences in habitat and age-sex structure between the two populations.     

Genetic isolation in an endemic African habitat specialist

The Chestnut‐banded Plover Charadrius pallidus is a Near‐Threatened shorebird species endemic to mainland Africa. We examined levels of genetic differentiation between its two morphologically and geographically distinct subspecies, C. p. pallidus in southern Africa (population size 11 000–16 000) and C. p. venustus in eastern Africa (population size 6500). In contrast to other plover species that maintain genetic connectivity over thousands of kilometres across continental Africa, we found profound genetic differences between remote sampling sites. Phylogenetic network analysis based on four nuclear and two mitochondrial gene regions, and population genetic structure analyses based on 11 microsatellite loci, indicated strong genetic divergence, with 2.36% mitochondrial sequence divergence between individuals sampled in Namibia (southern Africa) and those of Kenya and Tanzania (eastern Africa). This distinction between southern and eastern African populations was also supported by highly distinct genetic clusters based on microsatellite markers (global F_ST = 0.309,  = 0.510, D = 0.182). Behavioural factors that may promote genetic differentiation in this species include habitat specialization, monogamous mating behaviour and sedentariness. Reliance on an extremely small number of saline lakes for breeding and limited dispersal between populations are likely to promote reproductive and genetic isolation between eastern and southern Africa. We suggest that the two Chestnut‐banded Plover subspecies may warrant elevation to full species status. To assess this distinction fully, additional sample collection will be needed, with analysis of genetic and phenotypic traits from across the species’ entire breeding range.     

Diversity and genetic differentiation among populations of Indian and Kenyan tea (Camellia sinensis (L.) O. Kuntze) revealed by AFLP markers

AFLP markers were successfully employed to detect diversity and genetic differentiation among Indian and Kenyan populations of tea (Camellia sinensis (L.) O. Kuntze). Shannon's index of diversity was used to partition the total phenotypic variation into between and within population components. On average, most of the diversity was detected within populations, with 79% of the variation being within and 21% being between populations of Indian and Kenyan tea. A dendrogram constructed on the basis of band sharing distinctly separated the three populations of tea into China type (sinensis), Assam type (assamica) and Cambod type (assamica ssp. lasiocalyx) in a manner consistent with the present taxonomy of tea, the known pedigree of some of the genotypes and their geographical origin. Principal coordinate (PCO) analysis grouped Assam genotypes both from India and Kenya supporting the suggestion that the Kenyan clones have been derived from collections made in this region. The China types were more dispersed on the PCO plot which is a reflection of wider genetic variation. As would be expected, clones collected from the same region exhibited less overall genetic variation. AFLP analysis discriminated all of the tested genotypes from India and Kenya, even those which cannot be distinguished on the basis of morphological and phenotypic traits. Received: 2 May 1996 / Accepted: 14 June 1996     

Mitogenomic analysis for coelacanths (Latimeria chalumnae) caught in Tanzania

In recent years, a large number of individuals of the species Latimeria chalumnae, one of the living fossil coelacanths, have been landed off the coast of Tanzania. Although L. chalumnae specimens have also been landed at other localities in the western Indian Ocean, so far, viable populations of this species have been identified only at two localities, Comoros and South Africa. Therefore, the recent active catch off Tanzania suggests a new habitat for L. chalumnae. To examine the genetic background of the Tanzanian fish, we analyzed complete mtDNA sequences of two Tanzanian individuals (Kigombe-9 and Songo Mnara-1) collected from the north and south coasts of Tanzania. Using the recently reported criteria for six haplotypes established in a population genetic study for coelacanths living in the western Indian Ocean [Schartl, M., Hornung, U., Hissman, K., Schauer, J., Fricke, H., 2005. Relatedness among east African coelacanths. Nature 435, 901.], we characterized Songo Mnara-1 as haplotype 1 and Kigombe-9 as haplotype 5. We suggest that the Songo Mnara specimen is a member of the Comoran group, but was swept away by the South Equatorial current. The individual from Kigombe may be a member of an undiscovered population that exists near the boundary between Tanzania and Kenya. Further analysis using more than 19 individuals recently captured off the north coast of Tanzania will reveal whether a new population exists there. Our sequence data suggest additional variable sites in the mtDNA sequence that may define the population structure of coelacanths in the western Indian Ocean and also raise the possibility that the previously published Comoran coelacanth mtDNA sequence contains several critical errors including base changes and indels.     

Phylogeography of silver‐studded blue,Plebejus subsolanus (Lepidoptera: Lycaenidae), in the central mountainous regions of Japan

The silver‐studded blue, Plebejus subsolanus, is widely distributed in the Russian Altai mountains, northeastern China, the Korean Peninsula, and the Japanese archipelago. In Japan, the species is distributed across wide elevation ranges from the lowlands of Hokkaido to the subalpine zone of Honshu. Current subspecies classification in Japan is as follows: ssp. iburiensis, occurring in lowland grasslands in Hokkaido; ssp. yaginus in lower mountain grasslands in Honshu; and ssp. yarigadakeanus in higher mountain grasslands in Honshu. The habitat of this species has been markedly reduced due to recent habitat destruction and land‐use changes. Here, we undertook phylogeographic analyses of two subspecies, ssp. yaginus and yarigadakeanus in the central mountainous regions of Japan, based on two mitochondrial gene sequences, in order to collect information for establishing effective conservation strategies. From 57 samples from the four mountain ranges, we obtained a haplotype network comprised of 12 haplotypes. Because of the haplotype network topology, the geographic distribution of haplotypes and the correspondence of haplotype divergence to subspecies taxonomy, we provisionally divided the haplotypes into three haplogroups: YR1 and YR2, which comprised ssp. yarigadakeanus, and YG, which comprised ssp. yaginus. Mitochondrial DNA genetic differentiation generally agreed with morphological subspecies classification. The haplotype network suggested that ssp. yarigadakeanus populations had multiple origins, and the subspecies character of “bright blue of the male's wings” was assumed to have evolved independently in each subalpine meadow. We found that P. subsolanus was genetically differentiated depending upon the elevation at each mountain region, suggesting that each haplogroup should be a conservation unit.     

Effects of Forest Fragmentation on the Abundance of <Emphasis Type="Italic">Colobus angolensis palliatus</Emphasis> in Kenya’s Coastal Forests

We documented the occurrence and abundance patterns of Angola black-and-white colobus (Colobus angolensis palliatus) in 46 coastal forest fragments ranging from 1 ha to >1400 ha in the Kwale District, Kenya. In field surveys conducted in 2001, we also recorded forest spatial, structural, resource, and disturbance characteristics to determine the effects of habitat quality and fragmentation and the factors most critical to the continued survival of the little-known species. We tested 13 hypotheses to explain variation in patch occupancy and abundance patterns of Colobus angolensis palliatus in relation to habitat attributes. Minimal adequate models indicated that the occurrence of colobus in forest fragments is positively associated with fragment area and canopy cover, whereas the density of colobus in occupied fragments is attributable to forest area, the proportion of forest change over the previous 12 yr, and the basal area of 14 major food trees. Large-scale illegal extraction of major colobus food trees in the District for human resource use, in both protected and unprotected forests, together with ongoing forest clearance and modification, are the major threats to Colobus angolensis palliatus in Kenya.     

Phylogeny and genetic structure of the goitered gazelle (Artiodactyla,Bovidae) in north-western China indicated by the hypervariable mitochondrial control region

The goitered gazelle, Gazella subgutturosa, is a medium-sized ungulate inhabiting arid and semi-arid regions in the Middle East and central Asia. The intraspecific classification of the species remains unclear. We analysed the genetic diversity in mitochondrial DNA control region (CR) sequences (976?bp) from 104 wild samples from the Xinjiang Uyghur Autonomous Region (XUAR) in north-west China, and reconstructed phylogeny with additional sequences from across the species’ range. We detected 58 haplotypes in XUAR populations, all but three of which were specific to single sampling sites. The phylogenetic analysis displayed two obvious clades of mtDNA haplotypes and the other haplotypes differed from the two clades. A median-joining network showed three groups of haplotypes were to a high extent concordant with the phylogenetic tree. The haplotype clustering was consistent with their geographic distribution. Nei’s net sequence divergences amongst the three groups ranged from 0.010 to 0.018 and indicated three subspecies, two of which inhabit XUAR. We detected strong differentiation between northern (NX) and southern (SX) XUAR populations overall (F_ST?=?0.4448, P?相似文献