Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the african antelope, kob (Kobus kob)

The genetic differentiation among kob populations (Kobus kob) representing two recognized subspecies was examined using mitochondrial control region sequences. Two distinct lineages (estimated sequence divergence of 9.8%) exhibited different geographical distributions and do not coincide with previously recognized ranges of subspecies. The presence of the two lineages was further supported with sequences of mitochondrial cytochrome b gene. One lineage was predominant in the west and southern ranges of the populations studied and the other was commonly found in a more northern distribution (Murchison populations) in Uganda. Murchison and the geographically intermediate Toro populations (Uganda) represented the area of overlap. The existence of the two lineages in the area of overlap is hypothesized to have resulted from a range expansion and secondary contact of the two lineages of kob that evolved in allopatry. The existence of the kob during the Pleistocene offers a plausible explanation for the observed biogeographic pattern. Our mitochondrial data reveal two examples of discordance between a gene tree and presumed species tree as: (i) the two lineages co-occur in the kob subspecies, Kobus kob thomasi (Uganda kob); and (ii) the puku, which was included in the analysis because of its controversial taxonomic status (currently recognized as a distinct species from the kob), is paraphyletic with respect to the kob. Significant degrees of heterogeneity were detected between populations. Relatively high genetic variation was observed in the populations, however, the inclusion of distinct lineages influences the population structure and nucleotide diversity of the kob populations.     

Uganda kob prefer high-visibility leks and territories

In lekking species, where males provide estrous females withlittle more than sperm, it has been widely supposed that theonly possible benefits to females of mate choice are genetic.We studied female choice of leks and territories in a reduncineantelope, the Uganda kob (Kobus kob thomasi), and found thatfemales consistently preferred high-visibility mating sites.Leks were elevated and had shorter grass and fewer thicketsthan the surrounding areas. Changes in the number of male andfemale kob on 10 leks were correlated with changes in surroundinggrass height, and both females and males preferred leks withexperimentally reduced grass height over neighboring controls.Within a lek, territory popularity was the primary determinantof male daily mating success, and females preferred territoriesrelatively far from thickets, but removal of thickets did notaffect female territory preferences. Because lion hunting successon kob increases with grass height and thicket density, femalesmay benefit directly from these preferences by reducing therisk of predation.     

Uganda kob (Adenota kob thomast): Territoriality and the Spatial Distributions of Sexual and Agonistic Behaviors at a Territorial Ground4

Possible functions of territorial behavior were evaluated on the basis of observations of agonistic and reproductive activities of Uganda kob at a “territorial ground” (TG) in southwestern Uganda. We have found that male residents of a TG tend to occupy exclusive areas, and that agonistic interactions are concentrated along the boundaries separating adjacent occupied areas. Thus, we conclude that male kob do engage in the active defense of spatially exclusive territories at a TG.     

Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression

Two subspecies of waterbuck (Kobus ellipsiprymnus), common (Kobus ellipsiprymnus ellipsiprymnus) and defassa (Kobus ellipsiprymnus defassa), are recognized based on differences in rump pattern, coat colour and geographical distribution. These forms are parapatrically distributed with an area of range overlap in East Africa, where phenotypically intermediate populations occur. Variation in 478 bp of the mitochondrial DNA control region and 14 polymorphic microsatellite loci were used to describe the genetic structure and phylogeographical pattern of the species, and to assess if the intermediate populations are the results of hybridization. In total, 186 individuals from 11 localities were analysed. A high degree of genetic differentiation was found between subspecies, although this was most evident from the microsatellite data. Hybridization was suggested in the phenotypically and geographically intermediate Nairobi NP population in Kenya. A neighbour-joining (NJ) tree based on microsatellite population genetic distances grouped Nairobi between the common and defassa populations, and a Bayesian analysis clearly showed introgression. Individuals sampled in Samburu NP, Kenya, had a common waterbuck phenotype, but introgression was suggested by both markers. Although a high degree of maternal defassa input was indicated from the sequence data, the Samburu population grouped with the common waterbuck in the microsatellite population genetic distance tree, with high support. Analyses of linkage disequilibrium and maximum-likelihood estimates of genetic drift suggested that admixture between subspecies is a recent event. The fact that introgression is limited between subspecies could be caused by chromosomal differences, hindering gene flow between common and defassa waterbuck.     

Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity

Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Because of heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here, we describe the development of microsatellite markers for K. senegalensis using next-generation sequencing to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next-generation sequencing yielded 93,943 sequences with an average read length of 234 bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty-one microsatellite loci were tested with 11 showing reliable amplification and polymorphism in K. senegalensis. The 11 novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa.     

Lek Breeding and Territorial Aggression in White-eared Kob

Territorial aggression in a lek breeding population of white-eared kob (Kobus kob leucotis) was investigated in the Boma National Park region, southern Sudan. The frequency of aggression on leks was positively related to the number of females present, but generally declined over the course of the breeding season. Males fought most strenuously for central territories that were preferred by females. Males with females in their territories were more frequently engaged in fights than unaccompanied males. Such fights often induced females to leave their original partners, especially when large groups of females were involved. Territorial aggression led to damaging injuries in several instances, and mortality of breeding age males was disproportionately high. These results suggest that the intensity of aggression exhibited by territorial males was scaled to potential reproductive benefits.     

Artificial rearing of some East African antelopes

Six topi ( Damaliscus korrigum ), five Uganda kob ( Adenota kob thomasi ) and two kirk's dik-dik ( Rhynchotragus kirkii ) were artificially reared from a few days of age.
Foue kob and four topi were fed first on a humanized milk powder "Lactogen"; all four developed intestinal disorders which in two cases were fatal. The survivors recovered on a diet of pasteurized cows' milk on which they were satisfactorily reared. Two topi were satisfactorily reared on cows' milk from the time of capture.
One dik-dik was reared from two weeks on cows' milk enriched with egg yolk to the composition of eland ( Taurotragus oryx ) milk. weight gain was not significantly different to that of a second dik-dik reared on cows' milk alone.
Causes of ill health and death were: ( a ) dehydration during the first three days of captivity; ( b intestinal disorders during the milk-feeding period; and ( c ) heavy intestinal parasitic infections during the post-weaning period.     

Correlates of male mating success and female choice in a lek-breeding antelope

We investigated factors underlying variation in male matingsuccess in Uganda kob (Kobus kob thomasi), a lek-breeding antelope.We found that only heavy (and, possibly, relatively old) malesheld lek territories and that female choice was an importantdeterminant of nonrandom mating patterns at leks. Our measureof male mating success was closely related to the historicalpopularity of the territory that a male defended, and individualfemales showed consistent preferences for particular lek territories,despite changes in territory ownership. Male success increasedwith body weight and declined independently of territory effectsduring each bout of lek territory tenure. We also found someevidence that female kob copied one another's choice of matesbecause females arriving at a lek tended to join territoriesthat already had relatively large harems on them. When comparedacross leks, average male mating success increased with leksize. Our results suggest that female kob may use a suite ofmale- and territory-based cues in mate choice at leks and, asa result, mate with particularly large males. However, we wereunable to determine whether female kob gain any direct or indirectbenefits through mate choice at leks.     

A Ploceus sp. nov. from Uganda

A new species of weaverbird, Ploceus victoriae , is described from Entebbe, Uganda. Its nearest relatives are Ploceus taeniopterus of northeast Zaïre, Sudan, Ethiopia and northwest Kenya, and Ploceus velatus , widespread through East Africa and across the Sahel to the Atlantic, but it differs in several morphological and behavioural characteristics.     

Phylogeography of the Afromontane Prunus africana reveals a former migration corridor between East and West African highlands

Scattered populations of the same tree species in montane forests through Africa have led to speculations on the origins of distributions. Here, we inferred the colonization history of the Afromontane tree Prunus africana using seven chloroplast DNA loci to study 582 individuals from 32 populations sampled in a range-wide survey from across Africa, revealing 22 haplotypes. The predominant haplotype, HT1a, occurred in 13 populations of eastern and southern Africa, while a second common haplotype, HT1m, occurred in populations of western Uganda and western Africa. The high differentiation observed between populations in East Africa was unexpected, with stands in western Uganda belonging with the western African lineage. High genetic differentiation among populations revealed using ordered alleles (N(ST) = 0.840) compared with unordered alleles (G(ST) = 0.735), indicated a clear phylogeographic pattern. Bayesian coalescence modelling suggested that 'east' and 'west' African types likely split early during southward migration of the species, while further more recent splitting events occurred among populations in the East of the continent. The high genetic similarity found between western Uganda and west African populations indicates that a former Afromontane migration corridor may have existed through Equatorial Africa.     

Spatial and temporal habitat use of kob antelopes (Kobus kob kob, Erxleben 1777) in the Comoé National Park, Ivory Coast as revealed by radio tracking

Spatial and temporal habitat use of kob antelopes (Kobus kob kob) have been investigated in the Comoé National Park (Ivory Coast, West Africa) by use of radio telemetry. A total of 23 kob were equipped with radio collars and radio tracked for up to 15 months. Home ranges of males were smaller and those of females larger than expected from theoretical models. Adult males used smaller areas than adult females and did not show seasonal home range shifts. Daily distances travelled did not differ between sexes. Kob walked less during the night than by day and covered shorter distances in the wet season. Whereas an increase in home range overlap between females resulted in higher rates of association among individuals, association of adults of mixed sexes was not correlated with the degree of home range overlap. Territorial behaviour of males and predator avoidance by females are suggested to explain the sex‐specific differences in home range size of adults and the deviation from the predicted sizes. Predator avoidance is presumed as the main reason for the reduced walking distances at night as well as in the wet season. Reproductive behaviour and feeding ecology are assumed to determine the degree of association of conspecifics.     

Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion

Mitochondrial DNA control region sequence variation was obtained and the population history of the common hippopotamus was inferred from 109 individuals from 13 localities covering six populations in sub-Saharan Africa. In all, 100 haplotypes were defined, of which 98 were locality specific. A relatively low overall nucleotide diversity was observed (pi = 1.9%), as compared to other large mammals so far studied from the same region. Within populations, nucleotide diversity varied from 1.52% in Zambia to 1.92% in Queen Elizabeth and Masai Mara. Overall, low but significant genetic differentiation was observed in the total data set (F(ST) = 0.138; P = 0.001), and at the population level, patterns of differentiation support previously suggested hippopotamus subspecies designations (F(CT) = 0.103; P = 0.015). Evidence that the common hippopotamus recently expanded were revealed by: (i) lack of clear geographical structure among haplotypes, (ii) mismatch distributions of pairwise differences (r = 0.0053; P = 0.012) and site-frequency spectra, (iii) Fu's neutrality statistics (F(S) = -155.409; P < 0.00001) and (iv) Fu and Li's statistical tests (D* = -3.191; P < 0.01, F* = -2.668; P = 0.01). Mismatch distributions, site-frequency spectra and neutrality statistics performed at subspecies level also supported expansion of Hippopotamus amphibius across Africa. We interpret observed common hippopotamus population history in terms of Pleistocene drainage overflow and suggest recognising the three subspecies that were sampled in this study as separate management units in future conservation planning.     

Molecular markers provide insights into contemporary and historic gene flow for a non‐migratory species

Hairy woodpeckers Picoides villosus are a common, year round resident with distinct plumage and morphological variation across North America. We genotyped 335 individuals at six variable microsatellite loci and analyzed 322 mtDNA control region sequences in order to examine the role of contemporary and historical barriers to gene flow. In addition we combined genetic analyses with ecological niche modelling to test if hairy woodpeckers were isolated in northern refugia (Alaska, Newfoundland and the Queen Charlotte Islands) during the last glacial maximum. Genetic analyses revealed that gene flow among North American hairy woodpecker populations is restricted, but not to the extent predicted for a sedentary species. Populations clustered into two main genetic groups, east and west of the Great Plains in the south and the Rocky Mountains in the north. Contact zones between the two main genetic groups exist in central British Columbia and Washington, but are narrow. Within each group we found additional population structure with genetic breaks between subgroups in the geographic west corresponding to breaks in forested habitat and physical barriers like open expanses of water. Population genetic patterns for hairy woodpeckers have resulted from isolation in multiple southern refugia with the current distribution of genetic groups resulting from post‐glacial expansion and subsequent reduction in gene flow. While populations in Alaska, Newfoundland and the Queen Charlotte Islands are genetically distinct from other populations, we found no evidence of these areas acting as refugia throughout the Pleistocene. Atlantic Canada populations contained unique haplotypes raising the possibility of a separate colonization from the rest of eastern Canada. The endemic subspecies on the island of Newfoundland is not genetically distinct from their closest mainland population unlike the Queen Charlotte Island subspecies.     

Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long‐range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilizations across time. Archaezoological and linguistic evidence suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D‐loop analysis revealing the presence of five distinct haplogroups in East African village chickens. It supports the importance of the region in understanding the history of the species and indirectly of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur in both Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda's hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chickens and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilizations in Asia and East Africa.     

Food limitation and demography of a migratory antelope,the white-eared kob

Summary Although it is commonly presumed that many populations of large-herbivores are limited by food availability, supporting evidence is scarce. This hypothesis was investigated in a population of over 800,000 white-eared kob in the Boma National Park region of the southern Sudan. Food availability, body condition, and mortality rates of adults and calves were measured during the dry seasons of 1982 and 1983. Sampled age distributions from both the live population and carcasses were used to calculate age-specific rates of mortality. In 1982, food supplies during the dry season were augmented by substantial rainfall, which produced regrowth of grass in areas that ordinarily had little green forage. As a result, fat reserves declined little, and rates of adult mortality showed no increasing trend. Total adult mortality was 5%. In 1983, there was no rainfall during the dry season and food intake was insufficient to meet the estimated energy requirements of kob. As a result, fat reserves declined and adult mortality rates increased fourfold. Total adult mortality was 10% (equivalent to the recruitment rate of yearling into the population). Calf mortality during the dry season was similar in both years (50%), based on field estimates of mortality rates and calf/female ratios. Lactation throughout the dry season possibly provided a buffer for calves against variations in food availability. The age structure of the live population in 1983 suggests that a drought in 1980 reduced kob numbers by 40%. These results suggest that adult survival is influenced strongly by the availability of food during the dry season. However, the duration of the dry season also plays an important role. During the dry season, declining fat reserves make an increasing proportion of the population vulnerable to mortality. As a result, even moderate droughts may lead to substantial changes in population numbers.     

Phylogeography of the Guinea multimammate mouse (Mastomys erythroleucus): a case study for Sahelian species in West Africa

Aim To investigate the phylogeographical structure of the Guinea multimammate mouse, Mastomys erythroleucus (Temminck, 1853), a widespread murid rodent in sub‐Saharan (Sahel and Sudan) savannas, for a better understanding of the impacts of geographical and historical factors on the evolutionary history of this species, in the context of the growing database of phylogeographical studies of African savanna mammal species. Location Sahel and Sudan savannas, Africa. Methods We sequenced the whole cytochrome b gene in 211 individuals from 59 localities distributed from Senegal to Ethiopia. Sequence data were analysed using both phylogenetic (several rooted tree‐construction methods, median‐joining networks) and population genetic methods (spatial analyses of molecular variance, mismatch distributions). Results Haplotypes were distributed into four major monophyletic groups corresponding to distinct geographical regions across a west–east axis. Diversification events were estimated to have occurred between 1.16 and 0.18 Ma. Main conclusions Vicariance events related to the fragmentation of savanna habitats during the Pleistocene era may explain the phylogeographical patterns observed. Genetic structure was consistent with a role of major Sahelian rivers as significant barriers to west–east dispersal. Recent demographic expansions probably occurred during arid phases of the Holocene with the southward expansion of savannas.     

Genetic relationships among Kenyan and other East African indigenous chickens

In this study, 30 microsatellite markers recommended by the International Society for Animal Genetics and the Food and Agriculture Organization were used to determine the extent of genetic differentiation and phylogenetic relationships among indigenous chicken populations sampled in Kenya, Uganda, Ethiopia and Sudan. Genetic differentiation (F(ST)) and chord genetic distances (D(C)) indicated that the indigenous chickens were genetically related but distinct from commercial broiler and egg layer lines. Genetic divergence among the indigenous chickens determined using the Mantel test was significantly influenced (P < 0.001) by geographic (reproductive) isolation. Genetic subdivisions were found between the Kenyan/Ugandan chicken populations and Ethiopian/Sudanese chicken populations. The Marsabit chicken population from northern Kenya was the most genetically distinct population within the Kenyan and Ugandan chicken cluster, thus warranting further investigation.     

Rapid divergence and postglacial colonization in western North American Steller's jays (Cyanocitta stelleri)

Post-Pleistocene avian colonization of deglaciated North America occurred from multiple refugia, including a coastal refugium in the northwest. The location of a Pacific Coastal refugium is controversial; however, multiple lines of evidence suggest that it was located near the Queen Charlotte Islands (also known as Haida Gwaii). The Queen Charlotte Islands contain a disproportionately large number of endemic plants and animals including the Steller's jay Cyanocitta stelleri carlottae. Using five highly variable microsatellite markers, we studied population structure among eight populations of Steller's jay (N = 150) from geographical areas representing three subspecies in western North America: C. s. carlottae, C. s. stelleri and C. s. annectens. Microsatellite analyses revealed genetic differentiation between each of the three subspecies, although more extensive sampling of additional C. s. annectens populations is needed to clarify the level of subspecies differentiation. High levels of population structure were found among C. s. stelleri populations with significant differences in all but two pairwise comparisons. A significant isolation by distance pattern was observed amongst populations in the Pacific Northwest and Alaska. In the C. s. carlottae population, there was evidence of reduced genetic variation, higher number of private alleles than northern C. s. stelleri populations and higher levels of divergence between Queen Charlotte Island and other populations. We were unable to reject the hypothesis that the Queen Charlotte Islands served as a refugium during the Pleistocene. Steller's jay may have colonized the Queen Charlotte Islands near the end of the last glaciation or persisted throughout the Pleistocene, and this subspecies may thus represent a glacial relic. The larger number of private alleles, despite reduced genetic variation, morphological distinctiveness and high divergence from other populations suggests that the Queen Charlotte Island colonization pre-dates that of the mainland. Furthermore, our results show rapid divergence in Steller's jay populations on the mainland following the retreat of the ice sheets.     

Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa

Chicken were possibly domesticated in South and Southeast Asia. They occur ubiquitously in East Africa where they show extensive phenotypic diversity. They appeared in the region relatively late, with the first undisputed evidence of domestic chicken in Sudan, around ~ 700 BC. We reveal through a detailed analysis of mitochondrial DNA D-loop sequence diversity of 512 domestic village chickens, from four East African countries (Kenya, Ethiopia, Sudan, Uganda), the presence of at least five distinct mitochondrial DNA haplogroups. Phylogeographic analyses and inclusion of reference sequences from Asia allow us to address the origin, ways of introduction and dispersion of each haplogroup. The results indicate a likely Indian subcontinent origin for the commonest haplogroup (D) and a maritime introduction for the next commonest one (A) from Southeast and/or East Asia. Recent introgression of commercial haplotypes into the gene pool of village chickens might explain the rare presence of two haplogroups (B and C) while the origin of the last haplogroup (E) remains unclear being currently observed only outside the African continent in the inland Yunnan Province of China. Our findings not only support ancient historical maritime and terrestrial contacts between Asia and East Africa, but also indicate the presence of large maternal genetic diversity in the region which could potentially support genetic improvement programmes.     

Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population

Fine‐scale genetic structure of large mammals is rarely analysed. Yet it is potentially important in estimating gene flow between the now fragmented wildlife habitats and in predicting re‐colonization following local extinction events. In this study, we examined the extent to which warthog populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection practices and the other (Luwero), not a protected area, is characterized by a great deal of hunting. In the total sample, significant genetic differentiation was observed at both the mtDNA locus (F_ST = 0.68; P < 0.001) and the microsatellite loci (F_ST = 0.14; P < 0.001). Despite the relatively short geographical distances between populations, significant genetic differentiation was observed in all pair‐wise population comparisons at the two marker sets (mtDNA F_ST = 0.21–0.79, P < 0.001; microsatellite F_ST = 0.074–0.191, P < 0.001). Significant heterozygote deficiency was observed at most loci within protected areas while no significant deviation from Hardy–Weinberg expectation was observed in the unprotected Luwero population. We explain these results in terms of: (i) a strong philopatry among warthogs, (ii) a Wahlund effect resulting from the sampling regime and (iii) break down of social structure in the disturbed Luwero population.