Genetic structure of Mediterranean populations of the sandfly Phlebotomus papatasi by mitochondrial cytochrome b haplotype analysis

Phlebotomus papatasi (Scopoli) (Diptera: Psychodidae) is the main vector of Leishmania major Yakimoff & Schokhor; which is the cause of self-limiting cutaneous leishmaniasis in the Old World. This sandfly is found in houses, animal shelters, caves and rodent burrows. It has a large geographical range, which includes the Middle East and the Mediterranean regions. A population analysis of colony and field specimens of P. papatasi was conducted on 25 populations originating from 10 countries. The distribution of haplotypes of the maternally inherited mitochondrial cytochrome b gene were analysed to assess the population differentiation of P. papatasi. Alignment of a 442-basepair region at the 3' end of the gene identified 21 haplotypes and 33 segregating sites from 131 sandflies. The pattern of sequence variations did not support the existence of a species complex. The median-joining network method was used to describe both the origin of the haplotypes and the population structure; haplotypes tended to cluster by geographical location, suggesting some level of genetic differentiation between populations. Our findings indicate the presence of significant population differentiation for populations derived from Syria, Turkey, Palestine, Israel, Jordan and Egypt. Knowledge of population differentiation among P. papatasi populations is important for understanding patterns of dispersal in this species and for planning appropriate control measures.     

Host-specific Wolbachia strains in widespread populations of Phlebotomus perniciosus and P. papatasi (Diptera: Psychodidae), and prospects for driving genes into these vectors of Leishmania

A single strain of Wolbachia (alpha-proteobacteria, Rickettsiales) was found in widespread geographical populations of each of two Phlebotomus species, within which there was no indication of 'infectious speciation'. The two strains were identified by sequencing a fragment of wsp (a major surface protein gene), amplified by polymerase chain reaction from DNA extracted from the body parts of individual sandflies. Infection rates were high in the males and females of both sandflies, but they were lower for the B-group wPrn strain of Wolbachia in Phlebotomus perniciosus Newstead (60.3% overall) than for the A-group wPap strain in P. papatasi (Scopoli) (81.7%). Infections were frequent in the thorax, where Leishmania develops infective forms, as well as in the abdomen, where Wolbachia must infect the reproductive tissues to ensure its vertical transmission. These findings were related to knowledge of the population biology of Wolbachia in other insects, leading to the conclusion that this endosymbiont could be useful for driving transgenes through wild populations of both sandflies. This will require characterizing the cytoplasmic incompatibility phenotypes of Wolbachia-sandfly combinations, as well as estimating for them the incidence of paternal transmission and the fidelity of maternal transmission. Paternal transmission is one explanation for finding a single Wolbachia strain associated with all mitochondrial haplotypes and lineages of each sandfly species. However, this distribution pattern could also result from multiple horizontal transmissions or the failure of wsp to provide strain markers.     

Incrimination of Phiebotomus papatasi as vector of Leishmania major in the southern Jordan Valley

he status of sandflies as vectors of cutaneous leishmaniasis in the southern Jordan Valley was investigated during 1992. Sandflies were collected from domestic habitats and from burrows of Psammomys obesus . Of 686 Phlebotomus papatasi females collected from burrows, fourteen harboured promastigotes in their guts. On the other hand, none of 1446 P.papatasi females collected from domestic habitats were found infected. The highest infection rate (5.5%) was recorded in November at the end of the sandfly season. Six leishmanial stocks isolated from P.papatasi females were typed by cellulose acetate electrophoresis using the six enzymes G6PDH, 6PGDH, PGI, PGM, FK and ME. Five of the leishmanial stocks were identical to a Leishmania major reference strain (MHOMISU/73/5-ASKH). The sixth isolate was a 6PGDH variant of L.major . These findings present the first direct evidence of the role of P.papatasi as a vector of L.major in Jordan.     

基于线粒体细胞色素b基因的中国大沙鼠系统地理格局

通过内蒙、新疆、甘肃的41个大沙鼠样品和1个伊朗撒拉克大沙鼠的mtDNA Cytb基因全序列的遗传分析,对我国大沙鼠(Rhombomys opimus)的分子系统地理学进行了初步探讨。结果表明,我国41个大沙鼠样品的Cytb基因包含了50个核苷酸变异位点(占全序列的4.39%),其中转换48个,颠换2个,共定义23个单倍型。在四个地理种群中,内蒙古中部半荒漠区和阿拉善荒漠区的单倍型多样性最高,甘新荒漠区的单倍型多样性最低;北疆荒漠区的核苷酸多样性最高,内蒙古中部半荒漠区的核苷酸多样性最低。分子变异分析(AMOVA)表明,种群间的遗传变异占51.68%,种群内的遗传变异占48.32%。FST统计结果表明,除内蒙古中部半荒漠区与阿拉善荒漠区地理种群之间差异显著外(P<0.05),其它地理种群间的差异均极显著(P<0.01)。基于单倍型的系统树显示,42只大沙鼠形成三支。其中,伊朗撒拉克地区大沙鼠和中国地区大沙鼠之间的亲缘关系比中国两支大沙鼠之间的亲缘关系远;分析表明,中国分布的大沙鼠两支之间分歧时间估计在0.093Ma前。嵌套支分析表明,大沙鼠历史种群曾发生过异域片段化、受阻碍基因流和持续种群扩张事件。种群扩张分析提示大沙鼠在0.0119Ma前曾经历过一次种群扩张事件,种群可能受到末次冰期波动的影响。     

Bionomics of phlebotomine sandflies in the Galilee focus of cutaneous leishmaniasis in northern Israel

The bionomics of phlebotomine sandflies (Diptera: Psychodidae) were studied for three years (2001-2003) in the Galilee focus of cutaneous leishmaniasis in northern Israel, where the causative Leishmania tropica (Kinetoplastida: Trypanosomatidae) is transmitted by Phlebotomus (Adlerius) arabicus Theodor and Phlebotomus (Paraphlebotomus) sergenti Parrot, comprising 22% and 8%, respectively, of the local sandfly fauna sampled by light traps. The predominant species overall was Phlebotomus (Larroussius) tobbi Adler & Theodor (51%) with lesser numbers of Phlebotomus (Adlerius) simici Theodor (11%), Phlebotomus (Larroussius) syriacus Adler & Theodor (5%), Phlebotomus (Larroussius) perfiliewi Perfil'ev (3%) and Phlebotomus (Phlebotomus) papatasi Scopoli (0.05%). Sandfly adult populations were prevalent from April to November and peaked between June and August, being more abundant through the summer in irrigated habitats, such as gardens and orchards, than in open grassland. Of the two cutaneous leishmaniasis vectors, P. sergenti preferred boulder mounds located at the outskirts of settlements, whereas P. arabicus was more abundant overall and near houses in particular. Females of all these sandfly species displayed a peak of activity after sunset (20.00-22.00 hours), whereas activity of males persisted longer through the night. Another slight increase in activity was noted before dawn (02.00-04.00 hours). Phlebotomus arabicus appears to be the main vector of L. tropica in the Galilee focus, due to its denser populations, more endophily and preference for peridomestic habitats than shown by P. sergenti in northern Israel.     

Phylogeographical structure of the Dover sole Microstomus pacificus: the larval retention hypothesis and genetic divergence along the deep continental slope of the northeastern Pacific Ocean

Population genetic variability and phylogeographical structure of the Dover sole, Microstomus pacificus (Teleostei: Pleuronectidae), were examined along the continental slope of the north-eastern Pacific Ocean using sequences of the left domain of the mitochondrial DNA (mtDNA) control region. Six sites were sampled in three primary biogeographical provinces (based on surface water temperatures), ranging from the subarctic to the warm temperate zones. Many haplotypes were discerned, totalling 90 for 110 individuals. Neighbour joining and parsimony analyses of the entire data set showed that some groups of haplotypes of adult Dover sole were widely distributed, suggesting either panmixia or homoplasy and reversals. However, a substantial number of groups of related haplotypes were geographically circumscribed, and there were significant differences among sites in the distribution of restricted haplotypes (based on a reduced number of characters), supporting geographical structure. Geographical differentiation of populations appeared to be consistent with the member-vagrant hypothesis for retention of the pelagic larvae in currents and recruitment to adult habitats, reducing long-distance dispersal. Results of this study indicate phylogeographical structure among some populations, despite extended pelagic larval periods, and apparent environmental homogeneity in the adult habitats along the continental slope.     

Bionomics of Phlebotomus papatasi (Diptera: Psychodidae) in an endemic focus of zoonotic cutaneous leishmaniasis in central Iran.

Following an epidemiological survey of zoonotic cutaneous leishmaniasis (ZCL) in several villages of Badrood, a rural district north of the city of Natanz, central Iran, Phlebotomus (Phlebotomus) papatasi Scopoli were found to be naturally infected with Leishmania (Leishmania) major zymodeme MON-26. Sand flies were collected and dissected biweekly from rodent burrows from May to October 2001. Leptomonad infection rates varied between 6.7% and 22.0%, being greatest in September, coinciding with peak activity of P. papatasi, two-three months before the highest incidence of ZCL human cases in November-December. The leptomonad infection rate was 1.1% of the 94 P. papatasi captured indoors. In ELISA testing of 520 P. papatasi blood meals during Sept. 2001 and Aug. 2002, the proportion giving positive reactions for human, sheep, cow, goat, rodent, and bird were 31.2%, 69.6%, 63%, 38.8%, 24.7%, and 21.8%, respectively. This report thus incriminates P. papatasi as the vector of zoonotic cutaneous leishmaniasis in this part of Iran.     

Genetic structure of populations of the human hookworm, Necator americanus, in China

Twenty-one to 58 individual Necator americanus were sampled from each of four villages in south-western China. Each nematode was sequenced for 588 bp of the mitochondrial cytochrome oxidase I gene. Allelic and nucleotide diversity varied two-fold among villages. Overall FST among populations was approximately 0.28, but this large value resulted from one low-diversity population that had a large genetic distance to the other three populations (F(ST) = 0.10 without that population). There was no correlation between geographical and genetic distance among sites. Thus, the genetic structure of this species in China may be characterized by variable effective sizes and uneven movement among sites. We discuss the implications of this genetic structure for vaccine development and the spread of drug resistance in human hookworms, and compare the genetic structure of hookworms with that of other nematodes.     

Variation in mitochondrial DNA in Far Eastern mullet pilengas, Liza haematocheilus Temminck and Schlegel, acclimatized in the Azov-Black Sea basin

This study continues the investigation of genetic variation in the populations of native and acclimatized in the Azov-Black Sea basin pilengas from the Sea of Japan. The previous comparison based on allozyme analysis was supplemented by analysis of restriction polymorphism of a mitochondrial DNA fragment containing the cytochrome b gene and the D-loop. Five out of fifteen endonucleases tested detected polymorphic sites. In the samples of native and acclimatized pilengas, five common haplotypes were found; ten and three "population-specific" haplotypes were detected in the Far Eastern and the Azov populations, respectively. The differences in haplotype distributions between these populations were highly significant (P < 0.001). The mtDNA variation was lower in the Azov than in the Far Eastern population (haplotype diversity mu respectively 6.35 +/- 0.27 and 9.14 +/- 0.55), which is in good agreement with the decrease in the number of polymorphic loci and the mean number of alleles per locus, found earlier for allozyme markers in this population. The reasons for these differences in the acclimatized population are discussed.     

Seasonal abundance patterns of the sandfly Phlebotomus papatasi in climatically distinct foci of cutaneous leishmaniasis in Israeli deserts

Among foci of cutaneous leishmaniasis in Israel, population densities of the vector sandfly Phlebotomus papatasi Scopoli (Diptera: Psychodidae) were assessed during April-October 1999 in the mesic Negev desert and the hyper-xeric Arava valley, using sticky traps placed overnight near host burrows of the fat sand rat, Psammomys obesus Cretzschmar (Cricetidae: Gerbillinae). Population dynamics of Ph. papatasi differed between the Negev (study sites on sand near Mount Keren and on loess at Nizzana ruins) and the Arava valley (study sites on sand at Shezaf and in a fallow field near irrigation at wadi Arava). At the Negev sites, sandfly abundance peaked in spring (April or May), whereas at Arava sites Ph. papatasi population densities were bi-modal, with peaks in both spring and autumn (September or October). This might be conducive to sustaining enzootic Leishmania major Yakimoff & Schokhor (Kinetoplastida: Trypanosomatidae). In both areas, Ph. papatasi densities were much higher at the site with moister soil, raising transmission risks of zoonotic cutaneous leishmaniasis.     

A quantitative comparison of frugivorous tephritids (Diptera: Tephritidae) in tropical forests and rural areas of the Democratic Republic of Congo

Most of the current knowledge about African tephritids originates from studies performed in agricultural areas, while information about their distribution in pristine or moderately disturbed environments is extremely scarce. This study aims at (i) describing levels of spatial variability of frugivorous tephritids in tropical forests and small rural villages of the Congo River basin and (ii) verifying if human-mediated activities, such as small-scale agriculture and trade, can affect their distribution patterns. Four locations were sampled along a 250?km stretch of the Congo River. At each location, pristine and disturbed habitats (i.e. tropical forests and small rural villages, respectively) were sampled, with three replicate sites in each combination of habitat and location. Sampling with modified McPhail traps baited with four different attractants yielded 819 tephritid specimens of 29 species from seven genera (Bactrocera, Carpophthoromyia, Ceratitis, Dacus, Celidodacus, Perilampsis, Trirhithrum). The three most abundant species sampled (Dacus bivittatus, D. punctatifrons, Bactrocera invadens) showed significant variations in abundance across locations and sites and accounted for 98.29% of the overall dissimilarity between habitats. Assemblages differed among locations and sites while they showed significant differences between pristine and disturbed habitats in two out of the four locations. This study shows that frugivorous tephritids in central Congo have remarkably patchy distributions with differences among locations and sites representing the main source of variability. Our data show that, in rural villages of central Democratic Republic of Congo, human activities, such as small-scale agriculture and local commerce, are not always sufficient to promote differences between the tephritid assemblages of villages and those of the surrounding tropical forests.     

Patterns of genetic connectivity among anchialine habitats: a case study of the endemic Hawaiian shrimp Halocaridina rubra on the island of Hawaii

Anchialine habitats, landlocked bodies of mixohaline water that fluctuate with the tides but have no surface connection to the sea, are known from around the world. Many anchialine organisms have widespread distributions and it has been hypothesized that high levels of gene flow and low levels of genetic differentiation are characteristic of populations from these habitats. However, the generality of this hypothesis requires further assessment, particularly in light of the significant negative impact these habitats and their biota have experienced from anthropogenic causes. This study investigated the population structure and demography of an endemic Hawaiian anchialine species, the atyid shrimp Halocaridina rubra, using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. A survey of 305 individuals from 16 populations collected on the island of Hawaii revealed 135 haplotypes. These haplotypes belonged to one of two divergent (2.7-4.9%) lineages; notably, no haplotypes were shared between the two coasts of the island. Along each coast, strong subdivision and little to no gene flow occurs between populations separated by > 30 km. The population structure and demography of H. rubra on Hawaii are influenced by regional hydrology, geology, volcanism and two distinct colonization events of the island. Thus, H. rubra on Hawaii demonstrates that populations of endemic anchialine organisms may exhibit significant levels of genetic structure and restricted levels of gene flow over limited geographic scales. This report brings novel insight into the biology of anchialine organisms and has important implications for the future management of these habitats and their biota.     

中国小菜蛾群体遗传变异的时空动态

【目的】小菜蛾 Plutella xylostella 是十字花科蔬菜最重要的迁移性害虫之一,在中国越冬区(OR)的群体和季节性繁殖区(SBR)的群体之间具有“源-汇”关系和复合群体的特征。本研究旨在揭示中国小菜蛾群体遗传变异的时空动态,以期进一步阐明该虫的迁移特性及其对区域灾变的影响。【方法】基于已经发表的4组不同采样时间中国小菜蛾 COI 序列(共1 567条)数据,将每个数据集细分为3组:OR群体、SBR群体以及特定采样时间(ST)的群体。对不同组(群体)进行遗传多样性、遗传分化、单倍型相似性和群体演化史的分析。【结果】基于 COI 序列的小菜蛾群体遗传变异分析结果表明,同一采样时间内,OR群体和SBR群体遗传多样性水平相当。虽然SBR群体在单倍型频率上不稳定,导致包含SBR的群体间遗传分化较大,但SBR群体单倍型均能够在同一采样时间的OR群体中找到,或SBR单倍型仅与OR单倍型相差2个碱基以内;SBR群体中单倍型频率在不同年份间变化大,遗传分化最大,而ST群体之间遗传分化的变异水平最低。不同采样时间样品 COI 序列的碱基错配分布图呈现相同的单峰状,且不同采样时间样本主要是由几种相同的单倍型构成。【结论】这些结果表明:迁移是影响中国季节性繁殖区小菜蛾群体遗传变异的主要因素;中国不同区域的小菜蛾群体遗传变异在时间尺度上具有稳定性和相关性。小菜蛾复合群体特征为阐明其季节性迁移特性提供了重要的生态学依据。     

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.     

Genetic variation and population differentiation in the lichen-forming ascomycete Xanthoria parietina on the island Storfosna, central Norway

Genetic diversity and fine-scale population structure in the lichen-forming ascomycete Xanthoria parietina was investigated using sequence variation in part of the intergenic spacer (IGS) and the complete internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA. Sampling included 213 and 225 individuals, respectively, from seven populations in two different habitats, bark and rock, on the island Storfosna off the central west coast of Norway. Both markers revealed significant variation and a total of 10 IGS and 16 ITS haplotypes were found. There were no signs of significant positive spatial autocorrelation at any spatial size class down to 10% of transect length, nor did we find significant deviations from neutrality or signs of historical population expansion. Analysis of molecular variance (amova) indicated that most of the genetic variance observed was within populations, but when populations were grouped according to habitat, more than a quarter of the variance was explained among groups. Pairwise comparisons of populations (F(ST), exact tests of population differentiation) revealed significant differentiation between populations in different habitats (on bark or rock), but not between populations in the same habitat. Haplotype networks show that internal and presumably old haplotypes are shared between habitats, whereas terminal haplotypes tend to be unique to a habitat, mostly bark. We interpret the observed pattern to mean that there is no evidence of restricted gene flow between populations in the same habitat at the present spatial scale (interpopulation distances one or a few kilometres). On the other hand, differentiation between habitats is considerable, which we attribute to restricted gene flow between habitats (habitat isolation). Evidence suggests that the observed differentiation did not evolve locally. Estimates of divergence time between populations in the respective habitats indicate that an ancestral population started to diverge at least 34,000 years ago but probably much further back in time.     

No genetic differentiation between geographically isolated populations of Clarias macrocephalus Günther in Malaysia revealed by sequences of mtDNA Cytochrome b and D‐loop gene regions

In the present study, we assessed the genetic variation of three Clarias macrocephalus Günther populations collected from Kedah, Perlis and Kelantan (Peninsular Malaysia) using sequences of partial mitochondrial cytochrome b (Cyt b) and D‐loop genes. A total of 57 individuals were sequenced and 1470 bp were obtained (1053 bp Cyt‐b; 417 bp D‐loop). The analysis revealed 21 haplotypes based on 81 polymorphic sites. Nucleotide diversity (π) was 0.003 in all populations while haplotype diversity ranged from 0.657 to 0.765. No significant genetic differentiation among the three populations was observed. Nevertheless, a number of private haplotypes was discovered, providing valuable information for selective breeding programs.     

Phylogeography of the Marsh Fritillary Euphydryas aurinia (Lepidoptera: Nymphalidae) in the UK

We sampled extant (and extinct) populations of Euphydryas aurinia to examine the phylogeography of the species in the UK. We were interested in whether the genetic structuring of populations reflects anything other than a single recent post-glacial colonization event. Four hundred base pairs of the mitochondrial Cytochrome b gene were sequenced from individuals from populations throughout the UK, as well as populations in France and Portugal and seven polymorphic allozyme loci resolved. The mean number of allozyme alleles per locus was 4 and isolation by distance was shown not to be a factor in the geographic structuring of genetic diversity either with or without the inclusion of the French data (Mantel statistic Z = 0.015 and 0.112 respectively, P >0.5). Cytochrome b nucleotide diversity (average number of nucleotide differences per site between two sequences) was low overall (0.003, n = 63) but mean cytochrome b gene diversity over all populations was 0.77. The presence of the Portuguese and French haplotype in Scottish populations indicates that the Iberian peninsula was likely to be one glacial refugium for E. aurinia populations. The pattern of mitochondrial DNA found in the UK could be interpreted in one of two ways: (1) two separate colonization events or (2) a single slow colonization event. Allele frequency distributions followed a similar geographical pattern as mitochondrial DNA haplotypes. An AMOVA assigned just 2.68% of allozyme genetic variation to the grouping tested, providing more support for the single colonization event theory.     

Mitochondrial DNA variation in European populations of Silurus glanis

Mitochondrial DNA diversity of 13 wild Silurus glanis populations (covering the entire range of the species) and eight hatchery populations was investigated. PCR-RFLP analysis of four regions of mitochondrial DNA (cytochrome b, control region, ND-5/6) was used. Nineteen haplotypes were found. Thirteen of them were private. The proportion of total genetic diversity attributable to population differentiation was almost 80%. Despite the existence of significant differentiation between populations for mtDNA variation, no consistent pattern of geographic structuring was revealed and nucleotide divergence among S. glanis populations was low. These phenomena are discussed with regard to the impact of glaciation events. The domesticated stocks show less genetic diversity than natural ones, possibly due to their mode of management. Analysis of three European catfish species S. glanis, S. aristotelis and Silurus triostegus (sampled in the Euphrates river) revealed several endonucleases which produced restriction phenotypes diagnostic for the three species.     

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.     

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.