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

Abstract

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 (p ¼ 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 ¼ 0.138; P ¼ 0.001), and at the population level, patterns of differentiation support previously suggested hippopotamus subspecies designations (F CT ¼ 0.103; P ¼ 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 ¼ 0.0053; P ¼ 0.012) and site-frequency spectra, (iii) Fu's neutrality statistics (F S ¼ À155.409; Po0.00001) and (iv) Fu and Li's statistical tests (D * ¼ À3.191; Po0.01, F * ¼ À2.668; P ¼ 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. Heredity (2005) 95, 206-215.

Genetic Variation and Phylogenetic Relationships of Indian Buffaloes of Uttar Pradesh

“…However, the negative and significant Fu’s Fs statistical value observed in Region 1, Region 2 and Region 3 populations provide strong evidence for past population expansion, and rule out the possibility of genetic hitching and background selection, and evolutionary force that produce a pattern similar to population expansion (Fu and Li, 1993; Fu, 1997; Okello et al, 2005). Beneficial genetic variation will generally be accumulated and maintained in a rapidly growing population (Su et al, 2001).…”

Endangered species in small habitat patches can possess high genetic diversity: the case of the Tana River red colobus and mangabey

“…Allowing for a large error associated with the estimation of divergence time and based on the molecular clock rate for primate mtDNA of 11.5-17.3% per million years (Vigilant et al 1991), the observed level of sequence divergence indicates that the haplotype groups observed in these primates have been diverging over the past 0.6-1 million years. Thus, these mtDNA polymorphisms seem to date back to the Pliocene-Pleistocene interval when major shifts occurred in the fauna of East African due to increased aridity (Bobe and Behrensmeyer 2004;Heller et al 2008;Okello et al 2008;Okello et al 2005;Storz et al 2002a, b). Subsequently, the mtDNA polymorphisms may have been maintained by habitat heterogeneity in the Tana River landscape as populations in different habitat fragments were isolated from each other.…”

“…In Africa, climate change caused major shifts in faunal assemblages during a time interval lasting 5.3 million years during the Pliocene-Pleistocene epochs (deMenocal 2004;Bobe and Behrensmeyer 2004). The genetic imprint of these habitat changes is evident in several mammals in East Africa; buffalo (Heller et al 2008), elephant , hippopotamus (Okello et al 2005) and baboons (Storz et al 2002a, b). During that interval, lower temperatures and increased aridity in East Africa reduced and fragmented tropical forests and left them as isolated patches along major rivers and on high elevation (Bobe and Behrensmeyer 2004).…”

Mitochondrial DNA diversity and population structure of a forest-dependent rodent, Praomys taitae (Rodentia: Muridae) Heller 1911, in the fragmented forest patches of Taita Hills, Kenya

“…We used primer pairs Ham1 (5'-CCACCATCAGCACCCAAA-3' and Ham2 (5'-CGAGATGTCTTATTTAAGGGGAA-3') 19 to amplify a 356-bp fragment of the 5' hyper-variable segment of the mitochondrial control region. Amplifications were done in 50 µl reaction volumes containing 2-5 ng of genomic DNA, 50 mM dNTPs, 10 pmol of each primer, 1 unit of Taq DNA polymerase enzyme and 20 mM of 10X PCR reaction buffer containing 1.5 mM MgCl 2 .…”