Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene

Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial–drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi‐aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range‐wide sampling. We documented a global demographic and spatial expansion approximately 0.1–0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent‐wide gene flow among hippopotamus populations, and hence, no clear continental‐scale genetic structuring remains. Nevertheless, present‐day hippopotamus populations are genetically disconnected, probably as a result of the mid‐Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah‐adapted ungulate mammals and should be further investigated in other water‐associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long‐term decline.     

Characterization of a SINE species from vicuna and its distribution in animal species including the family Camelidae

Twenty-six sequences of a short interspersed repetitive element (SINE) with a size of approximately 150 base pairs (bp) were isolated from the genomic DNA of Vicugna vicugna (vicuna). RNA polymerase III split promoter sequence was observed in most of them, and many had direct repeats flanking to SINEs as well as a poly(A)-like structure. The SINE sequences were designated as ``vic-1' sequences. Comparison of the vic-1 consensus sequence with sequences registered in the DNA database (DDBJ/EMBL/GENBANK) revealed that the vic-1 sequence had a 79% homology with mouse ala-tRNA gene. In addition, the tRNA-related region of the consensus sequence was folded into a cloverleaf structure as with mouse ala-tRNA. These findings strongly indicated that vic-1 was a retroposon derived from ala-tRNA gene. The vic-1 sequences were used as a probe for dot-blot hybridization to examine the distribution of their homologous sequences in the genomes of various animal species spanning 14 orders, of which, homologous sequences were found only in the Camelidae family. In order to examine the phylogenetical relationship among vicuna, llama, and camel, vic-1 insertion analysis and homology analysis of vic-1 sequences were performed at each locus. The analyses indicated that vic-1 sequences were generated in a common ancestor of the animal species, and that camels first branched off from the clade Camelidae, followed by vicunas and llamas. Received: 5 July 2000 / Accepted: 14 November 2000     

Establishment and characterization of fibroblast cultures derived from a female common hippopotamus (Hippopotamus amphibius) skin biopsy

The population decline of the common hippopotamus (Hippopotamus amphibius) has necessitated the preservation of their genetic resources for species conservation and research. Of all actions, cryopreservation of fibroblast cell cultures derived from an animal biopsy is considered a simple but efficient means. Nevertheless, preserving viable cell cultures of the common hippopotamus has not been achieved to our knowledge. To this end, we established and characterized fibroblast cell cultures from the skin sample of a newborn common hippopotamus in this study. By combining the tissue explant direct culture and enzymatic digestion methods, we isolated a great number of cells with typical fibroblastic morphology and high viability. Neither bacteria/fungi nor mycoplasma was detectable in the cell cultures throughout the study. The population doubling time was 34 h according to the growth curve. Karyotyping based on Giemsa staining showed that the cultured cells were diploid with 36 chromosomes in all, one pair of which was sex chromosomes. The amplified mitochondrial cytochrome C oxidase subunit I gene sequence of the cultured cells was 99.26% identical with that of the registered H. amphibius complete mitochondrial DNA, confirming the species of origin of the cells. Flow cytometry and immunofluorescence staining results revealed that the detected cells were positive for fibroblast markers, S100A4, and vimentin. In conclusion, we generated the fibroblast cell cultures from a common hippopotamus and identified their characteristics using multiple techniques. We believe the cryopreserved cells could be useful genetic materials for future research.     

Episodic Molecular Evolution of Pituitary Growth Hormone in Cetartiodactyla

The sequence of growth hormone (GH) is generally strongly conserved in mammals, but episodes of rapid change occurred during the evolution of primates and artiodactyls, when the rate of GH evolution apparently increased substantially. As a result the sequences of higher primate and ruminant GHs differ markedly from sequences of other mammalian GHs. In order to increase knowledge of GH evolution in Cetartiodactyla (Artiodactyla plus Cetacea) we have cloned and characterized GH genes from camel (Camelus dromedarius), hippopotamus (Hippopotamus amphibius), and giraffe (Giraffa camelopardalis), using genomic DNA and a polymerase chain reaction technique. As in other mammals, these GH genes comprise five exons and four introns. Two very similar GH gene sequences (encoding identical proteins) were found in each of hippopotamus and giraffe. The deduced sequence for the mature hippopotamus GH is identical to that of dolphin, in accord with current ideas of a close relationship between Cetacea and Hippopotamidae. The sequence of camel GH is identical to that reported previously for alpaca GH. The sequence of giraffe GH is very similar to that of other ruminants but differs from that of nonruminant cetartiodactyls at about 18 residues. The results demonstrate that the apparent burst of rapid evolution of GH occurred largely after the separation of the line leading to ruminants from other cetartiodactyls.     

Digestion in the hippopotamus

The hippopotamus (Hippopotamus amphibius Linn.) has an enlarged stomach, divided into: (a) two anterior diverticula; (b) a large median chamber, and (c) a posterior chamber, secreting gastric juice. Fermentative digestion occurs in (a) and (b). The anatomy and function of the stomach are discussed. Two experiments were performed to compare digestive efficiency with that of ruminants. Exp. 1. In a total collection experiment, chopped grass wasfedtoahippopotamusand five ruminants. Overall digestibility was lower in the hippopotamus, but this may have been due to keeping the animal out of water. Exp. 2. A hippopotamus and two sheep were fed chopped elephant grass (Pennisetum purpureum), digestibility being measured by total collection (in the sheep) and the chromogen ratio method. Dry matter digestibility was similar in all three animals, while digestibility of crude protein was higher in the hippopotamus.     

Genealogy of families of SINEs in cetaceans and artiodactyls: the presence of a huge superfamily of tRNA(Glu)-derived families of SINEs.

Several novel (sub)families of SINEs were isolated from the genomes of cetaceans and artiodactyls, and their sequences were determined. From comparisons of diagnostic nucleotides among the short interspersed repetitive elements (SINEs) in these (sub)families, we were able to draw the following conclusions. (1) After the divergence of the suborder Tylopoda (camels), the CHRS family of SINEs was newly created from tRNA(Glu) in a common ancestor of the lineages of the Suina (pigs and peccaries), Ruminantia (cows and deer), and Cetacea (whales and dolphins). (2) After divergence of the Suina lineage, the CHR-1 SINE and the CHR-2 SINE were generated successively in a common ancestor of ruminants, hippopotamuses, and cetaceans. (3) In the Ruminantia lineage, the Bov-tA SINE was generated by recombination between the CHR-2 SINE and Bov-A. (4) In the Suina lineage, the CHRS-S SINE was generated from the CHRS SINE. (5) In this latter lineage, the PRE-1 family of SINEs was created by insertion of part of the gene for tRNA(Arg) into the 5' region of the CHRS-S family. The distribution of a particular family of SINEs among species of artiodactyls and cetaceans confirmed the most recent conclusion for paraphyly of the order Artiodactyla. The present study also revealed that a newly created tRNA(Glu)-derived family of SINEs was subjected both to recombination with different units and to duplication of an internal sequence within a SINE unit to generate, during evolution, a huge superfamily of tRNA(Glu)-related families of SINEs that are now found in the genomes of artiodactyls and cetaceans.     

A note on the structure of tail hairs from a pygmy hippopotamus (Choeropsis liberiensis)

The pygmy hippopotamus (Choeropsis liberiensis), like the Nile hippopotamus (Hippopotamus amphibius), defecates by backing into vertical objects while making a series of rapid, propellerlike tail movements that spread a mixture of urine and feces in a wide swath. Split hairs from the distal ventral surface of the pygmy hippopotamus tail were studied with the scanning electron microscope to determine whether the splitting was a normal character of the hair or was due to damage. The results suggest that splitting is a normal feature of the hair that may facilitate the dispersal of urine and feces.     

Different Sex Allocations in Two Related Species: The Case of the Extant Hippopotamus

Social and reproductive systems remain among the main predictors affecting mammalian birth sex ratio. The two extant hippopotamus species differ in their social and reproductive systems. While common hippopotamus (Hippopotamus amphibius) form herds and tend to be polygynous, solitary living pygmy hippopotamus (Choeropsis liberiensis) are promiscuous. Although it is one of the most studied topics, only few empirical studies using large sample sizes have reported distorted birth sex ratio. We examined the birth sex ratio in both hippopotamus species using international studbooks including large data sets exceeding a thousand individuals (1138 for common hippopotamus and 1161 for pygmy ones). In both species, the birth sex ratio differed from 1:1. Whereas more males than females were recorded in common hippopotamus (53.9% males), the opposite was found in pygmy hippopotamus (41.5% males). We also found that the birth sex ratio was affected by individual dams in common hippopotamus, and by individual sires in pygmy hippopotamus. The most plausible explanation for differentially skewed birth sex ratios in both species may be related to differences in social and reproductive systems. Whereas the polygynous, sexually dimorphic common hippopotamus biased the birth sex ratio towards males, the promiscuous and sexually monomorphic pygmy hippopotamus skewed the sex ratio in favour of females. Our results are in line with recent studies showing that not only manipulation by the mother (in common hippopotamus), but also by the father (in pygmy hippopotamus), may be responsible for the birth sex ratio in different species.     

Stephanofilaria thelazioides n. sp. (Nematoda: Filariidae) from a hippopotamus and its affinities with the species parasitic in the African black rhinoceros

Stephanofilaria thelazioides n. sp. (Filarioidea: Filariidae: Stephanofilariinae) is described from a hippopotamus Hippopotamus amphibius. This nematode is close to S. dinniki Round, 1964, a parasite of the black rhinoceros Diceros bicornis in Africa, but differs from it in the number of cuticular spines surrounding the mouth, the arrangement of the cloacal papillae and the measurements of the spicules, gubernaculum and microfilariae. Species of the genus Stephanofilaria possess spines on the head which have been derived by modification of the sensory papillae. S. thelazioides is the most primitive species of the genus and has the least modified arrangement of these papillae, with six bifid internal labial spines, four bifid external labial spines and four cephalic papillae. The genus appears to have diversified in various mammals which have in common a thick skin, such as rhinoceroses, elephants, buffaloes and now the hippopotamus. It appears to have become adapted secondarily to domestic bovines, initially in Asia and subsequently in North America.     

Localization of swine PRE-1 homologues in 13 loci of Phacochoerus aethiopicus and Tayassu tajacu genomes, and their sequence divergence

In our previous study, PRE-1 (a swine short interspersed nuclear element, SINE) was found to be present in the genomes of animal species related to swine ( Sus scrofa ) i.e. warthog ( Phacochoerus aethiopicus ) and collared peccary ( Tayassu tajacu ) at almost the same frequency as in Sus scrofa . In the present study, we investigated whether PRE-1 was present in hippopotamus ( Hippopotamus amphibius ), which is in the same order but in a different family to Sus scrofa . Hippopotamus amphibius was found to contain no PRE-1. Then, in order to study the localization of PRE-1 sequences at locus level and the sequence divergence of the PRE-1 of individual loci among Sus scrofa , Phacochoerus aethiopicus and Tayassu tajacu , primer sets, which can amplify PRE-1 sequences at 13 loci of swine genome with the polymerase chain reaction, were prepared to identify any corresponding sequences in Phacochoerus aethiopicus and Tayassu tajacu . Twelve and nine of the 13 primer sets identified fragments in Phacochoerus aethiopicus and Tayassu tajacu respectively. Ten of the 12 Phacochoerus aethiopicus fragments and two of the nine Tayassu tajacu fragments contained PRE-1 sequences. Based on the divergence between the corresponding PRE-1 sequences at individual loci and on the mutation rate of the pseudogenes (r=4·6×10^–9), Phacochoerus aethiopicus and Tayassu tajacu are currently calculated to have been separated from Sus scrofa later than 1·4million years before present (MYBP) and 16·8 MYBP, respectively.     

Seasonal variation of thermoregulatory behaviour in the Hippopotamus (Hippopotamus amphibius)

The hippopotamus (Hippopotamus amphibius) spends more than 12 h a day in the water. Hippos are often submitted to water temperatures that vary with the seasons. We hypothesize that this difference between cool and warm water temperatures leads to variations in behavioural thermoregulation. We recorded the exposure of hippos to sunshine at the beginning and at the end of the dry season. Our results show that (1) sunshine exposure lasted much longer in cool water and (2) sun-bathing occurred during the hottest hours. It is therefore likely that in cool water hippos were cold and expressed an original behaviour of search for heat.     

Missing teeth: Discordances in the trade of hippo ivory between Africa and Hong Kong

As the global epicentre of wildlife trade, Hong Kong plays an important role in the preservation or demise of biodiversity, including species found continents away. If mismanaged, legal trade in threatened species can lead to unsustainable exploitation. Inaccurate and incomplete trade records from the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) undermine the regulation of this trade. We examine the trade of hippo (Hippopotamus amphibius) teeth to illustrate the extent of mismatched data between key trading nations. More than 90% of global hippo teeth trade is imported to, and re‐exported from, Hong Kong. Of that imported, over 75% originated in Tanzania or Uganda, but there are notable disparities in declared trade volumes. In most transactions, Hong Kong declares more volume imported than the volume declared exported by Uganda. Overall, Hong Kong has reported the import of 3,176 kg more hippo teeth than declared exported by Tanzania. This indicates that actual trade levels may exceed internationally agreed quotas. In total, over 14,000 kg of hippo teeth is unaccounted for between Uganda and Hong Kong, representing more than 2,700 individual hippos—2% of the global population. This gross discordance in trade data undermines regulatory measures and challenges the persistence of hippo populations in Africa.     

Identification and characterization of a new member of the SINE Au retroposon family (GmAu1) in the soybean, Glycine max (L.) Merr., genome and its potential application

A plant short interspersed element (SINE) was identified in Glycine max after re-sequencing of the soybean sequence characterized amplified region (SCAR) markers. Detailed analysis revealed that this newly recognized SINE element consisted of a tRNA-related region, a tRNA non-related region, direct flanking repeat sequences, and a short stretch of Ts at the 3′-terminal region. These features are similar to previously characterized SINEs. To investigate the evolution of the SINE retroposon, BLASTN was used to search against genome sequences of other plants. Since it is homologous with the retroposon Au in Aegilops umbellulata (wheat) and its homology in soybean, the SINE is named as GmAu1. Genome analysis of the Glycine max var. Willimas 82 uncovered more than 847 copies of GmAu1 per haploid genome of soybean. Examination of the regions flanking the inserted GmAu1 sequences indicated a preference for introns over exons or other noncoding regions. Considering the flanking insertion sequences, 146 primers were designed in order to detect insertion mutations by a PCR-based method. Seventy-seven primers displayed polymorphism and were used to develop corresponding GmAu1-based SCAR markers. The retroposon GmAu1 and its related SCAR markers identified in this study will prove valuable to future investigations into the genetic mapping, phylogeny, and evolution of the Glycine genus.     

Common evolutionary trends for SINE RNA structures

Short interspersed elements (SINEs) and long interspersed elements (LINEs) are transposable elements in eukaryotic genomes that mobilize through an RNA intermediate. Understanding their evolution is important because of their impact on the host genome. Most eukaryotic SINEs are ancestrally related to tRNA genes, although the typical tRNA cloverleaf structure is not apparent for most SINE consensus RNAs. Using a cladistic method where RNA structural components were coded as polarized and ordered multistate characters, we showed that related structural motifs are present in most SINE RNAs from mammals, fishes and plants, suggesting common selective constraints imposed at the SINE RNA structural level. Based on these results, we propose a general multistep model for the evolution of tRNA-related SINEs in eukaryotes.     

RNA sequence analysis using covariance models.

We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models 'covariance models'. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for additional tRNAs and tRNA-related sequences in sequence databases. A model can be built automatically from an existing sequence alignment. We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information. Models trained on unaligned tRNA examples correctly predict tRNA secondary structure and produce high-quality multiple alignments. The approach may be applied to any family of small RNA sequences.     

First documentation of flehmen in a common hippopotamus (Hippopotamus amphibius)

A male common hippopotamus (Hippopotamus amphibius) was observed giving a flehmen grimace on 14 occasions in July and August of 1998 at the Denver Zoo. Twelve instances of flehmen occurred after anogenital investigation of the female as she was exiting the pool. The two other instances of flehmen occurred in the terrestrial portion of the enclosure after the male examined samples of the female's freshly voided urine. The frequency of flehmen increased as the female approached estrus. Flehmen in common hippos may be an example of an evolutionary remnant. Zoo Biol 18:415–420, 1999. © 1999 Wiley‐Liss, Inc.     

A Comparative Study of Pygmy Hippopotamus (<Emphasis Type="Italic">Choeropsis liberiensis</Emphasis>) Karyotype by Cross-Species Chromosome Painting

The family Hippopotamidae is comprised of two genera with two living species, the common hippo (Hippopotamus amphibius) and the pygmy hippo (Choeropsis liberiensis). Unlike the common hippo, the karyotype of C. liberiensis has not yet been investigated via cross-species chromosome painting methods. We established chromosomal homologies between the pygmy hippo, pig, and cattle by fluorescence in situ hybridization using whole chromosome, arm-specific, region specific, and bacterial artificial chromosome (BAC) probes. Probes from the 18 pig autosomes painted 45 conserved chromosomal segments in the pygmy hippo genome. The pygmy hippo and cattle homology map was deduced from our hybridization results of painting probes to pygmy hippo chromosomes with a combination of previously published dromedary hybridization data. On the pygmy hippo and cattle homology map, 29 cattle autosomes revealed 39 conservative segments on pygmy hippo chromosomes. For a more detailed structural analysis of genome rearrangements and X chromosome structure, we used cattle region specific and BAC probes. Our report demonstrates that cattle probes are useful not only in comparative studies within Ruminantia, but also in more phylogenetically distant Artiodactyla species.     

Hippos alter their aggregations to mitigate density-dependent drought effects

Megaherbivores play a critical role in the ecology of African savannas and grasslands. In addition, these systems are forecast to experience more frequent and severe droughts as a product of changes in the global climate. Thus, the continued conservation of megaherbivores and their associated ecosystems will require a better understanding of how megaherbivores respond to drought by shifting their movement, diet and social behaviour. We address this need by investigating the factors affecting changes in the abundance of common hippopotamus (Hippopotamus amphibius; hereafter: ‘hippos’) throughout the six major rivers of Kruger National Park, South Africa, during and following the severe drought of 2015/2016. Specifically, we aimed to understand the role of two environmental characteristics that have relevance to hippos and that changed in response to drought: vegetation condition and the extent of pooled surface water. In addition, we investigated the extent to which pre-drought density affected changes in hippo abundance. Although vegetation and daytime refugia both appeared to influence pre-drought hippo abundance, these factors were less important to the change in hippo abundance related to the drought. Instead, the response to drought was most strongly related to the pre-drought abundance of hippos, where river segments supporting more than 50 individuals prior to the drought in 2015 decreased by more than half on average. Furthermore, we show that the degree of aggregation decreased from 2015 to 2016 because of the drought, but then began to increase again as the rains returned in 2017. Our results suggest that in addition to the large pools that support large aggregations of hippos in typical years, additional smaller pools are likely important for accommodating this drought-induced dispersion. However, maintaining this distribution of pools will likely become more challenging as southern Africa's population and water demands increase.     

Surgical castration of the male common hippopotamus (Hippopotamus amphibius)

In a prospective, clinical, surgery study we report here for the first time, in detail, on the surgical castration of 10 captive adult male common hippopotami (Hippopotamus amphibius). The successful procedures, a species-specific modification of standard equine castration techniques, provide valuable insight into the spatially dynamic nature of the common hippopotamus testis. The use of ultrasonography to locate the testis before and during the procedures and species-specific positioning during surgery greatly facilitated this distinctive procedure. Additionally, this surgical method provides an important additional tool for captive management of the common hippopotamus. Castration of individual males not only facilitates population control but can potentially also be employed to limit intermale aggression.     

Are hippos Africa's most influential megaherbivore? A review of ecosystem engineering by the semi-aquatic common hippopotamus

Megaherbivores perform vital ecosystem engineering roles, and have their last remaining stronghold in Africa. Of Africa's remaining megaherbivores, the common hippopotamus (Hippopotamus amphibius) has received the least scientific and conservation attention, despite how influential their ecosystem engineering activities appear to be. Given the potentially crucial ecosystem engineering influence of hippos, as well as mounting conservation concerns threatening their long-term persistence, a review of the evidence for hippos being ecosystem engineers, and the effects of their engineering, is both timely and necessary. In this review, we assess, (i) aspects of hippo biology that underlie their unique ecosystem engineering potential; (ii) evaluate hippo ecological impacts in terrestrial and aquatic environments; (iii) compare the ecosystem engineering influence of hippos to other extant African megaherbivores; (iv) evaluate factors most critical to hippo conservation and ecosystem engineering; and (v) highlight future research directions and challenges that may yield new insights into the ecological role of hippos, and of megaherbivores more broadly. We find that a variety of key life-history traits determine the hippo's unique influence, including their semi-aquatic lifestyle, large body size, specialised gut anatomy, muzzle structure, small and partially webbed feet, and highly gregarious nature. On land, hippos create grazing lawns that contain distinct plant communities and alter fire spatial extent, which shapes woody plant demographics and might assist in maintaining fire-sensitive riverine vegetation. In water, hippos deposit nutrient-rich dung, stimulating aquatic food chains and altering water chemistry and quality, impacting a host of different organisms. Hippo trampling and wallowing alters geomorphological processes, widening riverbanks, creating new river channels, and forming gullies along well-utilised hippo paths. Taken together, we propose that these myriad impacts combine to make hippos Africa's most influential megaherbivore, specifically because of the high diversity and intensity of their ecological impacts compared with other megaherbivores, and because of their unique capacity to transfer nutrients across ecosystem boundaries, enriching both terrestrial and aquatic ecosystems. Nonetheless, water pollution and extraction for agriculture and industry, erratic rainfall patterns and human–hippo conflict, threaten hippo ecosystem engineering and persistence. Therefore, we encourage greater consideration of the unique role of hippos as ecosystem engineers when considering the functional importance of megafauna in African ecosystems, and increased attention to declining hippo habitat and populations, which if unchecked could change the way in which many African ecosystems function.