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.     

Characterization of swine short interspersed repetitive sequences

Swine genomic DNA segments containing repetitive sequences were isolated from a porcine genomic library using genomic DNA as a probe. Three fragments containing the repetitive sequences from two of the primary phage clones were subcloned for sequence analysis, which revealed six new PRE-1 repetitive families other than those reported earlier by Singer et al. (Nucleic Acids Research 15, 2780, 1987). The frequency of the repetitive sequences in the swine genome was estimated at 2 x 10(6) per diploid genome. Sequence analysis revealed similarities between these repetitive sequences and that of arginine-tRNA gene.     

Chromosomal evolution and phylogenetic analyses in <Emphasis Type="Italic">Tayassu pecari</Emphasis> and <Emphasis Type="Italic">Pecari tajacu</Emphasis> (Tayassuidae): tales from constitutive heterochromatin

The mammalian family Tayassuidae (peccaries) is confined to the New World and comprises three recognized extant species, white-lipped (Tayassu pecari), collared (Pecari tajacu) and chacoan (Catagonus wagneri) peccaries, which exhibit distinct morphological and chromosomal features. The phylogenetic relationships among the tayassuids are unclear and have instigated debate over the palaeontological, cytogenetic and molecular aspects. Constitutive heterochromatin analysis can be used in understanding the phylogenetic relationships between related species. Here we describe, for the first time, the constitutive heterochromatin (C-positive heterochromatin) of two tayassuid species, Tayassu pecari and Pecari tajacu. We demonstrate that in situ restriction endonuclease digestion with sequential C-banding could be a complementary tool in the study of constitutive heterochromatin heterogeneity in chromosomes of the Tayassuidae. Our characterization of peccary chromosomes suggests that the Pecari tajacu autosomal karyotype is more primitive and has accumulated great diversity in its constitutive heterochromatin. This idea is supported by several other studies that analysed nuclear and mitochondrial sequences of the living peccary species. Finally, the tayassuid X chromosome primitive form seems to be the one of Tayassu pecari.     

Description of collared peccary (Tayassu tajacu) milk composition

Composition of collared peccary (Tayassu tajacu) milk was described for samples obtained from a group of four captive females maintained on a high quality diet and four wild-caught females inhabiting semiarid rangelands in southern Texas. The gross composition of peccary and porcine milks are fairly similar, with some differences in mineral composition. Results suggest that bottle formulations developed for domestic swine piglets would provide adequate nutrition for hand-rearing nursling peccaries.     

Distribution of the common warthog (Phacochoerus africanus) and the desert warthog (Phacochoerus aethiopicus) in the Horn of Africa

The Somali warthog, Phacochoerus aethiopicus delamerei, is the surviving relative of the Cape warthog, P. a. aethiopicus, which formerly inhabited Cape Province but became extinct in the last century. It is only recently that these two subspecies of Phacochoerus aethiopicus have been restored to the status of a species – the ‘desert warthog’– distinct from the common warthog, P. africanus ( Grubb, 1985 ; Grubb & Oliver, 1991 ; Grubb, 1993 ). Mitochondrial DNA analysis has recently confirmed that the common and desert warthogs are two different and widely divergent species (Randi et al., unpublished). This preliminary study maps their distribution in the Horn of Africa, and discusses the significance of ecological barriers that limit these distributions. One hundred and thirty‐three skulls from 64 different localities in five countries – mostly from museum collections – were identified. New material was obtained from the field and reliable literature data were also recorded. Locality records suggest that the optimal habitats of desert warthog are low altitude arid lands. The two species may overlap locally in northern Somalia, northern and eastern Kenya and southern and south‐eastern Ethiopia, but the desert warthog's precise range is still not accurately established and basic data about its conservation status, ecology and behaviour are still very poor.     

Uneven-distribution of short interspersed repetitive sequence, PRE-1, on swine chromosomes.

We investigated the distribution of PRE-1 sequences (a swine major SINE) on the swine chromosomes. The investigation demonstrated that PRE-1 sequences are unevenly distributed along the chromosomes as in the case of the human and mouse SINES. The distribution pattern, however, has no simple correlation with Q-band pattern as that of human and mouse SINES. The prominent difference is as follows; PRE-1 is localized on centromeric regions, but human and mouse SINES are not [KORENBERG and RYKOWSKI (1988). Cell, 53: 391-400; BOYLE, BALLARD, and WARD (1990). Proc. Natl. Acad. Sci. U.S.A. 87: 7751-7761].     

Environment and space as drivers of variation in skull shape in two widely distributed South‐American Tayassuidae,Pecari tajacu and Tayassu pecari (Mammalia: Cetartiodactyla)

The influence of the environment on the geographical variation of morphological traits has been recognized in a number of taxa. Pecari tajacu and Tayassu pecari are ideal models to investigate intraspecific geographic variation in skull because of their wide and heterogeneous geographical distribution in South America. We used geometric morphometric procedures to examine the geographical variation in skull shape of 294 adult specimens of these species from 134 localities. We quantified to what extent skull shape variation was explained by environment, skull size and geographical space using variation partitioning analysis. We detected a strong pattern of geographic variation for P. tajacu skull shape, but not for T. pecari. The environment seems to be the major selective force that drives skull shape variation in both species. Nevertheless, other spatially structured processes (e.g. genetic drift, gene flow) might also have affected variation in the skull shape of the more widespread species P. tajacu. Allometric relationships might reflect the biomechanical constraints that are thought to be strong enough to limit size‐related changes in T. pecari skull shape.     

Influence of digestive morphology on resource partitioning in Amazonian ungulates

Summary Resource partitioning of diet and habitat use was studied in the entire Amazonian ungulate community of Northeastern Peru, which comprises the red brocket deer (Mazama americana), grey brocket deer (M. gouazoubira), collared peccary (Tayassu tajacu), white-lipped peccary (T. pecari), and lowland tapir (Tapirus terrestris). Each ungulate species partitioned at least one type of resource from every other species. Digestive morphology had a greater influence on resource partitioning of diet than body size. Neither digestive morphology nor body size were related to segregation of habitats. However, species with similar diets partitioned habitats, whereas species with different diets often used the same type of forest. Increases in habitat breadth of ungulates were positively correlated with increases in dietary breadth.     

The Complete Mitochondrial DNA Sequence of the Pig (Sus scrofa)

The complete mitochondrial genome sequence of the pig, Sus scrofa, was determined. The length of the sequence presented is 16,679 nucleotides. This figure is not absolute, however, due to pronounced heteroplasmy caused by variable numbers of the motif GTACACGTGC in the control region of different molecules. A phylogenetic study was performed on the concatenated amino acid and nucleotide sequences of 12 protein-coding genes of the mitochondrial genome. The analysis identified the pig (Suiformes) as a sister group of a cow/whale clade, making Artiodactyla paraphyletic. The split between pig and cow/whale was molecularly dated at 65 million years before present. Received: 2 December 1997 / Accepted: 20 February 1998     

Genome-specific repetitive sequences in the genus Oryza

Summary Repetitive DNA sequences are useful molecular markers for studying plant genome evolution and species divergence. In this paper, we report the isolation and characterization of four genome-type specific repetitive DNA sequences in the genus Oryza. Sequences specific to the AA, CC, EE or FF genome types are described. These genome-type specific repetitive sequences will be useful in classifying unknown species of wild or domestic rice, and in studying genome evolution at the molecular level. Using an AA genome-specific repetitive DNA sequence (pOs48) as a hybridization probe, considerable differences in its copy number were found among different varieties of Asian-cultivated rice (O. sativa) and other related species within the AA genome type. Thus, the relationship among some of the members of AA genome type can be deduced based on the degree of DNA sequence similarity of this repetitive sequence.     

Evaluation of fences for containing feral swine under simulated depopulation conditions

Populations of feral swine (Sus scrofa) are estimated to include >2 million animals in the state of Texas, USA, alone. Feral swine damage to property, crops, and livestock exceeds $50 million annually. These figures do not include the increased risks and costs associated with the potential for feral swine to spread disease to domestic livestock. Thus, effective bio-security measures will be needed to quickly isolate affected feral swine populations during disease outbreaks. We evaluated enclosures built of 0.86-m-tall traditional hog panels for containing feral swine during 35 trials, each involving 6 recently caught animals exposed to increasing levels of motivation. During trials, fences were 97% successful when enclosures were entered by humans for maintenance purposes; 83% effective when pursued by walking humans discharging paintball projectors; and in limited testing, 100% successful when pursued and removed by gunners in a helicopter. In addition to being effective in containing feral swine, enclosures constructed of hog panels required simple hand tools, took <5 min/m to erect, and were inexpensive ($5.73/m excluding labor) relative to other fencing options. As such, hog-panel fences are suitable for use by state and federal agencies for rapid deployment in disease response situations, but also exhibit utility for general control of other types of damage associated with feral swine. © 2011 The Wildlife Society.     

Observations on the Behavior of Rain Forest Peccaries in Perú: Why do White-lipped Peccaries Form Herds?

The ecology and behavior of Tayassu tajacu and T. pecari were studied for a total period of 16 months in the years 1975–1978 in the Manú National Park in southeastern Perú. It appears from 132 sightings of T. tajacu at the study site, and from reports from other regions, that groups of this species in rain forest usually contain fewer than 12 individuals. The more observers were at the study site, the more frequently this species was encountered. T. tajacu also repeatedly used wallows in the forest. These observations suggested that individuals of this species were relatively sedentary. Herds of T. pecari were encountered on 60 occasions. Five counts indicated that there were over 100 individuals in the herds. This species was encountered at practically random intervals, independent of number of observers at the site, but more frequently in the dry season than in the rainy season. Adults of both species are prey primarily of large cats and humans. Both species feed on green plant parts, fruits, nuts and seeds, but T. pecari feeds on more resistant seeds and nuts than T. tajacu. The hardest palm nuts that only T. pecari can consume are distributed in a patchy manner. Cracking these nuts between the teeth causes the animals to be heard more than 50 m away. The patchy distribution of the hard nuts and seeds prevents T. pecari from being sedentary, and group formation likely has several individual benefits for foraging efficiency and defense against predators. These may include (1) avoidance of searching for food in places recently visited by others, (2) benefitting from the knowledge of experienced foragers, (3) reducing the per capita probability of detection by predators, (4) reducing the probability of being captured after group detection by predators, (5) increasing the ability to counterattack as a group, (6) increasing the probability of detecting the predator before it can attack, and (7) “confusing” the predator through escape behavior. T. tajacu seems to live in small groups because its typical foods are distributed more evenly and because consumption of these foods does not cause individuals to be so noticeable to predators.     

Characterization of six new loci within the swine major histocompatibility complex class III region

A search for new potential coding sequences was conducted within two overlapping cosmid genomic DNA clusters of about 170 and 45 kb from the swine major histocompatibility complex class III region. The sequences were detected with various probes, including pools of swine cDNA, homologous and heterologous genomic sequences, and synthetic oligonucleotides. The 170 kb cluster was centered on the tumor necrosis factor genes (TNF), and the 45 kb cluster contained the heat-shock protein 70 genes (HSP70). The TNF cluster revealed the presence of five new genes: lymphotoxin , BAT1, BAT2, BAT3, and a sequence related to DNA-binding factors. No sequence homologous to B144 was found in the TNF cluster, although other unidentified coding sequences may be present in this cluster. The HSP70 cluster contained a gene identified as BAT6, that is, tRNA-valyl synthetase. These results provide new evidence that the genomic maps of these various genes in the TNF and HSP70 sub-regions are similar in swine and human.     

Nuclear and mitochondrial evolutionary analyses of Collared, White-lipped, and Chacoan peccaries (Tayassuidae)

The three extant peccary species, the Chacoan (Catagonus wagneri), the White-lipped (Tayassu pecari) and the Collared (Pecari tajacu), are morphologically and chromosomally distinct and confined to the New World. There is ongoing paleontological, cytogenetic, and molecular debate about phylogenetic relationships among them. To contribute to the understanding of Tayassuidae phylogeny, three mitochondrial (control region, cytochrome b, and 12S rRNA) and five nuclear (K-casein, thyrotropin, tyrosinase, and swine short interspersed nuclear elements PRE-1 P27 and P642) peccary DNA fragments were amplified, cloned and sequenced from Chacoan, White-lipped, and Collared peccaries. Phylogenetic analyses were performed using maximum likelihood and neighbor joining methods. K-casein, thyrotropin, and tyrosinase sequences did not resolve the phylogeny, while control region, cytochrome b, 12S rRNA, and PRE-1 P27 and P642 sequences were more informative in deciphering phylogenetic relationships. When pig and warthog were used as an outgroup, Chacoan and White-lipped peccaries clustered distinct from Collared peccaries. Furthermore, control region and cytochrome b sequence variation within Collared peccaries was as extreme as that between White-lipped and Chacoan peccaries, supporting subspecific and possibly even specific variation within the widely distributed Collared peccary. This study supports the existence of two independent genera within the Tayassuidae family consisting of Collared and Chacoan/White-lipped peccaries, in contrast with classical morphological taxonomy which clusters White-lipped and Collared peccaries in the genus Tayassu or which alternatively clusters the Collared peccary in the genus Dicotyles as a related sister clade of the Chacoan peccary (genus Catagonus).     

The swine steroid 21-hydroxylase gene (CYP21): cloning and mapping within the swine leucocyte antigen complex

A swine genomic cosmid library constructed from a genotypically SLA homozygous Large White individual was screened with a murine genomic 21-hydroxylase probe. A clone which contained a pig 21-hydroxylase gene was isolated and after subcloning, the 5' region of the gene was sequenced. The deduced amino acid sequence corresponded almost exactly to the NH2 terminal portion of the steroid 21-hydroxylase from porcine adrenal microsomes. Comparison of the first 99 amino acid residues of both sequences revealed three substitutions comprising two leucine residues in positions 10 and 13, and one arginine residue in position 55 for our sequence, instead of threonine in position 10 and lysine in position 13 and 55 for the isolated enzyme. A swine homologous probe was derived from the isolated 21-hydroxylase gene and used for gene assignment by RFLP studies in two swine leucocyte antigen (SLA) informative families. The results demonstrate that the swine 21-hydroxylase gene is located within or close to the swine MHC. Taken together, the present results suggest the existence of a single 21-hydroxylase gene per haploid genome.     

Behaviours of collared and white-lipped peccaries (Tayassu tajacu andT. pecari) in relation to sexual receptivity of the female

Changes in behaviours of the two peccary species,Tayassu tajacu Linnaeus, 1758 andT. pecari Link, 1795 between non-receptive and receptive periods were followed by presenting females to males daily for 15 minutes. InT. tajacu, the rank order of behaviours, similar in both sexes during the non-receptive period, differs during receptivity. Contact behaviours decrease in males, whereas sexual ones progress. The same tendency appears in females. Inhibited bites replace markings of partner as the most common behaviour in both sexes. InT. pecari, the rank order of behaviours always differs between sexes. When females become receptive, the differences from the non-receptive period are neither numerous nor significant. The most common behaviour of males, previously markings of partner, becomes mounts, whereas in females agonistic behaviours reinforce their dominance. In this species, the only behaviours that increase are those leading directly to copulation or those of an agonistic nature. In both species, females show more agonistic behaviours than males (mainly inhibited bites inT. tajacu, truly aggressive ones inT. pecari). When females are receptive, males ofT. pecari become less active, contrary toT. tajacu where both sexes double their activity. InT. tajacu, most behaviours vary significantly in relation to the progesterone level, contrary to the other species. These pecularities appear correlated to herd composition and organisation.     

Diet Overlap and Foraging Activity between Feral Pigs and Native Peccaries in the Pantanal

Inter-specific competition is considered one of the main selective pressures affecting species distribution and coexistence. Different species vary in the way they forage in order to minimize encounters with their competitors and with their predators. However, it is still poorly known whether and how native species change their foraging behavior in the presence of exotic species, particularly in South America. Here we compare diet overlap of fruits and foraging activity period of two sympatric native ungulates (the white-lipped peccary, Tayassu pecari, and the collared peccary, Pecari tajacu) with the invasive feral pig (Sus scrofa) in the Brazilian Pantanal. We found high diet overlap between white-lipped peccaries and feral pigs, but low overlap between collared peccaries and feral pigs. Furthermore, we found that feral pigs may influence the foraging period of both native peccaries, but in different ways. In the absence of feral pigs, collared peccary activity peaks in the early evening, possibly allowing them to avoid white-lipped peccary activity peaks, which occur in the morning. In the presence of feral pigs, collared peccaries forage mostly in early morning, while white-lipped peccaries forage throughout the day. Our results indicate that collared peccaries may avoid foraging at the same time as white-lipped peccaries. However, they forage during the same periods as feral pigs, with whom they have lower diet overlap. Our study highlights how an exotic species may alter interactions between native species by interfering in their foraging periods.     

On the intestinal yeast flora of free living hippopotami(Hippopotamus amphibius), wart hogs(Phacochoerus aethiopicus) and bush pigs(Potamochoerus choeropotamus)

Summary From the faeces of 35 free-living hippopotami (Hippopotamus amphibius), sampled in south Mozambique, 13 yeast isolates were obtained, distributed as shown (in brackets) among the following species:Candida guilliermondii (3),C. tropicalis (2),C. krusei (2),C. brumptii (1),Debaryomyces globosus (2),Trichosporon cutaneum (1), not identified (2). From the caecal contents of 9 free-living wart hogs (Phacochoerus aethiopicus), shot in north Mozambique 5 isolates were obtained:C. albicans (2),C. lusitaniae (2),C. parapsilosis (1). From the caecal contents of 9 free-living bush pigs (Potamochoerus choeropotamus), shot in north Mozambique, 18 isolates were obtained:C. krusei (6),C. tropicalis (5),Pichia fermentans (2),C. slooffii (2),C. albicans (1),Torulopsis glabrata (1),Trichosporon cutaneum (1). The low total yeast indices of the hippopotami (0.37) and the wart hogs (0.56) are believed to be correlated with the type of diet of these animals (rich in cellulose, poor in starch and simple carbohydrates). The bush pigs, which like the domestic pig, use a diet rich in starch and simple carbohydrates, had a very high total yeast index (2.00).Candida slooffii an obligate saprophyte of the digestive tract of domestic swine was found in two of the bush pig samples.     

A photographic ageing technique used on warthog

The ratios of tusk-length: snout-width from a series of warthog (Phacochoerus aethiopicus) photographs were calculated and plotted against the date the photographs were taken. Regression lines, as well as the 95% confidence intervals, were calculated from the photographs and plotted. These regression lines fell into four distinct groups, representing Age Classes II through V. The average degree of error in the tusk-length: snout-width ratio was 3-01 units, a figure well within the above 95% confidence intervals.     

Evolutionary genetics of the suiformes as reconstructed using mtDNA sequencing

We have amplified and sequnced the entire mitochondrial DNA cytochromeb gene from four species of Suidae: babirusa, warthog, bearded pig, and some specimens belonging to different subspecies and populations of wild and domestic pigs (Sus scrofa). These sequences were aligned with additional mammalian sequences retrieved from the literature and were used to obtain phylogenetic trees of the Suiformes (Artiodactyla). Several species of Carnivora, Perissodactyla. Cetacea, and other Artiodactyla were used as outgroups. Molecular phylogenetic relationships among the Suiformes reflect their current taxonomy: Hippopotamidae, Tayassuidae, and Suidae are separated by deep genetic gaps, and the division of the Suidae into the subfamilies Babyrousinae., Phacochoerinae, and Suinae has strong genetic correlates. Cytochromeb sequences show differences among Asian and Western populations ofSus scrofa, agreeing with other genetic information (karyotypes blood groups, and protein variability). The two Italian subspecies of wild boar have unique mtDNA cytochromeb haplotypes. The evolutionary rates of cytochromeb sequences are different at transitions versus transversions as well as at first, second, and third positions of codons. Therefore, these classes of substitutions reached different levels of mutational saturation. Only transversions and the conservative first and second position substitutions are linearly related to genetic distances among the Suiformes. Therefore, divergence times were computed using unsaturated conserved nucleotide substitutions and calibrated using paleontological divergence times between some Artiodactyla. Transversions apparently evolve at remarkably regular rates in ungulate taxa which have accumulated less than 20% estimated sequence divergence, corresponding to about 40–45 million years of independent evolution. Molecular, information suggests that Hippopotamidae and Tayassuidae are not closely related (as stated by Pickford, 1986, 1989, 1993) and that the origin of babirusa and warthog (about 10–19 and 5–15 million years ago, respectively) is more recent than supported by current evolutionary reconstructions. The inferred origin of bearded pig is about 2.1 million years old, and genetic divergence among differentSus scrofa populations is probably a Pleistocene event. The addition of new sequences of Suiformes does not help in resolving the phylogenetic position ofHippopotamus amphibius, which shows weak but recurrent linkages with the cetacean evolutionary lineage.To whom correspondence should be addressed.