Article

Complete DNA sequence analysis of the mitochondrial 16s rRNA and cytochrome b genes of the Visayan warty pig (Sus cebifrons)

Authors:
To read the full-text of this research, you can request a copy directly from the authors.

Abstract

The Visayan warty pig (Sus cebifrons) is one of the world's most endangered pigs and is found only on the islands of Negros, Masbate and Panay in the Philippines. Its taxonomy and phylogeny has largely been based on morphology but a limited number of studies have been conducted to correlate morphological data with DNA sequences of key genes. In this study, PCR primers targeting mitochondrial 16s rRNA and cytochrome b genes were designed using DNAsis based on pig (Sus) mitochondrial DNA sequences available in the ENTREZ online database. The newly designed primers amplified mitochondrial 16s rRNA and cytochrome b genes using DNA templates from S. cebifrons, two other Philippine wild pig samples and two samples of the domesticated pig, Sus scrofia. The mitochondrial genes of the pigs used in this study were found to closely match their counterparts in the ENTREZ online database, with the mitochondrial 16s rRNA genes of wild pigs matching those of domestic pigs by as much as 98%, and the mitochondrial cytochrome b genes of wild pigs matching those of domestic pigs by as much as 95%. Sequence data and analysis of sequence alignments suggest that the S. cebifrons could be a distinct species and is phylogenetically separate from other species of wild pig from various localities around the world. Phylogenetic tree construction using data from the mitochondrial 16s rRNA and cytochrome b genes showed that S. cebifrons was grouped with mixtures of both European and Asian wild boar species in their specific clades but belonged to a separate clade, indicating a cross-continental introgression consistent with the introduction of Asian wild boars into European populations in the 19(th) century. The gene sequences in this study are the first ever reported for any wild pig species in the Philippines and the approach taken in phylogenetic analysis is expected to contribute to better conservation strategies for S. cebifrons.

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the authors.

... The Visayan warty pig S. cebifrons was originally described from Cebu Island on the basis of only one skull, but only in 1993 it was recognized as a full species. Initially considered a subspecies of S. philippensis (Groves 1997), two phylogenetic studies suggest that S. cebifrons is a taxon very different from S. philippensis (Groves 1997;De Leon et al. 2008). This new species could be the most archaic member of the Sus genus. ...
Chapter
Names Genus: Sus Linnaeus, 1758 Species: Sus cebifrons Heude, 1888 Subspecies: Sus cebifrons cebifrons Heude, 1888, Cebu Island, Philippines (extinct); Sus cebifrons negrinus Sandborn, 1952, Negros Island, Philippines Names in other languages: French: Sanglier des Visayas; German: Visayas-Pustelschwein; Italian: Cinghiale di Visayas; Cinghiale verrucoso di Visayas; Spanish: Jabalì de Bisayas Taxonomy The Visayan warty pig S. cebifrons was originally described from Cebu Island on the basis of only one skull, but only in 1993 it was recognized as a full species. Initially considered a subspecies of S. philippensis (Groves 1997), two phylogenetic studies suggest that S. cebifrons is a taxon very different from S. philippensis (Groves 1997; De Leon et al. 2008). This new species could be the most archaic member of the Sus genus. As S. cebifrons seems to be a sister species to all other members of the genus Sus, it is possible that this species became separated from the other taxa early in the evolution of this genus, probably in the Pliocene. The frequent glacial-interglacial cycles during this period and concomitant sea level falls and rises may have facilitated the dispersal of the ancestors of these species through bridges between islands, after which they became isolated, following their own unique evolutionary paths. Presently, two subspecies are recognized in Visayan warty pig (Groves 1997). The nominal form from Cebu has become extinct, but the other subspecies, S. c. negrinus, still occurs on Negros Island. Recent genetic studies describe the possibility of a third subspecies but this assumption is based only on one specimen from Panay Island and needs further genetic evidence (Oliver 2004, 2008). However, animals in zoos from the two islands (Panay animals are in the USA, Negros animals in Europe) seem to look consistently different; for example, Panay animals seem to have a more pronounced colour difference between the flanks and the more backward-reaching mane (R. Wirth, personal communication and also see below). Subspecies and Distribution This species has been eradicated from most of its native range of the Visayan Islands in the central region of the Philippines (Figure 14.1). Currently it occurs in the West Visayan Islands (Negros and Panay islands). On the Cebu, Guimaras, and Ticao Islands the species is thought to be extinct, although it occurred on Cebu at least until the 1960s (Groves & Grubb 1993; Oliver 1995; Oliver 2008).
Article
Full-text available
Unlabelled: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. Availability: http://www.megasoftware.net. Contact: s.kumar@asu.edu
Article
There are more taxa of wild pig in South-east Asia (SEA) than in any other comparable area in the world, but the number of species and subspecies is still uncertain. The taxonomy of some wild pig populations distributed in Malaysia, Indonesia and the Philippines, was investigated using molecular and morphometric techniques. Our results suggest the existence of two main evolutionary clades that are likely to have diverged during the Pliocene in SEA: one including wild pig populations distributed in the Philippines (Sus cebifrons) and Sulawesi (S. celebensis); the other including the Indonesian and Malaysian bearded pigs (S. barbatus), and the widespread Eurasian wild boar (S. scrofa). A possible scenario for pig speciation in SEA is developed, and the need for a taxonomic revision of bearded pigs suggested, particularly concerning the taxonomic status of S. b. ahoenobarbus from Palawan Island, and the existence a new species distributed in the Tawi Tawi Islands (Philippines). Unexpectedly, bearded pigs in the Malay Peninsula are closely related to the Bornean population, but distinct from Sumatran S. barbatus, and they should be considered as belonging to a different subspecies.
Article
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to downweight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
Article
Mitochondrial genetic variations were used to investigate the relationships between two Japanese wild boars, Japanese wild boar (Sus scrofa leucomystax) and Ryukyu wild boar (S.s. riukiuanus). Nucleotide sequences of the control (27 haplotypes) and cytochrome b (cyt-b) regions (19 haplotypes) were determined from 59 Japanese wild boars, 13 Ryukyu wild boars and 22 other boars and pigs. From phylogenetic analyses, the mtDNA of Ryukyu wild boar has a distinct lineage from that of Japanese wild boar, which was classified into the Asian pig lineage. This result suggests that the Ryukyu wild boar has a separate origin from the Japanese wild boar.