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International audience; The nearly cosmopolitan tribe Desmodieae (Fabaceae) includes many important genera for medicine and forage. However, the phylogenetic relationships among the infratribal groups circumscribed using morphological traits are still poorly known. In this study, we used chloroplast (rbcL, psbA-trnH) and nuclear (ITS-1) DNA sequences to investigate the molecular phylogeny and historical biogeography of Desmodieae, and infer ancestral states for several vegetative and reproductive traits. Three groups, corresponding to the Desmodium, Lespedeza, and Phyllodium groups sensu Ohashi were retrieved in the phylogenetic analyses. Conflicts in the topologies inferred from the chloroplast and nuclear datasets were detected. For instance, the Lespedeza clade was sister to the groups Phyllodium + Desmodium based on chloroplast DNA, but nested within the Desmodium group based on ITS-1. Moreover, the New Caledonian endemic genera Arthroclianthus and Nephrodesmus were not monophyletic but together formed a clade, which also included Hanslia and Ohwia based on chloroplast DNA. The hypothetical common ancestor of Desmodieae was dated to the Middle Oligocene (ca. 28.3 Ma) and was likely an Asian shrub or tree producing indehiscent loments. Several colonization events towards Oceania, America, and Africa occurred (all less than ca. 17.5 Ma), most probably through long distance dispersal. The fruits of Desmodieae repeatedly evolved from indehiscence to dehiscence. We also showed that indehiscent loments allow for more variability in the number of seeds per fruit than indehiscent legumes. Modularity seems here to allow variability in the number of ovules produced in a single ovary.

In 1994, several unusual horns collected from markets in Vietnam and Cambodia were described as a new genus and species of wild bovid, Pseudonovibos spiralis (Peter and Feiler, 1994a,b). The horn sheaths possessed a unique and distinct lyriform twist, as well as annulations throughout their entire length. This animal, named ‘‘linh duong’’ in Vietnam or ‘‘kting voar’’ in Cambodia (but see Brandt et al., 2001), was known only from detached horn sheaths or frontlets (partial frontal bones with bony horn cores) with horn sheaths. This lack of anatomical information was largely responsible for the confusion regarding the taxonomic status of this species, with morphologists debating whether it was a close relative of the tribe Antilopini (gazelles) (Peter and Feiler, 1994a), Caprini sensu lato (goats, sheep, and allies) (Nadler, 1997), or Bovini (oxen, bison, and buffaloes) (Dioli, 1997; Timm and Brandt, 2001). Given both the paucity and variable taxonomic interpretation of the morphological data, hopes were initially high that DNA sequence would resolve the issue of Pseudonovibos taxonomic status and phylogenetic position. However, three ensuing DNA sequencing studies using different putative P. spiralis specimens gave rise to mutually incompatible hypotheses: (1) Hammer et al. (1999), using a 415-bp DNA fragment of the mitochondrial cytochrome b gene, proposed affinities with the Caprini sensu lato. However, Hassanin and Douzery (2000) challenged the authenticity of the Hammer et al. (1999) sequence and interpreted it as the result of DNA contamination from chamois (Rupicapra) in the laboratory. (2) Hassanin et al. (2001) revealed that some horns assigned to P. spiralis are simply cow horns that had been artificially carved and twisted. Two DNA markers were sequenced from four trophies of P. spiralis collected in Indochina during 1925: a 243-bp fragment of the mitochondrial cytochrome b and a 327-bp fragment of the nuclear lactoferrin gene. The phylogenetic results showed that the enigmatic horns of the linh duong belonged to domestic cattle (Bos taurus) (Hassanin et al., 2001). Morphological inspection indicated that horn sheaths, originally smooth, were carved to create the annulations, while the twist in the upper part of the horns was made by artificial torsion (Thomas et al., 2001). This raised the question of whether all horns of the linh duong are fraudulent or not. In other words, did the species P. spiralis ever really exist (see review in Brandt et al., 2001)? (3) Most recently, Kuznetsov et al. (2001) suggested that P. spiralis was a new species of buffalo based on a 962-bp fragment of the mitochondrial 12S rRNA gene. However, one of us (Hassanin, 2002) demonstrated that the putative sequence of P. spiralis was a chimera obtained from three different species: B. taurus, Bubalus bubalus (domesticated Asian water buffalo), and Saiga tatarica (saiga antelope). In addition, several factors indicated that their specimen was artificially made using horns and a frontlet from domestic cattle, B. taurus. The ongoing and increasingly heated controversy surrounding P. spiralis has been covered in Science (Malakoff, 2001), Nature (Whitfield, 2002), and the New York Times (Mydans, 2002), with emphasis on both the folkloric portrayals of a snake-eating cow-like creature Molecular Phylogenetics and Evolution 27 (2003) 545–548

Mitochondrial sequences are widely used for species identification and for studying phylogenetic relationships among closely related species or populations of the same species. However, many studies of mammals have shown that the maternal history of the mitochondrial genome can be discordant with the true evolutionary history of the taxa. In such cases, the analyses of multiple nuclear genes can be more powerful for deciphering interspecific relationships. Here, we designed primers for amplifying 13 new exon-primed intron-crossing (EPIC) autosomal loci for studying shallow phylogeny and taxonomy of Laurasiatherian mammals. Three criteria were used for the selection of the markers: gene orthology, a PCR product length between 600 and 1200 nucleotides, and different chromosomal locations in the bovine genome. Positive PCRs were obtained from different species representing the orders Carnivora, Cetartiodactyla, Chiroptera, Perissodactyla and Pholidota. The newly developed markers were analyzed in a phylogenetic study of the tribe Bovini (the group containing domestic and wild cattle, bison, yak, African buffalo, Asian buffalo, and saola) based on 17 taxa and 18 nuclear genes, representing a total alignment of 13,095 nucleotides. The phylogenetic results were compared to those obtained from analyses of the complete mitochondrial genome and Y chromosomal genes. Our analyses support a basal divergence of the saola (Pseudoryx) and a sister-group relationship between yak and bison. These results contrast with recent molecular studies but are in better agreement with morphology. The comparison of pairwise nucleotide distances shows that our nuDNA dataset provides a good signal for identifying taxonomic levels, such as species, genera, subtribes, tribes and subfamilies, whereas the mtDNA genome fails because of mtDNA introgression and higher levels of homoplasy. Accordingly, we conclude that the genus Bison should be regarded as a synonym of Bos, with the European bison relegated to a subspecies rank within Bos bison. We compared our molecular dating estimates to the fossil record in order to propose a biogeographic scenario for the evolution of Bovini during the Neogene.

The genus Hemitragus includes three species of tahr distributed in distant geographical areas: the Himalayan tahr, H. jemlahicus, occupies the southern flanks of the Himalaya Mountains; the Nilgiri tahr, H. hylocrius, is endemic to southern India; and the Arabian tahr, H. jayakari, is unique to the mountains of south-east Arabia. All previous investigations were based on morphology, and these three species together have never been included in a molecular phylogenetic study. In this study, we constructed a molecular phylogeny of the tribe Caprini sensu lato to determine the taxonomic status of the three species of tahr. Phylogenetic analyses were carried out on a matrix including most extant species currently described in the tribe Caprini sensu lato, and 3165 nucleotide characters, coming from four different markers, i.e., an intron of the nuclear gene coding for the protein kinase C iota, and three mitochondrial genes (subunit II of the cytochrome c oxidase, cytochrome b, and 12S rRNA). The results show that the genus Hemitragus is polyphyletic, as H. jemlahicus is associated with Capra (goats), H. hylocrius is the sister-group of Ovis (sheep), and H. jayakari is allied with Ammotragus lervia (aoudad). In the light of these unexpected results, we revaluate the validity of the morphological characters originally used for defining the genus Hemitragus. At least, we propose a new taxonomy, where the three species of tahr are ranged into three monospecific genera: the genus Hemitragus is restricted to the Himalayan tahr, and two new genera are created: Arabitragus for the Arabian tahr and Nilgiritragus for the Nilgiri tahr.

The kouprey is a very rare bovid species of the Indochinese peninsula, and no living specimen has been described for a long time, suggesting that it is possibly extinct. Its systematic position within the tribe Bovini remains confused since the analyses of morphological characters have led to several conflicting hypotheses. Some authors have also suggested that it could be a hybrid species produced by the crossing of the banteng with gaur, zebu, or water buffalo. Here we performed a molecular phylogeny of the tribe Bovini to determine the taxonomic status of the kouprey. DNA was extracted from the holotype specimen preserved in the MNHN collections. Phylogenetic analyses were carried out on a matrix including all the taxonomic diversity described in the tribe Bovini, and 2065 nucleotide characters, representing three different markers, i.e., the promotor of the lactoferrin and two mitochondrial genes (cytochrome b and subunit II of the cytochrome c oxidase). The results show that the kouprey belongs to the subtribe Bovina, and that three different clades can be evidenced into this group: the first includes the domestic ox, zebu, and European bison; the second incorporates the yak and American bison; and the third contains the kouprey, banteng and gaur. All hypotheses involving hybridization for the origin of the kouprey can be rejected, confirming that it is a real wild species. Molecular datings and biogeographic inferences suggest that the kouprey diverged from banteng and gaur during the Plio-Pleistocene of Asia. In addition, several molecular signatures were detected in the cytochrome b gene, permitting a molecular identification of the kouprey. We propose a conservation project based on a molecular taxonomy approach for tracking the kouprey in Indochina in order to determine whether some populations still survive in the wild.