Global phylogeography of the genus Capreolus (Artiodactyla: Cervidae), a Palaearctic meso-mammal.

Zoological Journal of the Linnean Society, 2013. 13 Seiten, 3 Abb., DOI: 10.1111/zoj.12091.

Abstract:

Areas of sympatry and hybridization of closely related species can be difficult to assess through morphological differences alone. Species which coexist and are similar morphologically may be distinguished only with molecular techniques. The roe deer (Capreolus spp.) is a meso-mammal having a Palaearctic distribution, with two closely related species: the European C. capreolus and the Siberian C. pygargus. We analysed mtDNA sequences from 245 individuals, sampled through all the entire range of the genus, to investigate the distribution of genetic lineages and outline phylogeographical patterns. We found that: (1) a C. pygargus lineage occurs in Poland and Lithuania, much farther west than the area which so far was believed its westernmost limit; (2) no haplotype of this C. pygargus lineage matches any found in East Europe and Asia – this should rule out human introductions and may indicate Pleistocene–Holocene migrations from the east; (3) no geographical structuring of C. pygargus lineages occurs, questioning the existence of putative subspecies; (4) several genetic lineages of C. capreolus can be recognized, consistent with the existence of two subspecies, respectively in central–southern Italy and southern Spain. Coalescence times suggest that intraspecific variation in C. capreolus and C. pygargus developed approximately 100–10 kya. The extant mitochondrial lineages pre-dated the Last Glacial Maximum. Capreolus pygargus must have moved westward to Central Europe, where at least one genetic lineage still survives, coexisting with C. capreolus.

lorenzini-biblio

Ancient origin and evolution of the Indian wolf: Evidence from mitochondrial DNA typing of wolves from Trans-Himalayan region and Peninsular India.

Genome Biology 4(6). DOI:10.1186/gb-2003-4-6-p6

Abstract:

The two wolf types found in India are represented by two isolated populations and believed to be two sub-species of Canis lupus. One of these wolf, locally called Himalayan wolf (HW) or Tibetan wolf, is found only in the upper Trans-Himalayan region from Himachal Pradesh to Leh in Kasmir and is considered to be C. lupus chanco. The other relatively larger population is of Indian Gray wolf (GW) that is found in the peninsular India and considered to be C. lupus pallipes. Both these wolves are accorded endangered species status under the Indian Wildlife Protection Act. In 1998 for the first time in India, we initiated molecular characterization studies to understand their genetic structure and taxonomic status. Since then, we have analyzed the genetic variability in 18 of the total of 21 HW samples available in Zoological parks along with representative samples of GW, wild dogs and jackals. Our study of mitochondrial DNA diversity across three different taxonomically informative domains i.e., cytochrome-B gene, 16S rDNA and hypervariable d-loop control region revealed HW to be genetically distinct from the GW as well as from all other wolves of the world, including C. lupus chanco from China. Most importantly, d-loop haplotypic diversity revealed both HW and GW from India to be significantly diverse from other wolf populations globally and showed that these represent the most ancient lineages among them. Phylogenetic analysis revealed the Indian wolves as two independent lineages in a clade distinct and basal to the clade of all wolves from outside of India. Conservative estimate of evolutionary time-span suggests more than one million years of separation and independent evolution of HW and GW. We hypothesize that Indian wolves represent a post-jackal pre-wolf ancestral radiation that migrated to India about 1-2 mya and underwent independent evolution without contamination from other wolf like canids. The study thus, suggests that Indian subcontinent had been one major center of origin and diversification of the wolf and related canids. Further, the significant degree of genetic differentiation of HW from GW and of these two from other wolves, suggest the interesting possibility of them to be new wolf species/subspecies in evolution that may need to be described possibly as C. himalayaensis and C. indica (or as C. lupus himalyaensis and C. lupus indica), respectively. Thus for the first time, the study reveals new ancient wolf lineages in India and also highlights the need to revisit the origin, evolution and dispersion of wolf populations in Asia and elsewhere. Simultaneously, it increases the conservation importance of Indian wolves warranting urgent measures for their effective protection and management, especially of the small HW population that at present is not even recognized in the canid Red List.

aggarwal-biblio

Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo).

Sci Rep 6, 30807 (2016). https://doi.org/10.1038/srep30807

Abstract:

Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.

bertola-biblio

Phylogenetic relationships of Mesoamerican spider monkeys (Ateles geoffroyi): Molecular evidence suggests the need for a revised taxonomy.

Molecular Phylogenetics and Evolution 82: 484-494.

Abstract:

Mesoamerican spider monkeys (Ateles geoffroyi sensu lato) are widely distributed from Mexico to northern Colombia. This group of primates includes many allopatric forms with morphologically distinct pelage color and patterning, but its taxonomy and phylogenetic history are poorly understood. We explored the genetic relationships among the different forms of Mesoamerican spider monkeys using mtDNA sequence data, and we offer a new hypothesis for the evolutionary history of the group. We collected up to ~800 bp of DNA sequence data from hypervariable region 1 (HV1) of the control region, or D-loop, of the mitochondrion for multiple putative subspecies of Ateles geoffroyi sensu lato. Both maximum likelihood and Bayesian reconstructions, using Ateles paniscus as an outgroup, showed that (1) A. fusciceps and A. geoffroyi form two different monophyletic groups and (2) currently recognized subspecies of A. geoffroyi are not monophyletic. Within A. geoffroyi, our phylogenetic analysis revealed little concordance between any of the classifications proposed for this taxon and their phylogenetic relationships, therefore a new classification is needed for this group. Several possible clades with recent divergence times (1.7–0.8 Ma) were identified within Ateles geoffroyi sensu lato. Some previously recognized taxa were not separated by our data (e.g., A. g. vellerosus and A. g. yucatanensis), while one distinct clade had never been described as a different evolutionary unit based on pelage or geography (Ateles geoffroyi ssp. indet. from El Salvador). Based on well-supported phylogenetic relationships, our results challenge previous taxonomic arrangements for Mesoamerican spider monkeys. We suggest a revised arrangement based on our data and call for a thorough taxonomic revision of this group.

morales-biblio

Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)

Zootaxa 4455 (1): 068–098.  http://www.mapress.com/j/zt/. ISSN1175-5334(online edition).

Abstract:

Cobras are among the most widely known venomous snakes, and yet their taxonomy remains incompletely understood, particularly in Africa. Here, we use a combination of mitochondrial and nuclear gene sequences and morphological data to diagnose species limits within the African forest cobra, Naja (Boulengerina) melanoleuca. Mitochondrial DNA sequences reveal deep divergences within this taxon. Congruent patterns of variation in mtDNA, nuclear genes and mor-phology support the recognition of five separate species, confirming the species status of N. subfulva and N. peroescobari, and revealing two previously unnamed West African species, which are described as new: Naja (Boulengerina) guineensis sp. nov. Broadley, Trape, Chirio, Ineich & Wüster, from the Upper Guinea forest of West Africa, and Naja (Boulengerina) savannula sp. nov. Broadley, Trape, Chirio & Wüster, a banded form from the savanna-forest mosaic of the Guinea and Sudanian savannas of West Africa. The discovery of cryptic diversity in this iconic group highlights our limited under-standing of tropical African biodiversity, hindering our ability to conserve it effectively.

wüster-biblio

The Genetic Integrity of the Ex Situ Population of the European Wildcat (Felis silvestris silvestris) Is Seriously Threatened by Introgression from Domestic Cats (Felis silvestris catus).

PLoS ONE 9(8): e106083. https://doi.org/10.1371/journal.pone.0106083

Abstract:

Studies on the genetic diversity and relatedness of zoo populations are crucial for implementing successful breeding programmes. The European wildcat, Felis s. silvestris, is subject to intensive conservation measures, including captive breeding and reintroduction. We here present the first systematic genetic analysis of the captive population of Felis s. silvestris in comparison with a natural wild population. We used microsatellites and mtDNA sequencing to assess genetic diversity, structure and integrity of the ex situ population. Our results show that the ex situ population of the European wildcat is highly structured and that it has a higher genetic diversity than the studied wild population. Some genetic clusters matched the breeding lines of certain zoos or groups of zoos that often exchanged individuals. Two mitochondrial haplotype groups were detected in the in situ populations, one of which was closely related to the most common haplotype found in domestic cats, suggesting past introgression in the wild. Although native haplotypes were also found in the captive population, the majority (68%) of captive individuals shared a common mtDNA haplotype with the domestic cat (Felis s. catus). Only six captive individuals (7.7%) were assigned as wildcats in the STRUCTURE analysis (at K = 2), two of which had domestic cat mtDNA haplotypes and only two captive individuals were assigned as purebred wildcats by NewHybrids. These results suggest that the high genetic diversity of the captive population has been caused by admixture with domestic cats. Therefore, the captive population cannot be recommended for further breeding and reintroduction.

witzenberger-biblio

Multi-locus analyses reveal four giraffe species instead of one.

Current Biology 26 (18): 2543-2549.

DOI: https://doi.org/10.1016/j.cub.2016.07.036

Summary:

Traditionally, one giraffe species and up to eleven subspecies have been recognized; however, nine subspecies are commonly accepted. Even after a century of research, the distinctness of each giraffe subspecies remains unclear, and the genetic variation across their distribution range has been incompletely explored. Recent genetic studies on mtDNA have shown reciprocal monophyly of the matrilines among seven of the nine assumed subspecies. Moreover, until now, genetic analyses have not been applied to biparentally inherited sequence data and did not include data from all nine giraffe subspecies. We sampled natural giraffe populations from across their range in Africa, and for the first time individuals from the nominate subspecies, the Nubian giraffe, Giraffa camelopardalis camelopardalis Linnaeus 1758 , were included in a genetic analysis. Coalescence-based multi-locus and population genetic analyses identify at least four separate and monophyletic clades, which should be recognized as four distinct giraffe species under the genetic isolation criterion. Analyses of 190 individuals from maternal and biparental markers support these findings and further suggest subsuming Rothschild’s giraffe into the Nubian giraffe, as well as Thornicroft’s giraffe into the Masai giraffe . A giraffe survey genome produced valuable data from microsatellites, mobile genetic elements, and accurate divergence time estimates. Our findings provide the most inclusive analysis of giraffe relationships to date and show that their genetic complexity has been underestimated, highlighting the need for greater conservation efforts for the world’s tallest mammal.

fennessy-biblio

First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens.

European Journal of Taxonomy 703: 1–33. ISSN 2118-9773. https://doi.org/10.5852/ejt.2020.703

Volltext (PDF)

Abstract:

Intensified exploration of sub-Saharan Africa during the 18th and 19th centuries led to many newly described giraffe subspecies. Several populations described at that time are now extinct, which is problematic for a full understanding of giraffe taxonomy. In this study, we provide mitochondrial sequences for 41 giraffes, including 19 museum specimens of high importance to resolve giraffe taxonomy, such as Zarafa from Sennar and two giraffes from Abyssinia (subspecies camelopardalis), three of the first southern individuals collected by Levaillant and Delalande (subspecies capensis), topotypes of the former subspecies congoensis and cottoni, and giraffes from an extinct population in Senegal. Our phylogeographic analysis shows that no representative of the nominate subspecies camelopardalis was included in previous molecular studies, as Zarafa and two other specimens assigned to this taxon are characterized by a divergent haplogroup, that the former subspecies congoensis and cottoni should be treated as synonyms of antiquorum, and that the subspecies angolensis and capensis should be synonymized with giraffa, whereas the subspecies wardi should be rehabilitated. In addition, we found evidence for the existence of a previously unknown subspecies from Senegal (newly described in this study), which is now extinct. Based on these results, we propose a new classification of giraffes recognizing three species and 10 subspecies. According to our molecular dating estimates, the divergence among these taxa has been promoted by Pleistocene climatic changes resulting in either savannah expansion or the development of hydrographical networks (Zambezi, Nile, Lake Chad, Lake Victoria).

petzold-biblio

A preliminary analysis of phylogenetic relationships and biogeography of the dangerously venomous Carpet Vipers, Echis (Squamata, Serpentes, Viperidae) based on mitochondrial DNA sequences.

Amphibia-Reptilia 30(2):273-282. DOI: 10.1163/156853809788201090.

Abstract:

Phylogenetic analysis of 1117 bp of mitochondrial DNA sequences (731 bp of cytochrome b and 386 bp of 16S rRNA) indicate that Echis consists of four main clades: E. ocellatus, and the E. coloratus, E. pyramidum, and E. carinatus groups. In the E. coloratus group, E. coloratus itself shows substantial genetic divergence from E. omanensis, corroborating their separate species status. In the E. pyramidum clade, E. pyramidum from Egypt and E. leucogaster from West Africa are genetically very similar, even though samples are separated by 4000 km. South Arabian populations of the E. pyramidum group are much better differentiated from these and two species may be present, animals from Dhofar, southern Oman probably being referable to E. khosatzkii. In the E. carinatus group, specimens of E. carinatus sochureki and E. multisquamatus are very similar in their DNA. The phylogeny indicates that the split between the main groups of Echis was followed by separation of African and Arabian members of the E. pyramidum group, and of E. coloratus and E. omanensis. The last disjunction probably took place at the lowlands that run southwest of the North Oman mountains, which are likely to have been intermittently covered by marine incursions; they also separate the E. pyramidum and E. carinatus groups and several sister taxa of other reptiles. The E. carinatus group may have spread quite recently from North Oman into its very extensive southwest Asian range, and there appears to have been similar expansion of E. pyramidum (including E. leucogaster) in North Africa. Both these events are likely to be associated with the marked climatic changes of the Pleistocene or late Pliocene. Similar dramatic expansions have also recently occurred in three snake species in Iberia.

arnold-biblio

Molecular diversity and phylogenetic analysis of domestic and wild Bactrian camel populations based on the mitochondrial ATP8 and ATP6 genes.

Livestock Science 199 (May 2017): 95-100.

Highlights:

• We analyzed the diversity of mitochondrial ATP8/6 gene in Bactrian camel populations.
• All domestic Bactrian camel populations were clustered as a single major group in the haplotype network.
• A single haplotype was identified in the wild Bactrian camel population, which formed a separate branch.
• The phylogenetic tree showed the same patterns as the haplotype network.
• Wild and domestic Bactrian camels evolved from two distinct ancestors.

yi-biblio