Natural genetic polymorphism and phylogeography of Siberian sturgeon Acipenser baerii Brandt, 1869.
Russ. J. Genet. 53: 358–368. https://doi.org/10.1134/S1022795417030024
Five populations of Siberian sturgeon Acipenser baerii collected throughout the species distribution range (Lake Baikal, Lena, Yenisei, Kolyma, and Irtysh rivers) were examined for genetic polymorphism using five tetraploid microsatellite loci and the mitochondrial DNA control region. It was demonstrated that Siberian sturgeon was represented by genetically well-differentiated groups that corresponded to hydrographic basins, Ob–Irtysh, Baikal–Yenisei, Lena, and Kolyma. Population assignment of the Siberian sturgeon broodstock should be considered in the restocking programs.
Improved systematics of lorikeets reflects their evolutionary history and frames conservation priorities.
Emu - Austral Ornithology 120 (3): 201–215. doi:10.1080/01584197.2020.1779596. S2CID 222094508.
A well-supported genus-level classification of any group of organisms underpins downstream understanding of its evolutionary biology and enhances the role of phylogenetic diversity in guiding its conservation and management. The lorikeets (Psittaciformes: Loriini) are parrots for which genus-level systematics (phylogenetic relationships and classification) has long been unstable and unsatisfactory. Instability has manifested through frequently changing compositions of some genera (e.g. Trichoglossus and Psitteuteles). Other genera (e.g. Charmosyna, Vini) have become so large that their phenotypic heterogeneity alone at least questions whether they are monophyletic assemblages that genera should comprise. Recent molecular phylogenetic and phenotypic studies have improved the framework with which to rationalise genus-level systematics in lorikeets but some trenchant uncertainty has remained. Here we utilise published genomic data and tetrahedral analysis of plumage colour to develop a full review of the genus-level classification of lorikeets. Using existing phylogenetic relationships and a newly estimated time-calibrated tree for lorikeets, we show where paraphyletic assemblages have misled the classification of genera. We assign six species to three new genera and six other species to four previously described generic names that have been in synonymy in recent literature. Our taxonomic revision brings a new perspective informing and guiding the conservation and management of the lorikeets and their evolutionary biology.
A molecular phylogeny of the Australian monitor lizards (Squamata:Varanidae) inferred from mitochondrial DNA sequences.
Australian Journal of Zoology. 54: 253–269.
To date no complete phylogeny of all of the currently recognised Indo-Australian varanid species and subspecies has been published. This paper presents a comprehensive mitochondrial gene phylogeny of these lizards. A portion of the mitochondrial genome comprising part of the ND4 gene and three adjacent tRNA genes (hereafter referred to as ND4) was analysed alone and, for a subset of the taxa, combined with previously published mitochondrial data. Similar tree topologies were produced by both datasets although combining the data helped resolve some of the unresolved or weakly supported nodes in the ND4 analyses. The monophyly of the Indo-Australian group was strongly supported in all analyses. This group comprised three major lineages: the gouldii group, the Odatria group and the varius group. Mitochondrial ND4 nucleotide sequences were successfully amplified from all of the Indo-Australian monitor species and subspecies currently recognised and, as such, is the first comprehensive phylogenetic study of the Australian monitor lizards published. Analysis of the tempo of diversification and evolution of preferred habitat use identified six episodes of increased net speciation rate, with two closely adjacent episodes showing the highest rates of diversification and correlating with the appearance of all preferred habitat types. The comprehensive molecular phylogenetic framework will also be useful for the identification of varanid species and traded products derived from monitors and, as such, has important applications for wildlife management and conservation.
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.
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.
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
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.
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
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.
Phylogenetic relationships of Mesoamerican spider monkeys (Ateles geoffroyi): Molecular evidence suggests the need for a revised taxonomy.
Molecular Phylogenetics and Evolution 82: 484-494.
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.
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).
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.
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
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.
Multi-locus analyses reveal four giraffe species instead of one.
Current Biology 26 (18): 2543-2549.
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.