A Phylogenetic Foundation for Comparative Mammalian Genomics. 

Genome Informatics 12: 141–154.

Abstract: 

A major effort is being undertaken to sequence an array of mammalian genomes. Coincidentally, the evolutionary relationships of the 18 presently recognized orders of placental mammals are only just being resolved. In this work we construct and analyse the largest alignments of amino acid sequence data to date. Our findings allow us to set up a series of superordinal groups (clades) to act as prior hypotheses for further testing. Important findings include strong evidence for a clade of Euarchonta+ Glires (=Supraprimates) comprised of primates, flying lemurs, tree shrews, lagomorphs and rodents. In addition, there is good evidence for a clade of all placental mammals except Xenarthra and Afrotheria (=Boreotheria) and for the previously recognised clades Laurasiatheria, Scrotifera, Fereuungulata, Ferae, Afrotheria, Euarchonta, Glires, and Eulipotyphla. Accordingly, a revised classification of the placental mammals is put forward. Using this and molecular divergence-time methods, the ages of the superordinal splits are estimated. While results are strongly consistent with the earliest superordinal divergences all being > 65 mybp (Cretaceous period), they suffer from greater uncertainty than presently appreciated. The early primate split of tarsiers from the anthropoid lineage at ∼55 mybp is seen to be an especially informative fossil calibration point. A statistical framework for testing clades using SINE data is presented and reveals significant support for the tarsier/anthropoid clade, as well as the clades Cetruminantia and Whippomorpha. Results also underline our thesis that while sequence analysis can help set up hypothesised clades, SINEs obtainable from sequencing 1-2 MB regions of placental genomes are essential to testing them. In contrast, derivations suggest that empirical Bayesian methods for sequence data may not be robust estimators of clades. Our findings, including the study of genes such as TP53, make a good case for the tree shrew as a closer relative of primates than rodents, while also showing a slower rate of evolution in key cell cycle genes. Tree shrews are consequently high value experimental animals and a strong candidate for a genome sequencing initiative.

The Phylogenetic Position of the Talpidae Within Eutheria Based on Analysis of Complete Mitochondrial Sequences. 

Molecular Biology and Evolution. 17 (1): 60–67.
ISSN 0737-4038.

Abstract:

The complete mitochondrial (mt) genome of the mole Talpa europaea was sequenced and included in phylogenetic analyses together with another lipotyphlan (insectivore) species, the hedgehog Erinaceus europaeus, and 22 other eutherian species plus three outgroup taxa (two marsupials and a monotreme). The phylogenetic analyses reconstructed a sister group relationship between the mole and the fruit bat Artibeus jamaicensis (order Chiroptera). The Talpa/Artibeus clade constitutes a sister clade of the cetferungulates, a clade including Cetacea, Artiodactyla, Perissodactyla, and Carnivora. A monophyletic relationship between the hedgehog and the mole was significantly rejected by maximum parsimony and maximum likelihood. Consistent with current systematic schemes, analyses of complete cytochrome b genes including the shrew Sorex araneus (family Soricidae) revealed a close relationship between Talpidae and Soricidae. The analyses of complete mtDNAs, along with the findings of other insectivore studies, challenge the maintenance of the order Lipotyphla as a taxonomic unit and support the elevation of the Soricomorpha (with the families Talpidae and Soricidae and possibly also the Solenodontidae and Tenrecidae) to the level of an order, as previously proposed in some morphological studies.

Molecular and Genomic Data Identify the Closest Living Relative of Primates. 

Science  (02 Nov 2007) 318 (5851): 792-794.
DOI: 10.1126/science.1147555.

Abstract:

A full understanding of primate morphological and genomic evolution requires the identification of their closest living relative. In order to resolve the ancestral relationships among primates and their closest relatives, we searched multispecies genome alignments for phylogenetically informative rare genomic changes within the superordinal group Euarchonta, which includes the orders Primates, Dermoptera (colugos), and Scandentia (treeshrews). We also constructed phylogenetic trees from 14 kilobases of nuclear genes for representatives from most major primate lineages, both extant colugos, and multiple treeshrews, including the pentail treeshrew, Ptilocercus lowii, the only living member of the family Ptilocercidae. A relaxed molecular clock analysis including Ptilocercus suggests that treeshrews arose approximately 63 million years ago. Our data show that colugos are the closest living relatives of primates and indicate that their divergence occurred in the Cretaceous.

Phylogenetic relationships and biogeographical history of the genus Rhinoclemmys Fitzinger, 1835, and the monophyly of the turtle family Geoemydidae (Testudines: Testudinoidea).

Zoological Journal of the Linnean Society 153: 751-767.

Abstract:

Rhinoclemmys is an interesting genus of rtutles biogeographically and ecologically, being the only genus of the family Geoemydidae that occurs in the New Wc orld and inhabiting a wide range of habitats from aquatic to highly terrestrial. Here we present a molecular phylogeny of Rhinoclemmys using both mitochondrial and nuclear genes. Our results strongly support the monophyletiand subfamilial status of Rhinoclemmys within the monophyletic family Geoemydidae. Within RhinoclemR. areolata + R. punctularia  + R. diademata + R. funerea + R. melanosterna, but the positions of R. nasuta and R. rubida are still weakly supported. In terms of the biogeographical history, the results of this study, coupled withmys, two clades are strongly supported, i.e. R. annulata + R. pulcherrima and palaeontological evidence, corroborate the hypothesis that this group migrated from Asia to the Americas across the Bering Strait during the early Eocene. The radiation of Rhinoclemmys in Central and South America corresponds well with vicariance events, including the emergence of the Sierra Madres of Mexico and the Nuclear Highland, and dispersals across the Panama land bridge. Interestingly, our resulting phylogeny suggests this group invaded South America at least four times and that dispersal of R. nasuta to South America probably took place in the early Miocene before the emergence of the Isthmus of Panama. We finally discuss our phylogenetic results with regard to the monophyly of the family Geoemydidae and in the context of previous morphological analyses.

Molecular phylogeny and historical biogeography of West Indian boid snakes (Chilabothrus).

Molecular Phylogenetics and Evolution Volume 68 (3): 461–470.

Abstract:

The evolutionary and biogeographic history of West Indian boid snakes (Epicrates), a group of nine species and 14 subspecies, was once thought to be well understood; however, new research has indicated that we are missing a clear understanding of the evolutionary relationships of this group. Here, we present the first multilocus, species-tree based analyses of the evolutionary relationships, divergence times, and historical biogeography of this clade with data from 10 genes and 6256 bp. We find evidence for a single colonization of the Caribbean from mainland South America in the Oligocene or early Miocene, followed by a radiation throughout the Greater Antilles and Bahamas. These findings support the previous suggestion that Epicrates sensu lato Wagler is paraphyletic with respect to the anacondas (Eunectes Wagler), and hence we restrict Epicrates to the mainland clade and use the available name Chilabothrus Duméril and Bibron for the West Indian clade. Our results suggest some diversification occurred within island banks, though most species divergence events seem to have occurred in allopatry. We also find evidence for a remarkable diversification within the Bahamian archipelago suggesting that the recognition of another Bahamian endemic species C. strigilatus is warranted.

reynolds-biblio

Genetic differentiation between Príncipe Island and mainland populations of the grey parrot (Psittacus erithacus), and implications for conservation.

Mol Ecol. 2007 Apr;16(8):1673-85.

Abstract:

The range of the grey parrot (Psittacus erithacus), one of the most heavily harvested bird species for the international pet trade, spans the forest belt of Central and West Africa and includes the oceanic island of Príncipe (Gulf of Guinea). Morphological variation led to the recognition of two mainland subspecies (P. e. erithacus and P. e. timneh). The population from Príncipe was originally described as a separate species (P. princeps) but is currently included in the nominate race. We used 1932 bp of the mitochondrial genome to clarify the genealogical affinities between the two currently-recognized mainland subspecies and the Príncipe population. Sampling included 20 individuals from Príncipe, 17 from P. e. erithacus, and 13 from P. e. timneh. We found that the two mainland subspecies form two independent lineages, having diverged up to 2.4 million years ago (Ma), and that the Príncipe population is composed of two lineages that diverged in allopatry. The most common lineage is descended from the first colonizers and evolved in isolation for up to 1.4 Ma. Contrary to current understanding, this 'Príncipe lineage' is more closely related to the timneh than to the erithacus subspecies. The second lineage consists of P. e. erithacus birds from the nearby mainland that colonized the island in recent times. The evolutionary dynamics of the grey parrot population of Príncipe are primarily characterized by isolation, with new genetic variation being added through rare immigration events. The heavily harvested Príncipe grey parrot population should therefore be treated as an independent conservation unit.

melo-biblio

Evolutionary history and conservation significance of the Javan leopard Panthera pardus melas.

Journal of Zoology. Version of Record online: 3 MAY 2016 | DOI: 10.1111/jzo.12348 (zu diesem Zeitpunkt gedruckte Version noch nicht verfügbar)

Abstract:

The leopard Panthera pardus is widely distributed across Africa and Asia; however, there is a gap in its natural distribution in Southeast Asia, where it occurs on the mainland and on Java but not on the interjacent island of Sumatra. Several scenarios have been proposed to explain this distribution gap. Here, we complemented an existing dataset of 68 leopard mtDNA sequences from Africa and Asia with mtDNA sequences (NADH5 +  ctrl, 724 bp) from 19 Javan leopards, and hindcasted leopard distribution to the Pleistocene to gain further insights into the evolutionary history of the Javan leopard. Our data confirmed that Javan leopards are evolutionarily distinct from other Asian leopards, and that they have been present on Java since the Middle Pleistocene. Species distribution projections suggest that Java was likely colonized via a Malaya-Java land bridge that by-passed Sumatra, as suitable conditions for leopards during Pleistocene glacial periods were restricted to northern and western Sumatra. As fossil evidence supports the presence of leopards on Sumatra at the beginning of the Late Pleistocene, our projections are consistent with a scenario involving the extinction of leopards on Sumatra as a consequence of the Toba super volcanic eruption (~74 kya). The impact of this eruption was minor on Java, suggesting that leopards managed to survive here. Currently, only a few hundred leopards still live in the wild and only about 50 are managed in captivity. Therefore, this unique and distinctive subspecies requires urgent, concerted conservation efforts, integrating in situ and ex situ conservation management activities in a One Plan Approach to species conservation management.

wilting-biblio

Molekularbiologische Untersuchungen zur Phylogenie der Hornvögel (Aves: Bucerotiformes).

Diplomarbeit

ca. 57 Seiten

Fachbereich Biologie, Johann Wolfgang Goethe-Universität Frankfurt am Main
Betreuung:
Zoo Heidelberg

Zusammenfassung: siehe hier

hübner-biblio

A molecular phylogeny of the African plated lizards, genus Gerrhosaurus Wiegmann, 1828 (Squamata: Gerrhosauridae), with the description of two new genera.

Zootaxa 3750 (5): 465–493. DOI: http://dx.doi.org/10.11646/zootaxa.3750.5.3   

Abstract:

We constructed a molecular phylogeny of the African plated lizard family Gerrhosauridae using two mitochondrial markers (ND2, 732 bp; 16S, 576 bp) and one nuclear marker (PRLR, 538 bp). This analysis showed that the subfamily Gerrhosaurinae consists of five major clades which we interpret as representing five genera. The genera Tetradactylus and Cordylosaurus were each recovered as monophyletic, but Gerrhosaurus as currently conceived is paraphyletic, consisting of three distinct genus-level assemblages. The two clades consisting of Gerrhosaurus major Duméril, 1851 and Gerrhosaurus validus Smith, 1849 are both described here as new genera, namely Broadleysaurus Bates & Tolley gen. nov. and Matobosaurus Bates & Tolley gen. nov., respectively. Two subspecies of ‘Gerrhosaurus major’ that were historically separated on the basis of differences in colour pattern are not reciprocally monophyletic, so Gerrhosaurus bottegoi Del Prato, 1895 is relegated to the synonomy of Broadleysaurus major (Duméril, 1851) comb. nov., which is rendered monotypic. Gerrhosaurus validus maltzahni De Grys, 1938 is genetically and morphologically well differentiated from G. v. validus and the two taxa also occur in allopatry. We therefore re-instate the former as Matobosaurus maltzahni (De Grys, 1938) comb. nov., rendering Matobosaurus validus (Smith, 1849) comb. nov. a monotypic species. Our analysis also showed that Gerrhosaurus sensu stricto comprises two major subclades, one consisting of Gerrhosaurus typicus (Smith, 1837) + Gerrhosaurus skoogi Andersson, 1916, and the other containing the remaining species. In this latter subclade we show that west-Central African Gerrhosaurus nigrolineatus Hallowell, 1857 is most closely related to Gerrhosaurus auritus Boettger, 1887 rather than to G. nigrolineatus from East and Southern Africa. The west-Central African clade of G. nigrolineatus differs from the East and Southern African clade by a p-distance of 13.0% (ND2) and 6.9% (16S), and can be differentiated morphologically. We accordingly apply the name Gerrhosaurus intermedius Lönnberg, 1907 comb. nov. to populations from Kenya, Uganda, Rwanda, Tanzania, Malawi, Mozambique, Zimbabwe and South Africa previously identified under the name G. nigrolineatus. Our analysis also confirms that Gerrhosaurus bulsi Laurent, 1954 is a distinct species and sister taxon to a clade containing G. nigrolineatus, G. auritus and G. intermedius. The latter four taxa form a closely-related ‘G. nigrolineatus species complex’ with a widespread distribution in Africa. Most closely related to this complex of species is Gerrhosaurus flavigularis Wiegmann, 1828 which has an extensive range in East and Southern Africa, and displays genetic substructure which requires further investigation. The status of Gerrhosaurus multilineatus Bocage, 1866, and Angolan populations referred to G. nigrolineatus, remains problematic.

bates-biblio