Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences.

Mol. Biol. Evol. (1997) 14 (5): 550-559.
DOI: https://doi.org/10.1093/oxfordjournals.molbev.a025792.

Abstract:

A data set of complete mitochondrial cytochrome b and 12S rDNA sequences is presented here for 17 representatives of Artiodactyla and Cetacea, together with potential outgroups (two Perissodactyla, two Carnivora, two Tethytheria, four Rodentia, and two Marsupialia). We include seven sequences not previously published from Hippopotamidae (Ancodonta) and Camelidae (Tylopoda), yielding a total of nearly 2.1 kb for both genes combined. Distance and parsimony analyses of each gene indicate that 11 clades are well supported, including the artiodactyl taxa Pecora, Ruminantia (with low 12S rRNA support), Tylopoda, Suina, and Ancodonta, as well as Cetacea, Perissodactyla, Carnivora, Tethytheria, Muridae, and Caviomorpha. Neither the cytochrome b nor the 12S rDNA genes resolve the relationships between these major clades. The combined analysis of the two genes suggests a monophyletic Cetacea +Artiodactyla clade (defined as "Cetartiodactyla"), whereas Perissodactyla, Carnivora, and Tethytheria fall outside this clade. Perissodactyla could represent the sister taxon of Cetartiodactyla, as deduced from resampling studies among outgroup lineages. Cetartiodactyla includes five major lineages: Ruminantia, Tylopoda, Suina, Ancodonta, and Cetacea, among which the phylogenetic relationships are not resolved. Thus, Suiformes do not appear to be monophyletic, justifying their split into the Suina and Ancodonta infraorders. An association between Cetacea and Hippopotamidae is supported by the cytochrome b gene but not by the 12S rRNA gene. Calculation of divergence dates suggests that the Cetartiodactyla could have diverged from other Ferungulata about 60 MYA.

Freigegeben in M

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.

Freigegeben in J
Freitag, 24 Februar 2017 10:17

GRAUR, D., GOUY, M. & DURET, L. (1997)

Evolutionary Affinities of the Order Perissodactyla and the Phylogenetic Status of the Superordinal Taxa Ungulata and Altungulata. 

Molecular Phylogenetics and Evolution 7 (2): 195-200.  April 1997.
http://dx.doi.org/10.1006/mpev.1996.0391

Abstract: 

Contrary to morphological claims, molecular data indicate that the order Perissodactyla (e.g., horses, rhinoceroses, and tapirs) is neither part of the superordinal taxon Paenungulata (Sirenia, Proboscidea, and Hyracoidea) nor an immediate outgroup of the paenungulates. Rather, Perissodactyla is closer to Carnivora and Cetartiodactyla (Cetacea + Artiodactyla) than it is to the paenungulates. Therefore, two morphologically defined superordinal taxa, Altungulata (Proboscidea, Sirenia, Hyracoidea, and Perissodactyla) and Ungulata (Altungulata and Cetartiodactyla), are invalidated. Perissodactyla, Carnivora, and Cetartiodactyla are shown to constitute a rather tight trichotomy. However, a molecular analysis of 36 protein sequences with a total concatenated length of 7885 aligned amino acids indicates that Perissodactyla is closer to Cetartiodactyla than either taxa is to Carnivora. The relationships among Paenungulata, Primates, and the clade consisting of Perissodactyla, Carnivora, and Cetartiodactylaa could not be resolved on the basis of the available data.

Freigegeben in G

Multiple Loci and Complete Taxonomic Sampling Resolve the Phylogeny and Biogeographic History of Tenrecs (Mammalia: Tenrecidae) and Reveal Higher Speciation Rates in Madagascar's Humid Forests.

Syst Biol (2016) 65 (5): 890-909. DOI: https://doi.org/10.1093/sysbio/syw034. Published: 21 April 2016

Abstract:

The family Tenrecidae (tenrecs) is one of only four extant terrestrial mammal lineages to have colonized and diversified on Madagascar. Over the last 15 years, several studies have disagreed on relationships among major tenrec lineages, resulting in multiple reinterpretations of the number and timing of historical transoceanic dispersal events between Africa and Madagascar. We reconstructed the phylogeny of Tenrecidae using multiple loci from all recognized extant species and estimated divergence timing using six fossil calibrations within Afrotheria. All phylogenetic analyses strongly support monophyly of the Malagasy tenrecs, and our divergence timing analysis places their colonization of the island at 30–56 Ma. Our comprehensive phylogeny supports three important taxonomic revisions that reflect the evolutionary history of tenrecs: (1) we formally elevate the African otter shrews to their own family Potamogalidae, thereby rendering extant Tenrecidae entirely endemic to Madagascar; (2) we subsume the semiaquatic genus Limnogale within the shrew tenrec genus Microgale ; and (3) we re-elevate the two largest-bodied shrew tenrecs, Microgale dobsoni and Microgale talazaci , to the genus NesogaleThomas (1918) . Finally, we use recently summarized habitat data to test the hypothesis that diversification rates differ between humid and arid habitats on Madagascar, and we compare three common methods for ancestral biogeographic reconstruction. These analyses suggest higher speciation rates in humid habitats and reveal a minimum of three and more likely five independent transitions to arid habitats. Our results resolve the relationships among previously recalcitrant taxa, illuminate the timing and mechanisms of major biogeographic patterns in an extraordinary example of an island radiation, and permit the first comprehensive, phylogenetically consistent taxonomy of Madagascar's tenrecs

Freigegeben in E

Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia).

Biol. Rev. (1999) 74: 143-175.

Abstract:

One way to build larger, more comprehensive phylogenies is to combine the vast amount of phylogenetic information already available. We review the two main strategies for accomplishing this (combining raw data versus combining trees), but employ a relatively new variant of the latter : supertree construction. The utility of one supertree technique, matrix representation using parsimony analysis (MRP), is demonstrated by deriving a complete phylogeny for all 271 extant species of the Carnivora from 177 literature sources.

Beyond providing a "consensus" estimate of carnivore phylogeny, the tree also indicates taxa for which the relationships remain controversial (e.g. the red panda; within canids, felids, and hyaenids) or have not been studied in any great detail (e.g. herpestids, viverrids, and intrageneric relationships in the procyonids). Times of divergence throughout the tree were also estimated from 74 literature sources based on both fossil and molecular data. We use the phylogeny to show that some lineages within the Mustelinae and Canidae contain significantly more species than expected for their age, illustrating the tree's utility for studies of macroevolution. It will also provide a useful foundation for comparative and conservational studies involving the carnivores.

Freigegeben in B
Donnerstag, 14 Juni 2018 15:56

LE, M. & MCCORD, W. P. (2008)

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.

Freigegeben in L
Donnerstag, 14 Juni 2018 09:12

LE, M., HOANG, T. & LE, D. (2004)

Trade Data and Some Comments On the Distribution of Mauremys annamensis (Siebenrock, 1903).

Asiatic Herpetological Research 10: 110-113.

Abstract:

This trade survey of Annam Pond Turtle reveals that this species is likely to have larger distribution than previously thought. The records in the trade in Quy Nhon and Ho Chi Minh City suggest its range could extend much further south. In addition, given the one way south-north trade route, the absence of Mauremys mutica in the trade south of Hai Van Pass and the reported absence of M. annamensis in the trade north of the Pass support the hypothesis that the Pass is the natural barrier for the two species ranges. This hypothesis combined with the long existence of the Pass might indicate that the speciation between the two species happened when their ancestors dispersed across the Pass, and were subsequently isolated, by the means of rafting or walking through narrow land strip emerged during the low sea level period. In terms of conservation, M. annamensis has become much rarer even in the trade, suggesting immediate conservation measures to protect it.

Freigegeben in L

Taxonomic Reevaluation of Phrynops (Testudines: Chelidae) with the description of two new genera and a new species of Batrachemys.

Rev. biol. trop vol.49 n.2 San José Jun. 2001. Online-Version: ISSN 0034-7744.

Abstract:

Relationships among turtle species loosely categorized within the South American genus Phrynops are explored. Three once recognized genera (Batrachemys, Mesoclemmys and Phrynops) that were demoted to subgenera, and then synonymized with Phrynops, are demonstrated to warrant full recognition based on morphometric analysis, skull osteology, and mitochondrial and nuclear gene sequencing. Mesoclemmys  is resurrected from the synonymy of Phrynops as a monotypic genus including M. gibba. The genus Rhinemys, previously a synonym of Phrynops, is resurrected for the species R. rufipes. Ranacephala  gen. nov. is described to include the species R hogei. The genus Batrachemys  is resurrected from the synonymy of Phrynops and includes B. dahli, B. nasuta B. raniceps, B. tuberculata, and B. zuliae. The taxon vanderhaegei  is placed in Bufocephala  gen. nov. The genus Phrynops is redefined to include the taxa P. geoffroanus, P. hilarii, P. tuberosus and P.williamsi. Ciadistic analysis of morphological data supports this taxonomy. A new species of Batrachemys  is described from the western Amazon region, and is distinguished by having facial markings in juveniles, a relatively wide head, and a flattened shell. The new species, B. heliostemma  sp. nov., is sympatric with and most similar to the recently resurrected form Batrachemys raniceps in the upper Amazonian region of Peru and adjacent Brazil, Ecuador, Venezuela, and Colombia. Lastly, morphometric data from living and museum specimens of all species of Batrachemys are presented.

Freigegeben in M

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

Freigegeben in R
Donnerstag, 14 Juni 2018 09:48

MELO, M. & O'RYAN, C. (2007)

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

Freigegeben in M
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