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The complete mitochondrial ND2 gene (1037 bp) was sequenced to examine relationships within the bent-wing bat complex, Miniopterus schreibersii (Family Vespertilionidae). It was found that M. schreibersii is a paraphyletic assemblage comprising several species. Two major lineages were identified, one of which was restricted to the Palearctic-Ethiopian regions and the other to the Oriental-Australasian regions. This pattern of differentiation was mirrored by the genus as a whole. Speciation and differentiation within the genus Miniopterus appears to have a hierarchical geographical pattern. The earliest divergence corresponds to the Ethiopian-Palearctic and the Oriental-Australasian biogeographical zones. This early divergence is then followed by radiations within each of the Ethiopian, Oriental and Australasian regions. The study also revealed that the number of species currently recognized (11 or 13) is a gross underestimate of the number of actual species. The emerging picture is one of a relatively speciose genus with most species having relatively restricted distributions; few, if any, occur in more than one biogeographical region.
Mol Phylogenet Evol 2004 May
PMID:Molecular systematics and biogeography of the bent-wing bat complex Miniopterus schreibersii (Kuhl, 1817) (Chiroptera: Vespertilionidae). 1506 85

Subtraction hybridization was earlier used to obtain cDNA clones corresponding to human genes upregulated in HIV-associated centroblast lymphoma (CL) as compared with HIV-associated immunoblast lymphoma (IL). With inverse subtraction hybridization, clones were isolated that correspond to genes upregulated in IL compared with CL. In addition to cDNAs characterized earlier, the resulting clones contained several (seven CL-specific and three IL-specific) sequences with unknown functions. To identify the lymphoma-specific genes that are overexpressed in early carcinogenesis, Northern blotting was used to assess the level of gene transcription in two human fibroblast lines and in their derivatives immortalized with either a temperature-sensitive mutant of SV-40 or with pSV3neo carrying the SV-40 A gene, considering the latter as a model of early cell malignant transformation. Increased expression in at least one immortalized line compared with normal fibroblasts was observed for set, a-myb, ND1, ND2, ND4 (NADH dehydrogenase subunits 1, 2, and 4), COX2, COX3 (cytochrome-c-oxidase subunits 2 and 3), KIAA0129, and the gene corresponding to cDNA hss2-1-7-10. High expression of these genes was assumed to be associated not only with lymphomogenesis, but also with early transformation (immortalization) of other, nonlymphoid cells. Expression of the calpain gene and the gene corresponding to cDNA hss2-2-9-5 proved to be lower in immortalized than in normal fibroblasts. This was considered indicative of an alternative mechanism of fibroblast transformation or of different processes regulating the expression of these genes in early and late carcinogenesis.
Mol Biol (Mosk)
PMID:[Analysis of expression of a series of lymphoma-specific genes in human fibroblasts immortalized by SV40 virus]. 1512 32

Intrageneric lineages and the historical biogeography of toads, genus Bufo, are poorly resolved due to their conservative morphology, their highly conserved karyotypes (typically 2N = 22), and erratic patterns of interspecific hybridisation. Here, we use mitochondrial and nuclear DNA sequence data to reconstruct relationships of the 20-chromosome toads, a major component of the African bufonid fauna. Mitochondrial 12S and 16S sequences from 29 species revealed two independent transitions between phenotypically distinct savannah and forest adapted forms. Analyses of mitochondrial 12S, 16S, and ND2, along with nuclear ACTC and Rhodopsin sequences from 12 species greatly increased bootstrap, and likelihood support for internal branches including a basal split into two pan-African 20-chromosome clades. Hybridisation is a weak indicator of phylogenetic relationship as it occurs across these deeply divergent clades, between Bufo rangeri and Bufo gutturalis. These analyses suggest a secondary reversion to 22-chromosomes in Bufo pardalis, within the 20-chromosome group, although we could not reject an alternative hypothesis that this lineage forms a sister to all 2N = 20 toads. Other informally recognised 22-chromosome groups form independent phylogenetic lineages outside the 20-chromosome group, such as the Angusticeps and Vertebralis divisions. Bufo lindneri, from the Taitanus division, is closely related to Stephopaedes anotis, and these species should be considered congeners.
Mol Phylogenet Evol 2004 Sep
PMID:Molecular systematics of African 20-chromosome toads (Anura: Bufonidae). 1528 46

Nucleotide sequences of mitochondrial genes (ND1, ND2, COI, and tRNAs) were determined for 38 samples representing 15 taxa of tropidurid lizards from the Galapagos Islands and mainland South America. Phylogenetically informative characters (759 of 1,956) were analyzed under Bayesian, maximum likelihood, and parsimony frameworks. This study supports the hypothesis that tropidurid lizards dispersed to the Galapagos on at least two separate occasions. One dispersal event involved an eastern Galapagos clade (Microlophus habelii and M. bivittatus, on Marchena and San Cristobal islands, respectively) the sister taxon of which is M. occipitalis from coastal Ecuador and Peru; the closest mainland relative of the western Galapagos clade was not unambiguously identified. The wide-ranging M. albemarlensis is revealed to be a complex of weakly divergent lineages that is paraphyletic with respect to the insular species M. duncanensis, M. grayii, and M. pacificus.
Mol Phylogenet Evol 2004 Sep
PMID:Evolution of Galapagos Island Lava Lizards (Iguania: Tropiduridae: Microlophus). 1528 53

The African bush-shrikes and helmet-shrikes (Malaconotidae sensu [A Complete Checklist of the Birds of the World, third ed., Helm Editions, London, 2003]) include 10 genera and 52 species of predatory passerine birds for which monophyly, sister-group, and inter-generic relationships are disputed. To resolve their relationships, we analyzed 2313 bp of sequence data obtained from two nuclear introns (myoglobin intron-2, beta-fibrinogen intron-5) and a mitochondrial protein-coding gene (ND2) using parsimony, maximum likelihood, and Bayesian inference. A strongly supported clade that included representatives of the Malaconotidae, Platysteiridae, and Vangidae was found in all analyses. Three main groups emerged within this clade but relationships between these three groups were always poorly supported. The first group included the helmet-shrikes (Prionops), flycatcher-shrikes (Bias and Megabyas), and vangas (Cyanolanius and Pseudobias), currently placed in the families Malaconotidae, Platysteiridae, and Vangidae, respectively. The second group consisted of four Platysteiridae genera (Lanioturdus, Batis, Platysteira, and Dyaphorophyia), with the remaining Malaconotidae genera ('core malaconotids') forming the last group. Two main clades emerged within the 'core malaconotids,' with the position of the genus Nilaus being variable. The first clade included Malaconotus, Dryoscopus, Bocagia, and Tchagra and the second Chlorophoneus, Laniarius, Rhodophoneus, and Telophorus. Monophyly of the genus Chlorophoneus was never recovered, a result that is consistent with morphological data.
Mol Phylogenet Evol 2004 Nov
PMID:Phylogenetic relationships of the African bush-shrikes and helmet-shrikes (Passeriformes: Malaconotidae). 1533 76

The environmental and/or life history factors affecting genetic exchange in marine species with potential for high dispersal are of great interest, not only from an evolutionary standpoint but also with regard to effective management. Previous genetic studies have demonstrated substantial differentiation among populations of the Patagonian toothfish around the Southern Ocean, indicating breakdown of gene flow across large distances between inhabited shelf areas. The present study examined genetic structuring through analysis of microsatellite loci and restriction fragment length polymorphism (RFLP) of the mitochondrial ND2 gene and control region of the toothfish population in the SW Atlantic, allowing examination of the relative effects of the Antarctic Polar Front (APF), deep-water troughs and distance between sites. Mitochondrial DNA (mtDNA) data indicated a sharp genetic division between the Patagonian Shelf/North Scotia Ridge and the Shag Rocks/South Georgia samples, whereas microsatellite data showed much less distinct structuring and an intermediate position of the North Scotia Ridge samples. We suggest these data indicate that the APF, as a barrier to larval dispersal, is the major inhibitor of genetic exchange between toothfish populations, with deep-water troughs and distance between sites contributing to genetic differentiation by inhibiting migration of relatively sedentary adults. We also suggest that differences between mtDNA and nuclear DNA population patterns may reflect either genome population size effects or (putative) male-biased dispersal.
Mol Ecol 2004 Nov
PMID:Genetic structuring of Patagonian toothfish populations in the Southwest Atlantic Ocean: the effect of the Antarctic Polar Front and deep-water troughs as barriers to genetic exchange. 1548 90

Genomic size of animal mitochondrial DNA is usually minimized over time. Thus, when regional duplications occur, they are followed by a rapid elimination of redundant material. In contrast to this general view, we report here long-sustained tRNA pseudogenes in the mitochondrial genome (mitogenome) of teleost fishes of the family Scaridae (parrotfishes). During the course of a molecular phylogenetic study of the suborder Labroidei, we determined the complete nucleotide sequence of the mitogenome for a parrotfish, Chlorurus sordidus, and found a gene rearrangement accompanied by a tRNA pseudogene. In the typical gene order of vertebrates, a tRNA-gene cluster between ND1 and ND2 genes includes tRNA(Ile) (I), tRNA(Gln) (Q), and tRNA(Met) (M) genes in this order (IQM). However, in the mitogenome of the parrotfish, the tRNA(Met) gene was inserted between the tRNA(Ile) and the tRNA(Gln) genes, and the tRNA(Gln) gene was followed by a putative tRNA(Met) pseudogene (psiM). Such a tRNA gene rearrangement including a pseudogene (IMQpsiM) was found in all of the 10 examined species, representing 7 of the 10 currently recognized scarid genera. All sister groups examined (20 species of Labridae and a single species of Odacidae) had the typical gene order of vertebrate mitogenomes. Phylogenetic analysis of the tRNA(Met) genes and the resulting pseudogenes demonstrated that the ancestral tRNA(Met) gene was duplicated in a common ancestor of the parrotfish. Based on the fossil record, these results indicate that the pseudogenes have survived at least 14 million years. Most of the vertebrate mitochondrial gene rearrangements involving the IQM region have held the tRNA(Met) gene just upstream of the ND2 gene, and even in a few exceptional cases, including the present ones, the tRNA pseudogenes have been found in that position. In addition, most of these tRNA(Met) pseudogenes maintained clover-leaf secondary structures, with the remainder sustaining the clover-leaf structure in the "top half (TpsiC and acceptor arms). Considering their potential secondary structures (holding "top halves" of the clover-leaf structures), locations within mitogenomes (flanking the 5' ends of the ND2 genes) and stabilities over time (survived at least 14 Myr), it is likely that the tRNA pseudogenes retain function as punctuation marks for mitochondrial ND2 mRNA processing.
J Mol Evol 2004 Sep
PMID:Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae). 1555 84

The true thrushes (Passeriformes: Muscicapidae, subfamily Turdinae) are a speciose and widespread avian lineage presumed to be of Old World origin. Phylogenetic relationships within this assemblage were investigated using mitochondrial DNA (mtDNA) sequence data that included the cytochrome b and ND2 genes. Our ingroup sampling included 54 species representing 17 of 20 putative turdine genera. Phylogenetic trees derived via maximum parsimony and maximum likelihood were largely congruent. Most of the Turdine taxa sampled can be placed into one of six well supported clades. Our data indicate a polyphyletic Zoothera which can be divided into at least two (Afro-Asian and Austral-Asian) main clades. The genus Turdus, as presently recognized, is paraphyletic but forms a well supported clade with the addition of three mostly monotypic genera (Platycichla, Nesocichla, and Cichlherminia). We identify an exclusively New World clade that includes a monophyletic Catharus, Hylocichla, Cichlopsis, Entomodestes, Ridgwayia, and Ixoreus. Members of the morphologically and behaviorally distinct genera Sialia, Myadestes, and Neocossyphus unexpectedly form a basal clade. Using multiple outgroup choices, we show that this group is distantly related, but unequivocally the sister group to the remaining Turdines sampled. The Turdinae appear to be a relatively old songbird lineage, originating in the mid to late Miocene. If the Turdinae are indeed Old World in origin, our data indicate a minimum of three separate invasions of the New World.
Mol Phylogenet Evol 2005 Mar
PMID:A molecular phylogenetic analysis of the "true thrushes" (Aves: Turdinae). 1568 24

The phylogeny of swallows was reconstructed by comparing segments of three genes, nuclear beta-fibrinogen intron 7 (betafib7), mitochondrial cytochrome b (cytb), and mitochondrial ND2, in a variety of combinations using maximum likelihood and Bayesian methods. betafib7 was sequenced for 47 species, cytb for 74 species, and ND2 for 61 species to yield comparisons among 75 of the 84 currently recognized swallow species. The family Hirundinidae was confirmed to consist of two clades, Pseudochelidoninae (river martins) and Hirundininae (typical swallows). The Hirundininae is further divided into mud nesters (Hirundo sensu lato), core martins (Phedina, Riparia, and New World endemic genera), and basal relicts (Psalidoprocne, Cheramoeca, and Pseudhirundo). We did not resolve the hierarchy among these three hirundinine groups, but discovered many relationships within them. Mud-nesting genera have the following relationships: (Hirundo sensu stricto, Ptyonoprogne), (Delichon, (Petrochelidon, Cecropis)). Core martins have the following topology: (Phedina, Riparia cincta), (Riparia sensu stricto, Tachycineta, ((Stelgidopteryx, Progne), (Neotropical endemic genera))). Interspecific relationships among the Neotropical endemics were resolved completely; Atticora and Notiochelidon are paraphyletic, and all Neotropical endemics probably should be lumped into one or two genera. The final group of hirundinines, the basal relicts, consists of a sister pair, the Australian Cheramoeca and African Pseudhirundo. The African saw-wings (Psalidoprocne) are their likely sister group.
Mol Phylogenet Evol 2005 Apr
PMID:Phylogeny of swallows (Aves: Hirundinidae) estimated from nuclear and mitochondrial DNA sequences. 1573 95

The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear beta-fibrinogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; approximately 3750 bp) and combined mt and nuclear data (nine genes; approximately 6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manul within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear beta-fibrinogen intron 7.
Mol Phylogenet Evol 2005 May
PMID:Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores. 1580 17


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