Genetic variation within Saurodactylus and its phylogenetic relationships within the Gekkonoidea estimated from mitochondrial and nuclear DNA sequences

2008 ◽  
Vol 29 (1) ◽  
pp. 25-34 ◽  
Author(s):  
David James Harris ◽  
Catarina Rato
Keyword(s):  
Genetic Variation ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Taxonomic Position ◽  
Gene Region ◽  
12S Rrna ◽  
Nuclear Marker ◽  
Nuclear Markers ◽  
Mtdna Variability

Abstract Phylogenetic relationships of the three morphological forms within the gecko genus Saurodactylus were estimated using mtDNA (12S rRNA and ND4) sequences. High between morphological forms variation (up to 25% with ND4), confirms that all three deserve specific status. Saurodactylus mauritanicus and Saurodactylus brosseti are strongly supported as sister taxa. Our results again highlight the extremely high mtDNA variability almost universally reported from within gecko species. The position of Saurodactylus within the Gekkonoidea was also investigated. Although considered as a member of the sphaerodactyl geckos, its taxonomic position is still highly uncertain. Evaluation of C-mos nuclear DNA sequences supports many of the recent taxonomic rearrangements within the Gekkonoidea. Using this marker, Saurodactylus is paraphyletic, with S. mauritanicus and S. brosseti sister taxa to Teratoscincus przewalskii rather than Saurodactylus fasciatus. This is supported by a further nuclear marker, RAG1, although for this gene region sampling is more limited. Based on this paraphyly, supported by two independent nuclear markers, we suggest it likely that Saurodactylus will need to be partitioned into two genera, pending further investigations.

Phylogeny and evolution of the green lizards, Lacerta spp. (Squamata: Lacertidae) based on mitochondrial and nuclear DNA sequences

2005 ◽  
Vol 26 (3) ◽  
pp. 271-285 ◽  
Author(s):  
D. James Harris ◽  
Nuno Ferrand ◽  
Eduardo Crespo ◽  
Raquel Godinho
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Bird Species ◽  
Rrna Genes ◽  
12S Rrna ◽  
Lineage Sorting ◽  
Extant Species ◽  
Mitochondrial Cytochrome B

AbstractPartial DNA sequences from three mitochondrial (cytochrome b, 12S rRNA and 16S rRNA) and two nuclear (β-fibrinogen intron 7 and C-mos) genes were used to estimate the phylogenetic relationships among all eight extant species of green lizards, Lacerta sensu stricto, and many currently recognized subspecies. All eight species form a monophyletic group. L. agilis, L. schreiberi and L. strigata are genetically well differentiated species. L. trilineata and L. pamphylica are not monophyletic units based on analyses of the β-fibrinogen intron 7. Lacerta media is closely related to some Lacerta trilineata. L. bilineata and L. viridis are closely related, and recognition of L. bilineata as a distinct species makes L. viridis paraphyletic also. For both L. bilineata and L. viridis, some subspecies appear to remain in their southern glacial refugia, while a single genetic entity shows successfully postglacial expansion. The topology derived from C-mos variation is concordant with that derived from mtDNA, with substitutions occurring at a similar rate to that of transversions in the rRNA genes. Although C-mos is typically used at deeper taxonomic levels it is also phylogenetically informative within green lizards. β-fibrinogen intron 7, typically used for assessing phylogenetic relationships among bird species, is a useful phylogenetic marker for reptiles also, showing considerable variation between species. There is not complete concordance between estimates of relationships derived from the mtDNA and nuclear markers, probably because rapid diversification led to incomplete lineage sorting in the green lizards. Introgression could also be occuring between some species.

scholarly journals Phylogenetic relationships of Cranichidinae and Prescottiinae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences

2009 ◽  
Vol 104 (3) ◽  
pp. 403-416 ◽  
Author(s):  
Gerardo A. Salazar ◽  
Lidia I. Cabrera ◽  
Santiago Madriñán ◽  
Mark W. Chase
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Dna

Mitochondrial lineages or discrete species? Assessing diversity within Timon tangitanus (Lacertidae) using mitochondrial and nuclear DNA sequences

2020 ◽  
Vol 41 (1) ◽  
pp. 123-132
Author(s):  
João M. Abreu ◽  
Daniele Salvi ◽  
Ana Perera ◽  
D. James Harris
Keyword(s):  
North Africa ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Divergence ◽  
Lineage Sorting ◽  
Lizard Species ◽  
Nuclear Markers ◽  
Species Complexes ◽  
Mtdna Sequence ◽  
Mtdna Lineages

Abstract Identification of extremely high levels of mitochondrial DNA (mtDNA) sequence divergence within reptiles from North Africa is commonplace. This high divergence often compares with interspecific levels among widely accepted species, leading to the hypothesis of the occurrence of species complexes. Indeed, in many examples, data from nuclear markers support such taxonomic recognition. Such is the case of two recently recognized ocellated lizard species of the genus Timon, T. nevadensis, from Spain, and T. kurdistanicus, from the Middle East, which both showed notable genetic differentiation from their sister taxa. In North Africa, highly divergent mtDNA lineages of Timon tangitanus were previously identified but not corroborated with nuclear markers. Here we expand geographic sampling across the range of Timon tangitanus and complement mtDNA sequences with data from nuclear markers (MC1R and ACM4). We identify four divergent mtDNA lineages, at a level similar to some reptile species. However, the nuclear markers show limited differentiation and lack of lineage sorting. This and some other recent assessments within reptiles discourage the use of mtDNA data alone as a proxy for taxonomic units, demonstrating once more the need for integrative taxonomic approaches.

scholarly journals Pathogenic and Genetic Variation in the Japanese Strains of Fusarium oxysporum f. sp. melonis

1998 ◽  
Vol 88 (8) ◽  
pp. 804-810 ◽  
Author(s):  
Fumio Namiki ◽  
Toshiki Shiomi ◽  
Kazufumi Nishi ◽  
Tsuruo Kayamura ◽  
Takashi Tsuge
Keyword(s):  
Genetic Variation ◽  
Fusarium Oxysporum ◽  
Dna Sequences ◽  
Nuclear Markers ◽  
Oriental Melon ◽  
Genetic Groups ◽  
Pathogenic Variation ◽  
Pathogenicity Tests ◽  
Race 2 ◽  
Single Cluster

Pathogenic variation among 41 Japanese strains of Fusarium oxysporum f. sp. melonis was analyzed by pathogenicity tests with muskmelon, oriental melon, and oriental pickling melon cultivars. Based on pathogenicity to muskmelon cvs. Amus and Ohi and oriental melon cv. Ogon 9, 41 strains were divided into 3 groups that corresponded completely to Risser's races 0, 2, and 1,2y. To further characterize pathogenic variation within the forma specialis and races, strains were assayed for pathogenicity to 42 additional muskmelon, oriental melon, and oriental pickling melon cultivars. All strains of race 1,2y were pathogenic to all cultivars tested. Strains of race 0 were divided into six variants based on differences in pathogenicity to three muskmelon cultivars; strains of race 2 also were classified into six variants based on differences in pathogenicity to two muskmelon cultivars and one oriental melon cultivar. Genetic variation among strains was analyzed by DNA fingerprinting with four repetitive DNA sequences: FOLR1 to FOLR4. Thirty-six fingerprint types were detected among forty-one strains by pooling results of fingerprinting with four probes. Cluster analysis showed distinct genetic groups correlated with races: the fingerprint types detected in each of races 2 and 1,2y were grouped into a single cluster, and two distinct genetic groups were found in race 0. However, pathogenic variation detected within races 0 and 2 could not be differentiated based on the nuclear markers examined.

Phylogenetic Relationships of Zeugites (Poaceae: Centothecoideae) Inferred from Plastid and Nuclear DNA Sequences and Morphology

2007 ◽  
Vol 32 (4) ◽  
pp. 722-730
Author(s):  
Ana María Soriano Martínez ◽  
Gerardo A. Salazar ◽  
Patricia Dávila Aranda
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Dna

scholarly journals Multiloci analyses suggest synonymy among Rhomboplites, Ocyurus and Lutjanus and reveal the phylogenetic position of Lutjanus alexandrei (Lutjanidae: Perciformes)

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Ivana Veneza ◽  
Raimundo da Silva ◽  
Danillo da Silva ◽  
Grazielle Gomes ◽  
Iracilda Sampaio ◽  
...  
Keyword(s):  
Coastal Zone ◽  
Dna Sequences ◽  
Endemic Species ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Genetic Identity ◽  
Phylogenetic Position ◽  
Brazilian Coast ◽  
Western Atlantic ◽  
Phylogenetic Hypotheses

ABSTRACT Lutjanidae comprises 21 genera and 135 species widespread throughout Atlantic, Indian and Pacific oceans. Nonetheless, the phylogenetic relationships of Lutjaninae remain uncertain. Furthermore, phylogenetic hypotheses for Lutjanus alexandrei, an endemic species from northeastern Brazilian coast, in Lutjanidae are absent so far. Therefore, we carried out multiloci analyses, combining both mitochondrial and nuclear DNA sequences in Lutjaninae species from Western Atlantic focusing on the controversial relationships among Lutjanus, Rhomboplites, and Ocyurus. Besides, we determined the phylogenetic position and dated the origin of L. alexandrei. The phylogenetics trees based on the 4.4 kb for 11 species corroborated the synonym among Lutjanus and the putative monotypic genera. For the dating of L. alexandrei, another nucleotide dataset (3.0 kb; 40 species) validated the genetic identity of this species that diverged from the sister taxon L. apodus between 2.5 - 6.5 Mya, probably as a result of the barrier caused by the muddy outflow from Orinoco and Amazon rivers along the coastal zone. This report is the most robust multiloci analysis to confirm the synonymy of the three genera of Lutjaninae from Western Atlantic and the first reliable inference about the phylogenetic relationships and origin of L. alexandrei.

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