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 Rapid ecological specialization despite constant population sizes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6476 ◽  
Author(s):  
Andrinajoro R. Rakotoarivelo ◽  
Paul O’Donoghue ◽  
Michael W. Bruford ◽  
Yoshan Moodley
Keyword(s):  
East Africa ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Demographic History ◽  
12S Rrna ◽  
Surprising Result ◽  
Ecological Specialization ◽  
Lineage Sorting ◽  
Mt Dna ◽  
Data Set

Background The bushbuck, Tragelaphus scriptus, is a widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage (T. s. scriptus) inhabits the north-western half of the African continent while Sylvaticus (T. s. sylvaticus) is found in the south-eastern half. Here we test hypotheses of historical demography and adaptation in bushbuck using a higher-resolution framework, with four nuclear (MGF, PRKCI, SPTBN, and THY) and three new mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods Genealogies were reconstructed for the mitochondrial and nuclear data sets, with the latter dated using fossil calibration points. We also inferred the demographic history of Scriptus and Sylvaticus using coalescent-based methods. To obtain an overview of the origins and ancestral colonisation routes of ancestral bushbuck sequences across geographic space, we conducted discrete Bayesian phylogeographic and statistical dispersal-vicariance analyses on our nuclear DNA data set. Results Both nuclear DNA and mtDNA support previous findings of two genetically divergent Sylvaticus and Scriptus lineages. The three mtDNA loci confirmed 15 of the previously defined haplogroups, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane Menelik’s bushbuck (Sylvaticus) of the Ethiopian highlands, which formed a monophyletic group at three of four nuclear DNA loci. We dated the coalescence of the two lineages to a common ancestor ∼2.54 million years ago. Both marker sets revealed similar demographic histories of constant population size over time. We show that the bushbuck likely originated in East Africa, with Scriptus dispersing to colonise suitable habitats west of the African Rift and Sylvaticus radiating from east of the Rift into southern Africa via a series of mainly vicariance events. Discussion Despite lower levels of genetic structure at nuclear loci, we confirmed the independent evolution of the Menelik’s bushbuck relative to the phenotypically similar montane bushbuck in East Africa, adding further weight to previous suggestions of convergent evolution within the bushbuck complex. Perhaps the most surprising result of our analysis was that both Scriptus and Sylvaticus populations remained relatively constant throughout the Pleistocene, which is remarkable given that this was a period of major climatic and tectonic change in Africa, and responsible for driving the evolution of much of the continent’s extant large mammalian diversity.

Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)

2020 ◽  
Vol 194 (1) ◽  
pp. 84-99
Author(s):  
Inelia Escobar ◽  
Eduardo Ruiz-Ponce ◽  
Paula J Rudall ◽  
Michael F Fay ◽  
Oscar Toro-Núñez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Incomplete Lineage Sorting ◽  
Morphological Evolution ◽  
Strong Support ◽  
Plastid Dna ◽  
Lineage Sorting ◽  
Generic Level ◽  
Molecular Analyses ◽  
Floral Diversity

Abstract Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.

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.

A molecular phylogeny of the eastern group of ocellated lizard genus Timon (Sauria: Lacertidae) based on mitochondrial and nuclear DNA sequences

2012 ◽  
Vol 33 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Faraham Ahmadzadeh ◽  
Miguel Angel Carretero ◽  
D. James Harris ◽  
Ana Perera ◽  
Wolfgang Böhme
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Divergence Time ◽  
Taxonomic Status ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
12S Rrna ◽  
Zagros Mountains ◽  
Divergence Time Estimates ◽  
Eastern Group

Timon, a small genus of lacertid lizards, includes four species distributed in two separate ranges in the western and eastern part of the Mediterranean Basin. Phylogenetic relationships between the two groups have not been resolved, and the taxonomic situation of the two subspecies of the eastern representative of the genus, Timon princeps, is not clear. To address these questions, partial DNA sequences of two nuclear (β-fibrinogen intron 7 and C-mos) and three mitochondrial (cytochrome b, 12S rRNA and 16S rRNA) genes were analyzed. Based on the high genetic distance between the two subspecies of T. princeps we promote their taxonomic status to full species, Timon princeps and Timon kurdistanicus. Divergence time estimates based on other lacertid species suggest that the separation of the green (Lacerta) and ocellated (Timon) lizards took place around 12 My ago, and that the Eastern group underwent speciation around 4-5 my ago, perhaps associated with the uplifting of the Zagros mountains. As expected given this ancient divergence and complex paleogeography, considerable levels of genetic diversity are recovered within both taxa, with geographically close individuals showing very divergent haplotypes.

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
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