A general species delimitation method with applications to phylogenetic placements
- Jiajie Zhang, P. Kapli, P. Pavlidis, A. Stamatakis
- Biology, Environmental ScienceBioinform.
- 29 August 2013
The Poisson tree processes (PTP) model is introduced to infer putative species boundaries on a given phylogenetic input tree and yields more accurate results than de novo species delimitation methods.
Comparative phylogeography of six herpetofauna species in Cyprus: late Miocene to Pleistocene colonization routes
- N. Poulakakis, P. Kapli, P. Lymberakis
- Environmental Science
- 1 March 2013
A reconstruction of the evolutionary history of six herptiles in Cyprus shows that the colonization history of those species in Cyprus started in the late Miocene and extended into the Pliocene and Pleistocene, with geodispersal, transmarine dispersal, and human-mediated dispersal having their share in shaping the diversification of Cypriote herptile.
Molecular phylogeny of three Mesalina (Reptilia: Lacertidae) species (M. guttulata, M. brevirostris and M. bahaeldini) from North Africa and the Middle East: another case of paraphyly?
- P. Kapli, P. Lymberakis, N. Poulakakis, G. Mantziou, A. Parmakelis, M. Mylonas
- BiologyMolecular Phylogenetics and Evolution
- 1 October 2008
A review of phylogeographic analyses of animal taxa from the Aegean and surrounding regions
- N. Poulakakis, P. Kapli, M. Mylonas
- Environmental Science, Geography
- 1 February 2015
A critical review of more than 100 phylogeographic articles on 76 animal genera for Greece leads to the recognition of three types of distribution patterns: old ‘colonizers’ diversified in the Aegean before the formation of the mid-Aegean Trench, as well as new colonizers that inhabited the region in the Pleistocene or even the Holocene.
Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha
- P. Kapli, M. Telford
- BiologyScience Advances
- 1 December 2020
A data simulation approach shows that the contested origins of Ctenophora and Xenacoelomorpha are obscured by systematic errors, which would imply that the alternative Porifera-first and Xenambulacraria topologies are the most credible current alternatives.
Phylogenetic tree building in the genomic age
- P. Kapli, Ziheng Yang, M. Telford
- BiologyNature reviews genetics
- 13 May 2020
The principles, steps and computational tools for phylogenetic tree building are discussed, including identification of orthologous genes or proteins, multiple sequence alignment, and choice of substitution models and inference methodologies.
Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects
- B. Wipfler, H. Letsch, Sabrina Simon
- BiologyProceedings of the National Academy of Sciences
- 14 January 2019
The inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment and that social behavior was not part of the polyneopteran ground plan.
Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria
- P. Kapli, P. Natsidis, M. Telford
- BiologyScience Advances
- 2 July 2020
Simulation experiments show that support for Deuterostomia could be explained by systematic error, and the branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterally symmetric ancestor may have been deuterstome-like.
Separate histories in both sides of the Mediterranean: phylogeny and niche evolution of ocellated lizards
- F. Ahmadzadeh, Morris Flecks, D. Rödder
- Biology
- 1 June 2016
This study provides insights into the evolutionary history of the ocellated lizards and helps to understand the role of climatic niche evolution during the speciation process.
A re-analysis of the molecular phylogeny of Lacertidae with currently available data
- P. Kapli, N. Poulakakis, P. Lymberakis, M. Mylonas
- Biology
- 2 December 2011
A concatenated dataset of 5727 bp from six genes (two nuclear and four mitochondrial) and 40 genera was assembled based on GenBank database revealing that even a combined dataset of both mitochondrial and nuclear genes is not able to resolve the phylogenetic relationships of the Lacertidae family under the tribe level.
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