Evaluating the phylogenetic signal limit from mitogenomes, slow evolving nuclear genes, and the concatenation approach. New insights into the Lacertini radiation using fast evolving nuclear genes and species trees

Mendes, Joana; Harris, D. James; Carranza, Salvador; Salvi, Daniele

doi:10.1016/j.ympev.2016.04.016

Cited by 52 publications

(60 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Given that all the recent phylogenetic analyses including these two genera find them as sister taxa (e.g., Carranza et al, 2004;Arnold et al, 2007;Kapli et al, 2011;Mendes et al, 2016), our result indicates that either we did not find enough osteological characters to unite Lacerta to the exclusion of Timon, or that the osteological variability is too high to obtain a meaningful tree topology based on osteological characters only. In order to test this, we performed a second analysis, including a constraint forcing the software to find all the specimens of Lacerta as a monophyletic group.…”

Section: Phylogenetic Analysismentioning

confidence: 68%

Osteology, fossil record and palaeodiversity of the European lizards

et al. 2017

View full text Add to dashboard Cite

Abstract. The capability of palaeontologists to identify fossil remains of a particular group of vertebrates strongly depends on the knowledge they have of its comparative osteology and on the actual presence of diagnostic differences among the considered taxa. This could have a relevant influence on the study of palaeodiversity, since a low recognisability causes a loss of data when trying to reconstruct the history of taxa that lived on Earth in the past. Currently, more than 6000 extant species of lizards and worm lizards are known, and new ones continue to be discovered, mainly based on molecular data. But are we able to recognise this high diversity using osteology? As far as European taxa are concerned, the osteological recognisability of non-snake squamates is very low: only 31% of the extant European taxa can be identified based on their skeletal morphology. This is balanced partially by the fact that most recognisable taxa have been actually recognised in the fossil record, suggesting that the lost data are mainly due to the scarce knowledge of the comparative osteology of these reptiles and less influenced by other biases, such as taphonomic or collection biases. In this context, specimen-level phylogenetic analysis has proved to be a useful tool to identify diagnostic combinations of osteological features, at least for lacertid species, as evidenced by a case study focused on the genus Lacerta.

show abstract

Section: Phylogenetic Analysismentioning

confidence: 68%

Osteology, fossil record and palaeodiversity of the European lizards

et al. 2017

View full text Add to dashboard Cite

show abstract

“…We amplified two mitochondrial gene fragments, 12S rRNA ( 12S ) and NADH dehydrogenase subunit four with flanking tRNA Ser , tRNA His , and tRNA Leu ( nd4 ), and two nuclear gene fragments, Melanocortin receptor 1 ( mc1r ) and acetylcholinergic receptor M4 ( acm4 ), by polymerase chain reaction (PCR). Primers and PCR protocols used for the amplification of the molecular markers are described in [44]. …”

Section: Methodsmentioning

confidence: 99%

“…In doing so we sequenced 10 Podarcis species from the same two fragment used in this study and retrieved Genbank sequences from nine additional Podarcis species (Table 2). We designated Scelarcis perspicillata and Teira dugesii as outgroups based on the mitochondrial phylogeny of Lacertini [44]. We performed a Bayesian analysis in BEAST, using the same settings as in the BEAST analysis of the P. tiliguerta dataset but using a Yule process of speciation as tree prior.…”

Section: Methodsmentioning

confidence: 99%

Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta

Salvi

Pinho²,

Harris³

2017

BMC Evol Biol

Self Cite

View full text Add to dashboard Cite

BackgroundMediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity.ResultsWe analysed DNA sequences of mitochondrial (12S and nd4) and nuclear (acm4 and mc1r) gene fragments in 174 individuals of P. tiliguerta from 81 localities across the full range of the species in a geographic and genealogical framework. We found surprisingly high genetic diversity both at mitochondrial and nuclear loci. Seventeen reciprocally monophyletic allopatric mitochondrial haplogroups were sharply divided into four main mitochondrial lineages (two in Corsica and two in Sardinia) of Miocene origin. In contrast, shallow divergence and shared diversity within and between islands was observed at the nuclear loci. We evaluated alternative biogeographic and evolutionary scenarios to explain such profound discordance in spatial and phylogenetic patterning between mitochondrial and nuclear genomes. While neutral models provided unparsimonious explanations for the observed pattern, the hypothesis of environmental selection driving mitochondrial divergence in the presence of nuclear gene flow is favoured.ConclusionsOur study on the genetic variation of P. tiliguerta reveals surprising levels of diversity underlining a complex phylogeographic pattern with a striking example of mito-nuclear discordance. These findings have profound implications, not only for the taxonomy and conservation of P. tiliguerta. Growing evidence on deep mitochondrial breaks in absence of geographic barriers and of climatic factors associated to genetic variation of Corsican-Sardinian endemics warrants additional investigation on the potential role of environmental selection driving the evolution of diversity hotspots within Mediterranean islands.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0899-x) contains supplementary material, which is available to authorized users.

show abstract

“…We amplified three mitochondrial gene fragments— ribosomal 12S rRNA ( 12S ), cytochrome b ( cytb ), and NADH dehydrogenase 4 with flanking tRNAs Serine, Histidine, and Leucine ( nd4 )—and two nuclear genes— oocyte maturation factor mos ( cmos ) and melanocortin 1 receptor ( mc1r ). These markers have been successfully used in many intra‐ and interspecific studies on lacertid lizards (Mendes, Harris, Carranza, & Salvi, ; Salvi, Harris, Bombi, Carretero, & Bologna, ; Salvi, Schembri, Sciberras, & Harris, ; Tamar, Carranza et al., ). Amplification was performed through polymerase chain reaction (PCR).…”

Section: Methodsmentioning

confidence: 99%

“…Primers, PCR conditions, and references are listed in the Supporting Information (Table ; see also Mendes et al. () and Salvi et al. ()).…”

Section: Methodsmentioning

confidence: 99%

Hidden in the Arabian Mountains: Multilocus phylogeny reveals cryptic diversity in the endemicOmanosauralizards

Mendes

Salvi

Harris

et al. 2018

J Zool Syst Evol Res

Self Cite

View full text Add to dashboard Cite

An increase in studies in the Hajar Mountains from the southeastern Arabian Peninsula has revealed a high richness of endemic evolutionary lineages with many cryptic taxa. Omanosaura is the only lacertid lizard genus endemic to the Hajar Mountains, with two species O. cyanura and O. jayakari distributed throughout this mountain range. The phylogenetic relationships and genetic diversity between and within these species have been poorly studied. In this study, we collected mitochondrial (12S, cytb, and nd4) and nuclear (cmos and mc1r) sequences for 25 specimens of Omanosaura, including 15 individuals of O. jayakari and 10 of O. cyanura. We performed phylogenetic analyses based on network reconstruction, maximum likelihood and Bayesian inference to estimate the relationships and intraspecific genetic diversity of these species. We estimated the time of divergence between the two species in the Miocene, around 8.5 million years ago. Omanosaura jayakari shows little genetic diversity, while O. cyanura presents two differentiated lineages. These are reciprocally monophyletic at mitochondrial and nuclear genes and present a high genetic distance between them. These two lineages are associated with the geographic features of the Hajar Mountains, with one lineage distributed in the northernmost part of the Hajar Mountains and the other in the rest of the western Hajars, the Jebel Akhdar, and the eastern Hajars. This geographic relationship has been recovered previously in other reptile taxa and is generally associated with high levels of local genetic diversity. Our results suggest the existence of cryptic diversity within O. cyanura and support a general biogeographic pattern of high diversity and endemism in the northern Hajar Mountains that certainly deserves additional research in the future.

show abstract

Evaluating the phylogenetic signal limit from mitogenomes, slow evolving nuclear genes, and the concatenation approach. New insights into the Lacertini radiation using fast evolving nuclear genes and species trees

Cited by 52 publications

References 55 publications

Osteology, fossil record and palaeodiversity of the European lizards

Osteology, fossil record and palaeodiversity of the European lizards

Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta

Hidden in the Arabian Mountains: Multilocus phylogeny reveals cryptic diversity in the endemicOmanosauralizards

Contact Info

Product

Resources

About