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
Estimating the phylogeny of lacertid lizards, and particularly the tribe Lacertini has been challenging, possibly due to the fast radiation of this group resulting in a hard polytomy. However this is still an open question, as concatenated data primarily from mitochondrial markers have been used so far whereas in a recent phylogeny based on a compilation of these data within a squamate supermatrix the basal polytomy seems to be resolved. In this study, we estimate phylogenetic relationships between all Lacertini genera using for the first time DNA sequences from five fast evolving nuclear genes (acm4, mc1r, pdc, βfib and reln) and two mitochondrial genes (nd4 and 12S). We generated a total of 529 sequences from 88 species and used Maximum Likelihood and Bayesian Inference methods based on concatenated multilocus dataset as well as a coalescent-based species tree approach with the aim of (i) shedding light on the basal relationships of Lacertini (ii) assessing the monophyly of genera which were previously questioned, and (iii) discussing differences between estimates from this and previous studies based on different markers, and phylogenetic methods.
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| Language: | English |
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Elsevier
2016-07
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| Subjects: | Lacertini radiation, Hard polytomy, Species tree, Concatenation, Nuclear DNA, Multilocus phylogeny, |
| Online Access: | http://hdl.handle.net/10261/151391 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100001871 http://dx.doi.org/10.13039/501100003329 |
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Lacertini radiation Hard polytomy Species tree Concatenation Nuclear DNA Multilocus phylogeny Lacertini radiation Hard polytomy Species tree Concatenation Nuclear DNA Multilocus phylogeny |
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Lacertini radiation Hard polytomy Species tree Concatenation Nuclear DNA Multilocus phylogeny Lacertini radiation Hard polytomy Species tree Concatenation Nuclear DNA Multilocus phylogeny Mendes, Joana Harris, David James Carranza, Salvador Salvi, Daniele 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 |
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Estimating the phylogeny of lacertid lizards, and particularly the tribe Lacertini has been challenging, possibly due to the fast radiation of this group resulting in a hard polytomy. However this is still an open question, as concatenated data primarily from mitochondrial markers have been used so far whereas in a recent phylogeny based on a compilation of these data within a squamate supermatrix the basal polytomy seems to be resolved.
In this study, we estimate phylogenetic relationships between all Lacertini genera using for the first time DNA sequences from five fast evolving nuclear genes (acm4, mc1r, pdc, βfib and reln) and two mitochondrial genes (nd4 and 12S). We generated a total of 529 sequences from 88 species and used Maximum Likelihood and Bayesian Inference methods based on concatenated multilocus dataset as well as a coalescent-based species tree approach with the aim of (i) shedding light on the basal relationships of Lacertini (ii) assessing the monophyly of genera which were previously questioned, and (iii) discussing differences between estimates from this and previous studies based on different markers, and phylogenetic methods. |
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European Commission |
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European Commission Mendes, Joana Harris, David James Carranza, Salvador Salvi, Daniele |
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artículo |
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Lacertini radiation Hard polytomy Species tree Concatenation Nuclear DNA Multilocus phylogeny |
| author |
Mendes, Joana Harris, David James Carranza, Salvador Salvi, Daniele |
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Mendes, Joana |
| title |
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 |
| title_short |
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 |
| title_full |
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 |
| title_fullStr |
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 |
| title_full_unstemmed |
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 |
| title_sort |
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 |
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Elsevier |
| publishDate |
2016-07 |
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http://hdl.handle.net/10261/151391 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100001871 http://dx.doi.org/10.13039/501100003329 |
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AT mendesjoana evaluatingthephylogeneticsignallimitfrommitogenomesslowevolvingnucleargenesandtheconcatenationapproachnewinsightsintothelacertiniradiationusingfastevolvingnucleargenesandspeciestrees AT harrisdavidjames evaluatingthephylogeneticsignallimitfrommitogenomesslowevolvingnucleargenesandtheconcatenationapproachnewinsightsintothelacertiniradiationusingfastevolvingnucleargenesandspeciestrees AT carranzasalvador evaluatingthephylogeneticsignallimitfrommitogenomesslowevolvingnucleargenesandtheconcatenationapproachnewinsightsintothelacertiniradiationusingfastevolvingnucleargenesandspeciestrees AT salvidaniele evaluatingthephylogeneticsignallimitfrommitogenomesslowevolvingnucleargenesandtheconcatenationapproachnewinsightsintothelacertiniradiationusingfastevolvingnucleargenesandspeciestrees |
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1777668661826289664 |
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dig-ibe-es-10261-1513912018-09-27T07:29:46Z 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, David James Carranza, Salvador Salvi, Daniele European Commission Fundação para a Ciência e a Tecnologia (Portugal) Ministerio de Economía y Competitividad (España) Lacertini radiation Hard polytomy Species tree Concatenation Nuclear DNA Multilocus phylogeny Estimating the phylogeny of lacertid lizards, and particularly the tribe Lacertini has been challenging, possibly due to the fast radiation of this group resulting in a hard polytomy. However this is still an open question, as concatenated data primarily from mitochondrial markers have been used so far whereas in a recent phylogeny based on a compilation of these data within a squamate supermatrix the basal polytomy seems to be resolved. In this study, we estimate phylogenetic relationships between all Lacertini genera using for the first time DNA sequences from five fast evolving nuclear genes (acm4, mc1r, pdc, βfib and reln) and two mitochondrial genes (nd4 and 12S). We generated a total of 529 sequences from 88 species and used Maximum Likelihood and Bayesian Inference methods based on concatenated multilocus dataset as well as a coalescent-based species tree approach with the aim of (i) shedding light on the basal relationships of Lacertini (ii) assessing the monophyly of genera which were previously questioned, and (iii) discussing differences between estimates from this and previous studies based on different markers, and phylogenetic methods. Results uncovered (i) a new phylogenetic clade formed by the monotypic genera Archaeolacerta, Zootoca, Teira and Scelarcis; and (ii) support for the monophyly of the Algyroides clade, with two sister species pairs represented by western (A. marchi and A. fitzingeri) and eastern (A. nigropunctatus and A. moreoticus) lineages. In both cases the members of these groups show peculiar morphology and very different geographical distributions, suggesting that they are relictual groups that were once diverse and widespread. They probably originated about 11–13 million years ago during early events of speciation in the tribe, and the split between their members is estimated to be only slightly older. This scenario may explain why mitochondrial markers (possibly saturated at higher divergence levels) or slower nuclear markers used in previous studies (likely lacking enough phylogenetic signal) failed to recover these relationships. Finally, the phylogenetic position of most remaining genera was unresolved, corroborating the hypothesis of a hard polytomy in the Lacertini phylogeny due to a fast radiation. This is in agreement with all previous studies but in sharp contrast with a recent squamate megaphylogeny. We show that the supermatrix approach may provide high support for incorrect nodes that are not supported either by original sequence data or by new data from this study. This finding suggests caution when using megaphylogenies to integrate inter-generic relationships in comparative ecological and evolutionary studies. This study was partially funded by the Project “Genomics and Evolutionary Biology” cofinanced by North Portugal Regional Operational Programme 2007/2013 (ON.2–O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF). JM, DJH, and DS are supported by the Fundação para a Ciência e a Tecnologia (FCT, Portugal): JM, doctoral grant SFRH/BD/81528/2011; DS, post-doctoral grant SFRH/BPD/105274/2014. SC is supported by Grant CGL2012-36970 from the Ministerio de Economía y Competitividad, Spain (co-funded by Fondos FEDER – EU). Peer reviewed 2017-06-13T12:48:37Z 2017-06-13T12:48:37Z 2016-07 artículo http://purl.org/coar/resource_type/c_6501 Molecular Phylogenetics and Evolution 100: 254-267 (2016) 1055-7903 http://hdl.handle.net/10261/151391 10.1016/j.ympev.2016.04.016 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100001871 http://dx.doi.org/10.13039/501100003329 en https://doi.org/10.1016/j.ympev.2016.04.016 Sí none Elsevier |