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7 results on '"Rancilhac, Lois"'

4. Target-enriched DNA sequencing clarifies the identity of name-bearing types of the Gephyromantis plicifer complex and reveals a new species of mantellid frog from Madagascar

Author

Vences, Miguel, Köhler, Jörn, Andreone, Franco, Craul, Ann-Kristin, Crottini, Angelica, du Preez, Louis, Preick, Michaela, Rancilhac, Lois, Rödel, Mark-Oliver, Scherz, Mark D., Streicher, Jeffrey W., Hofreiter, Michael, and Glaw, Frank

Subjects
MALAGASY FROGS, MOLECULAR PHYLOGENY, AMPHIBIA, PATTERNS, AMPLIFICATION, SUBGENUS, TAXONOMY, PERFORMANCE, ANCIENT, EVOLUTION
Abstract

Mantellid frogs of the Madagascar-endemic Gephyromantis plicifer complex consist of three nominal species (G. luteus, G. plicifer and G. sculpturatus) as well as several genetically divergent lineages (candidate species), but uncertainties surround the identity of the name-bearing types of all three established nomina. We applied laboratory techniques to isolate archival DNA from the three old, liquid-preserved, name-bearing type specimens and conducted target-enriched DNA sequencing of a fragment of the mitochondrial 16S rRNA gene as basis for the revision of their taxonomy. Along with 16S sequences of 161 fresh samples, sequences of a fragment of the nuclear-encoded Rag-1 gene for 97 of these samples, a multi-gene data set of selected samples, and a comprehensive analysis of available advertisement call recordings, the new data suggest a novel taxonomic hypothesis: (1) The name G. plicifer applies to a highland clade of populations from the southern Central East, previously referred to as Gephyromantis sp. Ca21, with G. sculpturatus as a junior synonym. (2) The name G. luteus applies to a widespread clade distributed along most of Madagascar's eastern rainforest band, and more specifically, is assigned to a subclade occurring mostly in coastal regions of the northern Central East and North East. (3) Large-sized specimens from Ranomafana (southern Central East) and Andohahela (South East) previously considered to belong to G. plicifer in fact represent a hitherto undescribed species, which we here formally name as G. pedronoi sp. nov. The three species are distinguished by very high genetic distances (over 8 % in the 16S gene), an absence of haplotype sharing in Rag-1, as well as morphological and bioacoustic characteristics. Moreover, several infra-specific clades with 16S divergences > 4 % may represent distinct species, especially within the widespread G. luteus, but cannot be unambiguously delimited by available data. We suggest dedicated sampling at contact zones and more extensive bioacoustic study of genotyped call vouchers to clarify their taxonomic status.

Published
2021

5. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards

Author

Garcia-Porta, Joan, Irisarri, Iker, Kirchner, Martin, Rodriguez, Ariel, Kirchhof, Sebastian, Brown, Jason L., MacLeod, Amy, Turner, Alexander P., Ahmadzadeh, Faraham, Albaladejo, Gonzalo, Crnobrnja-Isailovic, Jelka, De la Riva, Ignacio, Fawzi, Adnane, Galan, Pedro, Gocmen, Bayram, Harris, D. James, Jimenez-Robles, Octavio, Joger, Ulrich, Glavas, Olga Jovanovic, Karis, Mert, Koziel, Giannina, Kunzel, Sven, Lyra, Mariana, Miles, Donald, Nogales, Manuel, Oguz, Mehmet Anil, Pafilis, Panayiotis, Rancilhac, Lois, Rodriguez, Noemi, Rodriguez Concepcion, Benza, Sanchez, Eugenia, Salvi, Daniele, Slimani, Tahar, S'khifa, Abderrahim, Qashqaei, Ali Turk, Zagar, Anamarija, Lemmon, Alan, Lemmon, Emily Moriarty, Carretero, Miguel Angel, Carranza, Salvador, Philippe, Herve, Sinervo, Barry, Muller, Johannes, Vences, Miguel, Valero, Katharina C. Wollenberg, Garcia-Porta, Joan, Irisarri, Iker, Kirchner, Martin, Rodriguez, Ariel, Kirchhof, Sebastian, Brown, Jason L., MacLeod, Amy, Turner, Alexander P., Ahmadzadeh, Faraham, Albaladejo, Gonzalo, Crnobrnja-Isailovic, Jelka, De la Riva, Ignacio, Fawzi, Adnane, Galan, Pedro, Gocmen, Bayram, Harris, D. James, Jimenez-Robles, Octavio, Joger, Ulrich, Glavas, Olga Jovanovic, Karis, Mert, Koziel, Giannina, Kunzel, Sven, Lyra, Mariana, Miles, Donald, Nogales, Manuel, Oguz, Mehmet Anil, Pafilis, Panayiotis, Rancilhac, Lois, Rodriguez, Noemi, Rodriguez Concepcion, Benza, Sanchez, Eugenia, Salvi, Daniele, Slimani, Tahar, S'khifa, Abderrahim, Qashqaei, Ali Turk, Zagar, Anamarija, Lemmon, Alan, Lemmon, Emily Moriarty, Carretero, Miguel Angel, Carranza, Salvador, Philippe, Herve, Sinervo, Barry, Muller, Johannes, Vences, Miguel, and Valero, Katharina C. Wollenberg

Abstract

Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genomewide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.

Published
2019
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6. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards

Author

Ministerio de Economía y Competitividad (España), García-Porta, Joan, Irisarri, Íker, Kirchner, Martin, Rodríguez, Ariel, Kirchhof, Sebastian, Brown, Jason L., MacLeod, Amy, Turner, Alexander P., Ahmadzadeh, Faraham, Albaladejo, Gonzalo, Crnobrnja-Isailovic, Jelka, De la Riva, Ignacio, Fawzi, Adnane, Galán, Pedro, Göçmen, Bayram, Harris, David James, Jiménez-Robles, Octavio, Joger, Ulrich, Jovanovic Glavaš, Olga, Karis, Mert, Koziel, Giannina, Künzel, Sven, Lyra, Mariana, Miles, Donald, Nogales, Manuel, Oguz, Mehmet A., Pafilis, Panauiotis, Rancilhac, Lois, Rodríguez, Noemí, Rodríguez Concepción, Benza, Sanchez, Eugenia, Salvi, Daniele, Slimani, Tahar, S'khifa, Abderrahim, Qashqaei, Ali Turk, Žagar, Anamarija, Lemmon, Alan, Moriarty Lemmon, Emily, Carretero, Miguel Ángel, Carranza, Salvador, Philippe, Hervé, Sinervo, Barry, Müller, Jhoannes, Vences, Miguel, Wollenberg Valero, Katherina C., Ministerio de Economía y Competitividad (España), García-Porta, Joan, Irisarri, Íker, Kirchner, Martin, Rodríguez, Ariel, Kirchhof, Sebastian, Brown, Jason L., MacLeod, Amy, Turner, Alexander P., Ahmadzadeh, Faraham, Albaladejo, Gonzalo, Crnobrnja-Isailovic, Jelka, De la Riva, Ignacio, Fawzi, Adnane, Galán, Pedro, Göçmen, Bayram, Harris, David James, Jiménez-Robles, Octavio, Joger, Ulrich, Jovanovic Glavaš, Olga, Karis, Mert, Koziel, Giannina, Künzel, Sven, Lyra, Mariana, Miles, Donald, Nogales, Manuel, Oguz, Mehmet A., Pafilis, Panauiotis, Rancilhac, Lois, Rodríguez, Noemí, Rodríguez Concepción, Benza, Sanchez, Eugenia, Salvi, Daniele, Slimani, Tahar, S'khifa, Abderrahim, Qashqaei, Ali Turk, Žagar, Anamarija, Lemmon, Alan, Moriarty Lemmon, Emily, Carretero, Miguel Ángel, Carranza, Salvador, Philippe, Hervé, Sinervo, Barry, Müller, Jhoannes, Vences, Miguel, and Wollenberg Valero, Katherina C.

Abstract

Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genome-wide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.

Published
2019

7. Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal

Author

Rancilhac, Loïs, Miralles, Aurélien, Geniez, Philippe, Mendez-Aranda, Daniel, Beddek, Menad, Brito, José Carlos, Leblois, Raphaël, and Crochet, Pierre-André

Subjects
Archaeology, CC1-960, Science
Abstract

Aim: Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be reliably differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting. Location: Morocco. Taxon: Spiny-footed lizard (Acanthodactylus erythrurus), Squamata: Lacertidae. Methods: Using 325 samples from 40 localities, we identified genetic discontinuities within A. erythrurus based on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks). Results: A. erythrurus is characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 6 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases. Main conclusions: The genetic diversity of A. erythrurus originates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations within A. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.

Published
2023
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