Genomic Evidence for Cryptic Speciation in Tree Frogs From the Apennine Peninsula, With Description of Hyla perrini sp. nov

Dufresnes, Christophe; Mazepa, Glib; Rodrigues, Nicolas; Brelsford, Alan; Litvinchuk, Spartak N.; Sermier, Roberto; Lavanchy, Guillaume; Betto‐Colliard, Caroline; Blaser, Olivier; Borzée, Amaël; Cavoto, Elisa; Fabre, Guillaume; Ghali, Karim; Grossen, Christine; Horn, Adolf Heinrich; Leuenberger, Julien; Phillips, Barret C.; Saunders, Paul A.; Savary, Romain; Maddalena, Tiziano; Stöck, Matthias; Dubey, Sylvain; Canestrelli, Daniele; Jeffries, Daniel L.

doi:10.3389/fevo.2018.00144

Cited by 39 publications

(37 citation statements)

References 87 publications

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“…This first result thus adds to a growing body of literature supporting that diverging lineages persisting in separate microrefugia can be on the path to speciation, despite occasional gene flow during secondary contacts (e.g., Díaz-Rodríguez et al, 2017;Dufresnes et al, 2018). For the cold-tolerant Rana frogs, this outcome is remarkable because Spanish populations expanded and thrived during the prolonged glacials rather than during the short interglacial cycles only (Figures 4 and 5; see also Galán et al, 2010 for the Galician populations of R. parvipalmata), thus experiencing longer opportunities for lineage fusion compared to species with Mediterranean affinities.…”

Section: Cryptic Speciation In a Sanctuary-type Refugiummentioning

confidence: 57%

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Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

et al. 2020

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Subdivided Pleistocene glacial refugia, best known as “refugia within refugia”, provided opportunities for diverging populations to evolve into incipient species and/or to hybridize and merge following range shifts tracking the climatic fluctuations, potentially promoting extensive cytonuclear discordances and “ghost” mtDNA lineages. Here, we tested which of these opposing evolutionary outcomes prevails in northern Iberian areas hosting multiple historical refugia of common frogs (Rana cf. temporaria), based on a genomic phylogeography approach (mtDNA barcoding and RAD‐sequencing). We found evidence for both incipient speciation events and massive cytonuclear discordances. On the one hand, populations from northwestern Spain (Galicia and Asturias, assigned to the regional endemic R. parvipalmata), are deeply‐diverged at mitochondrial and nuclear genomes (~4 My of independent evolution), and barely admix with northeastern populations (assigned to R. temporaria sensu stricto) across a narrow hybrid zone (~25 km) located in the Cantabrian Mountains, suggesting that they represent distinct species. On the other hand, the most divergent mtDNA clade, widespread in Cantabria and the Basque country, shares its nuclear genome with other R. temporaria s. s. lineages. Patterns of population expansions and isolation‐by‐distance among these populations are consistent with past mitochondrial capture and/or drift in generating and maintaining this ghost mitochondrial lineage. This remarkable case study emphasizes the complex evolutionary history that shaped the present genetic diversity of refugial populations, and stresses the need to revisit their phylogeography by genomic approaches, in order to make informed taxonomic inferences.

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Section: Cryptic Speciation In a Sanctuary-type Refugiummentioning

confidence: 57%

“…Accordingly, many closely-related endemics have been tentatively described from Mediterranean refugia (e.g., Díaz-Rodríguez et al, 2017;Dufresnes et al, 2018;Dufresnes, Strachinis, et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

et al. 2020

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“…Despite the rapid progress in high‐throughput sequencing technologies in the last decade, studies that harness the power of genomic data remain few (Struck et al, ). Moreover, studies that integrate genomic with publicly available environmental data, that is statistically derived and/or remotely sensed data, to identify cryptic diversity are scarce (Dufresnes et al, ). In this study, we combined genome‐wide polymorphisms (4,089 SNPs) with climate, soil and land cover data to identify cryptic genomic diversity and its environmental correlates within the cold‐adapted P. farinosa .…”

Section: Discussionmentioning

confidence: 99%

The role of cryptic diversity and its environmental correlates in global conservation status assessments: Insights from the threatened bird's‐eye primrose (Primula farinosa L.)

Bravo

Conti

2019

Diversity and Distributions

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Aim: Most of the fundamental questions in conservation biogeography require the description of species geographic boundaries and the identification of discrete biological units within these boundaries. International conservation efforts and institutions rely mainly on traditional taxonomic approaches for defining these boundaries, resulting in significant cryptic diversity going undetected and often extinct. Here, we combine high-throughput genomic data with publicly available environmental data to identify cryptic diversity in the threatened bird's-eye primrose (Primula farinosa).We aim to characterize evolutionary lineages and test whether they co-occur with changes in environmental conditions. These lineages can be used as intraspecific units for conservation to enhance assessments regarding the status of threatened species.Location: Europe and temperate Asia (latitude, 40-65°N; longitude, 10°E-115°W). Methods:We genotyped 93 individuals from 71 populations at 1,220 loci (4,089 SNPs) across the Eurasian distribution of P. farinosa. We used phylogenomic and population structure approaches to identify intraspecific lineages. We further extracted statistically derived and remotely sensed environmental information, that is land cover, climate and soil characteristics, to define the biotic and abiotic environment inhabited by each lineage and test for niche similarities among lineages. Additionally, we tested for isolation by distance among populations and applied linear and polynomial regressions to identify lineage-environment associations.Results: Analyses of genomic data revealed six major lineages within P. farinosa corresponding to distinct geographic areas. Niche similarity tests indicated that lineages occupy distinct abiotic and biotic space. Isolation by distance indicated that geography alone cannot explain genetic divergence within P. farinosa, while lineage-environment associations suggested potential adaptation to different abiotic conditions across lineages. However, relationships with the land cover classes, a proxy for habitat, were weaker.

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“…In order to provide an up-to-date and comprehensive overview of species distributions, range limits, and the extent of the ten contacts documented so far in W-Palearctic Hyla, we combined our new H. arborea/molleri population genetic data with those from 24 previously-published studies on the phylogeography and hybrid zones of this group, totaling records from 857 different localities. These included general phylogenetic/phylogeographic accounts 21,23,35 , intra-specific genetic work on H. meridionalis and H. carthaginiensis 36,37 , H. savignyi and H. felixarabica 38,39 , H. sarda 40,41 , H. intermedia and H. perrini 42,43 , H. arborea 26,44 , H. molleri 45,46 , and H. orientalis 38,39,47 , as well as targeted surveys of the transitions for H. meridionalis/arborea-molleri 22 , H. savignyi/felixarabica 48 , H. arborea/perrini 49,50 , H. intermedia/perrini 20 and H. arborea/orientalis 33,51 . Based on the distribution of genetic diversity and ecological niche modelling, these studies also inferred the location of glacial refugia and routes of post-glacial recolonization for each species, providing insights on the relative age of contact zones that we summarized in File S2.…”

Section: Methodsmentioning

confidence: 99%

“…For divergence times, we relied on the fully-resolved phylogeny of 20 , built from genome-wide nuclear sequences (~42 kb), and a molecular clock calibrated with the tree root at ~20 Mya 52,53 , and the Messinian divergence of the Tyrrhenian H. sarda 21,35,54 .…”

Section: Methodsmentioning

confidence: 99%

The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs

Dufresnes

Berroneau²,

Dubey

et al. 2020

Sci Rep

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Because it is indicative of reproductive isolation, the amount of genetic introgression across secondary contact zones is increasingly considered in species delimitation. However, patterns of admixture at range margins can be skewed by the regional dynamics of hybrid zones. In this context, we posit an important role for phylogeographic history: hybrid zones located within glacial refugia (putatively formed during the Late-Pleistocene) should be better defined than those located in post-glacial or introduced ranges (putatively formed during the Holocene and the Anthropocene). We test this hypothesis in a speciation continuum of tree frogs from the Western Palearctic (Hyla), featuring ten identified contacts between species spanning Plio-Pleistocene to Miocene divergences. We review the rich phylogeographic literature of this group and examine the overlooked transition between H. arborea and H. molleri in Western France using a multilocus dataset. Our comparative analysis supports a trend that contacts zones resulting from post-glacial expansions and human translocations feature more extensive introgression than those established within refugial areas. Integrating the biogeographic history of incipient species, i.e. their age since first contact together with their genetic divergence, thus appears timely to draw sound evolutionary and taxonomic inferences from patterns of introgression across hybrid zones.

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Genomic Evidence for Cryptic Speciation in Tree Frogs From the Apennine Peninsula, With Description of Hyla perrini sp. nov

Cited by 39 publications

References 87 publications

Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

The role of cryptic diversity and its environmental correlates in global conservation status assessments: Insights from the threatened bird's‐eye primrose (Primula farinosa L.)

The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs

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