Molecular evidence for cryptic candidate species in Iberian Pelodytes (Anura, Pelodytidae)

Abstract

Species delineation is a central topic in evolutionary biology, with current efforts focused on developing efficient analytical tools to extract the most information from molecular data and provide objective and repeatable results. In this paper we use a multilocus dataset (mtDNA and two nuclear markers) in a geographically comprehensive population sample across Iberia and Western Europe to delineate candidate species in a morphologically cryptic species group, Parsley frogs (genus Pelodytes). Pelodytes is the sole extant representative of an ancient, historically widely distributed anuran clade that currently includes three species: P. caucasicus in the Caucasus; P. punctatus in Western Europe, from Portugal to North-Western Italy; and P. ibericus in Southern Iberia. Phylogenetic analyses recovered four major well-supported haplotype clades in Western Europe, corresponding to well demarcated geographical subdivisions and exhibiting contrasting demographic histories. Splitting times date back to the Plio-Pleistocene and are very close in time. Species-tree analyses recovered one of these species lineages, corresponding to P. ibericus (lineage B), as the sister taxon to the other three major species lineages, distributed respectively in: western Iberian Peninsula, along the Atlantic coast and part of central Portugal (lineage A); Central and Eastern Spain (lineage C); and North-eastern Spain, France and North-western Italy (lineage D). The latter is in turn subdivided into two sub-clades, one in SE France and NW Italy and the other one from NE Spain to NW France, suggesting the existence of a Mediterranean-Atlantic corridor along the Garonne river. An information theory-based validation approach implemented in SpedeSTEM supports an arrangement of four candidate species, suggesting the need for a taxonomic revision of Western European Pelodytes.

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

“…Our complementary genetic approaches suggest that these two taxa are worthy of a specific status, in light of the current taxonomic divisions of other European amphibians. First, their deep, congruent mtDNA and nuclear divergence (averages: 2.5 and 3.5 Mya) is comparable to or older than that of several already established species, such as the Iberian and Oriental tree frogs, H. molleri and H. orientalis (∼3 Mya; Stöck et al, 2012, this study); the Parsley frogs Pelodytes hespericus, P. atlanticus and P. punctatus (2-3 Mya; Diaz-Rodriguez et al, 2015; the green toads Bufo (Bufotes) viridis, B. siculus and B. balearicus (2-3 Mya; Stöck et al, 2008a;Dufresnes et al, 2014); the pool frogs Pelophylax lessonae and P. bergeri (1-2 Mya, Canestrelli and Nascetti, 2008), the Cyprus water frog P. cypriensis (2-3 My, Lymberakis et al, 2007, but 5.3 Mya in Plötner et al, 2012, the Caucasian toad Bufo verrucossisimus (1-2 Mya; Recuero et al, 2012); it is barely younger than many Messinian taxa, e.g., H. arborea (5-6 Mya, Stöck et al, 2012, this study), Middle Eastern Triturus newts (Wielstra and Arntzen, 2011). Note that molecular dating is inherently sensitive to the marker(s) and calibration(s) used (e.g., Veith et al, 2016) and should obviously be interpreted cautiously.…”

Present and past climatic effects on the current distribution and genetic diversity of the Iberian spadefoot toad (Pelobates cultripes): an integrative approach

“…The French Atlantic coast may have been colonized from an additional refugium in south‐eastern France. In any case, migration through a corridor along the Garonne river from the Mediterranean to the Atlantic coast of France is likely, as previously suggested for another anuran, P. punctatus (Díaz‐Rodríguez et al ., ). Our mid‐Holocene projections, showing some continuity of relatively favourable areas between the Atlantic and Mediterranean coasts, provide support for this hypothesis, although the evidence is not conclusive in terms of the temporal framework involved, as similar continuity was also inferred in previous time intervals (see Fig.…”

“…Despite the inferred long evolutionary history of P. cultripes in Iberia, all extant haplogroups share a common ancestor within the last 1 Myr (95% HPDi: 230–994 ka). This contrasts with most other Iberian amphibians, for which geographically structured, old phylogroups provide evidence of survival in allopatric refugia across several Ice Ages (Díaz‐Rodríguez et al ., ; Gonçalves et al ., ; Teixeira et al ., ). This may result from massive extinction of lineages during the glaciations of the Pliocene and Pleistocene, although other processes, such as selective sweeps, cannot be ruled out.…”

“…This analysis simultaneously reconstructs gene trees, ancestral population sizes, and the geographical ranges of inferred nodes, which can be visualized through time provided appropriate calibrations or substitution rates are supplied. As no reliable estimates of substitution rates or calibrations based on fossils or geological events are available for Pelobates, we estimated a substitution rate for the mtDNA fragment used (ND4+ adjacent tRNAs) in a family‐level phylogenetic analysis including representatives of the families Scaphiopodidade ( Scaphiopus couchii Baird, 1854, accession: , and Spea bombifrons (Cope, 1863): , Zhang et al ., ), Pelodytidae ( Pelodytes caucasicus Boulenger, 1896: , P. ibericus Sánchez Herráiz, Barbadillo‐Escrivá, Machordom & Sanchiz, 2000: , and P. punctatus (Daudin, 1802): , Díaz‐Rodríguez et al ., ), Megophryidae ( Leptobrachium montanum Fischer, 1885: , Scutiger cf mammatus (Günther, 1896): , and Oreolalax jingdongensis Ma, Yang & Li, 1983: , Rao & Wilkinson, ), and Pelobatidae (including one sequence of P. cultripes – voucher PC935‐ , and another one of its sister taxon P. varaldii Pasteur & Bons, 1959 – voucher IMS1148‐). Based on the estimates of Roelants et al .…”

The roles of allopatric fragmentation and niche divergence in intraspecific lineage diversification in the common midwife toad (Alytes obstetricans)

“…Genetic effects of vicariant events associated with climate‐mediated range expansions and contractions during glacial cycles are well documented in phylogeographic studies, highlighting the existence of cryptic diversity in many Iberian taxa (e.g. Díaz‐Rodríguez et al., ; Gonçalves et al., ; Martínez‐Solano, Teixeira, Buckley, & García‐París, ; Pinho, Kaliontzopoulou, Harris, & Ferrand, ; Recuero & García‐París, ; Sequeira, Alexandrino, Weiss, & Ferrand, ). However, comparatively little is known about the potential role of ecological factors in the process of intraspecific lineage diversification (e.g.…”