Research Article |
Corresponding author: Christophe Dufresnes ( christophe.dufresnes@hotmail.fr ) Academic editor: Deepak Veerappan
© 2025 Christophe Dufresnes, Simeon Lukanov, Sven Gippner, Johanna Ambu, Ilias Strachinis, Dragan Arsovski, Benjamin Monod-Broca, Hugo Cayuela, Petros Lymberakis, Daniele Canestrelli, Dan Cogălniceanu, Nikolay A. Poyarkov, Spartak N. Litvinchuk, Tomasz Suchan, Mathieu Denoël, Daniel Jablonski.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Dufresnes C, Lukanov S, Gippner S, Ambu J, Strachinis I, Arsovski D, Monod-Broca B, Cayuela H, Lymberakis P, Canestrelli D, Cogălniceanu D, Poyarkov NA, Litvinchuk SN, Suchan T, Denoël M, Jablonski D (2025) Historical biogeography and systematics of yellow-bellied toads (Bombina variegata), with the description of a new subspecies from the Balkans. Vertebrate Zoology 75: 1-30. https://doi.org/10.3897/vz.75.e138687
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Abstract
The Balkan Peninsula hosts a great proportion of Europe’s biodiversity, and this is well illustrated by amphibian richness and endemism. Among them, the yellow-bellied toad Bombina variegata has been a model in ecology and evolution, but several aspects of its phylogeography and taxonomy remain surprisingly poorly understood. In this study, we combine cytochrome b DNA barcoding data (1238 individuals from 355 localities), mitogenome phylogenetics (17.2 kb), gene-based nuclear phylogenetics (3.7 kb from four gene fragments) and multilocus phylogenomics (4759 loci / ~554 kb obtained by double digest Restriction Associated DNA sequencing; ddRAD-seq) to re-assess the diversification of B. variegata, and revisit its nomenclatural history to assign scientific names to phylogeographic lineages. The analyses support four major lineages, one assigned to B. v. variegata (Carpathians and northwestern ranges), one assigned to B. v. pachypus (Apennine Peninsula), and two assigned to B. v. scabra (Dinarides, Hellenides and Balkanides vs. the Rhodope mountains). Spatiotemporal patterns of diversification suggest a role for a Late Miocene marine incursion in the Pannonian Plain (Paratethys) as the initial trigger of divergence, followed by a vicariance event in the Apennines and a “sky island” process of Pleistocene differentiation in the Balkan Peninsula. As it reached the Dinarides during the Late Pleistocene, B. v. variegata potentially hybridized with B. v. scabra and captured its mitochondrial DNA, which resulted in a massive cyto-nuclear discordance across all northwestern European populations. Finally, we show that the two lineages of B. v. scabra significantly differ in morphology and ventral coloration patterns, and describe the Rhodope lineage as a new subspecies.
Balkan Peninsula, cyto-nuclear discordance, glacial refugia, nomenclature, phylogeography, Rhodope Mountains
Authorship statement: Mathieu Denoël and Daniel Jablonski contributed equally to this work.
Southern European peninsulas are considered hotspots of diversity and endemism for the terrestrial fauna of the Western Palearctic (e.g.,
The Balkan Peninsula in its broad sense, defined as the landmass stretching from the Alps to the Black Sea in the north and to the Peloponnese in the south (
The yellow-bellied toad Bombina variegata is another case of the complex processes of population persistence, differentiation and reticulation that shape the historical biogeography of the Balkan Peninsula (
Despite a relatively strong focus by zoologists and molecular ecologists, notably for studying the hybrid zones it forms with B. bombina (
These discrepancies partly explain why the taxonomy of B. variegata has remained unsettled. For instance, some authors consider B. v. pachypus as a separate species (
A comprehensive overview of the phylogeographic diversity of B. variegata would be timely to guide systematic revisions, and more generally to understand what shaped its evolution in the context of the historical biogeography of the Balkan Peninsula. We aim to provide such an overview by (1) updating the distributions of the main mitochondrial lineages, (2) re-examining their evolutionary relationships and timing of divergence, (3) assessing how these correspond to the nuclear diversity, and (4) to the taxa proposed in the historical zoological literature. As this framework suggests two unique lineages within the taxon B. v. scabra, we further quantify morphological and color pattern variation between them, and provide the taxonomic description of a new subspecies.
Mitochondrial lineages affiliated with B. variegata were identified for 1238 individuals sampled in 355 localities based on sequences of the cytochrome b (cyt b) gene, as gathered from previous studies (Szymura et al. 2000;
Sequences were manually aligned and trimmed (1096 bp) in Seaview 5 (
For the purpose of a taxonomic description, which requires stating diagnostic characters, we further screened the cyt b haplotype alignment for substitutions unique to the Rhodope lineage using MOLD (
We gathered 19 full mitogenomes representative of the mitochondrial diversity of B. variegata (n = 8) and its closest relatives B. bombina (n = 9) and B. orientalis (n = 2) sequenced in previous work (
The dataset was used to infer time-calibrated Bayesian phylogenies with BEAST 2.6 (
In parallel, we also reconstructed a maximum-likelihood phylogeny in IQ-TREE 1.6 (
Moreover, pairwise divergence between lineages was computed in MEGA 11 (
We built a supermatrix spanning four polymorphic fragments of nuclear genes previously sequenced in Bombina, namely sodium-calcium exchanger gene intron 1 (ncx1, 702 bp), recombination activating gene intron 1 (rag-1, 1061 bp), intron 2 (rag-2, 578 bp) and rhodopsin gene (rho, 1374 bp), for a subset of nine samples representative of the mitochondrial diversity of B. variegata (n = 6), as well as B. bombina (n = 1) and B. orientalis (n = 2) as outgroups (sequence list in Table S3). The samples considered are composite, as they combine sequences from two independent studies (rag-2 and rho:
The supermatrix was analyzed with the multigene coalescent-based species tree method implemented in *BEAST (
For exploratory purposes, the concatenated alignment was also analyzed with IQ-TREE as for the mitogenome dataset above, but noting that unlike mitogenomes (where all genes are fully linked and share the same genealogy), such analysis can provide spurious topologies when the combined sequences are unlinked and form different gene trees (
To infer the nuclear diversity of B. variegata, we further analyzed double-digest Restriction Associated DNA sequencing (ddRAD-seq) data obtained for 10 samples representative of the mitochondrial lineages of that species, and one B. bombina sample to be used as outgroup (Table S4). These samples were included in a genomic library prepared with a custom protocol (http://dx.doi.org/10.17504/protocols.io.kxygx3nzwg8j/v1), as fully described in
Our analyses confirmed the occurrence of an evolutionarily unique population in the Rhodope mountains, previously confounded with its sister lineage B. v. scabra (see Results). To document morphological variation, we measured 58 adult specimens curated at the Museum Koenig Bonn (
To examine body shape without the effect of body size, we applied allometric corrections with the R package GroupStruct (
To find characters diagnosable in the field, we further computed simple body ratios (characters/L.) and visualized differences between lineages using boxplots (R package ggplot2;
Finally, we explored differences in body length (L.) by considering body length measurements of an additional 120 B. v. scabra specimens of known sex and origin, namely the 4 specimens of the type series of the new Rhodope taxon (see Results), 96 live specimens captured in Bulgaria during monitoring surveys, and 20 specimens curated at the Zoological Institute of Russian Academy of Sciences, St. Petersburg (
We quantified variation in the proportions of yellow/orange vs. dark coloration on the ventral side of 197 specimens of B. v. scabra of known geographic origin and attributable to lineages. To this end, we gathered photographs where the throat and belly are visible for (1) field-caught specimens, taken from our own libraries and the citizen-science platform
Each photo was processed using a modified version of a Python script published by
Differences in color-to-black ratios between the two lineages were analyzed with a Kruskal-Wallis test. Additionally, to account for the potential effect of museum preservation on coloration contrast, a two-way ANOVA was conducted (significance tested by a permutation procedure as above), treating specimen type (field-caught vs. museum) as a secondary explanatory variable.
We examined the nomenclature with the goal of attributing available names to phylogeographic lineages. To this end, we first mapped these lineages according to our results by updating the distribution shapefile of B. variegata designed by
The nomenclature of the yellow-bellied toad B. variegata is intertwined with the nomenclature of the fire-bellied toad B. bombina. Both were considered the same species for more than a century of Linnean classification (
Analyses of the cyt b gene (1096 bp) in 1238 toads from 355 localities revealed 202 B. variegata haplotypes grouped into the four main mitochondrial lineages retrieved by previous studies (Fig.
(1) the Carpathian lineage (C) is found in the B. v. variegata populations of the Carpathian Mountains and can be divided into two closely related mitogroups inhabiting the northern and southwestern ranges (C-W) and southeastern ranges (C-E);
(2) the Apennine lineage (A) extends across all the populations of the Apennine B. v. pachypus;
(3) the Rhodope lineage (R) is restricted to the easternmost B. v. scabra populations of the Balkan Peninsula;
(4) the Balkano-Western lineage (BW) ranges from the southern to the northwestern edges of the distribution, and can be divided in two closely related mitogroups, one found in the southern populations of the Balkan Peninsula, attributed to B. v. scabra (BW-S), and one found across the populations stretching from the Dinarides to Western Europe, attributed to B. v. variegata (BW-N). The BW-S mitogroup is also found in Central Italy and the Aegean islands due to human-mediated introductions (
The mitochondrial trees obtained with BEAST and IQ-TREE, based on full mitogenomes (17,240 bp), provided robustly supported topologies that recovered the four B. variegata lineages in two major clades, one including lineage C, and one regrouping lineages A, R, and BW (Figs
Bayesian phylogeny obtained with BEAST based on full mitogenomes (17,240 kb). Nodes are annotated with dating estimates and their 95% HPD (node bars) obtained from two calibrations (dark grey: calibration I; light grey: calibration II). Sequence labels indicate accession numbers, geographic origins, taxa and mitochondrial lineages. Asterisks denote full branch support (posterior probabilities of 1.0).
Pairwise sequence divergences at barcoding genes (Table
Pairwise distances between mitochondrial lineages at the DNA barcoding genes 16S, cox1 and cyt b. See Fig.
B. variegata | |||||||||
16S | BW-N | BW-S | R | C-W | C-E | A | B. bombina | B. orientalis | |
B. variegata | BW-N (variegata) | — | |||||||
BW-S (scabra) | 0.2% | — | |||||||
R (rhodopensis subsp. nov.) | 1.2% | 1.3% | — | ||||||
C-W (variegata) | 2.5% | 2.6% | 3.3% | — | |||||
C-E (variegata) | 2.6% | 2.6% | 3.3% | 0.3% | — | ||||
A (pachypus) | 1.6% | 1.7% | 2.0% | 2.7% | 2.8% | — | |||
B. bombina | 3.6% | 3.5% | 3.9% | 3.5% | 3.5% | 3.5% | — | ||
B. orientalis | 6.4% | 6.4% | 6.6% | 6.6% | 6.7% | 6.2% | 6.7% | — | |
B. variegata | |||||||||
cox1 | BW-N | BW-S | R | C- W | C- E | A | B. bombina | B. orientalis | |
B. variegata | BW-N (variegata) | — | |||||||
BW-S (scabra) | 0.3% | — | |||||||
R (rhodopensis subsp. nov.) | 1.6% | 1.6% | — | ||||||
C-W (variegata) | 5.1% | 4.8% | 4.9% | — | |||||
C-E (variegata) | 5.1% | 4.8% | 5.0% | 0.3% | — | ||||
A (pachypus) | 2.7% | 2.5% | 2.4% | 5.1% | 5.0% | — | |||
B. bombina | 6.8% | 6.6% | 7.0% | 6.3% | 6.3% | 7.2% | — | ||
B. orientalis | 9.1% | 9.1% | 9.7% | 9.3% | 9.3% | 10.3% | 9.7% | — | |
B. variegata | |||||||||
cyt b | BW-N | BW-S | R | C-W | C-E | A | B. bombina | B. orientalis | |
B. variegata | BW-N (variegata) | — | |||||||
BW-S (scabra) | 0.5% | — | |||||||
R (rhodopensis subsp. nov.) | 2.4% | 2.4% | — | ||||||
C-W (variegata) | 8.3% | 8.1% | 8.2% | — | |||||
C-E (variegata) | 8.6% | 8.4% | 8.5% | 0.7% | — | ||||
A (pachypus) | 4.7% | 4.4% | 4.8% | 9.6% | 9.7% | — | |||
B. bombina | 11.3% | 11.1% | 10.2% | 9.4% | 9.4% | 11.1% | — | ||
B. orientalis | 17.7% | 17.5% | 17.1% | 16.2% | 16.0% | 18.1% | 15.7% | — |
The nuclear species tree obtained with *BEAST based on the four gene fragments (3715 bp in total) recovered B. variegata as monophyletic and as the sister species of B. bombina (Fig.
Cloudogram of the nuclear species trees obtained with *BEAST based on four gene fragments (3715 bp) and distinguishing samples representative of the different B. variegata mitochondrial lineages. Node labels indicate Bayesian posterior probabilities; sequence labels indicate taxa and mitochondrial lineages; the thick and thin lines show the average tree root and all the sampled trees, respectively.
Support of the gene fragment tree is low to moderate, with posterior probabilities of nodes ranging from 0.62 to 0.92 within the B. variegata clade, a typical issue given the much lower level of polymorphism at nuclear than mitochondrial sequences.
The IQ-TREE analysis confirms the homogeneity among the B. v. variegata sequences, as well as the distinctiveness between the two lineages of B. v. scabra and compared to other taxa (Fig. S3). The topology should however be interpreted with caution, both due to the low polymorphism of the dataset and because such analysis inappropriately assumes a single genealogy shared among the nuclear genes. Accordingly, the IQ-TREE topology appears uninformative, as seen from the nested placement of B. bombina within B. variegata (Fig. S3).
The ddRAD-seq data (4759 loci totaling 553,608 bp) provided a robust phylogenomic tree that distinguished the different phylogeographic lineages of B. variegata (Fig.
Maximum-likelihood phylogeny obtained with IQ-TREE of 4759 concatenated RAD loci (553,608 bp). Colors distinguish the different B. variegata mitochondrial lineages. Sequence labels indicate sample names, geographic origins, taxa and mitochondrial lineages. Asterisks denote robust branch support (bootstrap >95). The tree is rooted by B. bombina.
Based on 11 morphological characters corrected by body length (L.), the two lineages of B. v. scabra differ in body shape (Fig.
Morphological comparison of specimens attributed to the two lineages of B. v. scabra. A PCA on 11 characters corrected by body length distinguishing the males (triangles) and females (circles) of each lineage; B boxplots showing variation in body length (L.) among sexes and lineages. For the list of characters, see Methods (section Morphometric analyses in Bombina variegata scabra).
Males and females from the Rhodope lineage were larger and smaller than their Balkano-Western counterparts, respectively, which resulted in a significant interaction between sex and lineage (F = 7.2, P = 0.007), but not for sex (F = 1.0, P = 0.29) and lineage (F = 0.15, P = 0.691) in the two-way ANOVA (significance tested by a permutation approach). Average raw measurements and their standard deviation are detailed per sex and lineage in Table
Average and standard deviation of the morphological characters measured in 58 specimens representing the Rhodope lineage and the south–northwestern Balkan populations of B. v. scabra, distinguishing females and males (in mm). Values for the extended body length dataset (178 specimens) are given on the last line. For character abbreviations, see Methods (section Morphometric analyses in Bombina variegata scabra).
rhodopensis subsp. nov. | scabra | |||
♀ | ♂ | ♀ | ♂ | |
Morphological measurements | ||||
n | 4 | 6 | 26 | 22 |
L. | 32.1 ± 2.3 | 36.6 ± 5.0 | 41.3 ± 4.5 | 40.5 ± 4.8 |
F. | 10.1 ± 1.2 | 12.3 ± 2.6 | 15.9 ± 1.7 | 15.8 ± 2.0 |
T. | 11.4 ± 1.0 | 13.4 ± 2.7 | 15.6 ± 1.4 | 16.0 ± 1.7 |
D.p. | 2.7 ± 0.2 | 3.2 ± 0.7 | 3.9 ± 0.6 | 3.9 ± 0.7 |
L.c. | 8.0 ± 0.3 | 9.2 ± 1.2 | 10.0 ± 1.1 | 10.5 ± 1.1 |
Lt.c. | 10.2 ± 1.0 | 11.6 ± 1.6 | 12.8 ± 1.3 | 13.2 ± 1.4 |
Sp.oc. | 4.4 ± 0.4 | 5.2 ± 0.6 | 5.7 ± 0.7 | 5.6 ± 0.6 |
D.r.o. | 6.5 ± 0.1 | 7.5 ± 1.3 | 8.6 ± 0.9 | 8.7 ± 0.7 |
Lt.p. | 2.2 ± 0.1 | 2.2 ± 0.2 | 2.4 ± 0.3 | 2.5 ± 0.3 |
Sp.p. | 2.8 ± 0.3 | 2.9 ± 0.2 | 3.1 ± 0.4 | 3.2 ± 0.6 |
L.o. | 3.6 ± 0.4 | 4.1 ± 0.6 | 4.3 ± 0.4 | 4.3 ± 0.4 |
Sp.n. | 2.0 ± 0.1 | 2.2 ± 0.3 | 2.4 ± 0.4 | 2.4 ± 0.3 |
Extended body length measurements | ||||
n | 12 | 36 | 72 | 58 |
L. | 39.5 ± 7.5 | 45.1 ± 5.0 | 43.4 ± 6.1 | 43.01 ± 5.8 |
Comparisons of body ratios (character/L.) between the two B. v. scabra lineages suggest overlapping distributions for all characters (males and females combined), but four of them show significant differences (Kruskal-Wallis tests, P < 0.05) (Fig.
Body ratios (character/body length L.) between the Rhodope (purple) and Balkano-Western (light green) lineages of B. v. scabra (males and females combined). Brackets indicate significant differences (Kruskal-Wallis test) at P < 0.05 (dash) and at the adjusted P < 0.0045 for multiple testing (plain). For character abbreviations, see Methods (section Morphometric analyses in Bombina variegata scabra).
Color/dark ratios range from 0.26 (almost entirely dark) to 10.3 (almost entirely colored) (Fig.
Our analyses suggest that the species B. variegata features four genuine evolutionary lineages eligible for a taxonomic classification. First, the nuclear similarity among the two divergent mitochondrial lineages attributed to nominal subspecies B. v. variegata (mtDNA C and BW-N) implies the existence of a single taxon among these populations, which extends from the Carpathians to Western Europe; the mitochondrial discordance is discussed below (see Discussion). Second, we confirm the independent evolution of the Apennine populations known as B. v. pachypus (mtDNA A). Third and fourth, we documented the mitochondrial, nuclear and morphological differentiation of two lineages among the populations attributed to B. v. scabra, one in the Western and Southern Balkans (mtDNA BW-S) and one in the Rhodope (mtDNA R). As argued below (see Discussion), we preliminarily consider these Northern, Apennine, Balkan and Rhodope lineages as four distinct subspecies of the yellow-bellied toad B. variegata. Their respective distributions are provided in Fig.
Geographic distributions of the four subspecies of B. variegata and location of the type localities of available names for each (stars). Red: Northern subspecies; yellow: Apennine subspecies; light green: Balkan subspecies; purple: Rhodope subspecies. The dashed and question-marked areas correspond to potential contact zones/introgression and regions of unclear subspecies assignment, respectively. Senior synonyms are shown by big stars and are labelled with capital letters; junior synonyms are shown by small stars and are labelled with numbers.
Illustrations of the ventral side of European Bombina toads in nomenclaturally important specimens (top) and summary of the nomenclatural history (bottom). A Bottom right specimen in plate XXVII of Rösel (1758, pl. XXII) considered by
Rana variegata Linnaeus, 1758 – First published in Systema Naturae 10th edition without mention of a specimen and a locality other than “Exteris regionibus [foreign countries]” (
Rana bombina Linnaeus, 1761 – Described from “Scaniae compestris fossis australibus [= southern Scania/Skåne]” in Sweden (
Bufo igneus Laurenti, 1768 – Given as “Rœsel. Tab XXIII. XXII.” and “Habitat in paludibus nostris Danubialibus ingenti in copia; autumno omnis via, qua itur in Nusdorff, iisdem scatet” [= lives in great abundance in our Danubian marshes; in the autumn every road that leads to Nusdorff is covered with it]” (
Bufo salsus Schrank in Schrank & Moll, 1785 – Documented from “Berchtesgaden” in the Bavarian Alps, with no mention of specimens (
Rana sonans Bonnaterre, 1789 – Originally mentioned in
Bufo ignicolor Fibig & Nau, 1789 – Originally mentioned in the Synopsis Methodica of
Bufo pluvialis Daudin, 1803 – Mentioned on a plate (
Rana cruenta Pallas, 1814 – Mentioned from “Rossia media [= central Russia]” with no reference to any specimen (Pallas’s collections are not known to exist,
Bombinator pachypus Bonaparte, 1838 – Identified in the Italian mountains and explicitly distinguished from Bombinator igneus (Laurenti, 1768) – the only accepted Bombina species at this time (see Fig.
Bombinator pachidactylus Quattrocchi & Battistelli in Bonaparte, 1838 – An alternative name for Bombinator pachypus that is mentioned only on the legend of the plate representing that species, signed by Quattrocchi, the illustrator, and by Battistelli, the lithographer. It is likely to be an error, which may have contributed to Boulenger’s open criticism of Bonaparte’s work (
Bombinator brevipes Blasius, 1839 – Reported in Blantenburg [Blankenburg (Harz)] with locality given as “am Unterharze, namentlich bei Goslar, in einem Sumpfe am Fusse des Hartzensteins und bei Osterode vorkommend [occurring in the Lower Harz, especially near Goslar, in a swamp at the foot of the Hartzenstein, and near Osterode]”, and no reference to any specimen (
Bombinator scaber Küster, 1843 – Discovered in Montenegro with locality given as “kleine Lache bei Cettigne [= small puddle near Cetinje]” and explicitly distinguished from Bombinator igneus (Laurenti, 1768), but with no reference to any specimen (
Bombinator appeninicus Gistel in Gistel & Bromme, 1850 – Distinguished from Bombinator igneus with distribution given as “Italien auf den Apenninen [Italy in the Apennine Mountains]”, without mention of a specific locality or any specimen (
Bombina maculatus Gistel, 1868 – Described from “Regensburg” in Bavaria, Germany, with no reference to any specimen (
Bombinator pachypus var. Kolombatovici Bedriaga, 1890 – Given as a variety of Bombinator pachypus (= the yellow-bellied toad, now B. variegata) of large size and documented from “Dalmatien [Dalmatia]”, based on specimens from “Spalato [Split, Croatia]” (
Bombinator pachypus var. nigriventris Dürigen, 1897 – Discussed as a black-bellied variety characteristic of “bosnischen Exemplaren [Bosnian specimens]” (
Bombina salsa var. csikii Fejérváry, 1923 – Described based on 4 specimens from “Ipek” (Mus. Hung. Amph. [MNH] 2540/5), 1 specimen from “Mount Korab collected, at 1800 m.” (MNH 2540/6) and 1 specimen from “Kula Lums (from the banks of the Luma)” (MNH 2561/3), all near the border of present Albania, Kosovo/Serbia and North Macedonia. The author refers to a form with extremely developed horny spines and a black ventral coloration, which
Bombina variegata gracilis Bolkay, 1929 – Described from “Zabrgje (Northeastern Bosnia) [=Zabrđe]” based on 9 males and 5 females (and “some younger larvae”), curated at the Bosnia-Hercegovina State Museum in Sarajevo (= now National Museum of Bosnia and Herzegovina, ZMBH). The author also mentions that specimens collected in the “Save [= Sava]” river belong to this form. The diagnosis emphasizes weakly developed warts compared to western Balkan populations attributed to B. variegata kolombatovici (
Bombina bombina danubialis Călinescu, 1931 – Described from several sets of unspecified specimens collected in south and southeastern Romania, namely 16 from “Lunca Mofleni, lânga Caiova, judetul Dolj [Lunca Mofleni, near Craiova, Dolj county]”, 5 from “Lacul Herăstrău, lângă Bucureşti [Herastrau Lake, near Bucharest]”, 1 from “Băneasa”, 3 from “Olteniţa, judeţul Ilfov [Olteniţa, Ilfov county]”, 13 from “un izvor în pădurea Comana (Vlaşca) [a spring in the Comana forest (Vlasca)]”, 51 from “Craiova (canalul cald al moarei Mendel) şi împrejurimi (Lunca Mofleni, pârâul Izvorului din Luncă şi Balta Şerca) [Craiova (hot water canal of Mendel mill) and surroundings (Lunca Mofleni, Izvorului stream from Luncă and Balta Şerca]”, 39 from “Tulcea (bălţile şi smârcurile dinspre grădinării, sub dealul Monumentului) [Tulcea (the puddles and marshes from gardens, under the Monument hill)], 3 from “insula farului la Sf. Gheorghe, judeţul Tulcea [lighthouse island at Sf. Gheorghe, Tulcea county], 5 from “Periprava, judeţul Tulcea [Periprava, Tulcea county]” and 14 from “Vâlcov (canale părăsite), judeţul Ismail [Vâlcov (abandoned channels), Ismail county]” (now in Odesa Oblast, Ukraine). The author emphasized the distinctiveness of his taxon in terms of belly coloration (uneven yellow/yellow-orange blotches, never red), and the presence of dorsal spiny warts (
Bombina bombina var. viridis Marián, 1959 – Given as a color variety characterized by a greenish dorsum and grey-pink flanks, sighted in “vielen Stellen der ungarischen Ebene [numerous places in the Hungarian plain]” and in the same biotopes as the nominal form. The author mentions the collection and terrarium breeding of specimens (perhaps subsequently curated in Móra Ferenc Múzeum, Szeged, Hungary). From the geographic origin and description, Bombina bombina var. viridis Marián, 1959 clearly refers to Bombina bombina.
Bombina bombina arifiyensi Özeti & Yilmaz, 1987 – Described as a subspecies inhabiting Anatolian Turkey, with holotype SZE 9/1983-11 from “Arifiye” [Sakarya Province, Turkey]. This taxon was noted for differences in color and morphology patterns compared to specimens collected from Thrace Province (European Turkey). From the geographic origin, description, and photographs, Bombina bombina arifiyensi Özeti & Yilmaz, 1987 refers to Bombina bombina.
Finally, a few non-Bombina taxa have occasionally been associated with fire/yellow-bellied toads in some historical work, e.g., Rana Rubeta Linnaeus, 1758 (a synonym of Bufo bufo (Linnaeus, 1758)) as the “Feuerkröte” [= the fire-bellied toad] in
There are, to the best of our knowledge, no other names that apply to European Bombina populations. While three of our B. variegata lineages delimited as subspecies have already been named (B. v. variegata, B. v. pachypus, B. v. scabra), the Rhodope populations seem to have never been the focus of any taxonomic work. We therefore describe it as a new subspecies in the next section.
Previously identified as a divergent mitochondrial (cyt b) lineage, attributed to the subspecies Bombina variegata scabra by
BG-IBER-VER-000010561, adult male collected on 23 April 2024 by SL, MD, DJ and CD in a water fountain at the northeastern exit of Kostino, Kardzhali Municipality, Kardzhali Province, Bulgaria (41.7039°N, 25.3028°E; elevation: 563 m a. s. l.), and curated at the Institute of Biodiversity and Ecosystem Research of the Bulgarian Academy of Sciences (
BG-NMNHS-HER-000000000552 (L. 41.6 mm), adult male collected on 23 April 2024 by SL, MD, DJ and CD at the type locality and curated at the National Museum of Natural History of the Bulgarian Academy of Sciences (
General characteristics similar to those of the yellow-bellied toad B. variegata. It is the sister taxon of the Balkan subspecies B. v. scabra, from which it is distinguished by substantial mitochondrial, nuclear (especially phylogenomic) and morphological divergence. Specifically, B. v. rhodopensis subsp. nov. differs from B. v. scabra by 1.3% of sequence divergence at 16S, 1.6% of sequence divergence at cox1, and 2.4% of sequence divergence at cyt b (Table
The name rhodopensis is a Latin toponymic adjective given in reference to the Rhodope Mountains in the southeastern part of the Balkan Peninsula (Bulgaria and Greece) where the new taxon is mostly distributed. It spotlights a rare case of Rhodope endemism in vertebrates – Rhodope endemics are so far known only from plants and invertebrates.
Rhodope yellow-bellied toad (English), Родопска жълтокоремна бумка (Bulgarian), Κιτρινομπομπίνα της Ροδόπης (Greek), Rodop Sarılı Kurbağa (Turkish), Sonneur à ventre jaune des Rhodopes (French), Kunka žltobruchá rodopská (Slovak).
Bombina v. rhodopensis subsp. nov. is essentially restricted to the Rhodope Mountains and their foothills (from sea level up to 1600 m a.s.l.) in southeastern Bulgaria, northeastern Greece, and the adjacent part of Turkish Thrace (
The new subspecies inhabits similar habitats as B. v. scabra, being found in various aquatic sites such as mountain brooks, rivers, ponds, natural and artificial lakes or water-filled ruts and puddles (
Bombina v. rhodopensis subsp. nov. was reported widespread over the eastern Rhodopes of Greece and Bulgaria (
Our study confirmed the existence of four phylogeographic lineages within B. variegata, clarified their evolutionary relationships and distributions, and associated them with subspecies after an extensive overview of the nomenclatural history of European Bombina – no less than 21 existing names. These include B. v. variegata in northern ranges, B. v. pachypus in the Apennine Peninsula, B. v. scabra in the Balkans, and the newly described B. v. rhodopensis subsp. nov. in the Rhodopes. A tentative biogeographic scenario is presented in Fig.
Hypotheses for the historical biogeography of B. variegata in the Balkan Peninsula in respect to paleo-mountain ranges and the time-calibrated phylogeny (Fig.
The phylogenetic position of the Apennine B. v. pachypus, which branches with the Balkan subspecies B. v. scabra and B. v. rhodopensis subsp. nov. in the mtDNA and phylogenomic trees suggests historical dispersal between the Apennine and Balkan Peninsula after the diversification of B. variegata was initiated (Fig.
The taxonomic rank of B. v. pachypus remains controversial (
The Balkano-western populations of B. v. variegata carry mtDNA derived from B. v. scabra (Fig.
This remarkable situation yet appears common among Balkan amphibians examined with both mitochondrial and nuclear data. For instance, mtDNA of the Anatolian green toad Bufotes viridis sitibundus segregates in about half of the populations of the European green toad B. v. viridis, following refugial hybridization and post-glacial expansion (
Cyto-nuclear discordance offers opportunities to detect past hybridization events, but it stresses the need to reconstruct mitochondrial and nuclear phylogenies independently in phylogeography and species delimitation. For the latter especially, it is often tempting to combine mitochondrial and nuclear sequences in order to obtain more robust species trees (e.g., with the multispecies coalescent), but these trees are “chimeric” if the mitogenome reflects a divergent evolutionary history than the nuclear genome. Accordingly, previous Bombina studies explored variation at only two nuclear fragments, either separately using haplotype networks (ncx1 and rag-1:
Spatial patterns of diversification in the Balkans emphasize the Dinarides/Balkanides (scabra/variegata), and Pirin/Rila massifs (scabra/rhodopensis subsp. nov.) as major phylogeographic breaks (Fig.
In the south, the distribution of B. v. rhodopensis subsp. nov. shares similarities with the European ranges of the newts Lissotriton vulgaris schmidtleri (
Besides molecular divergence, B. v. scabra and B. v. rhodopensis subsp. nov. also quantitatively differ in morphology and in their ventral color patterns. In particular, we retrieved in both subspecies the sexual dimorphism in body shape previously established for B. v. scabra (
The various aspects surrounding the evolution of B. variegata (and their equivalents in other herpetofauna) illustrate well the processes by which the Balkan Peninsula generates and preserves phylogeographic diversity (e.g.,
The generic term “refugium” traditionally designates specific geographic areas where populations survived the Pleistocene climatic fluctuations, either through range shifts from unsuitable areas (“true” refugium) or by persistence on the spot (“sanctuary” refugium, sensu
We are grateful to A. Schmitz for access to the MNHG collection, to F. Tillack and M.-O. Rödel for access to the
Figures S1–S3
Data type: .docx
Explanation notes: Figure S1. Schematic of the morphological characters measured. — Figure S2. Maximum-likelihood phylogeny of the mitogenome alignment obtained with IQ-TREE. — Figure S3. Maximum-likelihood phylogeny of the four nuclear gene fragments obtained with IQ-TREE.
Tables S1–S6
Data type: .docx
Explanation notes: Table S1. Locality information and number of cyt b sequences attributed of the B. variegata lineages. — Table S2. Information on the mitogenomes used in the mitochondrial phylogeny. — Table S3. Information on the nuclear sequences used in the gene-based nuclear phylogeny. — Table S4. Information on the samples used in the phylogenomic analysis. — Table S5. Information on the specimens used in the morphological and coloration analyses. — Table S6. Variable loadings of the PCA on morphological characters.