Conflicting phylogenetic signal of nuclear vs mitochondrial DNA markers in midwife toads (Anura, Discoglossidae, Alytes): Deep coalescence or ancestral hybridization?

Gonçalves, Helena; Martínez‐Solano, Íñigo; Ferrand, Nuno; Garcı́a-Parı́s, Mario

doi:10.1016/j.ympev.2007.03.001

Cited by 44 publications

(59 citation statements)

References 36 publications

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“…While several studies have addressed patterns of variation in morphology, allozymes, and mitochondrial and nuclear DNA (Arntzen and García-París, 1995;Fonseca et al, 2003;Martínez-Solano et al, 2004;Gonçalves et al, 2007), several aspects of the evolutionary history of this species remain unsolved. Recently, a study by Maia-Carvalho et al (2014a), based on mitochondrial and microsatellite data in a set of populations representative of all currently recognized subspecies, revealed discordances with previous studies.…”

Section: Introductionmentioning

confidence: 99%

Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium

Gonçalves

Maia‐Carvalho

Sousa-Neves

et al. 2015

Molecular Phylogenetics and Evolution

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Recent investigations on the evolutionary history of the common midwife toad (Alytes obstetricans) revealed high levels of geographically structured genetic diversity but also a situation where delineation of major historical lineages and resolution of their relationships are much more complex than previously thought. We studied sequence variation in one mitochondrial and four nuclear genes throughout the entire distribution range of all recognized A. obstetricans subspecies to infer the evolutionary processes that shaped current patterns of genetic diversity and population subdivision. We found six divergent, geographically structured mtDNA haplogroups diagnosing population lineages, and varying levels of admixture in nuclear markers. Given the timeframe inferred for the splits between major lineages, the climatic and environmental changes that occurred during the Pleistocene seem to have shaped the diversification history of A. obstetricans. Survival of populations in allopatric refugia through the Ice Ages supports the generality of the "refugia-within-refugia" scenario for the Iberian Peninsula. However, lineages corresponding to subspecies A. o. almogavarii, A. o. pertinax, A. o. obstetricans, and A. o. boscai responded differently to Pleistocene climatic oscillations after diverging from a common ancestor. Alytes o. obstetricans expanded northward from a northern Iberian refugium through the western Pyrenees, leaving a signal of contrasting patterns of genetic diversity, with a single mtDNA haplotype north of the Pyrenees from SW France to Germany. Both A. o. pertinax and A. o. boscai are widespread and genetically diverse in Iberia, the latter comprising two divergent lineages with a long independent history. Finally, A. o. almogavarii is mostly restricted to the north-eastern corner of Iberia north of the Ebro river, with additional populations in a small region in south-eastern France. This taxon exhibits unparalleled levels of genetic diversity and little haplotype sharing with other lineages, suggesting a process of incipient speciation.

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Section: Introductionmentioning

confidence: 99%

Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium

Gonçalves

Maia‐Carvalho

Sousa-Neves

et al. 2015

Molecular Phylogenetics and Evolution

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“…For instance, Sequeira et al (2006) report intron sizes ranging from 400 bp in Pleurodeles waltl to 1123 bp in Salamandra atra; they were able to obtain good resolution in phylogenetic analyses within Salamandridae. Additionally, Gonçalves et al (2007) found significant levels of variation at both intra-and interspecific levels in the 634 bp-long sequences of midwife toads (Alytes) analyzed in their study. Pairwise Kimura-2 parameter-corrected genetic distances between species pairs in Alytes are 2.5 to 7.6 times higher in mtDNA (cob, data from Martínez-Solano et al, 2004) than in β-fibint7 (Gonçalves et al, 2007), and the corresponding values in Discoglossus are similar, 3.7-5 times higher in mtDNA than in β-fibint7 (this study).…”

Section: Discussionmentioning

confidence: 86%

“…The availability of nearly-universal primers and its relatively fast evolutionary rate have proven useful in recovering phylogenetic relationships in a variety of vertebrate taxa, from amphibians to birds and mammals (Prychitko and Moore, 1997;Weibel and Moore, 2002;Yu and Zhang, 2005;Sequeira et al, 2006;Gonçalves et al, 2007). In some cases, high levels of intraspecific variation have allowed characterization of phy-logeographic patterns, sometimes corresponding closely to those observed at the mtDNA level (Godinho et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

β-fibrinogen intron 7 variation in Discoglossus (Anura: Discoglossidae): implications for the taxonomic assessment of morphologically cryptic species

2008

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Abstract. The generalized use of nuclear introns in combination with mitochondrial DNA data in molecular systematic and intraspecific phylogeographical studies is providing new insights into the complex evolutionary histories of taxa surviving the Quaternary glaciations. Previous studies have highlighted the suitability of the beta-fibrinogen intron 7 (β-fibint7) for phylogenetic and phylogeographic studies in a wide variety of taxa, including amphibians. Here we use sequences of this marker to assess inter-and intraspecific variation in Discoglossus (Discoglossidae), with special emphasis on geographic patterns of genetic structure in the Iberian Peninsula, where recent studies have questioned the taxonomic status of D. jeanneae. We obtained 81 sequences of β-fibint7 from samples including all currently recognized species except D. montalentii and 37 populations in the Iberian Peninsula and compared levels of genetic variation with those observed in a fragment of similar length of the mtDNA gene cytochrome b. The sequence of β-fibint7 in Discoglossus is the shortest described for amphibians so far, 378 base pairs. In general, we found low levels of variability (only 26 parsimony-informative sites in the dataset), with no alternatively fixed haplotypes in samples attributed to D. galganoi or D. jeanneae based on their mtDNA. Values of pairwise sequence divergence between non-Iberian species ranged from 1.1% to 4.5% (13.3% to 20.9% in mtDNA). The patterns observed in samples from the Iberian Peninsula are consistent with either incomplete lineage sorting or ongoing gene flow between D. galganoi and D. jeanneae. We conclude by reviewing the genetic evidence available to address the taxonomic status of Iberian species of Discoglossus.

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“…Despite 12S and 16S mtDNA sequences have been largely used in phylogenetic studies of anurans (e.g., Darst and Cannatella 2004;Ron et al 2006), we must be aware that incongruences between the phylogenetic relationships inferred from mitochondrial and nuclear markers may occur (e.g., Gonçalves et al 2007;Koblmüller et al 2007 ) P S -l a n a n a B ( Fig. 7 A partial view of the strict consensus cladogram of Figure 1 showing some of the hypothetical transformations in NOR-bearing chromosomes (numbers in the branches).…”

Section: Karyotype Differentiation Within the Paratelmatobius + Scythmentioning

confidence: 99%

Molecular phylogeny and karyotype differentiation in Paratelmatobius and Scythrophrys (Anura, Leptodactylidae)

et al. 2007

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Paratelmatobius and Scythrophrys are leptodactylid frogs endemic to the Brazilian Atlantic forest and their close phylogenetic relationship was recently inferred in an analysis that included Paratelmatobius sp. and S. sawayae. To investigate the interspecific relationships among Paratelmatobius and Scythrophrys species, we analyzed a mitochondrial region (approximately 2.4 kb) that included the ribosomal genes 12S and 16S and the tRNAval in representatives of all known localities of these genera and in 54 other species. Maximum parsimony inferences were done using PAUP* and support for the clades was evaluated by bootstrapping. A cytogenetic analysis using Giemsa staining, C-banding and silver staining was also done for those populations of Paratelmatobius not included in previous cytogenetic studies of this genus in order to assess their karyotype differentiation. Our results suggested Paratelmatobius and Scythrophrys formed a clade strongly supported by bootstrapping, which corroborated their very close phylogenetic relationship. Among the Paratelmatobius species, two clades were identified and corroborated the groups P. mantiqueira and P. cardosoi previously proposed based on morphological characters. The karyotypes of Paratelmatobius sp. 2 and Paratelmatobius sp. 3 described here had diploid chromosome number 2n = 24 and showed many similarities with karyotypes of other Paratelmatobius representatives. The cytogenetic data and the phylogenetic analysis allowed the proposal/corroboration of several hypotheses for the karyotype differentiation within Paratelmatobius and Scythrophrys. Namely the telocentric pair No. 4 represented a synapomorphy of P. cardosoi and Paratelmatobius sp. 2, while chromosome pair No. 5 with interstitial C-bands could be interpreted as a synapomorphy of the P. cardosoi group. The NOR-bearing chromosome No. 10 in the karyotype of P. poecilogaster was considered homeologous to chromosome No. 10 in the karyotype of Scythrophrys sp., chromosome No. 9 in the karyotype of Paratelmatobius sp. 1, chromosome No. 8 in the karyotypes of Paratelmatobius sp. 2 and of Paratelmatobius sp. 3, and chromosome No. 7 in the karyotype of P. cardosoi. A hypothesis for the evolutionary divergence of these NOR-bearing chromosomes, which probably involved events like gain in heteochromatin, was proposed.

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Conflicting phylogenetic signal of nuclear vs mitochondrial DNA markers in midwife toads (Anura, Discoglossidae, Alytes): Deep coalescence or ancestral hybridization?

Cited by 44 publications

References 36 publications

Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium

Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium

β-fibrinogen intron 7 variation in Discoglossus (Anura: Discoglossidae): implications for the taxonomic assessment of morphologically cryptic species

Molecular phylogeny and karyotype differentiation in Paratelmatobius and Scythrophrys (Anura, Leptodactylidae)

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