Annemarie Ohler

The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

BackgroundUnderstanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae), Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti (Sooglossidae). These represent major clades not included in previous mitogenomic analyses, and most of them are remarkably species-poor compared to other neobatrachians.ResultsWe reconstructed a fully resolved and robust phylogeny of extant frogs based on the new mitochondrial and nuclear sequence data, and dated major cladogenetic events. The reconstructed tree recovered Heleophryne as sister group to all other neobatrachians, the Australasian Lechriodus and the South American Calyptocephalella formed a clade that was the sister group to Nobleobatrachia, and the Seychellois Sooglossus was recovered as the sister group of Ranoides. We used relative-rate tests and direct comparison of branch lengths from mitochondrial and nuclear-based trees to demonstrate that both mitochondrial and nuclear evolutionary rates are significantly higher in all neobatrachians compared to their non-neobatrachian relatives, and that such rate acceleration started at the origin of Neobatrachia.ConclusionsThrough the analysis of the selection coefficient (ω) in different branches of the tree, we found compelling evidence of relaxation of purifying selection in neobatrachians, which could (at least in part) explain the observed higher mitochondrial and nuclear substitution rates in this clade. Our analyses allowed us to discard that changes in substitution rates could be correlated with increased mitochondrial genome rearrangement or diversification rates observed in different lineages of neobatrachians.

Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana

We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas. On the contrary, R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ~3.5 mya for both species), but R. temporaria might have been characterized by larger ancestral and current effective population sizes than R. dalmatina. The high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a probably more recent event.

Phylogenetic Relationships of the Tribe Paini (Amphibia, Anura, Ranidae) Based on Partial Sequences of Mitochondrial 12s and 16s rRNA Genes

Abstract Partial sequences of mitochondrial 12S and 16S rRNA genes from 19 Asian frog species of the tribe Paini (Ranidae, Dicroglossinae) allowed a first molecular study of the phylogenetic relationships of this tribe. This analysis confirmed that this tribe is a monophyletic group, but suggested relationships did not agree with previous generic classification of this clade based on morphology. Two major clades were recognized within the Paini. For one of them, the generic name Quasipaa is available. Phylogenetic relationships within the other group are not yet fully clarified and need further study.

Does counting species count as taxonomy? On misrepresenting systematics, yet again

Recent commentary by Costello and collaborators on the current state of the global taxonomic enterprise attempts to demonstrate that taxonomy is not in decline as feared by taxonomists, but rather is increasing by virtue of the rate at which new species are formally named. Having supported their views with data that clearly indicate as much, Costello et al. make recommendations to increase the rate of new species descriptions even more. However, their views appear to rely on the perception of species as static and numerically if not historically equivalent entities whose value lie in their roles as “metrics”. As such, their one‐dimensional portrayal of the discipline, as concerned solely with the creation of new species names, fails to take into account both the conceptual and epistemological foundations of systematics. We refute the end‐user view that taxonomy is on the rise simply because more new species are being described compared with earlier decades, and that, by implication, taxonomic practice is a formality whose pace can be streamlined without considerable resources, intellectual or otherwise. Rather, we defend the opposite viewpoint that professional taxonomy is in decline relative to the immediacy of the extinction crisis, and that this decline threatens not just the empirical science of phylogenetic systematics, but also the foundations of comparative biology on which other fields rely. The allocation of space in top‐ranked journals to propagate views such as those of Costello et al. lends superficial credence to the unsupportive mindset of many of those in charge of the institutional fate of taxonomy. We emphasize that taxonomy and the description of new species are dependent upon, and only make sense in light of, empirically based classifications that reflect evolutionary history; homology assessments are at the centre of these endeavours, such that the biological sciences cannot afford to have professional taxonomists sacrifice the comparative and historical depth of their hypotheses in order to accelerate new species descriptions.

Discordant Patterns of Nuclear and Mitochondrial Introgression in Iberian Populations of the European Common Frog (Rana temporaria)

Amphibians often show complex histories of intraspecific and interspecific genetic introgression, which might differ in mitochondrial and nuclear genes. In our study of the genetic differentiation of the European common frog, Rana temporaria (159 specimens from 23 populations were analyzed for 24 presumptive allozyme loci; 82 specimens were sequenced for a 540-bp fragment of the mitochondrial 16S rRNA gene), multilocus correspondence analysis (CA) and Bayesian assignment tests of the nuclear data were concordant in identifying 2 population groups corresponding to 1) the Pyrenees in the east and 2) the Galicia and Asturias regions in the west, the latter corresponding to the subspecies R. temporaria parvipalmata. Geographically intermediate populations were genetically intermediate in the allozyme CA and, less clearly in the Bayesian assignment, with mitochondrial haplotypes exclusively belonging to the parvipalmata group. This indicates different degrees of introgression in the mitochondrial and nuclear genomes. Although Pyrenean high-altitude populations are morphologically distinct from low-altitude populations, these 2 groups were not separate clusters in any analysis. This suggests that the morphological differences may be due to fast adaptation to elevational gradients, likely under maintenance of gene flow, and that the underlying genetic changes are not detectable by the analyzed markers. We argue that a parsimonious explanation for the observed pattern along the east-west axis in northern Spain may be competition between invading and resident populations, with no need to invoke selection. However, in order to conclusively rule out selective processes, additional and finer scale data are required to test for asymmetric mating preference/behaviour, sex-biased gene flow, or sex-biased survival of potential hybrids.

Improving biodiversity assessment of anuran amphibians using DNA barcoding of tadpoles. Case studies from Southeast Asia.

Amphibian populations are dramatically declining, while their inventory is far from being achieved. Tadpoles are usually overlooked from biodiversity survey, whereas their consideration will optimize species counts and knowledge of their ecological and developmental requirements is essential in conservation planning. Two mitochondrial markers, 16S (397 new sequences obtained) and COI (343 new sequences obtained), are used to test DNA barcoding on a set of larval and adult Asian amphibians represented by 83 recognized species from 65 sites. The advantages and drawbacks of each marker are assessed, COI barcoding being advocated for global DNA barcoding, whereas 16S suits for taxonomically or geographically restricted DNA barcoding. About half of the collected tadpoles were badly identified or incompletely named in the field. All tadpole sequences (except one case of probable introgressive hybridization) were correctly assigned to their respective species. Finally six clusters of tadpole sequences without conspecific adults were revealed, stressing the importance of collecting and taking into account tadpoles in biodiversity survey and conservation planning.

The Holotype of Megalophrys weigoldi Vogt, 1924 (Amphibia: Anura, Pelobatidae)

The holotype of Megalophrys weigoldi Vogt, 1924 is described, compared to other species of Scutiger, and referred to the subgenus Scutiger (Aelurolalax).

The snake fauna of Togo: systematics, distribution and biogeography, with remarks on selected taxonomic problems

Segniagbeto G. H., Trape J. F., David P., Ohler A., Dubois A. & Glitho I. A. 2011. — The snake fauna of Togo: systematics, distribution and biogeography, with remarks on selected taxonomic problems. Zoosystema 33 (3): 325–360. ABSTRACT We present here an annotated list of the 91 snake species currently recorded from Togo, West Africa. Seven species are here recorded for the first time from this country: Calabaria reinhardtii, Hapsidophrys lineatus, Lycophidion nigromaculatum, Philothamnus carinatus, Leptotyphlops cf. narirostris, Letheobia crossi and Typhlops lineolatus. Main morphological data of examined specimens are provided. Some taxonomical problems are pointed out and discussed. The distribution of these species is detailed. We also provide a short discussion on the snake trade in Togo.

The identity of Elachyglossa gyldenstolpeiAndersson 1916 (Amphibia, Ranidae), with comments on some aspects of statistical support to taxonomy

Morphological and morphometric studies of the holotype of Elachyglossa gyldenstolpei Andersson 1916 , and comparison with specimens of the genus‐group taxa Limnonectes (Limnonectes), Limnonectes (Bourretia), Limnonectes (Fejervarya), Phrynoglossus and Occidozyga, provide evidence that the genus‐group name Elachyglossa Andersson (1916) is a senior subjective synonym of Bourretia Dubois (1987) | and that the species‐group name Elachyglossa gyldenstolpei is a senior subjective synonym of Rana pileata Boulenger 1916 . This case study supports the statement that univariate (non‐parametric Kruskal–Wallis, Tukey type b analysis) and multivariate (discriminant analysis) data analysis can support taxonomic decision, particularly in the case of taxa known by a single specimen (holotype).

Pyxicephalus khasianus Anderson, 1871 and Rana laticeps Boulenger, 1882 (Dicroglossidae, Anura, Amphibia) are Synonyms

ABSTRACT The study of publications and of museum specimens allows unequivocal identification of the type specimens of Pyxicephalus khasianus Anderson, 1871. These specimens were collected by Thomas Jerdon at the same time as the type specimens of Rana laticeps Boulenger, 1882 and belong to the same biological species. We describe and figure the lectotypes of Pyxicephalus khasianus and of Rana laticeps and give measurements of the other specimens seen by the authors of the original descriptions of both taxa. Thus, both names having been regularly used in literature, the valid name of this species is Limnonectes khasianus (Anderson, 1871), and Rana laticeps Boulenger, 1882 is its junior subjective synonym.