Molecular phylogeny and genetic identification of populations of two species of Feirana frogs (Amphibia: Anura, Ranidae, Dicroglossinae, Paini) endemic to China

Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species

The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.

Integrative taxonomy unveils a new species of Dugesia (Platyhelminthes, Tricladida, Dugesiidae) from the southern portion of the Taihang Mountains in northern China, with the description of its complete mitogenome and an exploratory analysis of mitochondrial gene order as a taxonomic character

A new species of Dugesia (Platyhelminthes, Tricladida, Dugesiidae) from northern China is described on the basis of an integrative approach, involving morphology, karyology, histology, molecular distance, molecular phylogeny, and mitochondrial gene order. Here, we present the complete mitogenome of the new species Dugesia constrictiva Chen & Dong, sp. nov. This new species is mainly characterized by the presence of the following features: asymmetrical openings of the oviducts; large, cuboidal copulatory bursa; vasa deferentia opening through the ventro-lateral wall of the seminal vesicle; laterally compressed seminal vesicle; ventrally displaced ejaculatory duct, opening at the blunt tip of the penis papilla; long duct intercalated between seminal vesicle and diaphragm; chromosome complement diploid, with 16 metacentric chromosomes; mitochondrial gene order as follows: cox1-E-nad6-nad5-S2-D-R-cox3-I-Q-K-atp6-V-nad1-W-cox2-P-nad3-A-nad2-M-H-F-rrnS-L1-Y-G-S1-rrnL-L2-T-atp8-C-N-cob-nad4l-nad4. In triclads, mitochondrial gene order is considerably conserved between freshwater planarians and land flatworms, whereas it is variable between marine planarians and both freshwater and land flatworms. The secondary structures of tRNAs are all equipped with 4 arms, excepting tRNA S1 and tRNA S2, which lack the D arm and have excessively enlarged loops. Numerous transpositions of tRNA are present between D. constrictiva and its congeners. Mitochondrial gene arrangements may form a new, additional tool for taxonomic studies. The phylogenetic tree based on analysis of the mitochondrial genome basically corroborates current classification of the higher taxa of planarian flatworms.

Unveiling the roles of interspecific competition and local adaptation in phenotypic differentiation of parapatric frogs

Understanding how ecological processes affect phenotypic evolution has been and continues to be an important goal of ecology and evolutionary biology. Interspecific competition for resources can be a selective force driving phenotypic differentiation that reduces competition among sympatric species (character divergence), enabling closely-related species to coexist. However, although patterns of character divergence are well documented in both empirical and theoretical researches, how local adaptation to abiotic environment affects trait evolution in the face of interspecific competition is less known. Here, we investigate how patterns in morphological traits of 2 parapatric frog species, Feirana quadranus and F. taihangnica, vary among allopatric and sympatric regions using range-wide data derived from extensive field surveys. Feirana quadranus was overall larger than F. taihangnica in body size (i.e., snout–vent length [SVL]), and the difference between SVL of both species in sympatry was larger than that in allopatry. From allopatry to sympatry, the 2 species diverged in foot and hand traits, but converged in eye size and interorbital span, even when we controlled for the effects of geographic gradients. Sympatric divergence in SVL, hand and foot traits is likely acting as a case of evolutionary shift caused by interspecific competition. In contrast, sympatric convergence of eye-related traits may derive at least partly from adaptation to local environments. These results imply the relative roles of interspecific competition and local adaptation in shaping phenotypic diversification. Our findings illustrate how traits evolve in parapatric species pair due to sympatric divergent and convergent evolution. It thus provides insights into understanding underlying evolutionary processes of parapatric species, that is, competition and local adaptation.

Inferring ecological explanations for biogeographic boundaries of parapatric Asian mountain frogs

Background

Identifying and understanding the mechanisms that shape barriers to dispersal and resulting biogeographic boundaries has been a longstanding, yet challenging, goal in ecology, evolution and biogeography. Characterized by stable, adjacent ranges, without any intervening physical barriers, and limited, if any, range overlap in a narrow contact zone, parapatric species are an interesting system for studying biogeographic boundaries. The geographic ranges of two parapatric frog species, Feirana quadranus and F. taihangnica, meet in a contact zone within the Qinling Mountains, an important watershed for East Asia. To identify possible ecological determinants of the parapatric range boundaries for two closely related frog species, we quantified the extent of their niche differentiation in both geographical and environmental space combining ecological niche models with an ordination technique. We tested two alternative null hypotheses (sharp environmental gradients versus a ribbon of unsuitable habitat dividing two highly suitable regions) for biogeographic boundaries, against the null expectation that environmental variation across a given boundary is no greater than expected by chance.

Results

We found that the niches of these two parapatric species are more similar than expected by chance, but not equivalent. No sharp environmental gradient was found, while a ribbon of unsuitable habitat did act as a barrier for F. quadranus, but not for F. taihangnica.

Conclusions

Integrating our findings with historical biogeographic information, our results suggest that at a contact zone, environmental tolerance restricted F. quadranus from dispersing further north, while interspecific competition most likely prevented the southward expansion of F. taihangnica. This study highlights the importance of both climate and competition in exploring ecological explanations for parapatric range boundaries between ecologically similar frog species, in particular under the effects of changing climate.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0160-5) contains supplementary material, which is available to authorized users.

Integrative taxonomy helps to reveal the mask of the genus Gynandropaa (Amphibia: Anura: Dicroglossidae)

Species of the genus Gynandropaa within the family Dicroglossidae are typical spiny frogs whose taxonomic status has long been in doubt. We used integrative methods, involving morphological and molecular analyses, to elucidate the phylogenetic relationships, and to determine identities and the geographic distribution of each valid species. We obtained DNA sequence data of 5 species of Gynandropaa (complete sequences of the mitochondrial NADH dehydrogenase subunit 2 [ND2] gene, and 890 bp of 12S rRNA and 16S rRNA partial sequences) from 37 localities (including the topotypes of 5 described species) and constructed Bayesian and maximum-likelihood trees to examine the patterns of phylogeography. A total of 28 morphological variables were taken on 624 specimens. Three clades with clear geographic patterns were recognized: clade C (from south-western Sichuan Province and central Yunnan Province), clade E (western Guizhou Province and eastern to central Yunnan Province) and clade W (western to southern Yunnan Province). Integrating morphological characteristics and distribution information, the clades W, E and C represent Gynandropaa yunnanensis, G. phrynoides and G. sichuanensis, respectively. We draw the following conclusions: (i) the taxon G. phrynoides, formerly evaluated as a junior synonym of G. yunnanensis, is revalidated herein at the rank of species; (ii) G. liui is a junior synonym of G. sichuanensis; and (iii) G. yunnanensis is a valid species while G. bourreti is probably a subspecies of G. yunnanensis, with the distribution range from Vietnam to southern Yunnan Province. This study clears up the taxonomic status of Gynandropaa and provides important information for understanding the evolution and conservation of these spiny frogs.

Species identification through mitochondrial rRNA genetic analysis

Inter-species and intraspecific variations in mitochondrial DNA (mtDNA) were observed in a bioinformatics analysis of the mitochondrial genomic sequences of 11 animal species. Some highly conserved regions were identified in the mitochondrial 12S and 16S ribosomal RNA (rRNA) genes of these species. To test whether these sequences are universally conserved, primers were designed to target the conserved regions of these two genes and were used to amplify DNA from 21 animal tissues, including two of unknown origin. By sequencing these PCR amplicons and aligning the sequences to a database of non-redundant nucleotide sequences, it was confirmed that these amplicons aligned specifically to mtDNA sequences from the expected species of origin. This molecular technique, when combined with bioinformatics, provides a reliable method for the taxonomic classification of animal tissues.

Phylogeographic patterns of mtDNA variation revealed multiple glacial refugia for the frog species Feirana taihangnica endemic to the Qinling Mountains

Diversification patterns and demography of montane species are affected by Pleistocene climate fluctuations. Empirical cases from the Qinling Mountains (QM) region, which is a major biogeographic divider of East Asia, are few. We used DNA sequence data of the complete mitochondrial ND2 gene to detect effects of the Pleistocene glaciations on phylogeographic profiles of a frog species, Feirana taihangnica, which is endemic to the QM. Four distinct lineages consisting of seven sublineages were revealed. The strongest signal of biogeographical structure (F(ct) = 0.971, P < 0.01) was found when populations were grouped according to these seven sublineages. One narrow secondary contact zone was detected in the middle QM between the lineage from middle QM and the lineage from eastern QM. Coalescent simulations indicated that this species colonized the QM region by a stepping-stone model. Divergences among lineages had likely been influenced by the uplift of the Tibetan Plateau during the late Miocene-to-late Pleistocene, as well as by the Pleistocene climatic cycles. Coalescent simulations also suggested that F. taihangnica populations have persisted through the Pleistocene glacial periods in multiple refugia across the QM region. Demographic analyses indicated that all lineages, except the lineage in the Funiu Mountains, have been experienced postglacial expansion of population size and distribution range. In conclusion, Pleistocene climate fluctuations and tectonic changes during the late Miocene-late Pleistocene have profoundly influenced the phylogeography and historical demography of F. taihangnica.

Postglacial colonization of the Qinling Mountains: phylogeography of the swelled vent frog (Feirana quadranus)

BACKGROUND

The influence of Pleistocene climatic fluctuations on intraspecific diversification in the Qinling-Daba Mountains of East Asia remains poorly investigated. We tested hypotheses concerning refugia during the last glacial maximum (LGM) in this region by examining the phylogeography of the swelled vent frog (Feirana quadranus; Dicroglossidae, Anura, Amphibia).

METHODOLOGY/PRINCIPAL FINDINGS

We obtained complete mitochondrial ND2 gene sequences of 224 individuals from 34 populations of Feirana quadranus for phylogeographic analyses. Additionally, we obtained nuclear tyrosinase gene sequences of 68 F. quadranus, one F. kangxianensis and three F. taihangnica samples to test for mitochondrial introgression among them. Phylogenetic analyses based on all genes revealed no introgression among them. Phylogenetic analyses based on ND2 datasets revealed that F. quadranus was comprised of six lineages which were separated by deep valleys; the sole exception is that the Main Qinling and Micang-Western Qinling lineages overlap in distribution. Analyses of population structure indicated restricted gene flow among lineages. Coalescent simulations and divergence dating indicated that the basal diversification within F. quadranus may be associated with the dramatic uplifts of the Tibetan Plateau during the Pliocene. Coalescent simulations indicated that Wuling, Daba, and Western Qinling-Micang-Longmen Mountains were refugia for F. quadranus during the LGM. Demographic analyses indicated that the Daba lineage experienced population size increase prior to the LGM but the Main Qinling and the Micang-Western Qinling lineages expanded in population size and range after the LGM, and the other lineages almost have stable population size or slight slow population size decline.

CONCLUSIONS/SIGNIFICANCE

The Qinling-Daba Mountains hosted three refugia for F. quadranus during the LGM. Populations that originated in the Daba Mountains colonized the Main Qinling Mountains after the LGM. Recent sharp expansion of the Micang-Western Qinling and Main Qinling lineages probably contribute to their present-day secondary contact.

Chromosomal evolution in Rattini (Muridae, Rodentia)

The Rattini (Muridae, Murinae) includes the biologically important model species Rattus norvegicus (RNO) and represents a group of rodents that are of clinical, agricultural and epidemiological importance. We present a comparative molecular cytogenetic investigation of ten Rattini species representative of the genera Maxomys, Leopoldamys, Niviventer, Berylmys, Bandicota and Rattus using chromosome banding, cross-species painting (Zoo-fluorescent in situ hybridization or FISH) and BAC-FISH mapping. Our results show that these taxa are characterised by slow to moderate rates of chromosome evolution that contrasts with the extensive chromosome restructuring identified in most other murid rodents, particularly the mouse lineage. This extends to genomic features such as NOR location (for example, NORs on RNO 3 are present on the corresponding chromosomes in all species except Bandicota savilei and Niviventer fulvescens, and the NORs on RNO 10 are conserved in all Rattini with the exception of Rattus). The satellite I DNA family detected and characterised herein appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). BAC-mapping using clones that span regions responsible for the morphological variability exhibited by RNO 1, 12 and 13 (acrocentric/submetacentric) and their orthologues in Rattus species, demonstrated that the differences are most likely due to pericentric inversions as exemplified by data on Rattus tanezumi. Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequence-based phylogenetic tree thus allowing an objective assessment of ancestral states for the reconstruction of the putative Rattini ancestral karyotype. This is thought to have comprised 46 chromosomes that, with the exception of a single pair of metacentric autosomes, were acrocentric in morphology.