Whole genome sequencing (WGS) is a very valuable resource to understand the evo- lutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non- model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at:
Montero-Mendieta S, Grabherr M, Lantz H, De la Riva I, Leonard JA, Webster MT, Vilà C. (2017) A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog. PeerJ 5, e3702 [PDF]
The genus Chalcides comprises about 30 species of scincid lizards mainly distributed across north Africa, its taxonomic status and distribution as described in the literature has fluctuated in recent years. in May 2014, the authors found a skink of the Chalcides type in Théniet el Had national Park (Algeria) initially classified as Chalcides mertensi Klausewitz, 1954, based on its morphological similarity and distribution. A region of 396-bp of the cytochrome b mitochondrial gene was sequenced as a reference against a preexisting phylogeny of the genus Chalcides. Surprisingly, this skink was genetically closely related with specimens of Chalcides minutus Caputo, 1993, found 300 km away. Comparison of the morphology between the new record and the original descriptions showed that this skink is likely to represent a new species of Chalcides, and that a major revision of Algerian skinks is needed to unravel the phylogeny of the C. minutus-mertensi species complex.
Montero-Mendieta S, Ferrer J, Hammou MA, Dahmani W, Sanuy D & Camarasa S (2017) Another record or a new taxon? A candidate species of Chalcides Laurenti, 1768, in North Africa (Squamata: Sauria: Scincidae). Herpetozoa. Volume 29 (3/4): 155-161[PDF]
We studied the variation in genetics, bioacustics, and morphology in Eleutherodactylus glamyrus, a regionally endemic frog species restricted to high elevations in the Sierra Maestra Massif, Western Cuba that was originally described as a cryptic species hidden under the name E. auriculatus. Genetic analysis of mtDNA sequences of the 16S and cob genes identify two allopatric and strongly supported mitochondrial clades (phylogroups) which also showed no haplotype sharing in the nuclear Rag-1 gene. Bioacustic, and morphological comparisons concordantly identify these two phylogroups as independent evolutionary lineages. Therefore, we herein restrict the name Eleutherodactylus glamyrus Estrada and Hedges to populations represented in our analyses as the western phylogroup (Cordillera del Turquino to Pico La Bayamesa) and consider specimens from the eastern phylogroup (Sierra del Cobre) to represent a new species described and named as Eleutherodactylus cattus. Our results add to the growing list of Eleutherodactylus species endemic to Cuba and highlight the importance of combining different sources of evidence for obtaining robust assessments of species limits in amphibians.
Rodríguez A, Dugo-Cota A, Montero-Mendieta S, Alonso R, Vences M, Vilà C. (2017) Cryptic within cryptic: genetics, morphometrics, and bioacoustics delimitate a new species of Eleutherodactylus (Anura: Eleutherodactylidae) from Eastern Cuba. Zootaxa 4221 (5): 501–522 [PDF]
A decade ago, DNA barcoding was proposed as a fast, cost-efficient and simple taxonomic method based on the use of a unique, short and standardized gene region for identifying existing species and speeding the discovery of new ones. Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra’s most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8–54.4%. This has implications in the species’ ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.
Vasconcelos R*, Montero-Mendieta S*, Simó-Riudalbas M, Sindaco R, Santos X, Fasola M, Llorente GA, Razzetti E, Carranza S. (2016) Unexpectedly high levels of cryptic diversity uncovered by a complete DNA barcoding of reptiles of the Socotra Archipelago. PLOS ONE 11(3): e0149985 (*Both authors contributed equally to this work) [PDF] [Press release] [IBOL press]
On 13th June 2014 we observed one population of Alpine newt (Ichthyosaura alpestris) outside its natural distribution range, near the natural space of "Parc del Castell de Montesquiu" in Barcelona, Catalonia Spain. This finding represents the first report of a breeding population of I. alpestris in Catalonia. On 18th and 25th June, we performed two samplings with the aim of: a) determining whether nearby water ponds were colonized, b) estimating population size, c) performing population biometrics, d) determining the origin of the introduced specimens, and e) detecting the presence of pathogens in the population. After doing molecular analyses, we found out that the introduced might be a mix of individuals from two different subspecies: I. a. apuanus and I. a. cyreni. Interestingly, these subspecies are commonly used in aquariums. We detected the presence of Ranavirus spp in the studied individuals, thus increasing the risk of transmission to native species, such as Alytes obstetricans. Additionally, we also observed the presence of two other breeding populations of I. alpestris near the study area, which might be a direct consequence of their invasive potential. We concluded that a drastic intervention is highly needed to prevent the expansion of I. alpestris and remove the species from this area.
Fibla M, Ubach A, Oromí N, Montero-Mendieta S, Camarasa S, Pascual-Pons M, Martínez-Silvestre A & Montori A. (2015) Población introducida de tritón alpino (Mesotriton alpestris) en el Prepirineo catalán. Bol. Asoc. Herpetol. Esp: 26(1) [PDF]