Tag Archives: phylogenetics

Deroceras in Mexico

Just published a paper by Araiza-Gómez et al. on the distribution in Mexico and phylogeny of three Deroceras species.

“This study reports the current distribution in Mexico of Deroceras laeve (Müller, 1774) and D. invadens Reise, Hutchinson, Schunack and Schlitt, 2011, both previously recorded, and the first records of D. reticulatum (Müller, 1774) in this country. The taxonomic identifications were made on the basis of morphology and DNA sequences of a fragment of the cytochrome oxidase I gene. A phylogenetic analysis by maximum likelihood was carried out in order to support the identification and to explore the association of Mexican specimens. D. reticulatum and D. invadens appear restricted to the central portion of the country while D. laeve is widely distributed. Due to the invasive and pest character of these species, it is important to know their distribution in the country and the possible risk to native fauna and crops”.

Schermafbeelding 2017-11-20 om 15.58.36

This study used only the CO1 marker and suggests that for D. laeve three subgroups may be distinguished. Further studies using other markers and phylogeographical analyses are suggested in the discussion.

Reference:
Araiza-Gómez, V. et al., 2017. The exotic slugs of the genus Deroceras (Agriolimacidae) in Mexico: Morphological and molecular characterization, and new data on their distribution. – American Malacological Bulletin, 35(2): 126-133.

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Phylogenetic data Achatinoidea

Phylogenetic studies tend to disrupt often the taxonomic grouping of snails, especially if it combined with anatomical data. Such a study was undertaken by Fontanilla et al. (2017) and a brief paper gives the first results.

This study presents a multi-gene phylogenetic analysis of the Achatinoidea and provides an initial basis for a taxonomic re-evaluation of family level groups within the superfamily. A total of 5028 nucleotides from the nuclear rRNA, actin and histone 3 genes and the 1st and 2nd codon positions of the mitochondrial cytochrome c oxidase subunit I gene were sequenced from 24 species, representing six currently recognised families. Results from maximum likelihood, neighbour joining, maximum parsimony and Bayesian inference trees revealed that, of currently recognised families, only the Achatinidae are monophyletic. For the Ferussaciidae, Ferussacia folliculus fell separately to Cecilioides gokweanus and formed a sister taxon to the rest of the Achatinoidea. For the Coeliaxidae, Coeliaxis blandii and Pyrgina umbilicata did not group together. The Subulinidae was not resolved, with some subulinids clustering with the Coeliaxidae and Thyrophorellidae. Three subfamilies currently included within the Subulinidae based on current taxonomy likewise did not form monophyletic groups”.

It is clear from this publication that within this superfamily further anatomical and molecular studies are needed, the results of which may drastically alter our current systematic treatment of several families in this group.

Reference:
Fontanilla, I.K. et al., 2017. Molecular phylogeny of the Achatinoidea (Mollusca, Gastropoda). – Molecular Phylogenetics and Evolution, 114: 382-385.

Phylogenetic data on Sagdoidea

As an advance online publication, recently appeared the paper by Sei et al. on the phylogenetic relationships within the Sagdoidea.

The abstract reads: “We performed multi-locus, time-calibrated phylogenetic analyses of Jamaican Pleurodontidae to infer their relationships within pulmonate land snails. These analyses revealed that Sagdoidea, with about 200 species in the Caribbean Basin and neighbouring regions, is the sister group of Helicoidea with about 4700 species worldwide and that these superfamilies diverged 61–96 Ma. Morphological disparity in Sagdoidea is similar to that in Helicoidea despite its much lower species richness. Helicoidea originated in the New World and colonized the Old World 46–64 Ma. Pleurodontids and sagdids colonized Jamaica 15.0–18.4 and 12.8–16.5 Ma, respectively, consistent with geological estimates of Jamaican subaerial emergence by mid-Miocene. Allopatric convergence in shell morphologies required caution in using fossils from outside the geographic range of ingroup taxa to calibrate molecular clock estimates. Estimates of ages of clades varied by 24–55%, depending on the calibration points included. We use these results to revise Helicoidea and Sagdoidea. Pleurodontids from Jamaica and the Lesser Antilles were reciprocally monophyletic but other putative pleurodontids grouped basally in Helicoidea as Labyrinthidae (new family), or with Sagdidae. Newly recognized members of Sagdoidea are Solaropsinae and Caracolinae (Solaropsidae), Polydontinae (Sagdidae) and Zachrysiidae (new family). Pleurodontidae is restricted to two subfamilies, Pleurodontinae, in the Lesser Antilles, with Gonostomopsinae, a synonym, and Lucerninae resurrected for the Jamaican endemic genera Lucerna, Dentellaria, Thelidomus and Eurycratera. Lucerna and Dentellaria have been treated as subgenera of Pleurodonte, but rendered it paraphyletic in our analyses”.

This is a nice piece of research for which the authors did extensive DNA research with 3 loci and divergence time analysis. This resulted in a major taxonomical revision of the group, defining the Pleurodontidae and erecting the Labyrinthidae and Zachrysiidae.

Reference:
Sei, M., Robinson, R.G., Geneva, A.J. & Rosenberg, G., 2017. Doubled helix: Sagdoidea is the overlooked sister group of Helicoidea (Mollusca: Gastropoda: Pulmonata). – Biological Journal of the Linnean Society, XX: 1-32 [advance online publication, hence the correct reference will be different].

Pinning down Tenuistemma

Under this (beginning of the) title, Uit de Weerd & Fernández has just made available a paper on the distribution and relationships of an Urocopitid species from eastern Cuba.

We report an extraordinary case of local and extreme shell-morphological differentiation within a group of otherwise relatively uniform eastern Cuban land snails. Analyses of multi-copy nuclear (ITS2) and of mitochondrial (COI) DNA sequences congruently place the ‘genus’ Tenuistemma, occurring monotypically on the Yunque de Baracoa mountain in eastern Cuba, within the more wide-spread species Pleurostemma perplicata from adjacent lower areas. This result is in sharp contrast with patterns of variation in supposedly diagnostic shell-morphological characters, namely (1) differences in both shell form and shell sculpture between Tenuistemma and P. perplicata, (2) the shell- morphological coherence of paraphyletic P. perplicata and (3) the resemblance between P. perplicata and phylogenetically and geographically more distant species placed in Pleurostemma. We conclude that Tenuistemma evolved from P. perplicata on the Yunque de Baracoa, a process that probably started between 0.01 and 1.42 million years ago. The remarkable set of shell features distinguishing Tenuistemma from P. perplicata probably evolved as a result of unique local selection pressures, possibly affecting multiple characters linked in shell development. This study provides a basis for further research into the evolutionary processes behind this remarkable morphological transition. To render the genus Pleurostemma monophyletic, we propose to transfer P. perplicata to the genus Tenuistemma”.

This research is interesting as it hypothesises on the local evolution of snails under different factors. As such there is a link to research on carinated species, of which a paper on Peruvian Bostryx is currently being prepared.

Reference:
Uit de Weerd, D.R. & Fernández V., A., 2017. Pinning down Tenuistemma (Pulmonata: Urocoptidae): local evolution of an extreme shell type. – Biological Journal of the Linnean Society, XX: 1-12. DOI: 10.1093/biolinnean/blx041

Cerion genomics

Harasewych and his team have focused on different aspects of the Cerionidae, but have now added a phylogenetic paper with state-of-the-art technique. “The complete mitochondrial genome of the neotype of Cerion incanum (Leidy, 1851) was sequenced using high-throughput sequencing and found to be a circular genome 15,117 bp in length with a GC content of 34.3%. It is the largest mitogenome presently known in Stylommatophora, with the difference in size due primarily to intergenic regions and to a lesser extent to larger sizes of individual genes. Gene content is identical to that of other stylommatophorans, but differs in having the tRNA-Gln gene situated on the major coding strand. Gene order of C. incanum was similar to that in Helicidae, differing in the regions between COX1 and NADH5, and between tRNA-Ser2 and tRNA-Ile. The potential origin of replication was located in a 50-bp noncoding region between COX3 and tRNA-Ile. Phylogenetic analyses using Bayesian inference and maximum-likelihood analyses of nucleotide data for all protein-coding and large and small ribosomal genes resulted in a well-resolved tree. This tree was similar to trees derived from nuclear or a combination of nuclear and mitochondrial genes, differing from previous phylogenetic reconstructions based on mitogenomes in the placement of Hygrophila. The phylogenetic position of Cerionidae as sister taxon to Helicoidea is consistent with previous findings after allowing for more limited taxon sampling in the mitogenome tree. The mitogenome tree is sufficiently populated to refute the inclusion of Cerionidae in Clausiloidea, as advocated by some authors, but at present lacks the representatives of the Orthalicoidea or Urocoptoidea needed to resolve more precisely its relationships with those taxa”.

Gonzalez16Cerion

The last sentence of their abstract is intriguing, and in Leiden we had hoped to be able to contribute to this knowledge by supplying data from a Bulimulus and a Drymaeus species. However, the PCRs have failed and the project has been dropped.

Reference:
González, V.L., Kayal, E., Halloran, M., Shresta, Y. & Harasewych, M.G., 2016. The complete mitichondrial genome of the land snail Cerion incanum (Gastropoda; Stylommatophora) and the phylogenetic relationships of Cerionidae within Panpulmonata. – Journal of Molluscan Studies: 1–9 (advance access doi:10.1093/mollus/eyw017).

Urocoptidae revisited

Uit de Weerd et al. (2016) have published a paper on the evolutionary history of biogeography of the land snail family Urocoptidae. It is a sequel following previous papers of Uit de Weerd dealing with the Caribbean region.

The authors reconstructed the phylogeny of Urocoptidae based on multi-locus (partial 28S, H3 and COI sequences) analyses (MrBayes, BEAST, GARLI) of 65 species, representing 44 recognized genera. Biogeographical analyses of a subset of the time-calibrated BEAST trees were made both with (DEC and DEC+J analysis in BioGeoBEARS) and without (S-DIVA in RASP) palaeo-geographical assumptions. In the DEC and DEC+J analyses we examined the effect of different settings for dispersal between directly connected areas relative to that between areas without direct land connection. Urocoptidae has been present on the Greater Antilles Arc from at least Middle Eocene onwards. Morphologically diverse and previously unrecognized clades evolved on most Caribbean (palaeo)islands. Jamaica was colonized at least twice. Dispersal multiplier matrices with moderately constrained dispersal between areas without direct land connections describe the phylogeographical history of the family with higher DEC and DEC+J lnL scores than uniform matrices. Urocoptids constitute an old element of the Greater Antillean biota, predating a proposed GAARlandia landspan connection to South America. The biogeographical history and evolution of Urocoptidae were shaped primarily by the geographical distribution of Caribbean landmasses, in combination with occasional oversea dispersal. Oversea dispersal allowed colonization of palaeogeographically isolated areas, such as Jamaica and present-day western Cuba, where presumably the absence of ecological competitors led to independent radiations into similar shell types. A follow-up paper will be dealing with the taxonomic consequences of this study.

Uitdeweerd16

With the representation of 44 genera out of the total 65 recognized genera within the family, this is a comprehensive molecular analysis. No other Caribbean family has been treated this way, thus this study provides unique insights and helps to test competing biogeographical theories about land snail distribution in this region.

Reference:
Uit de Weerd, D.R., Robinson, D.G. & Rosenberg, G., 2016. Evolutionary and biogeographical history of the land snail family Urocoptidae (Gastropoda: Pulmonata) across the Caribbean region. – Journal of Biogeography (early online access) http://wileyonlinelibrary.com/journal/jbi | doi:10.1111/jbi.12692

Reviving Galapagos snails

Under this short title as eye-catcher, Villanea et al. (2016) recently published about an improved method to apply ancient-DNA techniques to identify material obtained from empty shells. The full abstract reads as follows: “Snail shells represent an abundant source of information about the organisms that build them, which is particularly vital and relevant for species that are locally or globally extinct. Access to genetic information from snail shells can be valuable, yet previous protocols for extraction of DNA from empty shells have met with extremely low success rates, particularly from shells weathered from long-term exposure to environmental conditions. Here we present two simple protocols for the extraction and amplification of DNA from empty land snail shells from specimens of Galápagos endemic snails, including presumably extinct species. We processed 35 shells of the genus Naesiotus (Bulimulidae) from the Galápagos islands, some from species that have not been observed alive in the past 50 years. We amplified and sequenced short fragments (≤244 bp) of mitochondrial DNA (mtDNA) from 18 specimens. Our results indicate that the implementation of an ancient DNA extraction protocol and careful primer design to target short DNA fragments can result in successful recovery of mtDNA data from such specimens”. The crux is that the method seems to circumvent largely the PCR inhibitors that are co-extracted when using degraded shells. The resulting tree is given below.

Villanea16

One of the co-authors wrote me “We are really excited about this approach as it will allow us to include rare and potentially extinct species to our considerations of the evolutionary history of the Naesiotus group”. Methodical seems the approach sound, although it remains vague what exactly the inhibitors are. Given the more laborious extractions during aDNA work, it seems to me that the PCR will remain the bottle-neck. With more PCRs needed, this will remain a relatively costly procedure.

Reference:
Villanea, F.A., Parent, C.E. & Kemp, B.M., 2016. Reviving Galapagos snails: ancient DNA extraction and amplification from shells of probably extinct Galapagos endemic land snails. – Journal of Molluscan Studies (early online access; doi: 10.1093/mollus/eyw011).