Tag Archives: phylogenetics

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).

Phylogenetic relationships of Cerionidae

A recent paper by Harasewych et al. (2015) explores the phylogenetic relationships within the Cerionidae and its relations to other families. This makes this group one of the more well-studied Neotropical land snails since the work of Uit de Weerd and other recent publications by Harasewych and co-workers.

The new paper is summarized as follows: “Phylogenetic analyses of partial DNA sequences of the mitochondrial COI and 16S rDNA genes derived from Mexistrophia reticulata Thompson, 2011, the type species of the genus Mexistrophia, indicate that this genus is sister taxon to all remaining living Cerionidae, and that the family Cerionidae is most closely related to Urocoptidae. Relationships among representative cerionid taxa are consistent with the zoogeographic hypothesis that Mexistrophia has been isolated from the remaining living Cerionidae since the Cretaceous, and suggest that the near-shore, halophilic habitat that has commonly been associated with this family is likely a Cenozoic adaptation that coincided with the transition from continental to island habitats. The genus Protocerion is described to include the Late Cretaceous species Cerion acherontis Roth and Hartman, 1998, as its retention in Cerion would render this genus paraphyletic”.

Haresewych2015

Reference:
Harasewych, .G., Windsor, A.M., Lopez-Vera, E. & Thompson, F.G., 2015. On the phylogenetic relationships of the genus Mexistrophia and of the family Cerionidae (Gastropoda: Eupulmonata). – The Nautilus 129: 156–162.

Vertiginidae

Vertiginid land snails are tiny and constitute a tiny (but yet ill-studied) group of the Neotropical fauna. Apart from a monograph by Pilsbry in his Manual of Conchology, hardly any recent studies are known on this faunal element. For the Nearctic vertiginids Jeff Nekola has done much work and he has just published a note on the supraspecific taxonomy of the family (Nekola & Coles, 2016).

Nekola2016f2

A detailed phylogenetic study revealed that there are two clades, the Vertiginidae and Nesopupinae. The latter comprising tropical species. The paper discusses the use of genetical markers, and the interpretation of the results in the light of the number of taxa included in a family. The authors plead for a reconsideration of supraspecific concepts within the Orthurethra.

Reference:
Nekola, J.C. & Coles, B.F. Supraspecific taxonomy in the Vertiginidae (Gastropoda: Stylommatophora). – Journal of Molluscan Studies 82: 208–212.

Evolution and biogeography of Urocoptidae

Just published, the very interesting paper by Dennis Uit de Weerd et al. presents new data on the phylogenetics of the land snail family Urocoptidae. They also tested some biogeographical hypotheses using the phylogeny and present as results: “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”.

UitdeWeerd2016

As their main conclusions they present: “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 presentday western Cuba, where presumably the absence of ecological competitors led to independent radiations into similar shell types”. In a future paper a taxonomic revision of the family and of the genus Brachypodella will be published.

Reference:
Uit de Weerd, D., 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 [advanced access]: 1–15.