Monthly Archives: July 2016

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”.

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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).

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New list of types in MZSP

Cavallari et al. just published another list of type material in the Museu de Zoologia da Universidade de São Paulo. The abstract reads: “An alphabetical list of 352 type lots of molluscs housed in the Museu de Zoologia da Universidade de São Paulo is presented following the standards of the previous list by Dornellas & Simone (2011), with a few adjustments. Important items listed herein include types of species described after the previous compilation, as well as recently acquired paratypes of Asian Pomatiopsidae and Diplommatinidae (Gastropoda) taxa described by Rolf A.M. Brandt (1960s), P. Temcharoen (1970s) and W.J.M. Maassen (2000s), all of which belonged to the private collection of Jens Hemmen, Wiesbaden, Germany. Relevant items also include types of recently described species coming from the French- Brazilian Marion Dufresne MD55 expedition, and other types deposited by researchers from Brazil and the world. A list of authors and photographs of specimens are also provided”.

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Reference:
Cavallari D.C., Dornellas A.P.S. & Simone L.R.L., 2016. Second annotated list of type specimens of molluscs deposited in the Museu de Zoologia da Universidade de São Paulo, Brazil. – European Journal of Taxonomy 213: 1–59. http://dx.doi.org/10.5852/ejt.2016.213

Amazonian trees

Today a non-malacological topic, but still relevant in my opinion. Trees in Amazonia may host a largely unknown (at least a highly under-collected) malacofauna. Personally I’m convinced that if malacologists would explore canopies better, it would yield very interesting results.

Anyway, this post is provoked by a review on the Amazonian tree flora by ter Steege et al., (2016). Their abstract reads as follows “Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades. We find that a species’ range size is a better predictor of the number of times it has been collected than the species’ estimated basin-wide population size. Finding, describing, and documenting the distribution of the remaining species will require coordinated efforts at under-collected sites”.

terSteege2016

The article gives a historical overview of the collections made in Amazonia, i.e. French Guiana, Suriname, Guyana, Ecuador, Colombia, Brazil, Peru, Venezuela, and Bolivia, together with data of diversity and collection density, taxonomic patters, collection frequency, population size and range size. The discussion offers valuable suggestions for further research and concludes with a citation from Hubbell (2015) that is mutatis mutandis applicable also to malacology: ‘we need far better data on the geographic ranges and abundances of tropical tree species to finally put the “how many species?” question to rest. It seems to me that our priorities are misplaced. We spend many billions of dollars to look for extra-terrestrial life but far less to understand life and its distribution on our own planet’.

References:
Hubbell, S. P., 2015. Estimating the global number of tropical tree species, and Fischer’s paradox. – Proceedings of the National Academy of Science USA 112, 7343–7344.
ter Steege, H., Vaessen, R.W., Cárdenas-López, D., Sabatier, D., Antonelli, A., Mota de Oliveira, S., Pitman, N.C.A., Møller Jørgensen, P. & Salomão, R.P., 2016. The discovery of the Amazonian tree folra with an updated checklist of all known tree taxa. – Scientific Reports 6: 29549. Available at http://www.nature.com/articles/srep29549

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.

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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

To wait for print or not, that’s a question

One of my earlier, larger publications (though it’s not is my list here) was about biohistory (Breure & de Bruijn, 1979). It was quite voluminous and so it took time to write and to get it printed. Those were still the days of (relatively) ‘slow science’, and while this was a book, it will always be slower than publishing a paper. Today science is must faster is several ways, and one doesn’t necessarily have to wait till the final print has arrived to see your work being published. Although I have to admit it is always nice to see something in print, it more than often will remain as bits and bytes on your screen.

Several options for rapid, though informal, publication are nowadays available. Some journals offer ‘early access online’, others have the option of non-peer-reviewed preprints, and there is always the option to upload a manuscript as a working paper to ResearchGate or Academia. These latter two options are suitable when you want to use one manuscript as a building block for another, and need a formal reference using the DOI:

Yesterday one such manuscript was published as PeerJPreprint, and again it’s about biohistory. This time about research related to the collections made by a Spanish expedition in South America during the 1860s.

PeerJP160701

Although the manuscript is intended for publication in a peer-reviewed journal, this will take time. And probably (much) longer than the paper which will result of the research recently done in Madrid. That was an important reason for choosing this option. And although there are definitely pros and cons related to these different options for quick publication, sometimes it’s not so much a matter of impatience as well as practicality to making me decide this way.

Reference:
Breure, A.S.H. & Bruijn, J.G. de, 1979 (eds.). Leven en werken van J.G.S. van Breda (1788–1867): 1–429. Hollandsche Maatschappij der Wetenschappen, Haarlem / Tjeenk Willink, Groningen.