Tag Archives: dna

Taxonomy of Omalonyx

A group of Brazilian authors have made a comprehensive study on the succineid genus Omalonyx, with interesting results.

“The genus Omalonyx d’Orbigny, 1837, includes neotropical semi‐aquatic succineid slugs and comprises six recognized species to date. Field surveys across continental South America recovered five of the six recognized species. According to the morphological characters traditionally included in Omalonyx descriptions, the specimens were tentatively identified as O. matheroni, O. pattersonae, O. convexus, O. geayi and O. unguis. Employing sequences of mitochondrial cytochrome oxidase I (COI) alone or combined with the nuclear second internal transcribed spacer (ITS2) in discovery methods of species delimitation (GMYC and STACEY) led to species delimitation hypotheses that, except for unambiguously supporting O. convexus, have no correspondence to morphologically based assignments. To choose the delimitation model that best fit our data, the hypotheses recovered by GMYC, STACEY and morphology and created by merging species recovered by those methods had their marginal likelihood estimated and compared using the Bayes factors. The best‐supported hypothesis distinguished two species besides O. convexus: one widespread over most of South America and the other restricted to Rio de Janeiro State, Brazil. Furthermore, the pattern of genetic structuring supports pathways connecting the Amazonian and Atlantic forests. This pattern is similar to that observed in terrestrial taxa (e.g., forest‐dwelling small mammals) and is different from the pattern for fully aquatic taxa.”

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This is a well-executed study that uses different methods to formulate several hypotheses. The best-supported one leads the authors to conclude that there are two species to be recognised: O. convexus (Martens, 1868) and O. matheroni (Potiez & Michaud, 1835). This result is interesting, the more since this group is extremely difficult to study using the morphology alone. Such integrative studies are thus the way forward, and should be attempted also for other groups of Neotropical snails.


Vidigal, T.H.D.A. et al., 2018. Integrative taxonomy of the neotropical genus Omalonyx (Elasmognatha: Succineidae). – Zoologica Scripta, 47 (2): 174-186.

New Hispaniolan Annulariids

Already some months ago, Thomas Watters published a new revision dealing with Hispaniolan annulariids (Watters & Larson, 2017).

The annulariid genera Chondropomella, Chondropomium, and Clydonopoma are believed to have originated from the Tiburon/Barahona Peninsula in isolation from the rest of Hispaniola. Chondropomium has colonized the rift valley and adjacent river valleys between the Tiburon Peninsula and the remainder of Hispaniola. It is primarily limited to xeric lowlands, rarely found above 200 m elevation. Little is known about the rare Chondropomella but they seem to occur in the rift valley in xeric areas as well. In contrast, Clydonopoma is endemic to the Sierra Baoruco with a single species in the adjacent eastern Massif de la Selle and occupies the upland mesic forests and pine savannahs between 200–4000 m. The most widely distributed species, Chondropomium weinlandi, has been the subject of considerable confusion concerning the nature of its many color forms or subspecies, as well as its valid name. This species was investigated using phylogenetic methods and compared to congeners and related genera. A phylogenetic study aimed at elucidating relationships among these taxa analyzed a partitioned matrix of nuclear (ITS 1) and mitochondrial (CO1, 12S, 16S) DNA sequences in a Maximum-likelihood framework under the GTR+G substitution model. Contrary to Bartsch’s 1946 assessment that C. weinlandi is a complex of subspecies, it is here shown to be a single, highly polymorphic species for color. The new genus Superbipoma is recognized based on phylogenetic, radular, and conchological evidence. It contains two species: S. asymmetricum (Henderson and Simpson, 1902) and S. superbum (Pilsbry, 1933). Eleven species of Chondropomium are recognized including two new species: C. caelicum and C. sardonyx; three species of Chondropomella and nine species of Clydonopoma, including one new species, Clydonopoma titanum, are recognized. A calcified operculum is the ancestral condition for the Annulariidae. In Clydonopoma and Chondropomella the operculum is a particularly complex calcified structure termed the pseudolamella. This structure has been lost in Chondropomium and Superbipoma”.

As usual, this paper is very thorough, well organised and includes a phylogenetic study based on a multi-locus analysis.

Watters, G.T. & Larson, P., 2017. A revision of the Hispaniolan genera Chondropomella, Chondropomium, and Clydonopoma (Gastropoda: Annulariidae), with the recognition of a new genus, Superbipoma: phylogenetic, radular, and conchological evidence. – Nautilus, 131 (3):163-201.

Using microwaves to prepare gastropods

Today time for a tidbit about methodology and techniques. Already published some years ago, Galindo et al. (2014) provide a nice study about the use of microwaves to remove snails from their shells and the possible effect on DNA research of the animals.

Extracting DNA from gastropods presents particular difficulties due to the capacity of the living animal to retract into the shell, resulting in poor penetration of the ethanol into the tissues. Because the shell is essential to establish the link between sequences and traditional taxonomic identity, cracking the shell to facilitate fixation is not ideal. Several methods are currently in routine use to overcome this difficulty, including chemical relaxation, drilling the shell and boiling. Most of these methods are time-consuming, may be safety hazards and constitute a bottleneck in the preparation of large numbers of specimens in the field. We have experimented with a method traditionally used to clean shells that involves placing the living gastropods in a microwave (MW) oven; the electromagnetic radiation very quickly heats both the animal and the water trapped inside the shell, resulting in separation of the muscles that anchor the animal to the shell. Done properly, the body can be removed intact from the shell and the shell voucher is preserved undamaged. To test the method, the bodies of live-collected specimens from two gastropod species were separated from their shell by microwaving and by anesthetizing/drilling. After identical extraction and PCR procedures, the gels showed no difference in DNA quantity or quality, and the resulting sequences are identical within species. The method was then implemented on a large scale during expeditions, resulting in higher percentage of DNA extraction success. The MWs are also effective for quickly and easily removing other molluscs from their shells, that is, bivalves and scaphopods. Workflows implementing the MW technique show a three- to fivefold increase in productivity compared with other methods”.

This is an interesting method for those wanting to prepare material for DNA research and who have the equipment available during field work. Note that the authors are usually part of full-fletched expeditions with much more facilities than the average field worker. One disadvantage, also mentioned in the paper, of the procedure is its unsuitability for ethanol-preserved material. That is a pity, since material from collections is usually difficult to remove from their shells.


Galindo, L. et al., 2014. Using microwaves to prepare gastropods for DNA barcoding. – Molecular Ecology Resources, 14: 700-705.

Colombian Megalobulimus

Jaramillo et al. (2014) recently published a paper which combined anatomical and molecular research on Megalobulimus oblongus (Müller, 1774) (Strophocheilidae) from Colombia.

The abstract reads: “In this work was done morphological and molecular analysis to 28 land snails of Megalobulimus oblongus, collected in different departments of Colombia, deposited in a reference collection. For morphological characterization, the animals were dissected in a stereomicroscope. The reproductive system and the shell were described. Measures were taken to structures of the reproductive system. Of the shell were described its shape, color, number of whorls and ornamentation and equally basic measures were taken using a digital caliper. For molecular analysis were used two mitochondrial markers, 16S rRNA and cytochrome C oxidase subunit I (COI). Only one haplotype was obtained for each marker, even for individuals of different and distant biogeographical regions. This study suggests that M. oblongus is in danger, therefore are urgent investigations about reproduction, population genetics and biogeography to clarify its situation in Colombia. It also demonstrates that the reference collections and tissue banks are sources of valuable information since they allow knowing aspects related with the species’ risk that serve as an input for the design of conservation actions”.

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The Colombian specimens were collected at six different sites, three of which are in Dept. Antioquia, and one in adjacent Caldas; two originated from the eastern departments. The genetic invariability found was linked to human transportation due to illegal trade. The conclusion that this species, widespread in South America, in endangered in Colombia seems premature. Not all species need to be conserved everywhere anytime in any political-administrative region; this might be a misconception of what biodiversity really is.

The data in Table 2 can be supplemented with the locality of Megalobulimus parafragilior Leme & Indrusiak, 1990: Brazil, São Paulo, Peruibe (MZSP 86740), as mentioned in the source from which the sequence was derived.

Jaramillo Roldán, E., López Martínez, J., Ramírez, R. & Velásquez Trujillo, L. , 2014. Análisis morfológico del sistema reproductor e identificación molecular a través de los marcadores mitocondriales COI y 16S rRNA de Megalobulimus oblongus (Mollusca, Strophocheilidae) de Colombia. – Revista peruana de Biología 21: 79–88. http://bit.ly/1rGTAFs

Mollusca 2014 abstracts

During the congress of Neotropical malacologists in Mexico City, 22–27 June, many interesting talks and posters were presented. From the abstracts book (link here) I mention the following titles arranged alphabetically to (first) author.

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Borda, V. & Ramirez, R. Phylogenetic relationships of Megabuliminae (Mollusca, Gastropoda) reveal homoplasy in morpholicical evolution [p. 26]. Molluscan morphology involves characters that are under the influence of the environment. Megalobuliminae includes some of the largest neotropical land snails. One important problem with Megalobuliminae taxonomy is the plasticity of their anatomical characters. The goal of this work is to reveal the evolution of certain shell and reproductive characters using a molecular phylogeny based on 16S rRNA. For morphological and molecular analysis we used 10 species of Megalobulimus from Peru, three of them with red‐lip (M. capillaceus, M. florezi, and M. separabilis) and seven with white‐lip (M. maximus, M. popelairianus, M. huascari, M. lichtensteini, M. leucostoma leucostoma, M. leucostoma lacunosus and M. sp. nov.). We selected three species (Augustula braueri, Edentulina minor and Natalina knysnaensis) as outgroups. The alignment of the 16SrRNA fragments resulted in 341 positions. The GTR substitution model, obtained with JModelTest, was used to generate trees with RAxML and Mr.Bayes. Both trees showed similar topologies with two monophyletic groups. One clade includes M. huascari, M. separabilis, M. lichtensteini, M. sp. nov, M. leucostoma leucostoma, M. popelairianus and M. maximus. The other clade includes M. florezi, M. capillaceus and M. leucostoma lacunosus. This arrangement reveals the polyphyletic nature of the leucostoma complex that is supported by differences in male genitalia. The red‐lip character present in M. florezi, M. capillaceus and M. separabilis resulted in homoplasy. Likewise, both groups include species with different shell size; M. leucostoma lacunosus has a more slender and larger shell with respect to M. capillaceus and M. florezi. M. separabilis and M. huascari are sister species, they share the filiform aspect of male genitalia and an internal diverticulum in their oviducts despite having very different shell features. The complex distribution of shell characters in Megalobulimus could be a response to different ecological niches; however, certain reproductive characters reveal some evolutionary relationships.

Borrero, F.J. Systematic studies of terrestrial mollusks from Colombia and adjacent regions – current status, approaches and challenges [p. 29]. The non‐marine malacofauna of tropical America is still very poorly known. Major portions of northern South America and adjacent areas in Central America have not been the focus of sampling aimed at studying continental mollusks. However, these regions are also of significant interest for documenting the sheer magnitude of biodiversity, its geographic distribution, and possible relationships between species richness and environmental correlates including geologic history, forest types, and patterns of land utilization. Colombia is particularly well suited as a region of interest for assessing patterns of diversity distribution, due to its position at the junction of South and Central America, and to the complex geological events leading to the formation of the Isthmus of Panama and major mountain chains. The interaction of several major biogeographical regions, and the presence of recognized biodiversity hotspots for other biotic groups lend further support to this assertion. Important insights into continental‐level biotic exchange through the isthmus, and its effects on shaping current faunas may be gained from focusing studies in the junction of the Americas. Using examples from four relatively large, conspicuous and diverse genera of land snails, this presentation will describe an approach, currently in use, for assessing state of knowledge and progress in species delimitation and understanding of variation. These are required first steps towards estimating the magnitude of land snail diversity in Colombia. A collaborative program is being developed for garnering support from Colombian authorities towards facilitating surveys in poorly studied regions and habitats, including the existing network of protected areas in the country. This program is allowing a better understanding of the neotropical continental malacofauna and its distribution, will develop local expertise, and will provide insights into needed conservation actions.

Borrero, F.J., Lawless, A.S., Callomon, P. & Rosenberg, G. Digitatization of molluscan types at the Academy of Natural Sciences of Philadelphia [p. 30]. The collection of Recent mollusks at the ANSP is one of the largest worldwide, as well as the oldest and one of the most extensive in the Americas. Holdings include > 485,000 lots, and about 10 million specimens, including ~ 40,000 lots preserved in ethanol. Type material is present for about 10,000 nominal species described by more than 600 authors, encompassing all major groups of Mollusca and nearly worldwide representation. The type holdings are 56% terrestrial, 27% marine and 17% freshwater. The NSF‐supported Mollusk Type Digitization Project currently underway is studying the name‐bearing types of Recent Mollusca at the ANSP, updating the collection database, and posting project data online in a publicly accessible portal, including images of at least one specimen from each primary type lot. Information includes locality data and provenance, relevant citations affecting nomenclature and type status, measurements, and images of multiple standard views of each specimen. This is a major contribution to the nomenclature of Recent Mollusca, as well as a critical resource for systematic, ecological, conservation and phylogenetic studies. The goals, approach and main methodology used in this project are described, and specific examples of results to date are presented. Several protocols, techniques and sets of equipment have been developed specifically for this project, and details are given of their development and application, as well as the challenges encountered.

Cano-Santana, Z., Romero-Mata, A. & Rivera-García, A. Snails, slugs and clams of Mexico City [p. 39]. We conducted a bibliographic review of records of mollusks in México City. We found 54 species and subspecies, including four mussels and 50 gastropods. However, the gastropods reported for the city represent only 3.8% of the land mollusk diversity recorded for the whole country, and mussels represent 5.8% of the 69 species known for the country. The gastropods encompass one limpet, 41 snails, and eight slugs, and 26% of the species are exotic. Unfortunately, some species have been lost, as they were recorded in 1920 and nowadays they are not found. For example, the snail Drymaeus rudis has not been collected in the forest of Chapultepec since 1950. None of the land mollusks are protected by the government, but there are initiatives to protect green areas in specific patches of forest, and these sites provides habitat for native species of gastropods. Therefore, the urban and rural areas where the mollusks have not been recorded should be investigated to improve knowledge of this group in this region.

Correa-Sandoval, A. & Thompson, F.G. Biogeography of the terrestrial gastropods in southern Taumaulipas, Mexico [p. 49]. The terrestrial gastropods of the southern region of the state of Tamaulipas, México were surveyed (December, 1990 – November, 2006). This region has much elevational, topographic and climatic variation. Samples (525) were obtained from 121 localities, in different vegetational types. The primary zoogeographical relationships are characterized by the presence of endemics taxa (45 species or subspecies: 42.86%, highest value in northeastern México), and by the grouping of species of neotropical and neartic affinities (24 species: 22.86%) and those exhibiting neotropical distributions (15 species or subspecies: 14.29%). The family Spiraxidae has the largest number of endemic species (17 species and two subspecies). This family has the largest number of endemic species (29) in northeastern México.

Cuezzo, M.G., Pignataro de Lima, A.F. & Santos, S.B. dos. Anatomy of Solaropsis brasiliana (Deshayes, 1832): A contribution to the phylogeny of the Pleurodontidae (Stylommatophora, Helicoidea [p. 53]. The genus Solaropsis Beck, 1837 as well as the other South American taxa formerly classified into Camaenidae have a complex systematic history needed yet to be untangled. Its systematic position is problematic due to the scarce knowledge on anatomy, because the original descriptions are short, generally based only on shell characters. Solaropsis brasiliana (Deshayes, 1832) is an emblematic species from eastern Brazil, known just by shell morphology. The present study describes for the first time the anatomy of this species, updates the geographical range, and also introduces continuous characters that clarified the relationships among species in order to contribute to the solution of the Pleurodontidae phylogenetic puzzle. The shell of S. brasiliana is helicoid, depressed, spire moderately elevated, obtuse, with four to four 1⁄2 globose whorls, thin but solid, with periphery obsoletely angular; shell surface with regularly arranged rounded to oval granules, each bearing short hairs; dorsal surface with brown zigzagged bands; ventral side with dotted brown lines; shell aperture slightly oblique, with delicate slightly expanded peristome; basal lip of aperture with slightly undulating peristome; umbilicus only partially covered by peristomal columellar fold. Roof of pallial cavity system is distinctive by its dark pigmentation. Nephridium half the length of the pallial cavity roof, shorter than in other species; secondary ureter completely closed as in most of the Solaropsis species. Ovotestis forming a single, compact mass; bursa copulatrix with a thick and long diverticulum, flagellum thicker and longer than in other species of the genus; epiphallus straight, penis retractor muscle bifurcated with the vas deferens passing through it. The species seems to occur in Río de Janeiro, Espírito Santo and Minas Gerais states. The phylogenetic hypothesis of relationships obtained in the present study shows resolved relationships for the clade Solaropsis, supporting the genus as monophyletic.

Dourson, D.C. & Caldwell, R.S. Land snails of Belize [p. 59]. “Land Snails of Belize” documents 157 native and two exotic land snail species from 23 families. 122 species are recognized with a remaining 35 species undetermined, possibly new to science, endemic or range‐restricted to Belize. Belize belongs to a much larger biotic region including México and Central America that contains many biomes, different geological structures, complex physiographic features and a myriad of ecological settings. The number of recorded land snail species (an estimated 1,239 taxa) from this area is about 35% of the actual fauna predicted with as much as 65% remaining undiscovered (Thompson 2011: Bulletin Florida Museum Natural History, 50: 1‐299). Recent collection efforts and database searches have documented 85‐90% of the total fauna expected to occur in Belize based on Thompson’s predictions. Belize is divided into three distinct land snail ecoregions 1) the North (Corozal, Orange Walk and Belize Districts) which includes a unique biome, the Dry Tropical Forest, 2) Western Slopes of the Maya Mountain Divide (Cayo District) and 3) Eastern Slopes of the Maya Mountain Divide (Toledo and Stann Creek District). The Maya Mountains Massif (East and West) is one of the most important molluscan regions in Belize and indeed in Central America, due to its early geographic isolation as mountains. Northern Belize harbors one of the most endangered biomes in the world, the Dry Tropical Forest. Interesting subregions such as Towel Karst of the savanna of the Belize District and Yalbac Hills (border of Orange Walk and Cayo Districts) add to the overall biodiversity. Terrestrial gastropods are critical components in ecosystems as food sources to several taxonomic groups and dispersers of fungi and other taxonomic groups.

Espinosa, A. & Bastardo, R.H. Conservation status of terrestrial mollusks from the eastern part of Sierra de Bahoruco, Dominican Republic [p. 61]. Dominican Republic and Haiti share the island of Hispaniola, the second in size in the Greater Antilles. Based on a preliminary literature review, specimen collections and data bases, we have determined that 28 families and 741 species of terrestrial mollusks have been found on this island. The Southwest region of the Dominican Republic is regarded as one inhabited by the most diverse fauna of terrestrial mollusks on the island. This is caused, in part, by its karstic soils and habitat diversity due to the complex geological history of the region. Sierra de Bahoruco is the most prominent mountain of the region (2,367 msnm); its center exhibits a complex mosaic of vegetation with cloudy forest of broadleaves modified by cattle husbandry and agriculture (coffee and minor crops) since the beginning of the 20th Century. Thirteen families were found recently while sampling transects and plots in the Western part of Sierra de Bahoruco. According to the literature, Sierra de Bahoruco is the type locality for about 30 species, including the emblematic Oleacina voluta, which is found sporadically, and Coloniconcha prima, the only semi‐slug from La Hispaniola. It is necessary to be more precise assigning the type locality of many species that have been reported for the locality type “Sierra de Bahoruco” without specifying the side (Western or Eastern). The habitat loss due to the increasing use of land for agriculture is a threat for the permanence of terrestrial mollusk species, which are still poorly known.

Fields, A. & Robinson, D.G. Under treat – the molluscan fauna of Barbados [p. 67]. The island of Barbados is located in the Atlantic Ocean, 150 km east of the Lesser Antillean Archipelago, at 13°10′ N, 59°35′ W. It is a limestone island of low relief with a land area of 430 square kilometers and a maximum elevation of 330 metres. The island was settled by the English in 1627 and suffered severe loss of original vegetation to facilitate the cultivation of sugar cane. It is densely populated with an estimated population size of 290,000. Between 1862 and the present, 39 species of terrestrial molluscs have been confirmed from the island, 33 of which are snails and six are veronicellid slugs. The endemic snail, Pseudopineria barbadensis was rediscovered in 2003 but its continued existence is precarious as its preferred habitat is very fragmented. Current threats to the molluscan fauna include continued habitat loss due to urbanization and mortality resulting from efforts to eradicate the giant African snail. A potential threat is the presence of a parasitic mite, Riccardoella sp. that is found on molluscs in several locations on the island.

Herrera-Uria, J. Los tipos de la collección malacológica histórica “Miguel L. Jaum”, depositados en el Museo Nacional de Historia Natural de Cuba [p. 107]. We have revised the historic malacological collection “Miguel L. Jaume,” housed in the Cuban National Museum of Natural History. The original label data was copied and the veracity of the information was checked with the original descriptions of all species. The historic collection has 278 specimens included in 20 subspecies, 13 species, 12 generous and six families. The total of localities and collectors was 33 and 17 respectively.

Herrera-Uria, J., Breugelmans, K. & Backeljau, T. Molecular taxonomy of Viana regina (Morelet, 1849) in Cuba (Gastropoda, Neritinimorpha, Helicinidae) [p. 108]. Cuba has a rich terrestrial malacofauna with > 1300 species of which about 95% are endemic. One of the emblematic species is Viana regina (Morelet, 1849), which is an endemic taxon in the region of Pinar del Rio. Currently, the species is divided in three subspecies with relatively well‐defined distribution areas, viz. V. r. regina (Sierra de Viñales to Soroa), V. r. laevigata (Pfeiffer, 1865) (Sierra de los Organos) and V. r. subunguiculata (Poey, 1859) (Sierra de Guane to Sierra de Quemado). The three taxa differ only in a few subtle and highly variable conchological features, including shell color patterns and the form of the peristomal lip. Some authors have even suggested that the variation in these characters may reflect ecophenotypic, rather than subspecific, differentiation. As such, the significance of these supposedly taxon‐specific differences and the concomitant taxonomic interpretation of the three subspecies need corroboration. Therefore we analyzed nucleotide sequence variation of three mtDNA (COI, 16S rRNA, Cyt b) and two nuclear (ITS‐1, ITS‐2) gene fragments in nine V. regina populations (165 specimens), representing the three subspecies. These sequence data were used for phylogenetic reconstruction and DNA barcoding, showing that the three subspecies are consistently differentiated under a phylogenetic (lineage) species concept. The three taxa also seem to show a strong geographic structuring. The implications of these results will be discussed in the light of future conservation plans for V. regina.

Letelier, S., Báez, P., Rebolledo A. Exotic terrestrial mollusks in Chile: an updated review [p. 120]. The special geographic position of Chile in the south western edge of South America, separated from Argentina and Bolivia by the high peaks of the Andes Mountains, and from Peru by the northern desert zone, contributes to the geographical isolation of the country. However, through the reports of several authors, it has been possible to detect the presence of exotic terrestrial mollusks into the country. Therefore, the main objective of this work has been to do a scientific literature review and a registration of personal communications, including information on terrestrial mollusks introduced into Chile. For most of them, there isn’t systematic baseline data, which would allow to indicate the source or route of their introduction. For this reason they have been categorized as cryptogenic species. Nontheless, the major source of exotic species brought to the country has been through the transport of agricultural inputs, plants and related materials, which usually occurs accidentally or unintentionally. The exotic species recorded in Chile are concentrated in the Family Milacidae, Limacidae, Arionidae, Zonitidae, Helicidae, Achatinellidae, Elobiidae, Higromiidae and Carychiidae. Based on this information, we developed a checklist that included the updated specific taxonomy (Family, Genus, Species, Author) of the species included in these groups, the geographic location of the recorded species, and the authors who cited them. Places with more records are the Juan Fernández Archipelago and Easter Island, followed by other records made in continental Chile, both in the central region and the southern extreme of the country. This review allows to update the introduction of mollusk species situation in the country. At the same time it shows the existing weaknesses related to the registration of systematized information about introduced mollusks into Chile.

López, B., Mejia, O. & Gómez-Ortega. Population genetic structure and demographic history of Humboldtiana durangoensis (Solem, 1959) estimated through microsatellite loci [p. 122]. Land snails represent an excellent model in evolutionary biology due to their high diversity and high rates of molecular evolution. Particularly, metapopulations, composed of ephemeral demes that have experienced several events of colonization and extinction through time are ideal to study the geographic distribution of genetic diversity in order to comprehend evolutionary dynamic of species. The genus Humboldtiana comprise nearly 50 recognized species, most of them known only from the type locality. Among the few exceptions is Humboldtiana durangoensis, an endemic species widely distributed in the Sierra Madre Occidental of Durango, México. At this moment, 110 specimens have been collected in 11 localities, besides, 13 microsatellite DNA loci have been standardized, five of them new from the previously published. These markers will be amplified on each individual and the results will be used to assess a) Genetic diversity b) Genetic divergence among populations c) Population‐Genetic structure and d) Demographic history. This study is only a portion of a wider project that includes also multilocus phylogeography and morphometric variation of the shells.

Naranjo-García, E., Castillo Rodriguez, Z.G. & Oliveira Carrasco, M.T. Moluscos introducidos e invasores en México [p. 148]. Mexico is a country that stands out because of its species richness, inland and marine ecosystems due to its geographic position and its complex geomorphology. Human activities have instigated conscious and unconscious introductions of mollusks. At a national level, 20 families of introduced species have been recorded of which 11 are terrestrial, 6 marine and 3 freshwater. The most frequent in terrestrial environments are the slugs in the families Veronicellidae and Limacidae, in the marine environment are the families Mytilidae and Teredinidae and in freshwater the Thiaridae and Corbiculidae. The veronicellid slug Sarasinula plebeia has caused economic problems in the agriculture of various regions of Mexico, including in vanilla cultivars in Veracruz. Other introduced terrestrial species do not seem to cause harm. In the marine environment, the most abundant introduced mollusks are the bivalves Bankia zeteki, B. destructa, Teredo bartschi and T. navalis. They cause damage to boats and fishing boats, and they are also responsible of displacement of native bivalve communities. The freshwater species Melanoides tuberculata and Corbicula fluminea now have large distributions in Mexico. The freshwater gastropod Tarebia granifera has been recorded in the south‐east region of the country. Foreign commerce, the development of numerous human activities such as fishing, aquaculture, navigation, the aquarium industry, agriculture and/ or natural biological transportation foster the entry of alien species some of which have become invasive. The earliest records of introduced species date back 150 years. Since then the rate of introductions has increased, so it is imperative to take legislative and regulatory actions to avoid the entrance of new species and their harmful ecologic, social and economic impacts.

Pool Canche, A., Herrera Góngora, M. de, León, L.V. & Lizama, R. Gasterópodos terrestres de Buctzots, Yucatán, México [p. 168]. La clase Gastropoda es el grupo más diversificado de los moluscos. La característica principal del grupo Pulmonata es la aparición de un “pulmón“, producto de la vascularización del manto y carecen de opérculo; se distribuyen en regiones tropicales, subtropicales y templadas. En el caso de México se encuentran registradas un total de 41 familias de moluscos terrestres. Para el Estado de Yucatán, y zona sureste de la Republica, no se conocen estudios detallados de la malacofauna continental. Por ello el presente estudio tiene como propósito incrementar el conocimiento de la diversidad malacológica enfocándose a la zona de Buctzots, Yucatán. La recolecta de los macromoluscos fué por el método de colecta manual, modificado para zonas de vegentación densa, por lo cual se emplearon dos transectos de 75 m, dentro de los cuales se delimitaron 5 cuadrantes de 7 x 7 m para cada uno, con una separación de 10 m entre cuadrantes, y 23 m de separación entre cada transecto. La superficie total de muestreo fue 1725 mts2. Se realizó la identificación de 11 especies, agrupadas en cinco familias pertenecientes a 3 ordenes (Neotaenioglossa, Mesogastropoda, Stylommatophora). Con la información obtenida se realizó un listado taxonómico además del análisis de diversidad y riqueza para la zona de estudio. Los organismos más abundantes fueron los miembros del género Chondropoma, sin embargo el género Orthalicus presentó mayor número de organismos completos (organismo y concha). El estudio presente permitirá la realización de futuros trabajos ecológicos, así como la evaluación de especies invasoras, y un mayor acercamiento al estudio de los moluscos terrestres.

Richling, I. Towards the Costa Rican continental molluscan fauna [p. 174]. Up to date there exists no comprehensive work on the Costa Rican continental molluscan fauna despite its biogeographically interesting position as corridor between the North and South American faunas and as a hotspot area. After the epochal Biologia Centrali‐Americana by Martens (1890‐1901) mainly Pilsbry contributed in various publications to the fauna roughly between 1906 and 1948, but hereafter the interest faded. In 1993 with the foundation of the Instituto Nacional de Biodiversidad de Costa Rica (INBio) a new and highly motivated approach began to tackle the molluscan fauna, which resulted in a regional check‐list (Barrientos 2003: Revista Biología Tropical, 51 [Suppl. 3]: 293‐304) reviewing the literature from 1862 through 2001. Unfortunately, INBio had to focus its research goals and closed its malacological department about ten years ago resulting in a significantl interruption of these new efforts. The most recent compilation for Costa Rica is included in the elaborated check‐list for México and Central America by Thompson (2011: Bulletin Florida Museum Natural History, 50: 1‐299), but again without illustrations. The current work in progress aims to study all accessible type material of the species reported and found in the area. In a second step the historical information shall be combined with recent collecting data (e.g. the former INBio collection and other sources) and available ecological information. Although clearly below the level of revisions, the goal is to provide for the first time an illustrated guide to the Costa Rican continental mollusc fauna which summarizes the current state of taxonomic knowledge, shows roughly distribution ranges and moreover exposes the limits of the exploration of the Costa Rican fauna.

Rivera-García, A. & Naranjo-Garciía, E. Land mollusks in the Ecological Reserve of Pedregal de San Angel, Mexico [p. 175]. The ecological reserve Pedregal de San Angel is a volcanic area produced by the eruption of the volcano Xitle about 1670 ±35 years ago. This reserve is situated 2,300 meters above sea level, creating subhumid temperate weather, with two marked seasons: dry and rainy season. The ecological reserve covers about 237 hectares, which have been protected for 30 years. In recent years, students of the UNAM (University National Autonomous of México) searched for land mollusks in this area. A total of 23 species were found. Only six species represent the 89.8% of the abundance, indicating low diversity. However, the ecological reserve represents only a shadow of the complex ecosystem that previously existed. Nowadays mollusks and other groups are under constant pressure for several reasons: for example, human disturbance, introduction of exotic organisms and ecological changes.

Robinson, D.G. The increasing number of invasive terrestrial mollusks in the USA and the efforts to control them [p. 176]. For the first few centuries of colonization of the United States, most of the invasive snails and slugs were of European origin. Most of these species have become widespread throughout the lower 48 states, and cause significant damage to agriculture and the environment. It is estimated that it the United States loses $120 billion to invasive species in general, but the proportion attributed to mollusks is increasing significantly. Over the last century, and especially with expanded globalization of trade in the last thirty years, the rate of introduction of invasive species from the world over passing through quarantine barriers has correspondingly increased. Currently there are sixteen eradication, control, suppression or containment programs in the country for recently introduced mollusk species; a variety of integrated methods of control are being used, including public education, ongoing surveys, hand‐collecting (for larger species), baiting, and canine units. But as resources are becoming increasingly strained, some programs may have to be cut back. There are over 350 airports, seaports, and border crossing into the country, and more being created to cope with increasing world trade.

Robinson, D.G. & Fields, A. Preliminary report on the terrestrial malacofauna of Puerto Rico and associated islands [p. 177]. There has been no comprehensive inventory of the malacofauna of the island of Puerto Rico since Henry van der Schalie’s 1948 book, and none on the islands of Culebra, and Vieques. Carlos Aguayo created a checklist of Puerto Rican snails and slugs in 1966 with a number of undescribed species. The snails of the islands of Mona and Monito were inventoried by Fred Thompson in 1987. Little work has been done in the US Virgin Islands. Since van der Schalie’s work, Puerto Rico has undergone considerable change, and many if not most of the area has been drastically altered by human activity, including deforestation, agriculture, and urbanization. Many of the native or endemic species’ distributions have been greatly diminished, and the ranges of invasive and synanthropic species have expanded to replace them. Since the discovery of the giant African snail (Lissachatina fulica) in Guadeloupe in 1984, it became necessary to make an inventory of native species throughout the West Indies before the inevitable spread of this serious pest. Currently we can document some 185 species and subspecies in 28 families in Puerto Rico and its associated islands, including a number of invasive species from Africa, southeastern Asia, Florida, South America and the Lesser Antilles. Puerto Rico can be divided into 3 distinct zoogeographic zones, the Central Mountain chain, El Yunque massif, and the coastal karstic regions, and its malacofauna shows strong affinities with that of Hispaniola, with very few affinities with the Lesser Antilles.

Romero, P., Kussmann-Kolb, A. & Pfenninger, M. Signs of molecular adaptation related to land invasion in the mitochondrial genomes of Euthyneura [p. 185]. Euthyneura is one of the most diverse groups of gastropods considering ecological adaptations and species richness. One key innovation within this group was the evolution of air‐breathing in pulmonate snails and slugs which allowed the radiation into terrestrial and freshwater niches. We consider that the adaptations to these new niches left a trace in the euthyneuran genomes. Thus, our main objective was to find out possible signs of Darwinian selection related to land transitions. We used data from mitochondrial genomes as a first step to test this hypothesis. We sequenced three new mitogenomes from eupulmonates (two from Stylommatophora: Arion and Helicella, and one from an Ellobiidae: Carychium). We annotated each mt‐genome using the MITOS web server, and then performed phylogenetic analyses using the thirteen mitochondrial coding sequences: cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4l, nad5, nad6, atp6, and atp8. Then, we used the tree topology as a framework to test positive selection (PS) events using site or branch models. Tests of PS were performed in PAML 4.7, models M1a vs. M2a (sites) and Model A vs. Model A1 (branches) were compared using the Likelihood Ratio Test (LRT). Our results support the Panpulmonata / Euopistobranchia hypotheses in concordance with previous multi‐loci nuclear and mitochondrial topologies. The comparison of site‐specific models showed that nad2, nad5, and nad6 presented positions affected by PS, these proteins belong to the OXPHOS Complex I. Aminoacid changes in these proteins related to proton pump could have influenced the fitness during the radiation to land. For branch‐specific models, we found PS comparing Stylommatophora (land snails) with other marine and intertidal taxa. However, we did not find significant differences in other fully terrestrial adapted snails (Carychium, Ellobiidae) or slugs (Rhopalocaulis, Veronicellidae). Future analyses considering complete transcriptomes would shed light into more regions related to the land transition.

Sánchez-Méndez, E. & Gárces-Salazar, J.L. Diversidad de moluscos terrestres en la Estación Biológica de los Tuxtlas Veracruz [p. 196]. En el presente estudio se da a conocer la diversidad de moluscos terrestres de la Reserva de los Tuxtlas, en el estado de Veracruz, además se resalta su importancia ecológica en la selva como parte importante de los descomponedores de materia orgánica del suelo y su papel en la remoción de sustrato que beneficia a otras especies de invertebrados terrestres y de plantas. Para la realización de este trabajo, se hizo una salida a campo en el mes de abril de 2014 (correspondiente al período de secas) a la Estación Biológica de los Tuxtlas, donde se realizaron los muestreos en tres senderos establecidos (Lyell, Darwin y Circuito 1), en cada uno de ellos se recorrió una distancia de 200 m. En los tres senderos se utilizó el método de búsqueda directa, donde participaron cuatro personas y el tiempo en cada sendero fue de tres horas. Se encontraron 11 morfoespecies de organismos vivos y 24 morfoespecies de conchas vacías.

Santos, S.B. Conservation of terrestrial mollusks in Brazil: a vacuum of information [p. 199]. Brazil is a country of continental dimensions, harboring high diversity of biomes that support a huge species richness, deserving the status of one of the megadiverse countries. However, current knowledge about our biota is still scarce and heterogeneous, focused on just a few groups, especially when talking about invertebrates. Despite the advanced process of deforestation, it is surprising the small number of terrestrial mollusks that are listed as threatened with extinction, totalizing 17 species, considering federal and regional lists. This ignorance is an impediment to conservation actions. It will be presented the story of mollusks in the Red Book of Brasilian Fauna Threatened with Extinction, in the States regional listings and, status of species according to the IUCN criteria. A revision of the Red List of Brazilian mollusks is being prepared by Federal Government to this year, under organization of Chico Mendes Institute for the Conservation of Biodiversity (ICMBio), headquartered in Brasilia, through its “Coordination Assessment of the Status of Biodiversity Conservation ‐ COABIO”, that is responsible for leading the process of analyzing and assessing the risk of extinction of species of the Brasilian fauna.

Santos, S.B., Oliveira J.L. de & Vasconcelos, M.C. The RAPELD (Rapid Surveys in Long-term Ecological Research) in the study of terrestrial molluscs: an effort to optimize data [p. 199]. The RAPELD program is integrated into PPBio (Biodiversity Research Program), coordinated and funded by the Brazilian Ministry of Science and Technology. It was first designed by Dr. Magnusson team for use in the Amazon region and subsequently adopted by PPBio to develop biodiversity monitoring programs that allow comparison of the same biological group among different Brazilian regions and of different groups in the same region. The great advantage of using the RAPELD methodology is the rapid inventories of the flora and fauna, standardization of data, integration of different studies (soil, topography, etc.), costs reduction and rapid availability of data. Integrated studies performed by this methodology will provide more accurate information about biological communities, providing support for better management of Conservation Units. Several RAPELD study sites (totalizing 70 collecting sites) are already established in almost all Brazilian biomes generating many publications, which mostly focus on plants, fungi, fish, amphibians, reptiles, birds, mammals and invertebrates, especially arthropods; none of them addresses land or freshwater snails. We are developing pioneering studies addressing ecology and distribution of terrestrial molluscs in Brazil using the RAPELD methodology in Ilha Grande, Rio de Janeiro, one of the most important remnants of Atlantic Forest in Southeast Brazil, where two modules were established. Ten regularly spaced plots were marked out in each module. The plots have a 250 m central transect line that follows the elevational contour. We use a collecting protocol based on previous studies, collecting litter down to the soil surface from ten regularly spaced quadrats of 25 × 75 cm, for subsequent screening of snails. We will show the obtained preliminary data and hope this presentation encourage other researchers to deploy the RAPELD methodology in their countries, in order to obtain integrated data that contribute to the conservation of terrestrial molluscs.

Sei, M., Rosenberg, G., Köhler, F., Taesdale, L & Moussalli, A. Phylogenetics and evolution of Pleurodontidae and Sagdidae: Jamaica and beyond [p. 201]. Pulmonate families Pleurodontidae (formerly placed in Camaenidae) and Sagdidae are among the eight endemic‐rich families of land snails in Jamaica. Evolutionary histories of Jamaican genera within their respective families have not been rigorously examined, and placement of Sagdidae at a superfamily level has been subject to debate. We obtained partial sequences of mitochondrial cytochrome c oxydase subunit II (COII) gene, 16S ribosomal RNA (rRNA) gene, and nuclear 28S rRNA gene from 113 pleurodontid individuals (71 from Jamaica and 42 from elsewhere), 20 sagdid individuals (11 from Jamaica and nine from elsewhere), 38 individuals representing 14 helicoid families (Hygromiidae, Cepolidae, Monadeniidae, Camaenidae, Xanthonychidae, Helminthoglyptidae, Epiphragmophoridae, Humboldtianidae, Helicidae, Bradybaenidae, Polygyridae, Sphincterochilidae, Thysanophoridae and Helicodontidae), and two outgroups (Systrophiidae and Oreohelicidae). Using targeted enrichment and the Illumina platform, we also obtained more than 200 exon fragment sequences for a subset of taxa to resolve deeper nodes, using an exon capture technique based on ‘Next Generation’ Sequencing technology. The results suggest that Pleurodontidae in the dataset includes only Lesser Antillean and Jamaican genera, groups with Trichodiscinini and nests in the New World xanthonychoids (sensu Schileyko). Other supposed Pleurodontidae including Caracolus, Solaropsis, Zachrysia, and Polydontes s.l. group with Sagdidae, with Polydontes s.l. and Zachrysia forming clades within Sagdidae. Labyrinthus and Isomeria group with Thysanophoridae and Cepolidae. The exon capture results also suggest a New World origin of Helicoidea with Eurasian and Australian families at a more derived position.

Shoobs, N.F. & Coote, T.W. The terrestrial and freshwater gastropods of Montserrat: an unprecendented survey of Montserratian neotropical snails [p. 202; poster below, courtesy Nate Shoobs]. Montserrat is a small, volcanic island in the Caribbean Lesser Antilles, which is home to an unknown number of Neotropical gastropod taxa. We conducted the most extensive survey of the island to date, sampling over 30 sites across most of the inhabited portion of the island, and collecting specimens in order to better understand the biodiversity and ecology of its terrestrial and freshwater gastropod fauna. We have identified at least 21 different species of land and freshwater snails, compared to a total of 15 previously reported. Two of the freshwater snail species, (Biomphalaria glabrata Say, Potamopyrgus sp.) previously thought to have been present on the island were not present at any of our survey sites, and we believe that recent volcanic activity on the island has either eradicated them or substantially limited their range, if they were ever truly present on the island. Of the 20 species we collected, one is a poorly understood Montserrat endemic species (Amphibulima rawsonis Bland), which had been overlooked for more than a century before we identified and collected specimens; one is a land snail (Amphibulima browni Pilsbry) previously thought to have been endemic to the island of Dominica; two are currently unidentified potentially novel species, three (Veronicellidae spp., Megalobulimus oblongus Müller) are economically important invasive pests; and one (Neritilia succinea Récluz) is a rediscovered freshwater snail previously thought to have been a potentially extinct Montserrat endemic.

Shoobs poster Mollusca2014

Strenth, N.E., Rilling, R.K. & Correa-Sandoval, A. A morphological comparison of Holospira monclovana and Holospira picta (Gastropoda: Urocoptidae) from Coahuila, Mexico using X-ray computed tomography [p. 209]. Analyses of similarities (ANOSIM) were conducted on morphological measurements derived from X‐ray CT scans of two species of holospirids which were described from near Monclova in Coahuila, México by Paul Bartsch in 1925. These included the type and paratypic series of both Holospira monclovana (N=25) and Holospira picta (N=25) as well as a series of specimens assigned to H. picta (USNM 361966: N=24) from south of Monclova. X‐ray CT scanning allows for a non‐invasive re‐examination of the internal shell morphology that was not available at the time of the original descriptions in 1926. Images of external and internal morphology of specimens were measured using the program ImageJ. An ANOSIM conducted using the program R compared specimens of all three populations and revealed that dissimilarities between groups were greater than dissimilarities within groups (R=0.3977, p<0.001). Pairwise post‐hoc ANOSIM tests revealed that dissimilarities between groups were greater than within groups for each pair of populations; thus H. monclovana is distinct from both H. picta (R=0.612, p<0.001) and USNM 361966 (R=0.466, p<0.001), and H. picta and USNM 361966 are themselves distinct (R=0.098, p<0.006). Bartsch’s 1926 assignment of Holospira monclovana to the subgenus Holospira was found to be supported, while Thompson’s 2011 designation of the Mexican “Eudistemma” as a synonym for Holospira s.s was not. Both Holospira picta and USNM 361966 were found to belong to the subgenus Bostrichocentrum. The results of this analysis does not justify elevating USNM 361966 to its own species, but does support its elevation to at least a subspecies of H. picta.


Andean slugs

Slugs are sometimes difficult to identify, their external appearance does not always give a clue. In the Neotropics, the family Veronicellidae is known for giving taxonomists often a hard time. Gomes et al. (2013) have now published a paper that sheds some light on species from the northwestern part of South America and are prone to be introduced with agricultural products in other countries. The abstract reads:

In this study, we propose C. confusus, new species, an Andean slug of the genus Colosius Thomé, 1975, and a newly recognized pest of coffee and cultivated flowers from Colombia, Ecuador and Peru. We compare it with C. pulcher(Colosi, 1921), a poorly known species with which it has been confused. Our study is based on morphological analysis of a large number of specimens, including interceptions on cut-flowers and live plants by federal agricultural inspectors of the United States Department of Agriculture (USDA) and the Department of Homeland Security (DHS), and material from eight museum collections. Genetic diversity within C. confusus, n. sp. and C. pulcher is also analysed based on fragments of cytochrome oxidase I (COI), and 16S rRNA. They are differentiated by reproductive characters and genes studied. In C. confusus, n. sp., the phallus has a deep longitudinal groove from the base, near the retractor muscle, to its distal region, close to the papilla. In C. pulcher, there is an oval to rectangular swelling on the basal region of the phallus. Some important differences between these species are also found in the digitiform gland and bursa copulatrix. We describe, illustrate and discuss the color variation, morphological similarities, diagnostic characters and its variation, habitat and distribution for each species. Genetic diversity within C. confusus, n. sp., and C. pulcher is low. In order to analyze their relationship with C. propinquus (Colosi, 1921) (currently a junior synonym of C. pulcher) and C. lugubris (Colosi, 1921) (type-species of Colosius), fragments of COI, 16S, and 28S rRNA genes are also analyzed in a sample of these species. C. confusus, n. sp., is a distinct lineage within the genus Colosius. It is not a sister species of C. pulcher, which has C. propinquusas a sister species, here recognized as valid. Colosius confusus, n. sp., is closer to the clade that includes C. pulcher and C. propinquus than it is to C. lugubris. Based on the phylogenetic reconstruction, C. lugubris is sister to all the other Colosius, although additional studies are required to formally test phylogenetic placements and monophyly of the genus. Associated imports and number of interceptions per year of C. confusus, n. sp., by agricultural inspectors are also presented.

The combination of morphological and molecular studies may give a better insight in this economically important group. Hopefully the authors continue their useful work.

Gomes, S.R., Robinson, D.G., Zimmerman, F.J., Obregón, O. & Barr, N.B. (2013). Morphological and Molecular Analysis of the Andean Slugs Colosius confusus, n. sp., A Newly Recognized Pest of Cultivated Flowers and Coffee from Colombia, Ecuador and Peru, and Colosius pulcher (Colosi, 1921) (Gastropoda, Veronicellidae).

DNA barcodes in Systrophia

A paper that appeared already last year is Pedro Romero’s study on Systrophia from Peruvian Amazonia (Romero & Ramirez, 2011). 

DNA barcoding analysis is based on the comparison of genetic distances to identify species using a segment of Cytochrome C Oxidase I (COI) gene. Species identification through DNA barcoding challenges problems in groups with high genetic diversity as molluscs. Thus, our aim was to estimate intraspecific divergence in the Amazonian land snail Systrophia helicycloides (Gastropoda, Scolodontidae) and evaluate the use of DNA barcoding in molecular identification of this land snail. Nucleotide sequences were compared with Genbank and BOLD (Barcode of Life Data Systems) databases. We conducted distance analyses using the Neighbour Joining method. Systrophia helicycloides showed two groups of haplotypes and intraspecific genetic distances higher than 4%. We observed an overlap between intraspecifical and interspecific distances. The high divergence may be related to rapid mutation rate in the snail mitochondrial genome, to population distribution that influences genetic isolation and differentiation, and to ancestral DNA polymorphisms. COI profiles uploaded in BOLD are the first records of this species and can identify Systrophia helcycloides from other species. These profiles corroborated the high variation in the land snail genome. Therefore, species identification in this group needs a combined analysis of genetic distances, informative sites, and conventional taxonomy.
Romero, P. & R. Ramirez, 2011. Divergencia intraespecifica y codigo de barras de ADN en Systrophia helicycloides (Gastropoda, Scolodontidae). – Revista Peruana de Biologia 18(2): 201-208. 

An experiment with tissue sampling

New technology is finding its way to simplify the work of the field biologist. A technique developed for forensic purposes are specially prepared cards to collect and store DNA. These Whatman FTA cards were mentioned during my visit to the Natural History Museum in London last year. Now I’ve tested it with a common snail species from my own garden.


This version of the card allows four samples. In this case I decided on using all for the same species, but trying different circumstances: a) live ‘in the field’, b) live ‘in the lab’, c) fixed in alcohol 96%, and d) drowning the snail for 24h and fixation in alcohol 70%. The card is here photographed after two of the four sample fields (black circles) had been used.

Here is how I took the sample ‘in the field’:

After bringing the snail to the lab, I let it walk in a petri dish and cut off the tail. Although this may sounds awful, the snail contracts but soon continue to walk as if nothing had happened.

A second slice – this time alongside the tail – was made for fixation in pure alcohol. The fourth sample was taken when the snail was kept in tapwater for 24 hours (a method commonly applied to prepare the snails for dissection, although drowning is usually limited to overnight hours), followed by fixation in diluted alcohol (70%). The time between fixation in alcohol and pressing the tissue sample onto the FTA card was 1 hour and 3 days respectively.

Finally I sent the FTA card to the molecular lab for barcoding. On my request they applied the standard procedure but stopped after the extraction. The colleagues from the lab sent me a picture of the gels.

In the red box 8 gel bands correspond to the four different situations as follows:

1,2 = in vivo tail (b)

3,4 = in vivo (a)

5,6 = 1 hr alc 96 (c)

7,8 = 24 hr tapwater + alc 70 (d)

The negative results of number 5 and 6 may be due to a mistake in the lab. Since punches are taken from the sample fields on the card, the tissue sample of the “1 hr alc 96” field seems to have been missed.

The conclusion is that over all the in vivo samples scored better. This opens up useful perspectives for easier sampling during field work. It could make the life of a malacologist a bit more cheerful… At least this ‘proof of principle’ was successful.

Thanks to Camiel, Dick and Frank for coorperation during testing.

Some humor today

Time for some light-weight post that I found on the irregular Systematics and Biogeography blog (http://urhomology.blogspot.com/). Enjoy!

Title: Adventures with my DNA barcoder

But humanity is bioilliterate. Yes, there is a high priest for the name and natural history of some species. That person, however, is almost never standing by your side. But with Google, can you get it? No, there is no hole in your computer or handheld into which to insert the biobit to link through Google. Who is going to give you that name in the dark, the rain, the backyard, or the rain forest? True bioliteracy is being able to link what humanity knows to the biodiversity in hand, eye, or mouth, and build on it. What is the cost to let all seven billion of us read wild biodiversity, now? The barcorder in the back pocket” (Janzen, 2010,Biotropica, 42:540-542).

Thursday, 25th
I am so excited! Today I bought my DNA Barcoder from the gift shop at my local natural history museum. It comes with a two page booklet that tells me I need 6 AAA batteries and something to barcode.

Friday, 26th
I went down to the university to show my new barcoder to my sister. She needs lots of fresh tissue to do her molecular work and always complains that her specimens are either too old or contaminated. “Not with this!” I told her. She looked at me and my barcoder and started laughing. Stuck-up cow.

Saturday, 27th
Today is my first barcoding day (it rained all week, so there was nothing to barcode). I barcoded my cat, which it turns out, is ‘human’. Perhaps it’s because humans and cats are closely related? Perhaps I need something more distantly related?

Sunday, 28th
I barcoded an ant that I found crawling behind the sofa. The barcoder tells me it’s a fungus. I see no other ants. Later on I find a honey bee trapped in my kitchen window. It comes up as a ‘geranium’. The barcoder really needs to be calibrated or something.

Wednesday, 1st
Finally, a hot and sunny day! I tried to entice a bird with bread crumbs. No luck. 

Thursday, 2nd
Couldn’t get close enough to the house sparrows in my park to barcode them. I barcoded various trees in the arboretum. Amazing! The barcoder gets it right every time. There was only one plant sign in the whole park that was wrong!

Sunday, 5th
What a day! Yesterday morning I found a whip snake sunning itself on my porch. I managed to barcode it before it bit me in self defense. Luckily the hospital knew which anti-venom to use because my trusty barcoder got it right again!

Tuesday, 7th
I???m going to be famous! I barcoded a cicada and found that it was 7 different species! I rushed down to the local natural history museum to tell them of the news. Perhaps they can name a news species after me? Apparently the museum barcodes species from all over world and no longer employs taxonomists (the ones who describe new species). A barcoding technician pointed out several local amateur entomological groups I could join. “That’s where you find taxonomists now” he said. Perhaps I???ll try Google.

Puzzling with trees

One of the irritating jobs during DNA analyses is often the preparation for input files for different programs. Although the Nexus-format is becoming a standard more and more, some older programs require different formats, e.g. Newick or Phylip. While most programs are very forgiving for the type of input (interleaved or not), some are very strict in their requirements.


For several reasons I liked to try the program TreePuzzle (www.tree-puzzle.de). This program requires all input files in the interleaved Phylip format, so I set up CLUSTALW to export my alignment in that format. As the Phylip format only allows 10 positions for the taxon name, I had to manually edit these names to remain meaningful to me.

When I had overcome this hurdle, the program runs in a Terminal window and allows various options to be set.


One of the options allows likelihood mapping. This is based on quartet puzzling and produces a graphical output indicating the number of resolved and conflicting quartets as percentage.


In my data set the percentage resolved quartets is 95.5%, which seems sufficiently high to explore the data further.


Likely to be continued.