Tag Archives: phylogenetics

New Bunnya species from Mexico

Mexican papers are plentiful this moment, but I am sure it is coincidental…

Just published, a paper by a mixed Mexican-Costa Rican author team, whose abstract reads as follows: “We describe a new helicoidean semi-slug based on morphological and molecular evidence. The new species belongs to the genus Bunnya and is described from a small agricultural area in Zinacantepec, San Juan de las Huertas, México. The genus Bunnya is externally similar to Xanthonyx, another Helicoidea genus; both genera have similar shell and body form, and both have a tail horn. Internally, Bunnya is similar to Humboldtiana, since both have dart-sacs (3 in Bunnya, 3−4 in Humboldtiana) surrounding the vagina, two dart-bulbs associated with each dart sac, and a gland number similar to the dart-sacs number. Four adult specimens of Bunnya metli n. sp. were dissected and compared with the two described species: B. bernardinae from Cuajimalpa, México City, and B. naranjoe from Sierra de Manantlan, Jalisco. Bunnya metli n. sp. is characterized by: very closely-spaced radial riblets (about 23 per mm) crossed by fine spiral wavy threads on the embryonic whorls; unfused glands inserted on the vagina above the dart-sacs and only one dart per sac; a short, swollen penis with a large spherical verge about half the penis size; an elongated bursa copulatrix with a slight constriction in the middle; a long bursa copulatrix duct; and dart sacs with a muscular pad within the vaginal lumen, surrounding the basal part of the genitalia. We performed a phylogenetic analyses using data from fragments of 16S rRNA mtDNA and 28S rRNA genes from one of the collected specimens, as well as other helicoidean sequences from GenBank. Our analyses support the membership of Bunnya metli n. sp. in Xanthonychidae. This suggests that the taxonomic position of Bunnya in Humboldtianidae or Xanthonychidae warrants reevaluation”.

Schermafbeelding 2019-04-08 om 14.40.11

This appears to be a very well-executed study on this novelty, which also question the familiar placement of the species. No other Bunnya species have been sequenced, while only two taxa of the Xanthonychidae are currently included in GenBank. Further research may solve this situation.

Reference:
Araiza-Gómez, V. et al., 2019. A new species of the genus Bunnya H.B. Baker, 1942 (Helicoidea) from Mexico. – Malacologia, 62 (2): 237-246.

Clessinia from Argentina

A recent paper by Cuezzo et al. provides a revision of Argentinian species. Their abstract reads in full:

“Background: Land gastropods of the Dry Chaco merit special attention because they comprise a highly diverse but barely studied group. Clessinia Doering, 1875 are typical inhabitants of this ecoregion. The inclusion of their distribution areas into Spixia range, their shell shape similarities, and a former molecular study raised doubts on the monophyly of this genus. The present study review the species of Clessinia, under a morphological, geometric morphometrics, and molecular combined approach.
Methods: Adults were collected, photographed, measured, and dissected for anatomical studies. Shell ultrastructure was studied with scanning electron microscope. Geometric morphometric analyses on shells were performed testing if they gave complementary information to anatomy. Two mitochondrial genes, and a nuclear region were studied. Phylogenetic reconstructions to explore the relationships of DNA sequences here obtained to those of Clessinia and Spixia species from GenBank were performed.
Results: Species description on shell, periostracal ornamentation and anatomy is provided. We raised former Clessinia cordovana striata to species rank, naming it as Clessinia tulumbensis sp. nov. The periostracum, consisting of hairs and lamellae, has taxonomic importance for species identification. Shell morphometric analyses, inner sculpture of penis and proportion of the epiphallus and penis, were useful tools to species identification. Nuclear markers do not exhibit enough genetic variation to determine species relationships. Based on the mitochondrial markers, genetic distances among Clessinia species were greater than 10%, and while C. cordovana, C. nattkemperi, and C. pagoda were recognized as distinct evolutionary genetic species, the distinction between C. stelzneri and C. tulumbensis sp. nov. was not evident. Clessinia and Spixia were paraphyletic in the molecular phylogenetic analyses. Species of Clessinia here treated have narrow distributional areas and are endemic to the Chaco Serrano subecoregion, restricted to small patches within the Dry Chaco. Clessinia and Spixia are synonymous, and the valid name of the taxon should be Clessinia Doering, 1875 which has priority over Spixia Pilsbry & Vanatta, 1894.
Discussion: Our results support the composition of C. cordovana complex by three species, C. cordovana, C. stelzneri, and C. tulumbensis sp. nov. The low genetic divergence between C. stelzneri and C. tulumbensis sp. nov. suggests that they have evolved relatively recently. The former Spixia and Clessinia are externally distinguished because Clessinia has a detached aperture from the body whorl forming a cornet, periostracal microsculpture extended over dorsal portion of the peristome, five inner teeth on the shell aperture instead of three–four found in Spixia. Morphological similarities exists between both genera in shell shape, type of periostracum microsculpture, reproductive anatomy, besides the overlap in geographic ranges”.

Schermafbeelding 2018-12-15 om 15.59.37

This is an interesting paper for me, as more than 6 years ago I did research on type material in the London museum and found the species of the two ‘genera’ difficult to entangle, the more when phylogenetic results proved a paraphyletic relationship (Breure & Romero, 2012). This study comes to the same phylogenetic outcome as shown in the figure below. And for clarity: the Clessinia specimens used in our 2012 study were identified and supplied to us by one of the current authors and another Argentinian malacologist; they had more expertise and resources available.

Schermafbeelding 2018-12-15 om 15.53.44

The conclusion of the study by Cuezzo et al. is that Clessinia and Spixia are synonyms, with the older name (Clessinia) taking precedence. As such this is correct, but at the same time they conclude that the two ‘genera’ are morphological distinguishable (see the Discussion in their abstract). As taxonomists we have a solution for this: the subgenus…, which is treated in MolluscaBase as ‘alternate representation’. So instead of complete synonymisation, I would say there seems enough reason to distinguish the two as subgenera despite not being strictly monophyletic. The nomenclature then becomes:

Clessinia Doering, 1875
Clessinia (Clessinia) Doering, 1875 – type species Bulimus (Clessinia) stelzneri Doering, 1875.
Clessinia (Spixia) Pilsbry & Vanatta, 1898 – type species Clausilia striata Spix in Wagner, 1827.
See Cowie et al. (2004) for details on the names of Spix and Wagner.

Screenshot 2018-12-11 at 05.30.48

In this paper also one new species is described. The authors say “The new species, Clessinia tulumbensis sp. nov. include Clessinia cordovana striata (Parodiz, 1939). The name striata has not been used here to avoid homonymy with Pupa striata Spix, 1827 [= Clausilia striata Spix in Wagner, 1827], the type species of Spixia, since in the present study the genera Clessinia and Spixia are proposed as synonymous. The new species with its own holotype and paratypes is defined based on live-collected material from which DNA sequences were obtained and the anatomy described. In this sense, although the Parodiz name is preoccupied, we are not replacing the name proposed by him in 1939 but creating a new species with its own type series”.

With Parodiz’ name mentioned by the authors as a full synonym, I fail to see the reason to introduce the name tulumbensis as a species novum. Although it is correct to replace the name of Parodiz to avoid homonymy, it is nonsense to say that you can introduce a replacement name with its own type series. The name tulumbensis is thus not a ‘sp.nov.’ but a nomen novum. And the holotype of Clessinia cordovana striata Parodiz, 1939 (MACN-In 9127) becomes automatically the holotype of Clessinia tulumbensis! The “holotype IBN 883” and the paratype material mentioned in this paper has no status other than being vouchers for this study.

References:
Breure, A.S.H. & Romero, P.D., 2012. Support and surprises: a new molecular phylogeny of the land snail superfamily Orthalicoidea (Gastropoda, Stylommatophora) using a multi-locus gene analysis. – Archiv für Molluskenkunde, 141: 1–20.
Cowie, R.H. et al., 2004. The South American Mollusca of Johann Baptist Ritter von Spix and their publication by Johann Andreas Wagner. – The Nautilus, 118: 71-87.
Cuezzo, M.G. et al., 2018. From morphology to molecules: a combined source approach to untangle the taxonomy of Clessinia (Gastropoda, Odontostomidae), endemic land snails from the Dry Chaco ecoregion. – PeerJ, 6: e5986 (54 pp.).

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.”

Schermafbeelding 2018-07-26 om 07.52.50

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.

 

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

Genetic structure in a Humboldtiana species

López et al. (2017) published about the genetic structure of a Humboldtiana species in north-western Mexico. The abstract reads “Phylogeographic studies of different montane biological groups in Mexico have revealed complex patterns in a broad scale but an absence of genetic structure within local mountain systems such as the Sierra Madre Occidental. In this study, we estimate the genetic structure and demographic history of the endemic land snail Humboldtiana durangoensis within this mountain range. Nine polymorphic microsatellite loci in 178 individuals from 16 localities throughout the complete geographic distribution were analyzed. Strong deviations from Hardy–Weinberg equilibrium and low levels of heterozygosity were detected in the seven genetic clusters. The gene flow between two of the main geographic regions (North and South) was symmetric (~4 individuals). In addition, the analysis detected changes in the effective population size indicating that both geographic regions experienced a drastic reduction in their effective population size probably associated with the Pleistocene climatic changes”.

This is a specialised study but with an interesting methodology.

Reference:
López, B. et al. , 2017. Strong genetic structure and signs of population bottlenecks in the land snail Humboldtiana durangoensis in the Sierra Madre Occidental of Western Mexico. – Journal of Zoological Systematics and Evolutionary Research, 55 (4): 288-297.

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.

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].