Chelid Turtles of the Australasian Archipelago: II. A New Species of Chelodina from Roti Island, Indonesia.

Breviora 498: 1-31. Museum of Comparative Zoology; US ISSN 0006-9698; Cambridge, Mass.

Abstract:

A new species of Chelodina (Testudines: Pleurodira: Chelidae) is described from Roti Island, west of Timor, East Nusa Tenggara Province, in the southeastern Indonesian Archipelago. The species is endemic to Roti, a small and relatively xeric island. It is most similar and most closely related to Chelodina pritchardi from Papua New Guinea and C. longicollis from Australia, less closely related to C. novaeguineae and C. reimanni from New Guinea.

rhodin-biblio

Tortoise (Reptilia, Testudinidae) radiations in Southern Africa from the Eocene to the present.

Zoologica Scripta 46(4): 389-400

Abstract:

Africa, inclusive of the West Indian Ocean islands, harbours 11 of the world's 16 extant testudinid genera. Fossil records indicate that testudinids originated in Asia and dispersed first to North America and Europe (Early Eocene) and later to Africa (Late Eocene). We used mitochondrial (1870 bp) and nuclear (1416 bp) DNA sequence data to assess whether molecular data support the late cladogenesis of Southern African testudinid lineages. Our results revealed strong support for the monophyly of a clade consisting of Kinixys, the two Malagasy genera and four Southern African genera (Psammobates, Stigmochelys, Homopus and Chersina). Kinixys diverged from this clade in the Late Palaeocene, suggesting that testudinids occupied Africa at an earlier date than indicated by fossil records. The Southern African tortoises consist of three, strongly supported clades: Psammobates + Stigmochelys; the five-toed Homopus + Chersina; and the four-toed Homopus. Due to the paraphyly of Homopus, we propose the taxonomic resurrection of Chersobius for the five-toed Homopus species (boulengeri, signatus and solus). Cladogenesis at the genus level occurred mainly in the Eocene, with Chersina and Chersobius diverging in the Oligocene. The latter divergence coincided with species-level radiations within Homopus (areolatus and femoralis) and Psammobates (oculifer, geometricus and tentorius). Our phylogeny could not resolve relationships within Psammobates, indicating rapid speciation between the Late Oligocene and Early Miocene. The Chersobius species were the last to diverge in the Early to Mid-Miocene. By the Mid-Miocene, P. tentorius started to differentiate into four lineages instead of the three recognized subspecies: P. t. tentorius, P. t. trimeni and two P. t. verroxii subclades occurring north and south of the Orange River, respectively. Terminal radiations in several taxa suggest the existence of cryptic species and a more diverse tortoise fauna than currently recognized. Factors contributing to this diversity may include the early origin of African testudinids and climatic fluctuations over a heterogeneous landscape.

hofmeyr-biblio

Skiffia francesae, a New Species of Goodeid Fish from Western Mexico.

Copeia 1978 (3): 503–508. doi:10.2307/1443618. JSTOR 1443618.

Abstract:

A new species of Skiffia from the Río Teuchitlán on the Pacific slope of western México is based on both preserved and live material. It is regarded as most closely related to Skiffia multipunctata, as determined by meristic and morphometric data. It differs in shape and form of head and lips, size of orbit and head, diploid number of chromosomes and male coloration.

kingston-biblio

Eschmeyer's Catalog of Fishes: Genera, Species, References.

http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp).
Electronic version accessed 14.09.2023.

Diese vom Institute for Biodiversity Science and Sustainability der California Academy of Sciences unterhaltene Datenbank ist die taxonomische Standardreferenz für Fische und eine Grundlage für die breiter angelegte Datenbank FISH BASE.

fricke-biblio; eschmeyer-biblio

Phylogenetic classification of bony fishes.

Evolutionary Biology 17: Article number: 162 (2017)

Volltext

Abstract

Background

Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson’s volumes of Fishes of the World and W. Eschmeyer’s Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny (www.deepfin.org). We here update the first version of that classification by incorporating the most recent phylogenetic results.

Results

The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified.

Conclusions

This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.

betancur-biblio

Genetics and taxonomy of Chilean smooth-shelled mussels, Mytilus spp. (Bivalvia: Mytilidae).

Comptes Rendus Biologies 335 (1): 51-61.

Volltext

Abstract:

It has been previously established that native smooth-shelled mussels in southern South America possess close evolutionary affinities with Northern-Hemisphere Mytilus edulis L. 1758 (McDonald et al. (1991) [5]). This result has since been challenged by authors claiming that Chilean mussels should be considered a local subspecies of M. galloprovincialis Lmk. 1819. Moreover, morphological, physiological, ecotoxicological and molecular genetic studies on Chilean smooth-shelled mussels still frequently refer to ‘M. chilensis’ Hupé 1854, even though the previous discovery of alien M. galloprovincialis and considerable heterogeneity in shell morphology among samples collected along the Chilean shores raise concerns that different Mytilus spp. species might have been included under ‘M. chilensis’. Here we reviewed the molecular and morphological data available on smooth-shelled mussels from Chile in an attempt to clarify both their genetic composition and their taxonomic status. Using multivariate analysis on sample × allozyme-frequency matrices, we confirmed the widespread occurrence of the Southern-Hemisphere form of M. edulis along the shores from the North Patagonia region of Chile to the southern tip of the South American continent. The populations sampled in southern central Chile showed some evidence of slight introgression from Southern-Hemisphere M. galloprovincialis. Morphological characterization of a sample from Dichato in southern central Chile was consistent with its previous genetic identification as Mediterranean M. galloprovincialis. The occurrence of Southern-Hemisphere M. galloprovincialis in Punta Arenas at the southern tip of the South American continent was also reported. Southern-Hemisphere M. edulis, including native Chilean smooth-shelled Mytilus, should be assigned subspecific rank and named M. edulis platensis d’Orbigny 1846.

borsa-biblio

In praise of subgenera: taxonomic status of cobras of the genus Naja Laurenti (Serpentes: Elapidae).

ZOOTAXA 2236 (1): 26-36. 21 Sep. 2009.
DOI: https://doi.org/10.11646/zootaxa.2236.1.2

Abstract:

The genus Naja Laurenti, 1768, is partitioned into four subgenera. The typical form is restricted to 11 Asian species. The name Uraeus Wagler, 1830, is revived for a group of four non-spitting cobras inhabiting savannas and open formations of Africa and Arabia, while Boulengerina Dollo, 1886, is applied to four non-spitting African species of forest cobras, including terrestrial, aquatic and semi-fossorial forms. A new subgenus is erected for seven species of African spitting cobras. We recommend the subgenus rank as a way of maximising the phylogenetic information content of classifications while retaining nomenclatural stability.

wallach-biblio

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements.

Preprint: doi: https://doi.org/10.1101/717520
Molecular Phylogenetics and Evolution 146: 106731

Volltext (Preprint): https://www.biorxiv.org/content/10.1101/717520v1.full.pdf+html

Abstract:

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread “generalist” clades. This is especially true in the Australasia, where the monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately “derived” parachute geckos of the genus Ptychozoon.

Here we employ sequence capture targeting 5060 ultraconserved elements to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyzed multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods.

Our sampling scheme was designed to address four persistent systematic questions in this group:

(1) Are Luperosaurus and Ptychozoon monophyletic and are any of these named species truly nested within Gekko?

(2) Are prior phylogenetic estimates of Sulawesi’s L. iskandari as sister to Melanesian G. vittatus supported by our genome-scale dataset? (

3) Is the high elevation L. gulat of Palawan Island correctly placed within Gekko? (

4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny?

We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not related to Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our final, well-supported topologies, we recognize seven newly defined subgenera to accommodate ∼60 species within the more broadly defined and maximally-inclusive Australasian genus Gekko. The newly defined subgenera will aide taxonomists and systematists in species descriptions by allowing them to only diagnose putatively new species from the most relevant members of the same subgenus, not necessarily the phenotypically variable genus Gekko as a whole, and we argue that it appropriately recognizes geographically circumscribed units (e.g., a new subgenus for a novel clade, entirely endemic to the Philippines) while simultaneously recognizing several of the most systematically controversial, phenotypically distinct, and phylogenetically unique lineages. An added benefit of recognizing the most inclusive definition of Gekko, containing multiple phylogenetically-defined subgenera, is that this practice has the potential to alleviate taxonomic vandalism, if widely adopted, by creating formally available, supraspecific taxa, accompanied by character-based diagnoses and properly assigned type species, such that future, more atomized classifications would necessarily be required to adopt today’s subgenera as tomorrow’s genera under the guidelines of The Code of Zoological Nomenclature. Not only does this simple practice effectively eliminate the nefarious motivation behind taxonomic vandalism, but it also ensures that supraspecific names are created only when accompanied by data, that they are coined with reference to a phylogenetic estimate, and that they explicitly involve appropriate specifiers in the form of type species and, ultimately, type specimens.

wood-biblio

Molecular Systematics and Phylogeny of Old and New World Ratnakes, Elaphe AUCT., and Related Genera (Reptilia, Squamata, Colubridae.

Russian J. Herpetology 9(2): 105-124.

Abstract:

The phylogenetic relationships of the Holarctic ratsnakes (Elaphe auct.) are inferred from portions of two
mitochondrial genes, 12S rRNA and COI. Elaphe Fitzinger is made up of ten Palaearctic species. Natrix
longissima Laurenti (type species) and four western Palaearctic species (hohenackeri, lineatus, persicus,
and situla) are assigned to Zamenis Wagler. Its phylogenetic affinities with closely related genera, Coronella and Oocatochus, remain unclear. The East Asian Coluber porphyraceus Cantor is referred to a new genus. This taxon and the western European Rhinechis scalaris have an isolated position among Old World ratsnakes. Another new genus is described for four Oriental species (cantoris, hodgsonii, moellendorffi, and taeniurus). New World ratsnakes and allied genera are monophyletic. Coluber flavirufus Cope is referred to Pseudelaphe Mertens and Rosenberg. Pantherophis Fitzinger is revalidated for Coluber guttatus L. (type species) and further Nearctic species (bairdi, obsoletus, and vulpinus). Senticolis triaspis is the sister taxon of New World ratsnakes including the genera Arizona, Bogertophis, Lampropeltis, Pituophis, and Rhinocheilus. The East Asian Coluber conspicillatus Boie and Coluber mandarinus Cantor form a monophyletic outgroup with respect to other Holarctic ratsnake genera and are referred to Euprepiophis Fitzinger. Three Old World species, viz. Elaphe (sensu lato) bella, E. (s.l.) frenata, and E. (s.l.) prasina remain unassigned. The various groups of ratsnakes (tribe Lampropeltini) show characteristic hemipenis features.

utiger-biblio

Systematic revision of the living African Slender-snouted Crocodiles (Mecistops Gray, 1844).

ZOOTAXA 4504(2): 151-193. 24 Oct. 2018. DOI: 10.11646/zootaxa.4504.2.1.

Abstract:

Molecular and morphological evidence has shown that the African slender-snouted, or sharp-nosed, crocodile Mecistops cataphractus (Cuvier, 1824) is comprised of two superficially cryptic species: one endemic to West Africa and the other endemic to Central Africa. Our ability to characterize the two species is compromised by the complicated taxonomic history of the lineage and overlapping ranges of variation in distinguishing morphological features. The name M. cataphractus was evidently originally based on West African material, but the holotype is now lost. Although types exist for other names based on the West African form, the name M. cataphractus is sufficiently entrenched in the literature, and other names sufficiently obscure, to justify retypification. Here, we designate a neotype for M. cataphractus and restrict it to West Africa. We resurrect M. leptorhynchus as a valid species from Central Africa and identify exemplary referred specimens that, collectively, overcome the obscurity and diagnostic limits of the extant holotype. We additionally indicate suitable neotype material in the event the holotype is lost, destroyed, or otherwise needing replacement, and we rectify the previously erroneous type locality designation. We provide a revised diagnosis for crown Mecistops, and revise and update previous descriptions of the two living species, including providing both more complete descriptions and discussion of diagnostic characters. Finally, we provide considerable discussion of the current state of knowledge of these species’ ecology, natural history, and distribution.

shirley-biblio