Using historical genome‐wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild.

Evol. Appl. 2021 Mar; 14(3): 698–709.

Published online 2020 Nov 7. doi: 10.1111/eva.13149

Abstract:

Urgent conservation action for terminally endangered species is sometimes hampered by taxonomic uncertainty, especially in illegally traded animals that are often cross‐bred in captivity. To overcome these problems, we used a genomic approach to analyze historical DNA from museum samples across the Asian Pied Starling (Gracupica contra) complex in tropical Asia, a popular victim of the ongoing songbird crisis whose distinct Javan population (“Javan Pied Starling”) is extinct in the wild and subject to admixture in captivity. Comparing genomic profiles across the entire distribution, we detected three deeply diverged lineages at the species level characterized by a lack of genomic intermediacy near areas of contact. Our study demonstrates that the use of historical DNA can be instrumental in delimiting species in situations of taxonomic uncertainty, especially when modern admixture may obfuscate species boundaries. Results of our research will enable conservationists to commence a dedicated ex situ breeding program for the Javan Pied Starling, and serve as a blueprint for similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.

bavej-biblio

Is the northern chevrotain, Tragulus williamsoni Kloss, 1916, a synonym or one of the least-documented mammal species in Asia?

Raffles Bull. Zoology 65: 506–514.

Abstract:

The northern chevrotain, Tragulus williamsoni Kloss, 1916, was described, and for nearly a century remained known, from only one specimen. This had been collected from Meh Lem in northern Thailand in 1916. Following a taxonomic revision of the genus Tragulus, its taxonomic status was regarded as uncertain. New information from a Tragulus specimen from Xishuangbanna, Yunnan province, China, stored in the Kunming Institute of Zoology, corroborates the status of T. williamsoni as a distinct taxon based on skull measurements. The conservation implications of this finding include the urgent need to determine conclusively the taxonomic status of T. williamsoni, and its distribution and conservation status.

meijaard-biblio

Is the northern chevrotain, Tragulus williamsoni Kloss, 1916, a synonym or one of the least-documented mammal species in Asia?

Raffles Bulletin of Zoology 65: 506-514.

Abstract:

The northern chevrotain, Tragulus williamsoni Kloss, 1916, was described, and for nearly a century
remained known, from only one specimen. This had been collected from Meh Lem in northern Thailand in 1916.
Following a taxonomic revision of the genus Tragulus, its taxonomic status was regarded as uncertain. New
information from a Tragulus specimen from Xishuangbanna, Yunnan province, China, stored in the Kunming
Institute of Zoology, corroborates the status of T. williamsoni as a distinct taxon based on skull measurements. The
conservation implications of this finding include the urgent need to determine conclusively the taxonomic status
of T. williamsoni, and its distribution and conservation status.

meiijaard-biblio

The Identity of Mousedeer (Mammalia: Artiodactyla: Tragulidae) observed at Lower Peirce Fotest, Singapore.

NATURE IN SINGAPORE 2009 2: 467–473.

Volltext (PDF)

Conclusion:

The napu and the kanchil are usually distinguished from each other by the number of white stripes on their throat and
neck. However, in rare cases, this does not hold true at least for the kanchil. When coat colour and dark mid-ventral
stripe are taken into consideration, the mousedeer from Lower Peirce, thought to be a napu, Tragulus napu, should be a
kanchil, Tragulus kanchil fulviventer. Therefore, there is no recent record of wild napu on Singapore Island.

low-biblio

A review of the leucogaster species complex of the Indo-Pacific pomacentrid genus Amblyglyphidodon, with descriptions of two new species.

aqua, J. Ichthyol. Aquat. Biol. 5(4):139-152.

Zusammenfassung:

Bisher wurde angenommen, dass der indo-pazifische Pomacentride Amblyglyphidodon leucogaster aus verschiedenen, geografischen Farbvarianten bestesteht. Die vorliegende Untersuchung deutet jedoch auf einen aus vier Arten bestehenden Komplex hin: A. leucogaster (Bleeker) aus dem westlichen Pazifik und ostlichen Randgebiet des indischen Ozeans; A. orbicularis (Hombron u. Jacquinot) von Samoa, Fiji und Neu Kaledonien und zwei hier neu beschriebene Arten - A. indicus vom Roten Meer und Indischenr Ozean und A. melanopterus von Tonga. Die einzelnen Arten des leucogaster-Komplexes unterscheiden sich hautsachlich durch Kombinationen von Farbmustern und Anzahl der Kiemenreusen. Ein Bestimmungsschlussel fur Amblyglyphidodon-Arten liegt bei.

allen-biblio

Four new species of Cyprinodon from southern Nuevo León, Mexico, with a key to the C. eximius complex (Teleostei: Cyprinodontidae).

Ichthyological Explorations of Freshwaters, 4(4):295-308.

Abstract:

lozano-biblio

Four New Pupfishes of the Genus Cyprinodon from Mexico, with a Key to the C. eximius Complex.

Bull. Southern California Academy of Sciences 75(2): 68-75.

Volltext: http://www.nativefishlab.net/library/textpdf/15362.pdf

Abstract:

The pupfishes (genus Cyprinodon) referable to the C. eximius complex comprise seven species that are restricted to, or had their origin in, the Chihuahuan Desert region of Mexico and adjacent parts of Texas and New Mexico. Four are described as new; the remainder are C. eximius, C. atrorus, and C. latifasciatus. Most are of restricted distribution; one is extinct and another may be. Keys, diagnoses, and ranges are given for each species and all are illustrated. The distinctive morphometric characters of the new species are given. Life colors and color patterns are important in distinguishing species

miller-biblio

Evolution of Oviposition Techniques in Stick and Leaf Insects (Phasmatodea).

Front. Ecol. Evol., 19 December 2018. Sec. Phylogenetics, Phylogenomics, and Systematics. https://doi.org/10.3389/fevo.2018.00216.

Zusammenfassung:

Stick and leaf insects (Phasmatodea) are large, tropical, predominantly nocturnal herbivores, which exhibit extreme masquerade crypsis, whereby they morphologically and behaviorally resemble twigs, bark, lichen, moss, and leaves. Females employ a wide range of egg-laying techniques, largely corresponding to their ecological niche, including dropping or flicking eggs to the forest floor, gluing eggs to plant substrate, skewering eggs through leaves, ovipositing directly into the soil, or even producing a complex ootheca. Phasmids are the only insects with highly species-specific egg morphology across the entire order, with specific egg forms that correspond to oviposition technique. We investigate the temporal, biogeographic, and phylogenetic pattern of evolution of egg-laying strategies in Phasmatodea. Our results unequivocally demonstrate that the ancestral oviposition strategy for female stick and leaf insects is to remain in the foliage and drop or flick eggs to the ground, a strategy that maintains their masquerade. Other major key innovations in the evolution of Phasmatodea include the (1) hardening of the egg capsule in Euphasmatodea; (2) the repeated evolution of capitulate eggs (which induce ant-mediated dispersal, or myrmecochory); (3) adapting to a ground or bark dwelling microhabitat with a corresponding shift in adult and egg phenotype and egg deposition directly into the soil; and (4) adhesion of eggs in a clade of Necrosciinae that led to subsequent diversification in oviposition modes and egg types. We infer at minimum 16 independent origins of a burying/inserting eggs into soil/crevices oviposition strategy, 7 origins of gluing eggs to substrate, and a single origin each of skewering eggs through leaves and producing an ootheca. We additionally discuss the systematic implications of our phylogenetic results. Aschiphasmatinae is strongly supported as the earliest diverging extant lineage of Euphasmatodea. Phylliinae and Diapheromerinae are both relatively early diverging euphasmatodean taxa. We formally transfer Otocrania from Cladomorphinae to Diapheromerinae and recognize only two tribes within Diapheromerinae: Diapheromerini sensu nov. and Oreophoetini sensu nov. We formally recognize the clade comprising Necrosciinae and Lonchodinae as Lonchodidae stat. rev. sensu nov.

robertson-biblio

Toward a tree-of-life for the boas and pythons: multilocus species-level phylogeny with unprecedented taxon sampling.

Molecular Phylogenetics and Evolution 71: 201–213. doi:10.1016/j.ympev.2013.11.011.

Abstract:

Snakes in the families Boidae and Pythonidae constitute some of the most spectacular reptiles and comprise an enormous diversity of morphology, behavior, and ecology. While many species of boas and pythons are familiar, taxonomy and evolutionary relationships within these families remain contentious and fluid. A major effort in evolutionary and conservation biology is to assemble a comprehensive Tree-of-Life, or a macro-scale phylogenetic hypothesis, for all known life on Earth. No previously published study has produced a species-level molecular phylogeny for more than 61% of boa species or 65% of python species. Using both novel and previously published sequence data, we have produced a species-level phylogeny for 84.5% of boid species and 82.5% of pythonid species, contextualized within a larger phylogeny of henophidian snakes. We obtained new sequence data for three boid, one pythonid, and two tropidophiid taxa which have never previously been included in a molecular study, in addition to generating novel sequences for seven genes across an additional 12 taxa. We compiled an 11-gene dataset for 127 taxa, consisting of the mitochondrial genes CYTB, 12S, and 16S, and the nuclear genes bdnf, bmp2, c-mos, gpr35, rag1, ntf3, odc, and slc30a1, totaling up to 7561 base pairs per taxon. We analyzed this dataset using both maximum likelihood and Bayesian inference and recovered a well-supported phylogeny for these species. We found significant evidence of discordance between taxonomy and evolutionary relationships in the genera Tropidophis, Morelia, Liasis, and Leiopython, and we found support for elevating two previously suggested boid species. We suggest a revised taxonomy for the boas (13 genera, 58 species) and pythons (8 genera, 40 species), review relationships between our study and the many other molecular phylogenetic studies of henophidian snakes, and present a taxonomic database and alignment which may be easily used and built upon by other researchers.

reynolds-biblio

Systematics of Pythons of the Morelia amethistina Complex (Serpentes: Boidae) with the Description of three new Species.

Herpetological Monographs. 14: 139–185. doi:10.2307/1467047.

Description:

The scrub pythons (Morelia amethistina complex) are revised based on museum specimens and new material recently collected in eastern Indonesia. Morelia kinghorni (formerly M. amethistina kinghorni) and M. amethistina (formerly M. amethistina amethistina) are recognized as species, and three new species are described. The phylogenetic relationships of scrub pythons are resolved using morphological and molecular characters Scrub pythons are most closely related to Morelia boeleni and have undergone both ancient divergences and a relatively recent radiation. The distribution of scrub pythons corresponds well with areas of endemism recognized in earlier studies of other taxa. Their distribution and evolution appears to have been shaped by combined effects of dispersal and vicariance. Scrub python populations exhibit interesting color and pattern polymorphism and ontogenetic change, and these characteristics vary among populations.

harvey-biblio