Absence Of Molecular Evidence Research Articles

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.

Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible aDNA post-mortem degradation2 has so far limited aDNA recovery to the past ~0.5 million years (Ma)3. Contrarily, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1)4 and suggested the presence of protein residues in Cretaceous fossil remains5, although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae7–9 using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)10. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates11, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

Re-establishment of species from synonymies based on DNA barcoding and phylogenetic analysis using Diplopterygium simulans (Gleicheniaceae) as an example.

Because synonymy treatment traditionally relies on morphological judgments, it usually causes many problems in species delimitation and in the biodiversity catalogue. For example, Diplopterygium simulans, which belongs to the Gleicheniaceae family, has been considered to be synonymous with D. glaucum or D. giganteum based mainly on the morphology of its pinna rachis and blade. In the absence of molecular evidence, these revisions remain doubtful. DNA barcoding, which is considered to be a powerful method for species-level identification, was employed to assess the genetic distance among 9 members of the Diplopterygium genus. The results indicate that D. simulans is an independent species rather than a synonymy of D. glaucum or D. giganteum. Moreover, phylogenetic analysis uncovered the sisterhood of D. simulans and D. cantonense, which is supported by their geographical distributions and morphological traits. Incorrect synonymy treatment is prevalent in the characterization of biological diversity, and our study proposes a convenient and effective method for validating synonym treatments and discovering cryptic species.

Genetic Variation and Evolution of the Alpine Bamboos (Poaceae: Bambusoideae) using DNA Sequence Data

Difficulties in phylogenetic reconstruction are common within the woody bamboos due to their unique life cycles, a lack of morphological characters and even an absence of molecular evidence. The genetic variability and population structure of the bamboos are also poorly understood which impedes their exploitation via breeding. In this paper, ITS sequence data were used to examine the degree of genetic variation within the alpine bamboos and to explore their phylogeny. Twenty-three species representing three genera, Thamnocalamus, Fargesia and Yushania, of the alpine bamboos and one species of Ampelocalamus as an outgroup were studied. The results indicated that Thamnocalamus spathiflorus var. crassinodus and the Fargesia spathacea clade form the basal groups but bootstrap support was weak. Among the rest of the species, including species previously placed in Fargesia (plus Borinda) and Yushania, the F. yunnanensis subclade and the F. communis subclade were recognized but internal support for such groups was again low. The result indicated that, Fargesia and Yushania as delimited by morphological characters, are not monophyletic in the ITS phylogeny and require further resolution. We revealed relatively high levels of genetic variability in the alpine bamboos and showed that the ITS region could be used to improve generic delimitation of the woody bamboos in general.