Search results for "phylogenetics"

BioTIME: A database of biodiversity time series for the Anthropocene

2018

Abstract Motivation The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, th…

How Hox genes can shed light on the place of echinoderms among the deuterostomes.

2014

19 pages; International audience; BACKGROUND: The Hox gene cluster ranks among the greatest of biological discoveries of the past 30 years. Morphogenetic patterning genes are remarkable for the systems they regulate during major ontogenetic events, and for their expressions of molecular, temporal, and spatial colinearity. Recent descriptions of exceptions to these colinearities are suggesting deep phylogenetic signal that can be used to explore origins of entire deuterostome phyla. Among the most enigmatic of these deuterostomes in terms of unique body patterning are the echinoderms. However, there remains no overall synthesis of the correlation between this signal and the variations observ…

Evolution of Early Metazoa: Phylogenetic Status of the Hexactinellida Within the Phylum of Porifera (Sponges)

1998

The evolution of the Metazoa from their protozoan ancestors is one of the greatest puzzles of phylogeny (Willmer 1994; Cavalier-Smith et al. 1996). The emergence of multicellular animals has been explained by two major theories: the syncytial theory (Hadzi 1963) - origin from a multinucleated ciliate - and the colonial theory (Haeckel 1868) - origin from a colonial flagellate - both of which assume a di(poly)phyletic origin of the Metazoa. Numerous attempts to resolve whether the Metazoa are of mono- or polyphyletic origin have sought evidence from a wide variety of developmental and morphological data such as body symmetry, type of development (protostome vs. deuterostome), type of body ca…

Unusual Assortment of Segments in 2 Rare Human Rotavirus Genomes

2010

Using full-length genome sequence analysis, we investigated 2 rare G3P[9] human rotavirus strains isolated from children with diarrhea. The genomes were recognized as assortments of genes closely related to rotaviruses originating from cats, ruminants, and humans. Results suggest multiple transmissions of genes from animal to human strains of rotaviruses.

Molecular phylogenetics of the Dissochaeta alliance (Melastomataceae): Redefining tribe Dissochaeteae

2021

Exploring the major depletions of conodont diversity during the Triassic

2014

International audience; In this paper, we show that the Triassic fossil record reflects just two great depletions of conodont diversity before the Rhaetian, which occurred in the Smithian (Olenekian, Early Triassic) and in the Julian (Carnian, Late Triassic). By exploring this context, our results highlighted that they respond to different origination?extinction dynamics. Thus, while the Smithian diversity depletion can be interpreted as a consequence of elevated extinction, the Julian diversity depletion was triggered by fluctuations in origination regime. This evidence suggests that, despite the role of extinction on diversity losses, conodonts suffered crucial changes on the origination …

The never-ending story of geologically ancient DNA: was the model plantArabidopsisthe source of Miocene Dominican amber?

2013

Studies characterizing geologically ancient DNA in plants are rare, and all have reportedly obtained plastid DNA sequences from Miocene fossils in a remarkable state of preservation. Recently, a group made the extraordinary claim of having amplified a geologically ancient Miocene plastid DNA fragment (the rbcL gene) from Dominican amber nuggets, and the organismal source of this DNA was identified as Hymenaea protera (Fabaceae), the plant that produced the fossilized Dominican amber. Assuming that the Miocene sequence is error-free, reanalysis of the sequence indicates it is probably a technical artifact or an rbcL pseudogene. Furthermore, BLAST similarity searches and phylogenetic analyses…

Gene arrangement phylogeny of the E element in Drosophila species of the Obscura group

1993

Ecdysteroid titres in a tenebrionid beetle, Zophobas atratus: effects of grouping and isolation.

1997

Metamorphosis in Zophobas atratus is dependent on isolation: when kept in grouped conditions, larvae undergo numerous supernumerary moults, growing in size, without pupating. This beetle thus represents an interesting model for the analysis of possible differences in the endocrine regulation of normal vs. supernumerary larval moults. In this study, the ecdysteroid titres have been analysed in this species, using enzyme immunoassay. The hormonal variations of larvae undergoing normal or supernumerary larval cycles were particularly examined, in either grouped or isolated conditions. Normal larval cycles presented very similar ecdysteroid variations in grouped as well as isolated conditions, …

Testing alternative vicariance scenarios in Western Mediterranean discoglossid frogs

2004

Dated molecular phylogenies are often used to interpret evolutionary history with respect to paleogeographic events. Where more than one interpretation is possible, it is desirable but difficult to assess the alternatives in an objective manner. The present work demonstrates a formalized method for testing molecular clock calibrations and biogeographic scenarios based on them. We assessed the plausibility of several previously published biogeographic hypotheses, using the frog genera Alytes, Discoglossus, and Bombina as model groups. Our data set comprised ca. 900bp of partial mitochondrial 16S and 12S rRNA gene sequences (both genes evolved in a clock-like manner across genera) from nearly…