Search results for "Molecular clock"

Phylogeny, biogeography, and morphological ancestral character reconstruction in the Mediterranean genus Fumana (Cistaceae)

2020

Fumana is a diverse genus of the Cistaceae family, consisting of 21 currently accepted species. In this study, nuclear (ITS) and plastid (matK, trnT‐L) molecular markers were used to reconstruct the phylogeny and to estimate divergence times, including 19 species of Fumana. Phylogenetic analyses (Bayesian Inference, Maximum Parsimony and Maximum Likelihood) confirmed the monophyly of Fumana and did not support the infrageneric divisions previously established. The results support four main clades that group species that differ in vegetative and reproductive characters. Given the impossibility to define morphological characters common to all species within the clades, our proposal is to reje…

Phylogeny, biogeography and systematics of Dysphanieae (Amaranthaceae)

2021

After a rather turbulent taxonomic history, Dysphanieae (Chenopodioideae, Amaranthaceae) were established to contain five genera, four of which are monospecific (Cycloloma, Neomonolepis, Suckleya, Teloxys) and geographically restricted, and the fifth genus, Dysphania, having a nearly worldwide distribution and comprising ca. 50 species. This study investigates the phylogeny, biogeography and taxonomy of Dysphanieae. We studied specimens from 32 herbaria to infer morphological differences and distribution areas of the species and sampled 121 accessions representing 39 accepted species of the tribe for molecular phylogenetic analyses. The molecular phylogeny tested generic relationships of th…

Multilocus phylogenetics of smooth clam shrimps (Branchiopoda, Laevicaudata)

2021

International audience; Laevicaudatan branchiopods, also called ‘smooth clam shrimps’ or ’pea shrimps’, are rare crustaceans found exclusively in temporary, small freshwater bodies, which stay dry most of the year. Only 42 laevicaudatan species have been described so far, 90% of which belong to the genus Lynceus. The first multilocus phylogeny of the group is provided here, based on 15 Lynceus species from North and South America, Europe, Africa, Asia, Australia and New Caledonia and using nine molecular markers (two mitochondrial and seven nuclear genes, including newly designed primers). Genetic data suggest populations of Lynceus brachyurus from Europe and North America to represent a co…

Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale.

2007

International audience; Genome reduction, a typical feature of symbiotic bacteria, was analyzed in the last stages of evolution of Buchnera aphidicola, the primary aphid endosymbiont, in two neutrally evolving regions: the pseudogene cmk and an intergenic region. These two regions were examined in endosymbionts from several lineages of their aphid host Rhopalosiphum padi, and different species of the same genus, whose divergence times ranged from 0.62 to 19.51 million years. Estimates of nucleotide substitution rates were between 4.3 and 6.7 x 10(-9) substitution/site/year, with G or C nucleotides being substituted around four times more frequently than A or T. Two different types of indel …

The substitution rate of HIV-1 subtypes: a genomic approach

2017

Abstract HIV-1M causes most infections in the AIDS pandemic. Its genetic diversity is defined by nine pure subtypes and more than sixty recombinant forms. We have performed a comparative analysis of the evolutionary rate of five pure subtypes (A1, B, C, D, and G) and two circulating recombinant forms (CRF01_AE and CRF02 AG) using data obtained from nearly complete genome coding sequences. Times to the most recent common ancestor (tMRCA) and substitution rates of these HIV genomes, and their genomic partitions, were estimated by Bayesian coalescent analyses. Genomic substitution rate estimates were compared between the HIV-1 datasets analyzed by means of randomization tests. Significant diff…

Evolutionary distances corrected for purifying selection and ancestral polymorphisms.

2019

Abstract Evolutionary distance formulas that take into account effects due to ancestral polymorphisms and purifying selection are obtained on the basis of the full solution of Jukes–Cantor and Kimura DNA substitution models. In the case of purifying selection two different methods are developed. It is shown that avoiding the dimensional reduction implicitly carried out in the conventional model solving is instrumental to incorporate the quoted effects into the formalism. The problem of estimating the numerical values of the model parameters, as well as those of the correction terms, is not addressed.

2015

Molecular clock analyses estimate that crown-group animals began diversifying hundreds of millions of years before the start of the Cambrian period. However, the fossil record has not yielded unequivocal evidence for animals during this interval. Some of the most promising candidates for Precambrian animals occur in the Weng'an biota of South China, including a suite of tubular fossils assigned to Sinocyclocyclicus , Ramitubus , Crassitubus and Quadratitubus , that have been interpreted as soft-bodied eumetazoans comparable to tabulate corals. Here, we present new insights into the anatomy, original composition and phylogenetic affinities of these taxa based on data from synchrotron radiat…

Historical biogeography of Melastomataceae: the roles of Tertiary migration and long-distance dispersal

2001

Melastomataceae and Memecylaceae are pantropically distributed sister groups for which an ndhF gene phylogeny for 91 species in 59 genera is here linked with Eurasian and North American fossils in a molecular clock approach to biogeographical reconstruction. Nine species from the eight next-closest families are used to root phylogenetic trees obtained under maximum likelihood criteria. Melastomataceae comprise ∼3000 species in the neotropics, ∼1000 in tropical Asia, 240 in Africa, and 225 in Madagascar in 150-166 genera, and the taxa sampled come from throughout this geographic range. Based on fossils, ranges of closest relatives, tree topology, and calibrated molecular divergences, Mel…

A broader model for C 4 photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.)

2012

C 4 photosynthesis is a fascinating example of parallel evolution of a complex trait involving multiple genetic, biochemical and anatomical changes. It is seen as an adaptation to deleteriously high levels of photorespiration. The current scenario for C 4 evolution inferred from grasses is that it originated subsequent to the Oligocene decline in CO 2 levels, is promoted in open habitats, acts as a pre-adaptation to drought resistance, and, once gained, is not subsequently lost. We test the generality of these hypotheses using a dated phylogeny of Amaranthaceae s.l. (including Chenopodiaceae), which includes the largest number of C 4 lineages in eudicots. The oldest chenopod C 4 lineage da…

La evolución en los tribunales: aplicaciones forenses de las filogenias moleculares

2013

En las dos últimas décadas se ha generalizado el uso de pruebas genéticas en los tribunales, permitiendo la identificación de criminales a partir de restos biológicos, la determinación de paternidades o la identificación de cadáveres. Menos conocidas son las periciales basadas en el uso de filogenias moleculares. En ellas se estudia la ancestralidad común de organismos, normalmente virus o bacterias, para establecer su asociación a una fuente de infección. Desde el caso del dentista de Florida, que infectó con el VIH a varios de sus pacientes, hasta el más próximo del anestesista Juan Maeso, que transmitió el VHC a cerca de 300 pacientes, la teoría evolutiva tiene un papel esencial en estas…