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      Redefining the Distributional Boundaries and Phylogenetic Relationships for Ctenomids From Central Argentina

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          Abstract

          With about 68 recognized living species, subterranean rodents of the genus Ctenomys are found in a multiplicity of habitats, from the dunes of the Atlantic coast to the Andes Mountains, including environments ranging from humid steppes of Pampas to the dry deserts of Chaco region. However, this genus needs an exhaustive reevaluation of its systematic and phylogenetic relationships regarding the different groups that compose it. This knowledge is essential to propose biodiversity conservation strategies both at species level and at higher hierarchical levels. In order to clarify the taxonomy and the recent evolutionary history from populations of Ctenomys in the Pampas region, Argentina, phylogenetic relationships among them were evaluated using mitochondrial DNA sequences: gene encoding cytochrome b protein (1,140 bp) and the non-coding D-loop region (434 bp). To infer the divergence times inside the Ctenomys clade, a Bayesian calibrate tree using fossil remains data from different families within Caviomorpha was performed at first. Secondly, that calibration data was used as priors in a new Bayesian phylogenetic inference within the genus Ctenomys. This phylogenetic tree emphasized on species currently distributed on the Pampas region, more precisely considering both the talarum and mendocinus groups. Bayesian inferences (BI) were integrated with the results of a Maximum Likelihood approach (ML). Based on these results, the distributional limits of the mendocinus and talarum groups appear to be related to the physiognomy of the Pampas region soils. On the other hand, the validity of C. pundti complex as a differentiated species of C. talarum is debated. According to previous evidence from morphological and chromosomal studies, these results show a very low divergence between those species that originally were classified within the talarum group. Mitochondrial DNA sequences from populations associated with these putative species have not recovered as reciprocal monophyletic groups in the phylogenetic analyses. In conclusion, C. talarum and C. pundti complex might be considered as the same biological species, or lineages going through a recent or incipient differentiation process. The results obtained in this study have important implications for conservation policies and practices, since both species are currently categorized as Vulnerable and Endangered, respectively.

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          MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

          We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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            Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

            Abstract Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.
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              BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

              Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
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                Author and article information

                Contributors
                Journal
                Front Genet
                Front Genet
                Front. Genet.
                Frontiers in Genetics
                Frontiers Media S.A.
                1664-8021
                04 August 2021
                2021
                : 12
                : 698134
                Affiliations
                [1] 1Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICBA) / Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires CITNOBA (UNNOBA-CONICET) , Pergamino, Argentina
                [2] 2Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICBA) , La Plata, Argentina
                [3] 3Grupo de Investigación: Ecología y Genética de Poblaciones de Mamíferos, Instituto de Investigaciones Marinas y Costeras (IIMyC, CONICET), Universidad Nacional de Mar del Plata (UNMdP) , Mar del Plata, Argentina
                Author notes

                Edited by: Gislene Lopes Goncalves, Federal University of Rio Grande do Sul, Brazil

                Reviewed by: Mauro Tammone, National University of Comahue, Argentina; Ulyses Pardiñas, CONICET Instituto de Diversidad y Evolución Austral (IDEAus), Argentina

                *Correspondence: Gabriela Paula Fernández, gabriela.fernandez@ 123456nexo.unnoba.edu.ar

                This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Genetics

                Article
                10.3389/fgene.2021.698134
                8372524
                5e8aceba-7319-4b5c-8bf6-749ce95aea66
                Copyright © 2021 Carnovale, Fernández, Merino and Mora.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 20 April 2021
                : 06 July 2021
                Page count
                Figures: 3, Tables: 6, Equations: 0, References: 103, Pages: 16, Words: 0
                Categories
                Genetics
                Original Research

                Genetics
                ctenomys,phylogeny,talarum group,pampas region,conservation,mendocinus group,distributional boundaries,subterranean rodents

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