Phylogenetic relationships in the Sceloporus variabilis (Squamata: Phrynosomatidae) complex based on three molecular markers, continuous characters and geometric morphometric data
TL;DR: A parsimony‐based ancestral reconstruction on body size, femoral pores and dorsal scales and related morphological changes to geographic distribution of the species will allow best designs of comparative studies with species in the “variabilis group,” one of the earliest divergent lineages in the genus.
Abstract: The monophyly of the Sceloporus variabilis group is well established with five species and two species complexes, but phylogenetic relationships within species complexes are still uncertain. We studied 278 specimens in 20 terminals to sample all taxa in the “variabilis group,” including three subspecies in the “variabilis complex,” and two outgroups (Sceloporus grammicus and Sceloporus megalepidurus). We assembled an extensive morphological data set with discrete and continuous characters (distances and scale counts), including geometric morphometric data (landmark coordinates of three shapes), and a three‐marker molecular data set as well (ND4, 12S and RAG1). We conducted parsimony and Bayesian phylogenetic inferences on these data, including several partitioning and weighting schemes. We suggest elevating three subspecies to full species status. Therefore, we recommend recognition of nine species in the “variabilis group.” First, S. variabilis is sister to Sceloporus teapensis. In turn, Sceloporus cozumelae is sister to Sceloporus olloporus. These four species are a monophyletic group, which is sister to Sceloporus smithi. Finally, Sceloporus marmoratus is sister of the clade of five species. The other species in the “variabilis group” (Sceloporus chrysostictus, Sceloporus couchii and Sceloporus parvus) are a paraphyletic grade at the base of the tree. Our analyses reject the existence of the “variabilis complex.” We conducted a parsimony‐based ancestral reconstruction on body size (snout–vent length), femoral pores and dorsal scales and related morphological changes to geographic distribution of the species. Our phylogenetic hypothesis will allow best designs of comparative studies with species in the “variabilis group,” one of the earliest divergent lineages in the genus.
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01 Jan 2016
TL;DR: The systematics and the origin of species is universally compatible with any devices to read and is available in the book collection an online access to it is set as public so you can get it instantly.
Abstract: Thank you very much for downloading systematics and the origin of species. Maybe you have knowledge that, people have look numerous times for their chosen readings like this systematics and the origin of species, but end up in malicious downloads. Rather than enjoying a good book with a cup of coffee in the afternoon, instead they juggled with some infectious virus inside their desktop computer. systematics and the origin of species is available in our book collection an online access to it is set as public so you can get it instantly. Our book servers hosts in multiple countries, allowing you to get the most less latency time to download any of our books like this one. Kindly say, the systematics and the origin of species is universally compatible with any devices to read.
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TL;DR: The goal of this contribution is to provide conceptual elements for a basic understanding of morphometric and statistical methods useful in systematics under a phylogenetic approach, and give examples and recommendations on the use of linear measurements and landmark coordinates in morphometric analyses for the identification of species, the variation of taxonomic characters and in the inference of phylogeny and classification.
Abstract: Background and Aims: Quantitative methods have accumulated for the use of linear measurements and Cartesian coordinates of landmark points in analyses of morphometric variation. Unlike previous reviews, here I emphasize the theoretical bases of mathematical spaces and morphospace of a taxonomic character. The goal of this contribution is to provide conceptual elements for a basic understanding of morphometric and statistical methods useful in systematics under a phylogenetic approach.Methods: Morphometric data are being applied in comparative biology research, using a phylogeny as a reference. In contrast, applications of morphometrics in systematics have been with the aim of phenetic grouping and distinguishing taxonomic groups with overall similarity. Under a phylogenetic approach, morphometric data can also be used for the study of taxonomic character variation, character state identity and phylogenetic inference. Taxonomic groups should be proposed from monophyletic groups discovered with phylogenetic methods.Key results: I review the basic morphometric theory, vector geometry, Kendall shape space, Procrustes distance, projection of tangential spaces, and construction of morphospace hypercubes. Remainders of statistical concepts useful for the application of Principal Component Analysis and Canonical Variate Analysis in systematics are presented. Particularly, I give examples and recommendations on the use of linear measurements and landmark coordinates in morphometric analyses for the identification of species, the variation of taxonomic characters and in the inference of phylogeny and classification.Conclusions: The current broad collection of methods provides an opportunity to integrate morphometric data to discover taxic and transformational homology. This implies an epistemological change necessary to move from applications in systematics under a phenetic approach to the integration of morphometric analyses as part of phylogenetic research.
12 citations
Cites background from "Phylogenetic relationships in the S..."
...…con mediciones de largos y anchos analizados con códigos discretos (Guerrero-Enríquez et al., 2003) y también directamente con los valores continuos de los promedios y desviaciones estándar con métodos de parsimonia (De Bivort et al., 2010; Parins-Fukuchi, 2018; Solis-Zurita et al., 2019)....
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...También se incluyeron en el análisis tres configuraciones de coordenadas “x, y” para describir la forma de escamas cefálicas (Solis-Zurita et al., 2019)....
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...Ejemplos recientes de análisis filogenéticos que combinan las coordenadas con los datos moleculares en la inferencia de filogenias incluyen los de Botero-Trujillo et al. (2017), Bona et al. (2018) y Solís-Zurita et al. (2019)....
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...…la inclusión de los caracteres de las formas, al igual que el impacto de otros caracteres, tiene un efecto mínimo en la reconstrucción de las relaciones filogenéticas, especialmente cuando se combinan con muchos datos moleculares (Ospina-Garcés y De Luna, 2017; Solis-Zurita et al., 2019)....
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TL;DR: The present study shows the importance of incorporating size and shape variables into analyses of sexual dimorphism among populations of a single species with a wide distribution, as well as the degree of difference among populations that inhabit different environments.
6 citations
References
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TL;DR: The latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine, has been optimized for use on 64-bit computing systems for analyzing larger datasets.
Abstract: We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
33,048 citations
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Abstract: Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
Contact: clustalw@ucd.ie
25,325 citations
"Phylogenetic relationships in the S..." refers methods in this paper
...Nucleotide sequences were edited with MEGA 7.0.14 (Kumar, Stecher, & Tamura, 2016), and each marker was aligned with ClustalW (Larkin et al., 2007)....
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TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
Abstract: Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
20,627 citations
Additional excerpts
...1.2 (Altekar, Dwarkadas, Huelsenbeck, & Ronquist, 2004; Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck, 2003)....
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DOI•
27 Oct 2010
20,272 citations
"Phylogenetic relationships in the S..." refers background in this paper
...forest, pine–oak forest edge and coastal dunes (Canseco‐ Márquez & Gutiérrez Mayén, 2010; Chaves et al., 2013; Ramírez‐Bautista et al., 2010)....
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...…and southern Mexico, in diverse localities with more stable climatic conditions and high annual precipitation with montane moist | 435SOLIS‐ZURITA eT AL. forest, pine–oak forest edge and coastal dunes (Canseco‐ Márquez & Gutiérrez Mayén, 2010; Chaves et al., 2013; Ramírez‐Bautista et al., 2010)....
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Book•
01 Jun 1973
5,901 citations
"Phylogenetic relationships in the S..." refers background in this paper
...For example, morphological diagnosability by some quantitative difference defines a species (“phenetic species” concept, Sneath & Sokal, 1973) but also a subspecies (“subspecies criterion,” Patten, 2010)....
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