Novel Records of Rodent Species in the Sierra de Manantlán, Jalisco, México: Phylogenetic Insights and Taxonomic Implications

Martínez‐Borrego D., Arellano E., González‐Cózatl F.X., Ospina‐Garcés S.M., Rogers D.S.

AbstractSpecies boundaries are difficult to establish in groups with very similar morphology. As an alternative, it has been suggested to integrate multiple sources of data to clarify taxonomic problems in taxa where cryptic speciation processes have been reported. This is the case of the harvest mouse Reithrodontomys mexicanus, which has a problematic taxonomy history as it is considered a complex species. Here, we evaluate the cryptic diversity of R. mexicanus using an integrative taxonomy approach in order to detect candidate lineages at the species level. The molecular analysis used one mitochondrial (cytb) and two nuclear (Fgb‐I7 and IRBP) genes. Species hypotheses were suggested based on three molecular delimitation methods (mPTP, bGMYC, and STACEY) and cytb genetic distance values. Skull and environmental space differences between the delimited species were also tested to complement the discrimination of candidate species. Based on the consensus across the delimitation methods and genetic distance values, four species were proposed, which were mostly supported by morphometric and ecological data: R. mexicanus clade I, R. mexicanus clade IIA, R. mexicanus clade IIIA, and R. mexicanus clade IIIB. In addition, the evolutionary relationships between the species that comprise the R. mexicanus group were discussed from a phylogenetic approach. Our findings present important taxonomic implications for Reithrodontomys, as the number of known species for this genus increases. Furthermore, we highlight the importance of the use of multiple sources of data in systematic studies to establish robust delimitations between species considered taxonomically complex.

García-Mendoza D.F., López-González C., Salas-H T.

We report for the first time the presence of 2 shrew species (Sorex altoensis and S. emarginatus) and 4 rodent species (Peromyscus merriami, P. schmidlyi, Reithrodontomys zacatecae, and Sigmodon leucotis) in the state of Nayarit, Mexico, as well as the occurrence of P. carletoni and P. schmidlyi in Jalisco and Zacatecas. We extend the known distribution range of the squirrel Sciurus aureogaster to northern Nayarit and report the presence of 2 subspecies of P. eremicus and 3 of Neotoma mexicana in near sympatry. We also confirm the presence of Tlacuatzin sinaloae and P. micropus in Nayarit. Finally, we document the presence of Dasypus novemcinctus in the highlands of the Sierra Madre Occidental in Durango; these are the first records of the nine-banded armadillo in Durango in 57 years. Our results highlight the importance of continuing biological surveys and inventories in the least-explored areas of Mexico.

Magurran A.E.

As prehistoric cave paintings illustrate, our species has had an enduring appreciation of the variety and abundance of life on Earth. Today, however, concern is focused on the pressure humanity is placing on the natural world, and on the continued ability of ecosystems to deliver the services on which we all depend. To understand the extent of this 'biodiversity crisis' and develop strategies to ameliorate its impact, it is essential to be able to accurately measure biological diversity (a term often contracted to biodiversity) and make informed predictions about how and why this diversity varies over space and time.

Gutiérrez-Costa M.A., González-Cózatl F.X., Ramírez-Martínez, M.M., Iñiguez-Dávalos L.I., Rogers D.S.

Recent collecting surveys in the Sierra de Manantlán Biosphere Reserve, Jalisco (México), uncovered the existence of a new population of the Mexican spiny pocket mouse, Heteromys irroratus.  Because the subspecies H. i. bulleri and H. i. jaliscensis occur nearby, our objective was to properly determine the taxonomic identity of the novel sample.  Also, we evaluate its distinctiveness, both in terms of genetic divergence and phylogenetic placement, relative to other members of H. irroratus.  Preliminary, we compared external and cranial measurements of recently collected individuals to those reported for representatives of the subspecies of H. irroratus occurring close by.  In addition, we examined levels of genetic differentiation and phylogenetic relationships, based on sequence data of the Cytochrome b, among this population and other members of H. irroratus, including an individual from Sierra de Juanacatlán, Jalisco, the type locality of H. i. bulleri. Phylogenetic relationships were estimated using Maximum Likelihood and Bayesian Inference methods and levels of genetic divergence were assessed employing Kimura-2-parameters genetic distances.  Samples from Sierra de Manantlán and Sierra de Juanacatlán were grouped together in a well-supported haplogroup and genetic distances between them were lower than < 1.02 %.  Our phylogenetic hypothesis shows that H. i. bulleri represents the sister group to all other samples of H. irroratus but that, genetically, is a very divergent lineage.  Distances values between H. i. bulleri to any of the other groups were > 10.05 %.  Comparison of external and cranial measurements showed that, in average, individuals from Sierra de Manantlán are larger than those of H. i. jaliscensis, but more similar in size to H. i. bulleri.  Our results show that the new population of the Mexican spiny pocket mouse from Sierra de Manantlán belongs to H. i. bulleri.  In addition, the phylogenetic separation and the high levels of genetic divergence of H. i. bulleri, relative to other members of H. irroratus, suggest that the first should be recognized as a species-level taxon.  Considering the scarce collecting records of H. i. bulleri and the known area of occurrence, that is very restricted, this taxon may warrant special conservation status.

Kumar S., Stecher G., Li M., Knyaz C., Tamura K.

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Rambaut A., Drummond A.J., Xie D., Baele G., Suchard M.A.

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.

Kalyaanamoorthy S., Minh B.Q., Wong T.K., von Haeseler A., Jermiin L.S.

ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.

Sikes R.S.

Guidelines for use of wild mammal species in research are updated from Sikes et al. (2011). These guidelines cover current professional techniques and regulations involving the use of mammals in research and teaching; they also incorporate new resources, procedural summaries, and reporting requirements. Included are details on capturing, marking, housing, and humanely killing wild mammals. It is recommended that Institutional Animal Care and Use Committees (IACUCs), regulatory agencies, and investigators use these guidelines as a resource for protocols involving wild mammals, whether studied in the field or in captivity. These guidelines were prepared and approved by the American Society of Mammalogists (ASM), in consultation with professional veterinarians experienced in wildlife research and IACUCs, whose collective expertise provides a broad and comprehensive understanding of the biology of nondomesticated mammals. The current version of these guidelines and any subsequent modifications are available online on the Animal Care and Use Committee page of the ASM website (http://mammalogy.org/uploads/committee_files/CurrentGuidelines.pdf). Additional resources pertaining to the use of wild animals in research are available at: http://www.mammalsociety.org/committees/animal-care-and-use#tab3.

Nguyen L., Schmidt H.A., von Haeseler A., Minh B.Q.

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree.

Ramírez-Pulido J., González-Ruiz N., Gardner A.L., Arroyo-Cabrales J.

Ceballos G.

Minh B.Q., Nguyen M.A., von Haeseler A.

Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods such as the RAxML rapid bootstrap (RBS) and the Shimodaira-Hasegawa-like approximate likelihood ratio test have been introduced to speed up the bootstrap. Here, we suggest an ultrafast bootstrap approximation approach (UFBoot) to compute the support of phylogenetic groups in maximum likelihood (ML) based trees. To achieve this, we combine the resampling estimated log-likelihood method with a simple but effective collection scheme of candidate trees. We also propose a stopping rule that assesses the convergence of branch support values to automatically determine when to stop collecting candidate trees. UFBoot achieves a median speed up of 3.1 (range: 0.66-33.3) to 10.2 (range: 1.32-41.4) compared with RAxML RBS for real DNA and amino acid alignments, respectively. Moreover, our extensive simulations show that UFBoot is robust against moderate model violations and the support values obtained appear to be relatively unbiased compared with the conservative standard bootstrap. This provides a more direct interpretation of the bootstrap support. We offer an efficient and easy-to-use software (available at http://www.cibiv.at/software/iqtree) to perform the UFBoot analysis with ML tree inference.

Miller M.A., Pfeiffer W., Schwartz T.

The CIPRES Science Gateway (CSG) provides browser-based access to computationally demanding phylogenetic codes run on large HPC resources. Since its release in December 2009, there has been a sustained, near-linear growth in the rate of CSG use, both in terms of number of users submitting jobs each month and number of jobs submitted. The average amount of computational time used per month by CSG increased more than 5-fold since its initial release. As of April 2012, more than 4,000 unique users have run parallel tree inference jobs on TeraGrid/XSEDE resources using the CSG. The steady growth in resource use suggests that the CSG is meeting an important need for computational resources in the Systematics/Evolutionary Biology community.To ensure that XSEDE resources accessed through the CSG are used effectively, policies for resource consumption were developed, and an advanced set of management tools was implemented. Studies of usage trends show that these new management tools helped in distributing XSEDE resources across a large user population that has low-to-moderate computational needs.In the first quarter of 2012, 30% of all active XSEDE users accessed computational resources through the CSG, while the analyses conducted by these users accounted for 0.7% of all allocable XSEDE computational resources. User survey results showed that the easy access to XSEDE/TeraGrid resources through the CSG had a critical and measurable scientific impact: at least 300 scholarly publications spanning all major groups within the Tree of Life have been enabled by the CSG since 2009. The same users reported that 82% of these publications would not have been possible without access to computational resources available through the CSG. The results indicate that the CSG is a critical and cost-effective enabler of science for phylogenetic researchers with limited resources.

Okonechnikov K., Golosova O., Fursov M.

UNLABELLED Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. AVAILABILITY AND IMPLEMENTATION UGENE binaries are freely available for MS Windows, Linux and Mac OS X at http://ugene.unipro.ru/download.html. UGENE code is licensed under the GPLv2; the information about the code licensing and copyright of integrated tools can be found in the LICENSE.3rd_party file provided with the source bundle.

Crawford D.L., Dragoo J.W., Smith F.A., Chavez A.N.

To examine the partitioning of genetic variation within the Mexican vole (Microtus mexicanus), we analyzed variation within the cytochrome b (cytb, ca. 953 bp) from 44 samples of the Mexican vole from the mountains of the southwestern United States and Mexico. Phylogeographic analyses demonstrated strong support for a western clade and an eastern clade, corresponding to the Sierra Madre Occidental and mountains of the southwestern United States (western clade) and the Sierra Madre Oriental and the Sierra Madre del Sur (eastern clade). Levels of genetic distinctiveness among vole populations in Mexico and the southwestern United States support recognition of the Mogollon vole (Microtus mogollonensis). Estimates of lineage divergence suggested an older divergence for populations in Mexico and a more recent divergence for the presumptive M. mogollonensis. Ecological analyses demonstrated a distinct climate niche between vole lineages in the Southwest and Mexico, which indicated the possible role of environmental variation in diversification of the Mexican vole. A similar pattern of climatic separation was also demonstrated between clades of the codistributed taxa Sigmodon hispidus, Neotoma mexicana, and Peromyscus truei, suggesting a broader role for climatic variation in the origin and maintenance of the region's biodiversity.