Systematic Biology - Editorial Board
(Source: Systematic Biology)
Source: Systematic Biology - March 16, 2017 Category: Biology Source Type: research
Systematic Biology Volume 66, Number 2 March 2017 - Front Cover
(Source: Systematic Biology)
Source: Systematic Biology - March 16, 2017 Category: Biology Source Type: research
Dental Data Perform Relatively Poorly in Reconstructing Mammal Phylogenies: Morphological Partitions Evaluated with Molecular Benchmarks
AbstractPhylogenetic trees underpin reconstructions of evolutionary history and tests of evolutionary hypotheses. They are inferred from both molecular and morphological data, yet the relative value of morphology has been questioned in this context due to perceived homoplasy, developmental linkage, and nonindependence of characters. Nevertheless, fossil data are limited to incomplete subsets of preserved morphology, and different regions are treated as equivalent. Through meta-analysis of 40 data sets, we show here that the dental and osteological characters of mammals convey significantly different phylogenetic signals, a...
Source: Systematic Biology - March 14, 2017 Category: Biology Source Type: research
Species Delimitation with Gene Flow
We describe an approach to delimiting species using PHRAPL that attempts to account for both genetic drift and gene flow, and we compare the method ’s performance to that of a popular delimitation approach (BPP) using both simulated and empirical datasets. PHRAPL generally infers the correct demographic-delimitation model when the generating model includes gene flow between taxa, given a sufficient amount of data. When the generating model in cludes only isolation in the recent past, PHRAPL will in some cases fail to differentiate between gene flow and divergence, leading to model misspecification. Nevertheless, the expl...
Source: Systematic Biology - March 11, 2017 Category: Biology Source Type: research
Different from Trees, more than Metaphors: Branching Silhouettes —Corals, Cacti, and the Oaks
AbstractThere has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like visualization of phylogeny may also be done via other types of graphics, especially botanical (or literal) tree drawings. As a consequence, the meaning of such diagrams is not always clear: a given picture may have multiple interpretations in its different parts and two figures that look similar may a...
Source: Systematic Biology - March 11, 2017 Category: Biology Source Type: research
Species Concepts in Biology: Historical Development, Theoretical Foundations and Practical Relevance. —By Frank E. Zachos.
Species Concepts in Biology: Historical Development, Theoretical Foundations and Practical Relevance. —By ZachosFrank E.Switzerland: Springer Nature, 2016. xii+220 pp. ISBN 978-3-319-44964-7. € 144, US$ 159 (hardcover); ISBN 978-3-319-44966-1. € 107, US$ 119 (eBook). (Source: Systematic Biology)
Source: Systematic Biology - March 6, 2017 Category: Biology Source Type: research
Evolutionary Theory: A Hierarchical Perspective. —Edited by Niles Eldredge, Telmo Pievani, Emanuele Serrelli, and Ilya Tëmkin.
Evolutionary Theory: A Hierarchical Perspective. —Edited by EldredgeNiles, TelmoPievani, SerrelliEmanuele, and TëmkinIlya. Chicago: Chicago University Press, 2016. vii+385 pp. ISBN 978-0-226-42605-1 $US105 (hardcover); ISBN 978-0-226-42622-8 $US35 (paperback); ISBN 978-0-226-42619-8 $US35 (eBook). (Source: Systematic Biology)
Source: Systematic Biology - March 6, 2017 Category: Biology Source Type: research
Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola)
Parasitic “wing lice” (Phthiraptera:Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species ofColumbicola have switched to new host species. Understanding the ecological and evolutionary factors that influence...
Source: Systematic Biology - March 6, 2017 Category: Biology Source Type: research
ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability
AbstractThe computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often based on empirical amino acid substitution models that assume that all sites evolve at the same rate and under the same process. However, this assumption is frequently violated because protein evolution is highly heterogeneous due to different selective constraints among sites. Here, we presentProtASR, a new evolutionary framework to infer ancestral protein sequences acco...
Source: Systematic Biology - March 6, 2017 Category: Biology Source Type: research
Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola )
Parasitic “wing lice” (Phthiraptera:Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species ofColumbicola have switched to new host species. Understanding the ecological and evolutionary factors that influence...
Source: Systematic Biology - March 6, 2017 Category: Biology Source Type: research
ProtASR : An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability
AbstractThe computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often based on empirical amino acid substitution models that assume that all sites evolve at the same rate and under the same process. However, this assumption is frequently violated because protein evolution is highly heterogeneous due to different selective constraints among sites. Here, we presentProtASR, a new evolutionary framework to infer ancestral protein sequences acco...
Source: Systematic Biology - March 6, 2017 Category: Biology Source Type: research
Efficient Bayesian Species Tree Inference under the Multispecies Coalescent
AbstractWe develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we implement two efficient MCMC proposals: the first is based on the Subtree Pruning and Regrafting (SPR) algorithm and the second is based on a node-slider algorithm. Like the Nearest-Neighbor Interchange (NNI) algorithm we implemented previously, both new algorithms propose changes to the species tree, while simultaneously altering the gene trees at multiple genetic loci to automa...
Source: Systematic Biology - March 6, 2017 Category: Biology Source Type: research
Phylogenomics from Whole Genome Sequences Using aTRAM
AbstractNovel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes ($<$1000 Mbp) it is feasible to sequence the entire genome at modest coverage ($10-30\times$). Computational challenges for handling these large data sets c...
Source: Systematic Biology - March 6, 2017 Category: Biology Source Type: research
Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes
In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5 million base pairs collected across 35 representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher level (interordinal) relationships among ostariophysan fishes, focusing on the monophyly of the Characiformes —one of the most contentiously debated groups in fish systematics. As with most previous molecular studies, we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophys...
Source: Systematic Biology - February 27, 2017 Category: Biology Source Type: research
