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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<!-- saved from url=(0035)https://www.ncbi.nlm.nih.gov/pubmed -->
<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"></head><body><pre>PMID- 28173480
OWN - NLM
STAT- MEDLINE
DCOM- 20180213
LR - 20180808
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 1
DP - 2017 Jan 1
TI - Incomplete Lineage Sorting in Mammalian Phylogenomics.
PG - 112-120
LID - 10.1093/sysbio/syw082 [doi]
AB - The impact of incomplete lineage sorting (ILS) on phylogenetic conflicts among
genes, and the related issue of whether to account for ILS in species tree
reconstruction, are matters of intense controversy. Here, focusing on full-genome
data in placental mammals, we empirically test two assumptions underlying current
usage of tree-building methods that account for ILS. We show that in this data
set (i) distinct exons from a common gene do not share a common genealogy, and
(ii) ILS is only a minor determinant of the existing phylogenetic conflict. These
results shed new light on the relevance and conditions of applicability of
ILS-aware methods in phylogenomic analyses of protein coding sequences.
FAU - Scornavacca, Celine
AU - Scornavacca C
AD - UMR 5554-Institute of Evolutionary Sciences, University Montpellier, CNRS, IRD,
EPHE, Place E. Bataillon-CC64, Montpellier, France.
FAU - Galtier, Nicolas
AU - Galtier N
AD - UMR 5554-Institute of Evolutionary Sciences, University Montpellier, CNRS, IRD,
EPHE, Place E. Bataillon-CC64, Montpellier, France.
LA - eng
SI - Dryad/10.5061/dryad.1m3s2
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 0 (Proteins)
SB - IM
MH - Animals
MH - Computer Simulation
MH - Genome/*genetics
MH - Genomics/*standards
MH - Mammals/*classification/genetics
MH - *Phylogeny
MH - Proteins/genetics
OTO - NOTNLM
OT - *Coalescence
OT - *exon
OT - *Supertree
OT - *phylogeny
OT - *placental
EDAT- 2017/02/09 06:00
MHDA- 2018/02/14 06:00
CRDT- 2017/02/08 06:00
PHST- 2016/01/18 00:00 [received]
PHST- 2016/03/25 00:00 [revised]
PHST- 2016/09/04 00:00 [accepted]
PHST- 2017/02/08 06:00 [entrez]
PHST- 2017/02/09 06:00 [pubmed]
PHST- 2018/02/14 06:00 [medline]
AID - 2449707 [pii]
AID - 10.1093/sysbio/syw082 [doi]
PST - ppublish
SO - Syst Biol. 2017 Jan 1;66(1):112-120. doi: 10.1093/sysbio/syw082.
PMID- 28169404
OWN - NLM
STAT- MEDLINE
DCOM- 20180215
LR - 20180808
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 6
DP - 2017 Nov 1
TI - Age-Dependent and Lineage-Dependent Speciation and Extinction in the Imbalance of
Phylogenetic Trees.
PG - 912-916
LID - 10.1093/sysbio/syx031 [doi]
AB - It is known that phylogenetic trees are more imbalanced than expected from a
birth-death model with constant rates of speciation and extinction, and also that
imbalance can be better fit by allowing the rate of speciation to decrease as the
age of the parent species increases. If imbalance is measured in more detail, at
nodes within trees as a function of the number of species descended from the
nodes, age-dependent models predict levels of imbalance comparable to real trees
for small numbers of descendent species, but predicted imbalance approaches an
asymptote not found in real trees as the number of descendent species becomes
large. Age-dependence must therefore be complemented by another process such as
inheritance of different rates along different lineages, which is known to
predict insufficient imbalance at nodes with few descendent species, but can
predict increasing imbalance with increasing numbers of descendent species.
[Crump-Mode-Jagers process; diversification; macroevolution; taxon sampling; tree
of life.].
CI - (c) The Author(s) 2017. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists. All rights reserved. For Permissions, please
email: journals.permissions@oup.com.
FAU - Holman, Eric W
AU - Holman EW
AD - Department of Psychology, University of California, Los Angeles, CA 90095, USA.
LA - eng
SI - Dryad/10.5061/dryad.2q9r7
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - *Extinction, Biological
MH - *Genetic Speciation
MH - *Models, Biological
MH - *Phylogeny
MH - Time
EDAT- 2017/02/09 06:00
MHDA- 2018/02/16 06:00
CRDT- 2017/02/08 06:00
PHST- 2016/05/17 00:00 [received]
PHST- 2017/01/25 00:00 [accepted]
PHST- 2017/02/09 06:00 [pubmed]
PHST- 2018/02/16 06:00 [medline]
PHST- 2017/02/08 06:00 [entrez]
AID - 2972845 [pii]
AID - 10.1093/sysbio/syx031 [doi]
PST - ppublish
SO - Syst Biol. 2017 Nov 1;66(6):912-916. doi: 10.1093/sysbio/syx031.
PMID- 28169402
OWN - NLM
STAT- MEDLINE
DCOM- 20180129
LR - 20181202
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 4
DP - 2017 Jul 1
TI - Can We "Future-Proof" Consensus Trees?
PG - 611-619
LID - 10.1093/sysbio/syx030 [doi]
AB - Consensus methods are widely used for combining phylogenetic trees into a single
estimate of the evolutionary tree for a group of species. As more taxa are added,
the new source trees may begin to tell a different evolutionary story when
restricted to the original set of taxa. However, if the new trees, restricted to
the original set of taxa, were to agree exactly with the earlier trees, then we
might hope that their consensus would either agree with or resolve the original
consensus tree. In this article, we ask under what conditions consensus methods
exist that are "future proof" in this sense. While we show that some methods
(e.g., Adams consensus) have this property for specific types of input, we also
establish a rather surprising "no-go" theorem: there is no "reasonable" consensus
method that satisfies the future-proofing property in general. We then
investigate a second notion of "future proofing" for consensus methods, in which
trees (rather than taxa) are added, and establish some positive and negative
results. We end with some questions for future work.
CI - (c) The Author(s) 2017. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists. All rights reserved. For Permissions, please
email: journals.permissions@oup.com.
FAU - Bryant, David
AU - Bryant D
AD - Computational Modeling, Department of Mathematics and Statistics, University of
Otago, Dunedin, New Zealand.
FAU - Francis, Andrew
AU - Francis A
AD - Centre for Research in Mathematics, School of Computing, Engineering and
Mathematics, Western Sydney University, Sydney, Australia.
FAU - Steel, Mike
AU - Steel M
AD - Biomathematics Research Centre, Mathematics and Statistics, University of
Canterbury, Christchurch, New Zealand.
LA - eng
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Algorithms
MH - Biological Evolution
MH - Classification/*methods
MH - *Phylogeny
OTO - NOTNLM
OT - *Adams consensus
OT - *consensus
OT - *extension stability
OT - *phylogeny
EDAT- 2017/02/09 06:00
MHDA- 2018/01/30 06:00
CRDT- 2017/02/08 06:00
PHST- 2016/10/30 00:00 [received]
PHST- 2017/01/25 00:00 [accepted]
PHST- 2017/02/09 06:00 [pubmed]
PHST- 2018/01/30 06:00 [medline]
PHST- 2017/02/08 06:00 [entrez]
AID - 2972844 [pii]
AID - 10.1093/sysbio/syx030 [doi]
PST - ppublish
SO - Syst Biol. 2017 Jul 1;66(4):611-619. doi: 10.1093/sysbio/syx030.
PMID- 28158373
OWN - NLM
STAT- MEDLINE
DCOM- 20180228
LR - 20181113
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 1
DP - 2017 Jan 1
TI - Special Issue: Mathematical and Computational Evolutionary Biology-2015.
PG - 1-2
LID - 10.1093/sysbio/syw111 [doi]
FAU - Bryant, David
AU - Bryant D
AD - Department of Mathematics and Statistics, University of Otago, Dunedin, New
Zealand.
FAU - Gascuel, Olivier
AU - Gascuel O
AD - Unite Bioinformatique Evolutive C3BI, USR 3756 Institut Pasteur - CNRS Paris,
France.
AD - Institut de Biologie Computationnelle, LIRMM, UMR 5506, Universite de Montpellier
- CNRS Montpellier, France.
LA - eng
PT - Introductory Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - *Biological Evolution
MH - Classification
MH - *Computational Biology
MH - Congresses as Topic
PMC - PMC5410973
EDAT- 2017/02/06 06:00
MHDA- 2018/03/01 06:00
CRDT- 2017/02/04 06:00
PHST- 2017/02/04 06:00 [entrez]
PHST- 2017/02/06 06:00 [pubmed]
PHST- 2018/03/01 06:00 [medline]
AID - 2965347 [pii]
AID - 10.1093/sysbio/syw111 [doi]
PST - ppublish
SO - Syst Biol. 2017 Jan 1;66(1):1-2. doi: 10.1093/sysbio/syw111.
PMID- 28123117
OWN - NLM
STAT- MEDLINE
DCOM- 20180130
LR - 20181202
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 5
DP - 2017 Sep 1
TI - Phylogenomics from Whole Genome Sequences Using aTRAM.
PG - 786-798
LID - 10.1093/sysbio/syw105 [doi]
AB - Novel 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 can
be alleviated by assembling targeted reads, rather than assembling the entire
genome, to produce a phylogenomic data matrix. Here we demonstrate the use of
automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy
ortholog genes from whole genome sequencing of sucking lice (Anoplura) and
out-groups. We developed a pipeline to extract exon sequences from the aTRAM
assemblies by annotating them with respect to the original target protein. We
aligned these protein sequences with the inferred amino acids and then performed
phylogenetic analyses on both the concatenated matrix of genes and on each gene
separately in a coalescent analysis. Finally, we tested the limits of successful
assembly in aTRAM by assembling 100 genes from close- to distantly related taxa
at high to low levels of coverage.Both the concatenated analysis and the
coalescent-based analysis produced the same tree topology, which was consistent
with previously published results and resolved weakly supported nodes. These
results demonstrate that this approach is successful at developing phylogenomic
data sets from raw genome sequencing reads. Further, we found that with coverages
above $5-10\times$, aTRAM was successful at assembling 80-90% of the contigs for
both close and distantly related taxa. As sequencing costs continue to decline,
we expect full genome sequencing will become more feasible for a wider array of
organisms, and aTRAM will enable mining of these genomic data sets for an
extensive variety of applications, including phylogenomics. [aTRAM; gene
assembly; genome sequencing; phylogenomics.].
CI - (c) The Author(s) 2017. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists. All rights reserved. For Permissions, please
email: journals.permissions@oup.com.
FAU - Allen, Julie M
AU - Allen JM
AD - Illinois Natural History Survey, University of Illinois at Urbana-Champaign,
Urbana, IL 61801, USA.
FAU - Boyd, Bret
AU - Boyd B
AD - Illinois Natural History Survey, University of Illinois at Urbana-Champaign,
Urbana, IL 61801, USA.
AD - Florida Museum of Natural History, University of Florida, Gainesville, FL 32611,
USA.
FAU - Nguyen, Nam-Phuong
AU - Nguyen NP
AD - Carl R. Woese Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA.
FAU - Vachaspati, Pranjal
AU - Vachaspati P
AD - Department of Computer Science, University of Illinois at Urbana-Champaign,
Urbana, IL 61801, USA.
FAU - Warnow, Tandy
AU - Warnow T
AD - Carl R. Woese Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA.
AD - Department of Computer Science, University of Illinois at Urbana-Champaign,
Urbana, IL 61801, USA.
AD - Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana,
IL 61801, USA.
FAU - Huang, Daisie I
AU - Huang DI
AD - Biodiversity Research Centre, University of British Columbia, Vancouver V6T 1Z4,
Canada.
FAU - Grady, Patrick G S
AU - Grady PGS
AD - Illinois Natural History Survey, University of Illinois at Urbana-Champaign,
Urbana, IL 61801, USA.
FAU - Bell, Kayce C
AU - Bell KC
AD - Department of Biology and Museum of Southwestern Biology, University of New
Mexico, Albuquerque, NM 87131, USA.
FAU - Cronk, Quentin C B
AU - Cronk QCB
AD - Biodiversity Research Centre, University of British Columbia, Vancouver V6T 1Z4,
Canada.
FAU - Mugisha, Lawrence
AU - Mugisha L
AD - Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda.
AD - College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere
University, Uganda.
FAU - Pittendrigh, Barry R
AU - Pittendrigh BR
AD - Department of Entomology Michigan State University, East Lansing, MI 48823, USA.
FAU - Leonardi, M Soledad
AU - Leonardi MS
AD - Instituto de Biologia de Organismos Marinos, Centro Nacional Patagonico, Puerto
Madryn, Argentina.
FAU - Reed, David L
AU - Reed DL
AD - Florida Museum of Natural History, University of Florida, Gainesville, FL 32611,
USA.
FAU - Johnson, Kevin P
AU - Johnson KP
AD - Illinois Natural History Survey, University of Illinois at Urbana-Champaign,
Urbana, IL 61801, USA.
LA - eng
SI - Dryad/10.5061/dryad.26j38
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Classification/*methods
MH - Genomics/*methods
MH - *Phylogeny
MH - Sequence Analysis
EDAT- 2017/01/27 06:00
MHDA- 2018/01/31 06:00
CRDT- 2017/01/27 06:00
PHST- 2016/06/02 00:00 [received]
PHST- 2016/12/01 00:00 [accepted]
PHST- 2017/01/27 06:00 [pubmed]
PHST- 2018/01/31 06:00 [medline]
PHST- 2017/01/27 06:00 [entrez]
AID - syw105 [pii]
AID - 10.1093/sysbio/syw105 [doi]
PST - ppublish
SO - Syst Biol. 2017 Sep 1;66(5):786-798. doi: 10.1093/sysbio/syw105.
PMID- 28123116
OWN - NLM
STAT- MEDLINE
DCOM- 20180130
LR - 20181202
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 5
DP - 2017 Sep 1
TI - The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory
Systems - OArCS) and its Integration into a Novel Formalization Scheme for
Morphological Descriptions.
PG - 754-768
LID - 10.1093/sysbio/syw108 [doi]
AB - Morphology, the oldest discipline in the biosciences, is currently experiencing a
renaissance in the field of comparative phenomics. However,
morphological/phenotypic research still suffers on various levels from a lack of
standards. This shortcoming, first highlighted as the "linguistic problem of
morphology", concerns the usage of terminology and also the need for
formalization of morphological descriptions themselves, something of paramount
importance not only to the field of morphology but also when it comes to the use
of phenotypic data in systematics and evolutionary biology. We therefore argue,
that for morphological descriptions, the basis of all systematic and evolutionary
interpretations, ontologies need to be utilized which are based exclusively on
structural qualities/properties and which in no case include statements about
homology and/or function. Statements about homology and function constitute
interpretations on a different or higher level. Based on these "anatomy
ontologies", further ontological dimensions (e.g., referring to functional
properties or homology) may be exerted for a broad use in evolutionary phenomics.
To this end we present the first organ-based ontology for the most species-rich
animal group, the Arthropoda. Our Ontology of Arthropod Circulatory Systems
(OArCS) contains a comprehensive collection of 383 terms (i.e., labels) tied to
296 concepts (i.e., definitions) collected from the literature on phenotypic
aspects of circulatory organ features in arthropods. All of the concepts used in
OArCS are based exclusively on structural features, and in the context of the
ontology are independent of homology and functional assumptions. We cannot rule
out that in some cases, terms are used which in traditional usage and previous
accounts might have implied homology and/or function (e.g. heart, sternal
artery). Concepts are composed of descriptive elements that are used to classify
observed instances into the organizational framework of the ontology. That is,
descriptions in ontologies are only descriptions of individuals if they are
necessary/and or sufficient representations of attributes (independently)
observed and recorded for an individual. In addition, we here present for the
first time an entirely new approach to formalizing phenotypic research, a
semantic model for the description of a complex organ system in a highly
disparate taxon, the arthropods. We demonstrate this with a formalized
morphological description of the hemolymph vascular system in one specimen of the
European garden spider Araneus diadematus. Our description targets five
categories of descriptive statement: "position", "spatial relationships",
"shape", "constituents", and "connections", as the corresponding formalizations
constitute exemplary patterns useful not only when talking about the circulatory
system, but also in descriptions in general. The downstream applications of
computer-parsable morphological descriptions are widespread, with their core
utility being the fact that they make it possible to compare collective
description sets in computational time, that is, very quickly. Among other
things, this facilitates the identification of phenotypic plasticity and
variation when single individuals are compared, the identification of those
traits which correlate between and within taxa, and the identification of links
between morphological traits and genetic (using GO, Gene Ontology) or
environmental (using ENVO, Environmental Ontology) factors. [Arthropoda; concept;
function; hemolymph vascular system; homology; terminology.].
CI - (c) The Author(s) 2017. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists. All rights reserved. For Permissions, please
email: journals.permissions@oup.com.
FAU - Wirkner, Christian S
AU - Wirkner CS
AD - Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universitaet
Rostock, 18055 Rostock, Germany.
FAU - Gopel, Torben
AU - Gopel T
AD - Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universitaet
Rostock, 18055 Rostock, Germany.
FAU - Runge, Jens
AU - Runge J
AD - Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universitaet
Rostock, 18055 Rostock, Germany.
FAU - Keiler, Jonas
AU - Keiler J
AD - Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universitaet
Rostock, 18055 Rostock, Germany.
FAU - Klussmann-Fricke, Bastian-Jesper
AU - Klussmann-Fricke BJ
AD - Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universitaet
Rostock, 18055 Rostock, Germany.
FAU - Huckstorf, Katarina
AU - Huckstorf K
AD - Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universitaet
Rostock, 18055 Rostock, Germany.
FAU - Scholz, Stephan
AU - Scholz S
AD - Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universitaet
Rostock, 18055 Rostock, Germany.
FAU - Miko, Istvan
AU - Miko I
AD - Department of Entomology, Pennsylvania State University, University Park, PA
16802, USA.
FAU - J Yoder, Matthew
AU - J Yoder M
AD - Illinois Natural History Survey, University of Illinois, Champaign, IL 61820,
USA.
FAU - Richter, Stefan
AU - Richter S
AD - Allgemeine & Spezielle Zoologie, Institut fuer Biowissenschaften, Universitaet
Rostock, 18055 Rostock, Germany.
LA - eng
SI - Dryad/10.5061/dryad.kv62d
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Anatomy/*standards
MH - Animals
MH - Arthropods/*anatomy & histology
MH - Classification/*methods
MH - Phenotype
MH - Phylogeny
MH - *Terminology as Topic
EDAT- 2017/01/27 06:00
MHDA- 2018/01/31 06:00
CRDT- 2017/01/27 06:00
PHST- 2016/05/27 00:00 [received]
PHST- 2016/11/26 00:00 [accepted]
PHST- 2017/01/27 06:00 [pubmed]
PHST- 2018/01/31 06:00 [medline]
PHST- 2017/01/27 06:00 [entrez]
AID - syw108 [pii]
AID - 10.1093/sysbio/syw108 [doi]
PST - ppublish
SO - Syst Biol. 2017 Sep 1;66(5):754-768. doi: 10.1093/sysbio/syw108.
PMID- 28123115
OWN - NLM
STAT- MEDLINE
DCOM- 20180129
LR - 20181202
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 4
DP - 2017 Jul 1
TI - Homology-Aware Phylogenomics at Gigabase Scales.
PG - 590-603
LID - 10.1093/sysbio/syw104 [doi]
AB - Obstacles to inferring species trees from whole genome data sets range from
algorithmic and data management challenges to the wholesale discordance in
evolutionary history found in different parts of a genome. Recent work that
builds trees directly from genomes by parsing them into sets of small $k$-mer
strings holds promise to streamline and simplify these efforts, but existing
approaches do not account well for gene tree discordance. We describe a "seed and
extend" protocol that finds nearly exact matching sets of orthologous $k$-mers
and extends them to construct data sets that can properly account for genomic
heterogeneity. Exploiting an efficient suffix array data structure, sets of whole
genomes can be parsed and converted into phylogenetic data matrices rapidly, with
contiguous blocks of $k$-mers from the same chromosome, gene, or scaffold
concatenated as needed. Phylogenetic trees constructed from highly curated rice
genome data and a diverse set of six other eukaryotic whole genome,
transcriptome, and organellar genome data sets recovered trees nearly identical
to published phylogenomic analyses, in a small fraction of the time, and
requiring many fewer parameter choices. Our method's ability to retain local
homology information was demonstrated by using it to characterize gene tree
discordance across the rice genome, and by its robustness to the high rate of
interchromosomal gene transfer found in several rice species.
CI - (c) The Author(s) 2017. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists.
FAU - Sanderson, M J
AU - Sanderson MJ
AD - Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
85721, USA.
FAU - Nicolae, Marius
AU - Nicolae M
AD - Department of Computer Science and Engineering, University of Connecticut,
Storrs, CT 06269, USA.
FAU - McMahon, M M
AU - McMahon MM
AD - School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
LA - eng
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Classification/*methods
MH - Gene Transfer, Horizontal/genetics
MH - *Genomics
MH - Oryza/classification/genetics
MH - *Phylogeny
PMC - PMC5790135
OTO - NOTNLM
OT - *Oryza
OT - *k-mer
OT - *lineage sorting
OT - *phylogenomics
OT - *suffix array
EDAT- 2017/01/27 06:00
MHDA- 2018/01/30 06:00
CRDT- 2017/01/27 06:00
PHST- 2016/05/19 00:00 [received]
PHST- 2016/11/25 00:00 [accepted]
PHST- 2017/01/27 06:00 [pubmed]
PHST- 2018/01/30 06:00 [medline]
PHST- 2017/01/27 06:00 [entrez]
AID - syw104 [pii]
AID - 10.1093/sysbio/syw104 [doi]
PST - ppublish
SO - Syst Biol. 2017 Jul 1;66(4):590-603. doi: 10.1093/sysbio/syw104.
PMID- 28123114
OWN - NLM
STAT- MEDLINE
DCOM- 20180129
LR - 20181202
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 4
DP - 2017 Jul 1
TI - Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data.
PG - 620-636
LID - 10.1093/sysbio/syw103 [doi]
AB - Detecting variation in the evolutionary process along chromosomes is increasingly
important as whole-genome data become more widely available. For example, factors
such as incomplete lineage sorting, horizontal gene transfer, and chromosomal
inversion are expected to result in changes in the underlying gene trees along a
chromosome, while changes in selective pressure and mutational rates for
different genomic regions may lead to shifts in the underlying mutational
process. We propose the split score as a general method for quantifying support
for a particular phylogenetic relationship within a genomic data set. Because the
split score is based on algebraic properties of a matrix of site pattern
frequencies, it can be rapidly computed, even for data sets that are large in the
number of taxa and/or in the length of the alignment, providing an advantage over
other methods (e.g., maximum likelihood) that are often used to assess such
support. Using simulation, we explore the properties of the split score,
including its dependence on sequence length, branch length, size of a split and
its ability to detect true splits in the underlying tree. Using a sliding window
analysis, we show that split scores can be used to detect changes in the
underlying evolutionary process for genome-scale data from primates, mosquitoes,
and viruses in a computationally efficient manner. Computation of the split score
has been implemented in the software package SplitSup.
CI - (c) The Author(s) 2017. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists. All rights reserved. For Permissions, please
email: journals.permissions@oup.com.
FAU - Allman, Elizabeth S
AU - Allman ES
AD - Department of Mathematics and Statistics, PO Box 756660, University of Alaska
Fairbanks, Fairbanks, AK 99775-6660, USA.
FAU - Kubatko, Laura S
AU - Kubatko LS
AD - Department of Statistics and Department of Evolution, Ecology, and Organismal
Biology, The Ohio State University, Columbus, OH 43210, USA.
FAU - Rhodes, John A
AU - Rhodes JA
AD - Department of Mathematics and Statistics, PO Box 756660, University of Alaska
Fairbanks, Fairbanks, AK 99775-6660, USA.
LA - eng
GR - R01 GM117590/GM/NIGMS NIH HHS/United States
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - Classification/*methods
MH - Culicidae/classification/genetics
MH - Evolution, Molecular
MH - Gene Transfer, Horizontal
MH - Genome/genetics
MH - *Phylogeny
MH - Primates/classification/genetics
MH - Software
MH - Viruses/classification/genetics
PMC - PMC6075200
OTO - NOTNLM
OT - *General Markov model
OT - *genome-scale data analysis
OT - *matrix flattenings
OT - *phylogenetic trees
OT - *singular value decomposition
OT - *split scores
EDAT- 2017/01/27 06:00
MHDA- 2018/01/30 06:00
CRDT- 2017/01/27 06:00
PHST- 2016/08/02 00:00 [received]
PHST- 2016/10/28 00:00 [accepted]
PHST- 2017/01/27 06:00 [pubmed]
PHST- 2018/01/30 06:00 [medline]
PHST- 2017/01/27 06:00 [entrez]
AID - syw103 [pii]
AID - 10.1093/sysbio/syw103 [doi]
PST - ppublish
SO - Syst Biol. 2017 Jul 1;66(4):620-636. doi: 10.1093/sysbio/syw103.
PMID- 28123113
OWN - NLM
STAT- PubMed-not-MEDLINE
LR - 20180226
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 4
DP - 2017 Jul 1
TI - Erratum.
PG - 660
LID - 10.1093/sysbio/syw113 [doi]
LA - eng
PT - Journal Article
PT - Published Erratum
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
EFR - Syst Biol. 2017 Jan 1;66(1):e1-e29. PMID: 28173586
PMC - PMC5790131
EDAT- 2017/01/27 06:00
MHDA- 2017/01/27 06:01
CRDT- 2017/01/27 06:00
PHST- 2017/01/27 06:00 [pubmed]
PHST- 2017/01/27 06:01 [medline]
PHST- 2017/01/27 06:00 [entrez]
AID - syw113 [pii]
AID - 10.1093/sysbio/syw113 [doi]
PST - ppublish
SO - Syst Biol. 2017 Jul 1;66(4):660. doi: 10.1093/sysbio/syw113.
PMID- 28123112
OWN - NLM
STAT- MEDLINE
DCOM- 20180129
LR - 20181202
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 4
DP - 2017 Jul 1
TI - How the Aridification of Australia Structured the Biogeography and Influenced the
Diversification of a Large Lineage of Australian Cicadas.
PG - 569-589
LID - 10.1093/sysbio/syw078 [doi]
AB - Over the last 30 million years, Australia's landscape has undergone dramatic
cooling and drying due to the establishment of the Antarctic Circumpolar Current
and change in global CO$_{2}$ levels. Studies have shown that many Australian
organisms went extinct during these major cooling events, while others
experienced adaptive radiations and increases in diversification rates as a
result of exploiting new niches in the arid zone. Despite the many studies on
diversification and biogeography in Australia, few have been continent-wide and
none have focused on a group of organisms adapted to feeding on plants. We
studied 162 species of cicadas in the Australian Pauropsalta complex, a large
generic lineage within the tribe Cicadettini. We asked whether there were changes
in the diversification rate of Pauropsalta over time and if so: 1) which clades
were associated with the rate change? 2) did timing of rate shifts correspond to
known periods of dramatic historical climate change, 3) did increases in
diversification rate along select lineages correspond to adaptive radiations with
movement into the arid zone? To address these questions, we estimated a molecular
phylogeny of the Pauropsalta complex using ${\sim}$5300 bp of nucleotide sequence
data distributed among five loci (one mtDNA locus and four nDNA loci). We found
that this large group of cicadas did not diversify at a constant rate as they
spread through Australia; instead the signature of decreasing diversification
rate changed roughly around the time of the expansion of the east Antarctic ice
sheets ${\sim}$16 Ma and the glaciation of the northern hemisphere ${\sim}$3 Ma.
Unlike other Australian taxa, the Pauropsalta complex did not explosively radiate
in response to an early invasion of the arid zone. Instead multiple groups
invaded the arid zone and experienced rates of diversification similar to
mesic-distributed taxa. We found evidence for relictual groups, located in
pre-Mesozoic habitat, that have not diversified and continue to reside on mesic
hosts in isolated "habitat islands". Future work should focus on groups of
similar ages with similar distribution patterns to determine whether this tempo
and pattern of diversification and biogeography is consistent with evidence from
other phytophagous insects.
CI - (c) The Author(s) 2017. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists. All rights reserved. For Permissions, please
email: journals.permissions@oup.com.
FAU - Owen, Christopher L
AU - Owen CL
AD - Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N.
Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA.
AD - Computational Biology Institute, George Washington University, Innovation Hall,
Suite 305, 45085 University Drive, Ashburn, VA 20147-2766, USA.
FAU - Marshall, David C
AU - Marshall DC
AD - Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N.
Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA.
FAU - Hill, Kathy B R
AU - Hill KBR
AD - Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N.
Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA.
FAU - Simon, Chris
AU - Simon C
AD - Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N.
Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA.
LA - eng
SI - Dryad/10.5061/dryad.1580p
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - Australia
MH - *Biodiversity
MH - Climate Change
MH - Hemiptera/*classification/genetics
MH - *Phylogeny
MH - Phylogeography
OTO - NOTNLM
OT - *Aridification
OT - *Australia
OT - *Pauropsalta
OT - *cicadas
OT - *diversification
EDAT- 2017/01/27 06:00
MHDA- 2018/01/30 06:00
CRDT- 2017/01/27 06:00
PHST- 2014/04/03 00:00 [received]
PHST- 2016/08/24 00:00 [accepted]
PHST- 2017/01/27 06:00 [pubmed]
PHST- 2018/01/30 06:00 [medline]
PHST- 2017/01/27 06:00 [entrez]
AID - syw078 [pii]
AID - 10.1093/sysbio/syw078 [doi]
PST - ppublish
SO - Syst Biol. 2017 Jul 1;66(4):569-589. doi: 10.1093/sysbio/syw078.
PMID- 28108601
OWN - NLM
STAT- MEDLINE
DCOM- 20180215
LR - 20181113
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 6
DP - 2017 Nov 1
TI - Phylogenomics using Target-Restricted Assembly Resolves Intrageneric
Relationships of Parasitic Lice (Phthiraptera: Columbicola).
PG - 896-911
LID - 10.1093/sysbio/syx027 [doi]
AB - 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 of Columbicola have switched to new host species.
Understanding the ecological and evolutionary factors that influence coadaptation
and codiversification in this system will substantially improve our understanding
of coevolution in general. However, further work is hampered by the lack of a
robust phylogenetic framework for Columbicola spp. and their hosts. Previous
attempts to resolve the phylogeny of Columbicola based on sequences from a few
genes provided limited support. Here, we apply a new approach, target restricted
assembly, to assemble 977 orthologous gene sequences from whole-genome sequence
data generated from very small, ethanol-preserved specimens, representing up to
61 species of wing lice. Both concatenation and coalescent methods were used to
estimate the species tree. These two approaches yielded consistent and
well-supported trees with 90% of all relationships receiving 100% support, which
is a substantial improvement over previous studies. We used this new phylogeny to
show that biogeographic ranges are generally conserved within clades of
Columbicola wing lice. Limited inconsistencies are probably attributable to
intercontinental dispersal of hosts, and host switching by some of the lice.
[aTRAM; coalescent; coevolution; concatenation; species tree.].
CI - (c) The Author(s) 2017. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists. All rights reserved. For Permissions, please
email: journals.permissions@oup.com.
FAU - Boyd, Bret M
AU - Boyd BM
AD - Department of Entomology, University of Georgia Athens, 413 Biological Sciences
Building, Athens, GA 30602, USA.
AD - Illinois Natural History Survey, Prairie Research Institute, University of
Illinois Urbana-Champaign, Champaign, IL 61820, USA.
FAU - Allen, Julie M
AU - Allen JM
AD - Illinois Natural History Survey, Prairie Research Institute, University of
Illinois Urbana-Champaign, Champaign, IL 61820, USA.
AD - Florida Museum of Natural History, University of Florida, Gainesville, FL 32611,
USA.
FAU - Nguyen, Nam-Phuong
AU - Nguyen NP
AD - Department of Computer Science and Engineering, University of California San
Diego, La Jolla, CA 92093, USA.
FAU - Sweet, Andrew D
AU - Sweet AD
AD - Illinois Natural History Survey, Prairie Research Institute, University of
Illinois Urbana-Champaign, Champaign, IL 61820, USA.
FAU - Warnow, Tandy
AU - Warnow T
AD - Departments of Computer Science and Bioengineering, University of Illinois
Urbana-Champaign, Urbana, IL 61801, USA.
FAU - Shapiro, Michael D
AU - Shapiro MD
AD - Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
FAU - Villa, Scott M
AU - Villa SM
AD - Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
FAU - Bush, Sarah E
AU - Bush SE
AD - Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
FAU - Clayton, Dale H
AU - Clayton DH
AD - Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
FAU - Johnson, Kevin P
AU - Johnson KP
AD - Illinois Natural History Survey, Prairie Research Institute, University of
Illinois Urbana-Champaign, Champaign, IL 61820, USA.
LA - eng
SI - Dryad/10.5061/dryad.4812p
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - Columbidae/parasitology
MH - Genome/*genetics
MH - Host Specificity
MH - Host-Parasite Interactions
MH - Phthiraptera/*classification/*genetics/physiology
MH - *Phylogeny
PMC - PMC5837638
EDAT- 2017/01/22 06:00
MHDA- 2018/02/16 06:00
CRDT- 2017/01/22 06:00
PHST- 2016/09/06 00:00 [received]
PHST- 2017/01/06 00:00 [accepted]
PHST- 2017/01/22 06:00 [pubmed]
PHST- 2018/02/16 06:00 [medline]
PHST- 2017/01/22 06:00 [entrez]
AID - syx027 [pii]
AID - 10.1093/sysbio/syx027 [doi]
PST - ppublish
SO - Syst Biol. 2017 Nov 1;66(6):896-911. doi: 10.1093/sysbio/syx027.
PMID- 28057858
OWN - NLM
STAT- MEDLINE
DCOM- 20180215
LR - 20180808
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 66
IP - 6
DP - 2017 Nov 1
TI - ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with
Selection on Folding Stability.
PG - 1054-1064
LID - 10.1093/sysbio/syw121 [doi]
AB - The 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
present ProtASR, a new evolutionary framework to infer ancestral protein
sequences accounting for selection on protein stability. First, ProtASR generates
site-specific substitution matrices through the structurally constrained
mean-field (MF) substitution model, which considers both unfolding and misfolding
stability. We previously showed that MF models outperform empirical amino acid
substitution models, as well as other structurally constrained substitution
models, both in terms of likelihood and correctly inferring amino acid
distributions across sites. In the second step, ProtASR adapts a well-established
maximum-likelihood (ML) ASR procedure to infer ancestral proteins under MF
models. A known bias of ML ASR methods is that they tend to overestimate the
stability of ancestral proteins by underestimating the frequency of deleterious
mutations. We compared ProtASR under MF to two empirical substitution models (JTT
and CAT), reconstructing the ancestral sequences of simulated proteins. ProtASR
yields reconstructed proteins with less biased stabilities, which are
significantly closer to those of the simulated proteins. Analysis of extant
protein families suggests that folding stability evolves through time across
protein families, potentially reflecting neutral fluctuation. Some families
exhibit a more constant protein folding stability, while others are more
variable. ProtASR is freely available from
https://github.com/miguelarenas/protasr and includes detailed documentation and
ready-to-use examples. It runs in seconds/minutes depending on protein length and
alignment size. [Ancestral sequence reconstruction; folding stability; molecular
adaptation; phylogenetics; protein evolution; protein structure.].
CI - (c) The Author(s) 2017. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists. All rights reserved. For Permissions, please
email: journals.permissions@oup.com.
FAU - Arenas, Miguel
AU - Arenas M
AD - Instituto de Investigacao e Inovacao em Saude (i3S), University of Porto, Porto,
Portugal.
AD - Institute of Molecular Pathology and Immunology of the University of Porto
(IPATIMUP), Porto, Portugal.
AD - Centre for Molecular Biology Severo Ochoa (CBMSO), Consejo Superior de
Investigaciones Cientificas (CSIC), Madrid, Spain.
AD - Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo,
Spain.
FAU - Weber, Claudia C
AU - Weber CC
AD - Department of Biology and Center for Computational Genetics and Genomics, Temple
University, Philadelphia, PA 19122, USA.
FAU - Liberles, David A
AU - Liberles DA
AD - Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
AD - Department of Biology and Center for Computational Genetics and Genomics, Temple
University, Philadelphia, PA 19122, USA.
FAU - Bastolla, Ugo
AU - Bastolla U
AD - Centre for Molecular Biology Severo Ochoa (CBMSO), Consejo Superior de
Investigaciones Cientificas (CSIC), Madrid, Spain.
LA - eng
SI - Dryad/10.5061/dryad.bh213
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PT - Research Support, U.S. Gov't, Non-P.H.S.
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 0 (DNA, Ancient)
SB - IM
MH - *Algorithms
MH - Amino Acid Substitution
MH - Classification/*methods
MH - DNA, Ancient/chemistry