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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- 25239212
OWN - NLM
STAT- MEDLINE
DCOM- 20150416
LR - 20150217
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 64
IP - 2
DP - 2015 Mar
TI - Phylogeny, paleontology, and primates: do incomplete fossils bias the tree of
life?
PG - 169-86
LID - 10.1093/sysbio/syu077 [doi]
AB - Paleontological systematics relies heavily on morphological data that have
undergone decay and fossilization. Here, we apply a heuristic means to assess how
a fossil's incompleteness detracts from inferring its phylogenetic relationships.
We compiled a phylogenetic matrix for primates and simulated the extinction of
living species by deleting an extant taxon's molecular data and keeping only
those morphological characters present in actual fossils. The choice of
characters present in a given living taxon (the subject) was defined by those
present in a given fossil (the template). By measuring congruence between a
well-corroborated phylogeny to those incorporating artificial fossils, and by
comparing real vs. random character distributions and states, we tested the
information content of paleontological datasets and determined if extinction of a
living species leads to bias in phylogeny reconstruction. We found a positive
correlation between fossil completeness and topological congruence. Real fossil
templates sampled for 36 or more of the 360 available morphological characters
(including dental) performed significantly better than similarly complete
templates with random states. Templates dominated by only one partition performed
worse than templates with randomly sampled characters across partitions. The
template based on the Eocene primate Darwinius masillae performs better than most
other templates with a similar number of sampled characters, likely due to
preservation of data across multiple partitions. Our results support the
interpretation that Darwinius is strepsirhine, not haplorhine, and suggest that
paleontological datasets are reliable in primate phylogeny reconstruction.
CI - (c) The Author(s) 2014. 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 - Pattinson, David J
AU - Pattinson DJ
AD - Department of Zoology, Downing Street, Cambridge, CB2 3EJ; Division of Ecology
and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ;
Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7
5BD; and Department of Physics, Cavendish Laboratory, JJ Thomson Avenue,
Cambridge, CB3 0HE, UK Department of Zoology, Downing Street, Cambridge, CB2 3EJ;
Division of Ecology and Evolution, Imperial College London, South Kensington
Campus, London, SW7 2AZ; Department of Life Sciences, Natural History Museum,
Cromwell Road, London, SW7 5BD; and Department of Physics, Cavendish Laboratory,
JJ Thomson Avenue, Cambridge, CB3 0HE, UK Department of Zoology, Downing Street,
Cambridge, CB2 3EJ; Division of Ecology and Evolution, Imperial College London,
South Kensington Campus, London, SW7 2AZ; Department of Life Sciences, Natural
History Museum, Cromwell Road, London, SW7 5BD; and Department of Physics,
Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
FAU - Thompson, Richard S
AU - Thompson RS
AD - Department of Zoology, Downing Street, Cambridge, CB2 3EJ; Division of Ecology
and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ;
Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7
5BD; and Department of Physics, Cavendish Laboratory, JJ Thomson Avenue,
Cambridge, CB3 0HE, UK.
FAU - Piotrowski, Aleks K
AU - Piotrowski AK
AD - Department of Zoology, Downing Street, Cambridge, CB2 3EJ; Division of Ecology
and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ;
Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7
5BD; and Department of Physics, Cavendish Laboratory, JJ Thomson Avenue,
Cambridge, CB3 0HE, UK.
FAU - Asher, Robert J
AU - Asher RJ
AD - Department of Zoology, Downing Street, Cambridge, CB2 3EJ; Division of Ecology
and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ;
Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7
5BD; and Department of Physics, Cavendish Laboratory, JJ Thomson Avenue,
Cambridge, CB3 0HE, UK r.asher@zoo.cam.ac.uk djp65@cam.ac.uk.
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20140919
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - Extinction, Biological
MH - *Fossils
MH - Paleontology/standards
MH - *Phylogeny
MH - Primates/anatomy & histology/*classification
OTO - NOTNLM
OT - Artificial extinction
OT - Darwinius
OT - data combination
OT - missing data
OT - phylogeny reconstruction
OT - primates
OT - taphonomy
EDAT- 2014/09/23 06:00
MHDA- 2015/04/17 06:00
CRDT- 2014/09/21 06:00
PHST- 2014/09/21 06:00 [entrez]
PHST- 2014/09/23 06:00 [pubmed]
PHST- 2015/04/17 06:00 [medline]
AID - syu077 [pii]
AID - 10.1093/sysbio/syu077 [doi]
PST - ppublish
SO - Syst Biol. 2015 Mar;64(2):169-86. doi: 10.1093/sysbio/syu077. Epub 2014 Sep 19.
PMID- 25236959
OWN - NLM
STAT- MEDLINE
DCOM- 20150604
LR - 20181113
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 64
IP - 1
DP - 2015 Jan
TI - How much information is needed to infer reticulate evolutionary histories?
PG - 102-11
LID - 10.1093/sysbio/syu076 [doi]
AB - Phylogenetic networks are a generalization of evolutionary trees and are an
important tool for analyzing reticulate evolutionary histories. Recently, there
has been great interest in developing new methods to construct rooted
phylogenetic networks, that is, networks whose internal vertices correspond to
hypothetical ancestors, whose leaves correspond to sampled taxa, and in which
vertices with more than one parent correspond to taxa formed by reticulate
evolutionary events such as recombination or hybridization. Several methods for
constructing evolutionary trees use the strategy of building up a tree from
simpler building blocks (such as triplets or clusters), and so it is natural to
look for ways to construct networks from smaller networks. In this article, we
shall demonstrate a fundamental issue with this approach. Namely, we show that
even if we are given all of the subnetworks induced on all proper subsets of the
leaves of some rooted phylogenetic network, we still do not have all of the
information required to completely determine that network. This implies that even
if all of the building blocks for some reticulate evolutionary history were to be
taken as the input for any given network building method, the method might still
output an incorrect history. We also discuss some potential consequences of this
result for constructing phylogenetic networks.
CI - (c) The Author(s) 2014. Published by Oxford University Press, on behalf of the
Society of Systematic Biologists.
FAU - Huber, Katharina T
AU - Huber KT
AD - School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum
Wiskunde & Informatica (CWI), Amsterdam, Netherlands.
FAU - Van Iersel, Leo
AU - Van Iersel L
AD - School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum
Wiskunde & Informatica (CWI), Amsterdam, Netherlands.
FAU - Moulton, Vincent
AU - Moulton V
AD - School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum
Wiskunde & Informatica (CWI), Amsterdam, Netherlands
vincent.moulton@cmp.uea.ac.uk.
FAU - Wu, Taoyang
AU - Wu T
AD - School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum
Wiskunde & Informatica (CWI), Amsterdam, Netherlands.
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20140918
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Classification/*methods
MH - Cryptococcus gattii/classification/genetics
MH - Models, Theoretical
MH - *Phylogeny
PMC - PMC4265143
OTO - NOTNLM
OT - Evolutionary tree
OT - network reconstruction
OT - phylogenetic network
OT - reticulate evolution
EDAT- 2014/09/23 06:00
MHDA- 2015/06/05 06:00
CRDT- 2014/09/20 06:00
PHST- 2014/09/20 06:00 [entrez]
PHST- 2014/09/23 06:00 [pubmed]
PHST- 2015/06/05 06:00 [medline]
AID - syu076 [pii]
AID - 10.1093/sysbio/syu076 [doi]
PST - ppublish
SO - Syst Biol. 2015 Jan;64(1):102-11. doi: 10.1093/sysbio/syu076. Epub 2014 Sep 18.
PMID- 25209223
OWN - NLM
STAT- MEDLINE
DCOM- 20150604
LR - 20141216
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 64
IP - 1
DP - 2015 Jan
TI - ModelOMatic: fast and automated model selection between RY, nucleotide, amino
acid, and codon substitution models.
PG - 42-55
LID - 10.1093/sysbio/syu062 [doi]
AB - Molecular phylogenetics is a powerful tool for inferring both the process and
pattern of evolution from genomic sequence data. Statistical approaches, such as
maximum likelihood and Bayesian inference, are now established as the preferred
methods of inference. The choice of models that a researcher uses for inference
is of critical importance, and there are established methods for model selection
conditioned on a particular type of data, such as nucleotides, amino acids, or
codons. A major limitation of existing model selection approaches is that they
can only compare models acting upon a single type of data. Here, we extend model
selection to allow comparisons between models describing different types of data
by introducing the idea of adapter functions, which project aggregated models
onto the originally observed sequence data. These projections are implemented in
the program ModelOMatic and used to perform model selection on 3722 families from
the PANDIT database, 68 genes from an arthropod phylogenomic data set, and 248
genes from a vertebrate phylogenomic data set. For the PANDIT and arthropod data,
we find that amino acid models are selected for the overwhelming majority of
alignments; with progressively smaller numbers of alignments selecting codon and
nucleotide models, and no families selecting RY-based models. In contrast, nearly
all alignments from the vertebrate data set select codon-based models. The
sequence divergence, the number of sequences, and the degree of selection acting
upon the protein sequences may contribute to explaining this variation in model
selection. Our ModelOMatic program is fast, with most families from PANDIT taking
fewer than 150 s to complete, and should therefore be easily incorporated into
existing phylogenetic pipelines. ModelOMatic is available at
https://code.google.com/p/modelomatic/.
CI - (c) The Author(s) 2014. 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 - Whelan, Simon
AU - Whelan S
AD - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala
75236, Sweden and Faculty of Life Sciences, University of Manchester, Manchester,
UK Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala
75236, Sweden and Faculty of Life Sciences, University of Manchester, Manchester,
UK simon.whelan@ebc.uu.se.
FAU - Allen, James E
AU - Allen JE
AD - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala
75236, Sweden and Faculty of Life Sciences, University of Manchester, Manchester,
UK.
FAU - Blackburne, Benjamin P
AU - Blackburne BP
AD - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala
75236, Sweden and Faculty of Life Sciences, University of Manchester, Manchester,
UK.
FAU - Talavera, David
AU - Talavera D
AD - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala
75236, Sweden and Faculty of Life Sciences, University of Manchester, Manchester,
UK.
LA - eng
GR - BB/H000445/1/Biotechnology and Biological Sciences Research Council/United
Kingdom
GR - BB/H006818/1/Biotechnology and Biological Sciences Research Council/United
Kingdom
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20140909
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 0 (Amino Acids)
RN - 0 (Codon)
RN - 0 (Nucleotides)
SB - IM
MH - Amino Acids/genetics
MH - Animals
MH - Classification/*methods
MH - Codon/genetics
MH - *Models, Biological
MH - Nucleotides/genetics
MH - *Phylogeny
MH - Software
OTO - NOTNLM
OT - AIC
OT - model selection
OT - phylogenetics
OT - substitution models
EDAT- 2014/09/12 06:00
MHDA- 2015/06/05 06:00
CRDT- 2014/09/12 06:00
PHST- 2014/09/12 06:00 [entrez]
PHST- 2014/09/12 06:00 [pubmed]
PHST- 2015/06/05 06:00 [medline]
AID - syu062 [pii]
AID - 10.1093/sysbio/syu062 [doi]
PST - ppublish
SO - Syst Biol. 2015 Jan;64(1):42-55. doi: 10.1093/sysbio/syu062. Epub 2014 Sep 9.
PMID- 25209222
OWN - NLM
STAT- MEDLINE
DCOM- 20150604
LR - 20141216
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 64
IP - 1
DP - 2015 Jan
TI - The unsolved challenge to phylogenetic correlation tests for categorical
characters.
PG - 127-36
LID - 10.1093/sysbio/syu070 [doi]
FAU - Maddison, Wayne P
AU - Maddison WP
AD - Departments of Zoology and Botany and Beaty Biodiversity Museum, University of
British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada
V6T 1Z4; Departments of Zoology and Biodiversity Research Centre, University of
British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada
V6T 1Z4 and Department of Biological Sciences, Macquarie University, Sydney NSW
2109, Australia wayne.maddison@ubc.ca.
FAU - FitzJohn, Richard G
AU - FitzJohn RG
AD - Departments of Zoology and Botany and Beaty Biodiversity Museum, University of
British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada
V6T 1Z4; Departments of Zoology and Biodiversity Research Centre, University of
British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada
V6T 1Z4 and Department of Biological Sciences, Macquarie University, Sydney NSW
2109, Australia Departments of Zoology and Botany and Beaty Biodiversity Museum,
University of British Columbia, 6270 University Boulevard, Vancouver, British
Columbia, Canada V6T 1Z4; Departments of Zoology and Biodiversity Research
Centre, University of British Columbia, 6270 University Boulevard, Vancouver,
British Columbia, Canada V6T 1Z4 and Department of Biological Sciences, Macquarie
University, Sydney NSW 2109, Australia.
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20140909
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - Biodiversity
MH - *Classification
MH - Genetic Speciation
MH - Models, Biological
MH - *Phylogeny
EDAT- 2014/09/12 06:00
MHDA- 2015/06/05 06:00
CRDT- 2014/09/12 06:00
PHST- 2014/09/12 06:00 [entrez]
PHST- 2014/09/12 06:00 [pubmed]
PHST- 2015/06/05 06:00 [medline]
AID - syu070 [pii]
AID - 10.1093/sysbio/syu070 [doi]
PST - ppublish
SO - Syst Biol. 2015 Jan;64(1):127-36. doi: 10.1093/sysbio/syu070. Epub 2014 Sep 9.
PMID- 25190593
OWN - NLM
STAT- MEDLINE
DCOM- 20150604
LR - 20141216
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 64
IP - 1
DP - 2015 Jan
TI - Declining rates of species described per taxonomist: slowdown of progress or a
side-effect of improved quality in taxonomy?
PG - 144-51
LID - 10.1093/sysbio/syu069 [doi]
FAU - Sangster, George
AU - Sangster G
AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History,
P.O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Stockholm
University, SE-106 91 Stockholm, Sweden; and Department of Environmental Science
and Policy, George Mason University, 4400 University Drive, Fairfax, Virginia
22030 4444, USA Department of Bioinformatics and Genetics, Swedish Museum of
Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden; Department of
Zoology, Stockholm University, SE-106 91 Stockholm, Sweden; and Department of
Environmental Science and Policy, George Mason University, 4400 University Drive,
Fairfax, Virginia 22030 4444, USA g.sangster@planet.nl.
FAU - Luksenburg, Jolanda A
AU - Luksenburg JA
AD - Department of Bioinformatics and Genetics, Swedish Museum of Natural History,
P.O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Stockholm
University, SE-106 91 Stockholm, Sweden; and Department of Environmental Science
and Policy, George Mason University, 4400 University Drive, Fairfax, Virginia
22030 4444, USA.
LA - eng
PT - Journal Article
DEP - 20140903
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - *Classification
MH - Research/*standards/*trends
MH - Species Specificity
EDAT- 2014/09/06 06:00
MHDA- 2015/06/05 06:00
CRDT- 2014/09/06 06:00
PHST- 2014/09/06 06:00 [entrez]
PHST- 2014/09/06 06:00 [pubmed]
PHST- 2015/06/05 06:00 [medline]
AID - syu069 [pii]
AID - 10.1093/sysbio/syu069 [doi]
PST - ppublish
SO - Syst Biol. 2015 Jan;64(1):144-51. doi: 10.1093/sysbio/syu069. Epub 2014 Sep 3.
PMID- 25183706
OWN - NLM
STAT- MEDLINE
DCOM- 20150604
LR - 20181113
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 64
IP - 1
DP - 2015 Jan
TI - Concatabominations: identifying unstable taxa in morphological phylogenetics
using a heuristic extension to safe taxonomic reduction.
PG - 137-43
LID - 10.1093/sysbio/syu066 [doi]
FAU - Siu-Ting, Karen
AU - Siu-Ting K
AD - Department of Biology, National University of Ireland, Maynooth, Co. Kildare,
Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ,
UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK;
and Institute of Biological, Environmental & Rural Sciences, Aberystwyth
University, Aberystwyth SY23 3FG, UK Department of Biology, National University
of Ireland, Maynooth, Co. Kildare, Ireland; School of Biological Sciences,
University of Bristol, Bristol BS8 1TQ, UK; Department of Life Sciences, The
Natural History Museum, London SW7 5BD, UK; and Institute of Biological,
Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3FG, UK
Department of Biology, National University of Ireland, Maynooth, Co. Kildare,
Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ,
UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK;
and Institute of Biological, Environmental & Rural Sciences, Aberystwyth
University, Aberystwyth SY23 3FG, UK agalychnica@gmail.com.
FAU - Pisani, Davide
AU - Pisani D
AD - Department of Biology, National University of Ireland, Maynooth, Co. Kildare,
Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ,
UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK;
and Institute of Biological, Environmental & Rural Sciences, Aberystwyth
University, Aberystwyth SY23 3FG, UK.
FAU - Creevey, Christopher J
AU - Creevey CJ
AD - Department of Biology, National University of Ireland, Maynooth, Co. Kildare,
Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ,
UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK;
and Institute of Biological, Environmental & Rural Sciences, Aberystwyth
University, Aberystwyth SY23 3FG, UK.
FAU - Wilkinson, Mark
AU - Wilkinson M
AD - Department of Biology, National University of Ireland, Maynooth, Co. Kildare,
Ireland; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ,
UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK;
and Institute of Biological, Environmental & Rural Sciences, Aberystwyth
University, Aberystwyth SY23 3FG, UK.
LA - eng
GR - BB/K007440/1/Biotechnology and Biological Sciences Research Council/United
Kingdom
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20140902
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - Classification/*methods
MH - *Phylogeny
PMC - PMC4265141
EDAT- 2014/09/04 06:00
MHDA- 2015/06/05 06:00
CRDT- 2014/09/04 06:00
PHST- 2014/09/04 06:00 [entrez]
PHST- 2014/09/04 06:00 [pubmed]
PHST- 2015/06/05 06:00 [medline]
AID - syu066 [pii]
AID - 10.1093/sysbio/syu066 [doi]
PST - ppublish
SO - Syst Biol. 2015 Jan;64(1):137-43. doi: 10.1093/sysbio/syu066. Epub 2014 Sep 2.
PMID- 25173563
OWN - NLM
STAT- MEDLINE
DCOM- 20150604
LR - 20171116
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 64
IP - 1
DP - 2015 Jan
TI - Unveiling the diversification dynamics of Australasian predaceous diving beetles
in the Cenozoic.
PG - 3-24
LID - 10.1093/sysbio/syu067 [doi]
AB - During the Cenozoic, Australia experienced major climatic shifts that have had
dramatic ecological consequences for the modern biota. Mesic tropical ecosystems
were progressively restricted to the coasts and replaced by arid-adapted floral
and faunal communities. Whilst the role of aridification has been investigated in
a wide range of terrestrial lineages, the response of freshwater clades remains
poorly investigated. To gain insights into the diversification processes
underlying a freshwater radiation, we studied the evolutionary history of the
Australasian predaceous diving beetles of the tribe Hydroporini (147 described
species). We used an integrative approach including the latest methods in
phylogenetics, divergence time estimation, ancestral character state
reconstruction, and likelihood-based methods of diversification rate estimation.
Phylogenies and dating analyses were reconstructed with molecular data from seven
genes (mitochondrial and nuclear) for 117 species (plus 12 outgroups). Robust and
well-resolved phylogenies indicate a late Oligocene origin of Australasian
Hydroporini. Biogeographic analyses suggest an origin in the East Coast region of
Australia, and a dynamic biogeographic scenario implying dispersal events. The
group successfully colonized the tropical coastal regions carved by a rampant
desertification, and also colonized groundwater ecosystems in Central Australia.
Diversification rate analyses suggest that the ongoing aridification of Australia
initiated in the Miocene contributed to a major wave of extinctions since the
late Pliocene probably attributable to an increasing aridity, range contractions
and seasonally disruptions resulting from Quaternary climatic changes. When
comparing subterranean and epigean genera, our results show that contrasting
mechanisms drove their diversification and therefore current diversity pattern.
The Australasian Hydroporini radiation reflects a combination of processes that
promoted both diversification, resulting from new ecological opportunities driven
by initial aridification, and a subsequent loss of mesic adapted diversity due to
increasing aridity.
CI - (c) The Author(s) 2014. 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 - Toussaint, Emmanuel F A
AU - Toussaint EF
AD - SNSB-Bavarian State Collection of Zoology, Munchhausenstrasse 21, 81247 Munich,
Germany; CNRS, UMR 7641 Centre de Mathematiques Appliquees (Ecole Polytechnique),
Route de Saclay, 91128 Palaiseau cedex, France; South Australian Museum,
Adelaide, South Australia, Australia; Centre for Integrated Ecology & School of
Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood,
Victoria 3125, Australia; and GeoBioCenter, Ludwig-Maximilians University,
Munich, Germany. Toussaint@zsm.mwn.de.
FAU - Condamine, Fabien L
AU - Condamine FL
AD - SNSB-Bavarian State Collection of Zoology, Munchhausenstrasse 21, 81247 Munich,
Germany; CNRS, UMR 7641 Centre de Mathematiques Appliquees (Ecole Polytechnique),
Route de Saclay, 91128 Palaiseau cedex, France; South Australian Museum,
Adelaide, South Australia, Australia; Centre for Integrated Ecology & School of
Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood,
Victoria 3125, Australia; and GeoBioCenter, Ludwig-Maximilians University,
Munich, Germany.
FAU - Hawlitschek, Oliver
AU - Hawlitschek O
AD - SNSB-Bavarian State Collection of Zoology, Munchhausenstrasse 21, 81247 Munich,
Germany; CNRS, UMR 7641 Centre de Mathematiques Appliquees (Ecole Polytechnique),
Route de Saclay, 91128 Palaiseau cedex, France; South Australian Museum,
Adelaide, South Australia, Australia; Centre for Integrated Ecology & School of
Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood,
Victoria 3125, Australia; and GeoBioCenter, Ludwig-Maximilians University,
Munich, Germany.
FAU - Watts, Chris H
AU - Watts CH
AD - SNSB-Bavarian State Collection of Zoology, Munchhausenstrasse 21, 81247 Munich,
Germany; CNRS, UMR 7641 Centre de Mathematiques Appliquees (Ecole Polytechnique),
Route de Saclay, 91128 Palaiseau cedex, France; South Australian Museum,
Adelaide, South Australia, Australia; Centre for Integrated Ecology & School of
Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood,
Victoria 3125, Australia; and GeoBioCenter, Ludwig-Maximilians University,
Munich, Germany.
FAU - Porch, Nick
AU - Porch N
AD - SNSB-Bavarian State Collection of Zoology, Munchhausenstrasse 21, 81247 Munich,
Germany; CNRS, UMR 7641 Centre de Mathematiques Appliquees (Ecole Polytechnique),
Route de Saclay, 91128 Palaiseau cedex, France; South Australian Museum,
Adelaide, South Australia, Australia; Centre for Integrated Ecology & School of
Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood,
Victoria 3125, Australia; and GeoBioCenter, Ludwig-Maximilians University,
Munich, Germany.
FAU - Hendrich, Lars
AU - Hendrich L
AD - SNSB-Bavarian State Collection of Zoology, Munchhausenstrasse 21, 81247 Munich,
Germany; CNRS, UMR 7641 Centre de Mathematiques Appliquees (Ecole Polytechnique),
Route de Saclay, 91128 Palaiseau cedex, France; South Australian Museum,
Adelaide, South Australia, Australia; Centre for Integrated Ecology & School of
Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood,
Victoria 3125, Australia; and GeoBioCenter, Ludwig-Maximilians University,
Munich, Germany.
FAU - Balke, Michael
AU - Balke M
AD - SNSB-Bavarian State Collection of Zoology, Munchhausenstrasse 21, 81247 Munich,
Germany; CNRS, UMR 7641 Centre de Mathematiques Appliquees (Ecole Polytechnique),
Route de Saclay, 91128 Palaiseau cedex, France; South Australian Museum,
Adelaide, South Australia, Australia; Centre for Integrated Ecology & School of
Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood,
Victoria 3125, Australia; and GeoBioCenter, Ludwig-Maximilians University,
Munich, Germany. SNSB-Bavarian State Collection of Zoology, Munchhausenstrasse
21, 81247 Munich, Germany; CNRS, UMR 7641 Centre de Mathematiques Appliquees
(Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; South
Australian Museum, Adelaide, South Australia, Australia; Centre for Integrated
Ecology & School of Life and Environmental Sciences, Deakin University, 221
Burwood Highway, Burwood, Victoria 3125, Australia; and GeoBioCenter,
Ludwig-Maximilians University, Munich, Germany.
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20140829
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - Australia
MH - Coleoptera/*classification/genetics
MH - Fossils
MH - Genes, Insect/genetics
MH - Genetic Speciation
MH - *Genetic Variation
MH - *Phylogeny
OTO - NOTNLM
OT - Australian aridification
OT - Dytiscidae
OT - Hydroporini
OT - Pleistocene extinction
OT - diversification
OT - freshwater biota
OT - ground water organisms
EDAT- 2014/09/01 06:00
MHDA- 2015/06/05 06:00
CRDT- 2014/09/01 06:00
PHST- 2014/09/01 06:00 [entrez]
PHST- 2014/09/01 06:00 [pubmed]
PHST- 2015/06/05 06:00 [medline]
AID - syu067 [pii]
AID - 10.1093/sysbio/syu067 [doi]
PST - ppublish
SO - Syst Biol. 2015 Jan;64(1):3-24. doi: 10.1093/sysbio/syu067. Epub 2014 Aug 29.
PMID- 25164916
OWN - NLM
STAT- MEDLINE
DCOM- 20150604
LR - 20171116
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 64
IP - 1
DP - 2015 Jan
TI - Towards improving searches for optimal phylogenies.
PG - 56-65
LID - 10.1093/sysbio/syu065 [doi]
AB - Finding the optimal evolutionary history for a set of taxa is a challenging
computational problem, even when restricting possible solutions to be "tree-like"
and focusing on the maximum-parsimony optimality criterion. This has led to much
work on using heuristic tree searches to find approximate solutions. We present
an approach for finding exact optimal solutions that employs and complements the
current heuristic methods for finding optimal trees. Given a set of taxa and a
set of aligned sequences of characters, there may be subsets of characters that
are compatible, and for each such subset there is an associated (possibly
partially resolved) phylogeny with edges corresponding to each character state
change. These perfect phylogenies serve as anchor trees for our constrained
search space. We show that, for sequences with compatible sites, the parsimony
score of any tree [Formula: see text] is at least the parsimony score of the
anchor trees plus the number of inferred changes between [Formula: see text] and
the anchor trees. As the maximum-parsimony optimality score is additive, the sum
of the lower bounds on compatible character partitions provides a lower bound on
the complete alignment of characters. This yields a region in the space of trees
within which the best tree is guaranteed to be found; limiting the search for the
optimal tree to this region can significantly reduce the number of trees that
must be examined in a search of the space of trees. We analyze this method
empirically using four different biological data sets as well as surveying 400
data sets from the TreeBASE repository, demonstrating the effectiveness of our
technique in reducing the number of steps in exact heuristic searches for trees
under the maximum-parsimony optimality criterion.
CI - (c) The Author(s) 2014. 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 - Ford, Eric
AU - Ford E
AD - Department of Computer Science, Graduate Center, CUNY, New York, NY, 10016, USA;
Department of Mathematics and Computer Science, Lehman College, CUNY, Bronx, NY,
10468, USA; and Division of Invertebrate Zoology, American Museum of Natural
History, New York, NY, 10024, USA;
FAU - St John, Katherine
AU - St John K
AD - Department of Computer Science, Graduate Center, CUNY, New York, NY, 10016, USA;
Department of Mathematics and Computer Science, Lehman College, CUNY, Bronx, NY,
10468, USA; and Division of Invertebrate Zoology, American Museum of Natural
History, New York, NY, 10024, USA; Department of Computer Science, Graduate
Center, CUNY, New York, NY, 10016, USA; Department of Mathematics and Computer
Science, Lehman College, CUNY, Bronx, NY, 10468, USA; and Division of
Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024,
USA; stjohn@lehman.cuny.edu.
FAU - Wheeler, Ward C
AU - Wheeler WC
AD - Department of Computer Science, Graduate Center, CUNY, New York, NY, 10016, USA;
Department of Mathematics and Computer Science, Lehman College, CUNY, Bronx, NY,
10468, USA; and Division of Invertebrate Zoology, American Museum of Natural
History, New York, NY, 10024, USA;
LA - eng
PT - Journal Article
PT - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20140826
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - *Algorithms
MH - Animals
MH - Classification/*methods
MH - Fungi/classification
MH - Magnoliopsida/classification
MH - *Phylogeny
OTO - NOTNLM
OT - Character compatibility
OT - exact search
OT - maximum-parsimony optimality criterion
OT - phylogenetic islands
OT - tree search
EDAT- 2014/08/29 06:00
MHDA- 2015/06/05 06:00
CRDT- 2014/08/29 06:00
PHST- 2014/08/29 06:00 [entrez]
PHST- 2014/08/29 06:00 [pubmed]
PHST- 2015/06/05 06:00 [medline]
AID - syu065 [pii]
AID - 10.1093/sysbio/syu065 [doi]
PST - ppublish
SO - Syst Biol. 2015 Jan;64(1):56-65. doi: 10.1093/sysbio/syu065. Epub 2014 Aug 26.
PMID- 25164915
OWN - NLM
STAT- MEDLINE
DCOM- 20180110
LR - 20181202
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 65
IP - 3
DP - 2016 May
TI - Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence
of Incomplete Lineage Sorting.
PG - 366-80
LID - 10.1093/sysbio/syu063 [doi]
AB - Species tree estimation is complicated by processes, such as gene duplication and
loss and incomplete lineage sorting (ILS), that cause discordance between gene
trees and the species tree. Furthermore, while concatenation, a traditional
approach to tree estimation, has excellent performance under many conditions, the
expectation is that the best accuracy will be obtained through the use of species
tree estimation methods that are specifically designed to address gene tree
discordance. In this article, we report on a study to evaluate MP-EST-one of the
most popular species tree estimation methods designed to address ILS-as well as
concatenation under maximum likelihood, the greedy consensus, and two supertree
methods (Matrix Representation with Parsimony and Matrix Representation with
Likelihood). Our study shows that several factors impact the absolute and
relative accuracy of methods, including the number of gene trees, the accuracy of
the estimated gene trees, and the amount of ILS. Concatenation can be more
accurate than the best summary methods in some cases (mostly when the gene trees
have poor phylogenetic signal or when the level of ILS is low), but summary
methods are generally more accurate than concatenation when there are an adequate
number of sufficiently accurate gene trees. Our study suggests that
coalescent-based species tree methods may be key to estimating highly accurate
species trees from multiple loci.
CI - (c) The Author(s) 2014. 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 - Mirarab, Siavash
AU - Mirarab S
AD - Department of Computer Science, University of Texas at Austin, Austin, TX, 78712,
USA; and.
FAU - Bayzid, Md Shamsuzzoha
AU - Bayzid MS
AD - Department of Computer Science, University of Texas at Austin, Austin, TX, 78712,
USA; and.
FAU - Warnow, Tandy
AU - Warnow T
AD - Department of Computer Science, University of Texas at Austin, Austin, TX, 78712,
USA; and Departments of Bioengineering and Computer Science, University of
Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. warnow@illinois.edu.
LA - eng
SI - Dryad/10.5061/dryad.310q3
GR - HHMI/Howard Hughes Medical Institute/United States
PT - Journal Article
DEP - 20140826
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Classification/*methods
MH - Computer Simulation
MH - Gene Duplication
MH - *Phylogeny
MH - Probability
OTO - NOTNLM
OT - *MP-EST
OT - *MRL
OT - *MRP
OT - *concatenation
OT - *consensus methods
OT - *gene tree discordance
OT - *incomplete lineage sorting
OT - *multilocus bootstrapping
OT - *species tree estimation
OT - *supertree methods.
EDAT- 2014/08/29 06:00
MHDA- 2018/01/11 06:00
CRDT- 2014/08/29 06:00
PHST- 2013/12/16 00:00 [received]
PHST- 2014/08/18 00:00 [accepted]
PHST- 2014/08/29 06:00 [entrez]
PHST- 2014/08/29 06:00 [pubmed]
PHST- 2018/01/11 06:00 [medline]
AID - syu063 [pii]
AID - 10.1093/sysbio/syu063 [doi]
PST - ppublish
SO - Syst Biol. 2016 May;65(3):366-80. doi: 10.1093/sysbio/syu063. Epub 2014 Aug 26.
PMID- 25151624
OWN - NLM
STAT- MEDLINE
DCOM- 20141208
LR - 20141015
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 63
IP - 6
DP - 2014 Nov
TI - Popperian corroboration and phylogenetics.
PG - 1018-22
LID - 10.1093/sysbio/syu064 [doi]
FAU - de Queiroz, Kevin
AU - de Queiroz K
AD - Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian
Institution, Washington, DC 20560-0162, USA dequeirozk@si.edu.
LA - eng
PT - Journal Article
DEP - 20140822
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Classification/*methods
MH - Models, Biological
MH - *Phylogeny
EDAT- 2014/08/26 06:00
MHDA- 2014/12/15 06:00
CRDT- 2014/08/25 06:00
PHST- 2014/08/25 06:00 [entrez]
PHST- 2014/08/26 06:00 [pubmed]
PHST- 2014/12/15 06:00 [medline]
AID - syu064 [pii]
AID - 10.1093/sysbio/syu064 [doi]
PST - ppublish
SO - Syst Biol. 2014 Nov;63(6):1018-22. doi: 10.1093/sysbio/syu064. Epub 2014 Aug 22.
PMID- 25139888
OWN - NLM
STAT- MEDLINE
DCOM- 20141208
LR - 20141015
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 63
IP - 6
DP - 2014 Nov
TI - Reconciling hierarchical taxonomy with molecular phylogenies.
PG - 1010-7
LID - 10.1093/sysbio/syu061 [doi]
FAU - Holt, Ben G
AU - Holt BG
AD - Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot
SL5 7PY; and Department of Life Sciences, Natural History Museum, Cromwell Road,
London SW7 5BD, UK b.holt@imperial.ac.uk.
FAU - Jonsson, Knud Andreas
AU - Jonsson KA
AD - Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot
SL5 7PY; and Department of Life Sciences, Natural History Museum, Cromwell Road,
London SW7 5BD, UK Department of Life Sciences, Imperial College London, Silwood
Park Campus, Ascot SL5 7PY; and Department of Life Sciences, Natural History
Museum, Cromwell Road, London SW7 5BD, UK.
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20140819
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - Birds/classification/genetics
MH - *Classification
MH - Mammals/classification/genetics
MH - *Phylogeny
MH - Species Specificity
EDAT- 2014/08/21 06:00
MHDA- 2014/12/15 06:00
CRDT- 2014/08/21 06:00
PHST- 2014/08/21 06:00 [entrez]
PHST- 2014/08/21 06:00 [pubmed]
PHST- 2014/12/15 06:00 [medline]
AID - syu061 [pii]
AID - 10.1093/sysbio/syu061 [doi]
PST - ppublish
SO - Syst Biol. 2014 Nov;63(6):1010-7. doi: 10.1093/sysbio/syu061. Epub 2014 Aug 19.
PMID- 25123369
OWN - NLM
STAT- MEDLINE
DCOM- 20141208
LR - 20150528
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 63
IP - 6
DP - 2014 Nov
TI - Model selection in historical biogeography reveals that founder-event speciation
is a crucial process in Island Clades.
PG - 951-70
LID - 10.1093/sysbio/syu056 [doi]
AB - Founder-event speciation, where a rare jump dispersal event founds a new
genetically isolated lineage, has long been considered crucial by many historical
biogeographers, but its importance is disputed within the vicariance school.
Probabilistic modeling of geographic range evolution creates the potential to
test different biogeographical models against data using standard statistical
model choice procedures, as long as multiple models are available. I re-implement
the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package
BioGeoBEARS, and modify it to create a new model, DEC + J, which adds
founder-event speciation, the importance of which is governed by a new free
parameter, [Formula: see text]. The identifiability of DEC and DEC + J is tested
on data sets simulated under a wide range of macroevolutionary models where
geography evolves jointly with lineage birth/death events. The results confirm
that DEC and DEC + J are identifiable even though these models ignore the fact
that molecular phylogenies are missing many cladogenesis and extinction events.
The simulations also indicate that DEC will have substantially increased errors
in ancestral range estimation and parameter inference when the true model
includes + J. DEC and DEC + J are compared on 13 empirical data sets drawn from
studies of island clades. Likelihood-ratio tests indicate that all clades reject
DEC, and AICc model weights show large to overwhelming support for DEC + J, for
the first time verifying the importance of founder-event speciation in island
clades via statistical model choice. Under DEC + J, ancestral nodes are usually
estimated to have ranges occupying only one island, rather than the widespread
ancestors often favored by DEC. These results indicate that the assumptions of
historical biogeography models can have large impacts on inference and require
testing and comparison with statistical methods.
CI - (c) The Author(s) 2014. 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 - Matzke, Nicholas J
AU - Matzke NJ
AD - Department of Integrative Biology, University of California, Berkeley, CA
94720-3140, USA; and National Institute for Mathematical and Biological Synthesis
and Department of Ecology and Evolutionary Biology, University of Tennessee,
Knoxville, TN 37996-3410, USA Department of Integrative Biology, University of
California, Berkeley, CA 94720-3140, USA; and National Institute for Mathematical
and Biological Synthesis and Department of Ecology and Evolutionary Biology,
University of Tennessee, Knoxville, TN 37996-3410, USA matzke@nimbios.org.
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PT - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20140814
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
EIN - Syst Biol. 2015 Jan;64(1):167. PMID: 25504792
MH - *Computer Simulation
MH - Founder Effect
MH - Genetic Speciation
MH - *Models, Biological
MH - *Phylogeny
MH - Phylogeography/*methods
MH - Psychotria/classification
MH - Reproducibility of Results
OTO - NOTNLM
OT - BioGeoBEARS
OT - GeoSSE
OT - LAGRANGE
OT - cladogenesis
OT - extinction
OT - founder-event speciation
OT - historical biogeography
OT - jump dispersal
EDAT- 2014/08/16 06:00
MHDA- 2014/12/15 06:00
CRDT- 2014/08/16 06:00
PHST- 2014/08/16 06:00 [entrez]
PHST- 2014/08/16 06:00 [pubmed]
PHST- 2014/12/15 06:00 [medline]
AID - syu056 [pii]
AID - 10.1093/sysbio/syu056 [doi]
PST - ppublish
SO - Syst Biol. 2014 Nov;63(6):951-70. doi: 10.1093/sysbio/syu056. Epub 2014 Aug 14.
PMID- 25121824
OWN - NLM