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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- 19085332
OWN - NLM
STAT- MEDLINE
DCOM- 20090202
LR - 20101118
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 6
DP - 2008 Dec
TI - The influence of model averaging on clade posteriors: an example using the
triggerfishes (Family Balistidae).
PG - 905-19
LID - 10.1080/10635150802562392 [doi]
AB - Although substantial uncertainty typically surrounds the choice of the best model
in most phylogenetic analyses, little is known about how accommodating this
uncertainty affects phylogenetic inference. Here we explore the influence of
Bayesian model averaging on the phylogenetic inference of the triggerfishes
(Family: Balistidae), a charismatic group of reef fishes. We focus on clade
support as this area has received little attention and is typically one of the
most important outcomes of phylogenetic studies. We present a novel phylogenetic
hypothesis for the family Balistidae based on an analysis of two mitochondrial
(12S, 16S) and three nuclear genes (TMO-4C4, Rhodopsin, RAG1) sampled from 26
ingroup species. Despite the presence of substantial model uncertainty in almost
all partitions of our data, we found model-averaged topologies and clade
posteriors to be nearly identical to those conditioned on a single model.
Furthermore, statistical comparison of clade posteriors using the Wilcoxon
signed-rank test revealed no significant differences. Our results suggest that
although current model-selection approaches are likely to lead to
overparameterization of the substitution model, the consequences of conditioning
on this overparameterized model are likely to be mild. Our phylogenetic results
strongly support the monophyly of the triggerfishes but suggest that the genera
Balistoides and Pseudobalistes are polyphyletic. Divergence time estimation
supports a Miocene origin of the crown group. Despite the presence of several
young species-rich subclades, statistical analysis of temporal diversification
patterns reveals no significant increase in the rate of cladogenesis across
geologic time intervals.
FAU - Dornburg, Alex
AU - Dornburg A
AD - School of Biological Sciences, Washington State University, Pullman, Washington
99164, USA. dornburgalex@yale.edu
FAU - Santini, Francesco
AU - Santini F
FAU - Alfaro, Michael E
AU - Alfaro ME
LA - eng
SI - GENBANK/AY308790
SI - GENBANK/AY679622
SI - GENBANK/AY679623
SI - GENBANK/AY679624
SI - GENBANK/AY679625
SI - GENBANK/AY679626
SI - GENBANK/AY679627
SI - GENBANK/AY679628
SI - GENBANK/AY679629
SI - GENBANK/AY679630
SI - GENBANK/AY679631
SI - GENBANK/AY679632
SI - GENBANK/AY679633
SI - GENBANK/AY679634
SI - GENBANK/AY700238
SI - GENBANK/AY700239
SI - GENBANK/AY700240
SI - GENBANK/AY700241
SI - GENBANK/AY700242
SI - GENBANK/AY700243
SI - GENBANK/AY700244
SI - GENBANK/AY700245
SI - GENBANK/AY700246
SI - GENBANK/AY700247
SI - GENBANK/AY700248
SI - GENBANK/AY700249
SI - GENBANK/AY700250
SI - GENBANK/AY700251
SI - GENBANK/AY700308
SI - GENBANK/AY700310
SI - GENBANK/AY700311
SI - GENBANK/AY700312
SI - GENBANK/AY700313
SI - GENBANK/AY700314
SI - GENBANK/AY700315
SI - GENBANK/AY700316
SI - GENBANK/AY700317
SI - GENBANK/AY700318
SI - GENBANK/AY700319
SI - GENBANK/AY700320
SI - GENBANK/AY700321
SI - GENBANK/EU108801
SI - GENBANK/EU108802
SI - GENBANK/EU108803
SI - GENBANK/EU108804
SI - GENBANK/EU108805
SI - GENBANK/EU108806
SI - GENBANK/EU108807
SI - GENBANK/EU108808
SI - GENBANK/EU108809
SI - GENBANK/EU108810
SI - GENBANK/EU108811
SI - GENBANK/EU108812
SI - GENBANK/EU108813
SI - GENBANK/EU108814
SI - GENBANK/EU108815
SI - GENBANK/EU108816
SI - GENBANK/EU108817
SI - GENBANK/EU108818
SI - GENBANK/EU108819
SI - GENBANK/EU108820
SI - GENBANK/EU108821
SI - GENBANK/EU108822
SI - GENBANK/EU108823
SI - GENBANK/EU108824
SI - GENBANK/EU108825
SI - GENBANK/EU108826
SI - GENBANK/EU108827
SI - GENBANK/EU108828
SI - GENBANK/EU108829
SI - GENBANK/EU108830
SI - GENBANK/EU108831
SI - GENBANK/EU108832
SI - GENBANK/EU108833
SI - GENBANK/EU108834
SI - GENBANK/EU108835
SI - GENBANK/EU108836
SI - GENBANK/EU108837
SI - GENBANK/EU108838
SI - GENBANK/EU108839
SI - GENBANK/EU108840
SI - GENBANK/EU108841
SI - GENBANK/EU108842
SI - GENBANK/EU108843
SI - GENBANK/EU108844
SI - GENBANK/EU108845
SI - GENBANK/EU108846
SI - GENBANK/EU108847
SI - GENBANK/EU108848
SI - GENBANK/EU108849
SI - GENBANK/EU108850
SI - GENBANK/EU108851
SI - GENBANK/EU108852
SI - GENBANK/EU108853
SI - GENBANK/EU108854
SI - GENBANK/EU108855
SI - GENBANK/EU108856
SI - GENBANK/EU108857
SI - GENBANK/EU108858
SI - GENBANK/EU108859
SI - GENBANK/EU108860
SI - GENBANK/EU108861
SI - GENBANK/EU108862
SI - GENBANK/EU108863
SI - GENBANK/EU108864
SI - GENBANK/EU108865
SI - GENBANK/EU108866
SI - GENBANK/EU108867
SI - GENBANK/EU108868
SI - GENBANK/EU108869
SI - GENBANK/EU108870
SI - GENBANK/EU108871
SI - GENBANK/EU108872
SI - GENBANK/EU108873
SI - GENBANK/EU108874
SI - GENBANK/EU108875
SI - GENBANK/EU108876
SI - GENBANK/EU108877
SI - GENBANK/EU108878
SI - GENBANK/NC004416
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
SB - IM
MH - Animals
MH - Bayes Theorem
MH - Biological Evolution
MH - Classification/*methods
MH - Fishes/*classification/genetics
MH - Linear Models
MH - Molecular Sequence Data
MH - *Phylogeny
MH - Time Factors
EDAT- 2008/12/17 09:00
MHDA- 2009/02/03 09:00
CRDT- 2008/12/17 09:00
PHST- 2008/12/17 09:00 [entrez]
PHST- 2008/12/17 09:00 [pubmed]
PHST- 2009/02/03 09:00 [medline]
AID - 906545059 [pii]
AID - 10.1080/10635150802562392 [doi]
PST - ppublish
SO - Syst Biol. 2008 Dec;57(6):905-19. doi: 10.1080/10635150802562392.
PMID- 19085331
OWN - NLM
STAT- MEDLINE
DCOM- 20090202
LR - 20081216
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 6
DP - 2008 Dec
TI - The modified gap excess ratio (GER*) and the stratigraphic congruence of dinosaur
phylogenies.
PG - 891-904
LID - 10.1080/10635150802570809 [doi]
AB - Palaeontologists routinely map their cladograms onto what is known of the fossil
record. Where sister taxa first appear as fossils at different times, a ghost
range is inferred to bridge the gap between these dates. Some measure of the
total extent of ghost ranges across the tree underlies several indices of
cladistic/stratigraphic congruence. We investigate this congruence for 19
independent, published cladograms of major dinosaur groups and report exceptional
agreement between the phylogenetic and stratigraphic patterns, evidenced by sums
of ghost ranges near the theoretical minima. This implies that both phylogenetic
and stratigraphic data reflect faithfully the evolutionary history of dinosaurs,
at least for the taxa included in this study. We formally propose modifications
to an existing index of congruence (the gap excess ratio; GER), designed to
remove a bias in the range of values possible with trees of different shapes. We
also propose a more informative index of congruence--GER*--that takes account of
the underlying distribution of sums of ghost ranges possible when permuting
stratigraphic range data across the tree. Finally, we incorporate data on the
range of possible first occurrence dates into our estimates of congruence,
extending a procedure originally implemented with the modified Manhattan
stratigraphic measure and GER to our new indices. Most dinosaur data sets
maintain extremely high congruence despite such modifications.
FAU - Wills, Matthew A
AU - Wills MA
AD - Department of Biology and Biochemistry, The University of Bath, Claverton Down,
Bath, UK. m.a.wills@bath.ac.uk
FAU - Barrett, Paul M
AU - Barrett PM
FAU - Heathcote, Julia F
AU - Heathcote JF
LA - eng
GR - BB/C006682/1/Biotechnology and Biological Sciences Research Council/United
Kingdom
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 - Classification/*methods
MH - Dinosaurs/*classification
MH - *Phylogeny
EDAT- 2008/12/17 09:00
MHDA- 2009/02/03 09:00
CRDT- 2008/12/17 09:00
PHST- 2008/12/17 09:00 [entrez]
PHST- 2008/12/17 09:00 [pubmed]
PHST- 2009/02/03 09:00 [medline]
AID - 906549706 [pii]
AID - 10.1080/10635150802570809 [doi]
PST - ppublish
SO - Syst Biol. 2008 Dec;57(6):891-904. doi: 10.1080/10635150802570809.
PMID- 19085330
OWN - NLM
STAT- MEDLINE
DCOM- 20090202
LR - 20081216
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 6
DP - 2008 Dec
TI - Comparison of methods for species-tree inference in the sawfly genus Neodiprion
(Hymenoptera: Diprionidae).
PG - 876-90
LID - 10.1080/10635150802580949 [doi]
AB - Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity
to investigate the origin and maintenance of barriers to reproduction, but
obtaining a phylogenetic estimate for comparative studies of Neodiprion
speciation has proved difficult. Specifically, nonmonophyly within and
discordance between individual gene trees, both of which are common in groups
that diverged recently and/or rapidly, make it impossible to infer a species tree
using methods that are designed to estimate gene trees. Therefore, in this study,
we estimate relationships between members of the lecontei species group using
four approaches that are intended to estimate species, not gene, trees: (1)
minimize deep coalescences (MDC), (2) shallowest divergences (SD), (3) Bayesian
estimation of species trees (BEST), and (4) a novel approach that combines
concatenation with monophyly constraints (CMC). Multiple populations are sampled
for most species and all four methods incorporate this intraspecific variation
into estimates of interspecific relationships. We investigate the sensitivity of
each method to taxonomic sampling, and, for the BEST method, we assess the impact
of prior choice on species-tree inference. We also compare species-tree estimates
to one another and to a morphologically based hypothesis to identify clades that
are supported by multiple analyses and lines of evidence. We find that both
taxonomic sampling and method choice impact species-tree estimates and that, for
these data, the BEST method is strongly influenced by Theta and branch-length
priors. We also find that the CMC method is the least sensitive to taxonomic
sampling. Finally, although interspecific genetic variation is low due to the
recent divergence of the lecontei group, our results to date suggest that
incomplete lineage sorting and interspecific gene flow are the main factors
complicating species-tree inference in Neodiprion. Based on these analyses, we
propose a phylogenetic hypothesis for the lecontei group. Finally, our results
suggest that, even for very challenging groups like Neodiprion, an underlying
species-tree signal can be extracted from multi-locus data as long as
intraspecific variation is adequately sampled and methods that focus on the
estimation of species trees are used.
FAU - Linnen, Catherine R
AU - Linnen CR
AD - Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
clinnen@oeb.harvard.edu
FAU - Farrell, Brian D
AU - Farrell BD
LA - eng
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
SB - IM
MH - Animals
MH - Classification/*methods
MH - Genetic Variation
MH - Hymenoptera/*classification/genetics
MH - *Phylogeny
MH - Species Specificity
EDAT- 2008/12/17 09:00
MHDA- 2009/02/03 09:00
CRDT- 2008/12/17 09:00
PHST- 2008/12/17 09:00 [entrez]
PHST- 2008/12/17 09:00 [pubmed]
PHST- 2009/02/03 09:00 [medline]
AID - 906550332 [pii]
AID - 10.1080/10635150802580949 [doi]
PST - ppublish
SO - Syst Biol. 2008 Dec;57(6):876-90. doi: 10.1080/10635150802580949.
PMID- 19085329
OWN - NLM
STAT- MEDLINE
DCOM- 20090202
LR - 20101118
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 6
DP - 2008 Dec
TI - Phylogeny of the beaked whale genus Mesoplodon (Ziphiidae: Cetacea) revealed by
nuclear introns: implications for the evolution of male tusks.
PG - 857-75
LID - 10.1080/10635150802559257 [doi]
AB - With 14 species currently recognized, the beaked whale genus Mesoplodon (family
Ziphiidae) is the most speciose in the order Cetacea. Beaked whales are widely
distributed but are rarely seen at sea due to their oceanic distribution,
deep-diving capacity, and apparent low abundance. Morphological differentiation
among Mesoplodon species is relatively limited, with the exception of tooth form
in adult males. Based on scarring patterns, males appear to use their tusk-like
teeth as weapons in aggressive encounters with other males. Females are
effectively toothless. We used sequences from seven nuclear introns (3348 base
pairs) to construct a robust and highly resolved phylogeny, which was then used
as a framework to test predictions from four hypotheses seeking to explain
patterns of Mesoplodon tusk morphology and/or the processes that have driven the
diversification of this genus: (1) linear progression of tusk form; (2)
allopatric speciation through isolation in adjacent deep-sea canyons; (3)
sympatric speciation through sexual selection on tusks; and (4) selection for
species-recognition cues. Maximum-likelihood and Bayesian reconstructions
confirmed the monophyly of the genus and revealed that what were considered
ancestral and derived tusk forms have in fact arisen independently on several
occasions, contrary to predictions from the linear-progression hypothesis.
Further, none of the three well-supported species clades was confined to a single
ocean basin, as might have been expected from the deep-sea canyon-isolation or
sexual-selection hypotheses, and some species with similar tusks have overlapping
distributions, contrary to predictions from the species-recognition hypothesis.
However, the divergent tusk forms and sympatric distributions of three of the
four sister-species pairs identified suggest that sexual selection on male tusks
has likely played an important role in this unique radiation, although other
forces are clearly also involved. To our knowledge, this is the first time that
sexual selection has been explicitly implicated in the radiation of a mammalian
group outside terrestrial ungulates.
FAU - Dalebout, Merel L
AU - Dalebout ML
AD - School of Biological, Earth, and Environmental Sciences (BEES), University of New
South Wales, Kensington, NSW, Australia. m.dalebout@unsw.edu.au
FAU - Steel, Debbie
AU - Steel D
FAU - Baker, C Scott
AU - Baker CS
LA - eng
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
SB - IM
MH - Animals
MH - *Biological Evolution
MH - Cell Nucleus/*genetics
MH - Female
MH - Introns/*genetics
MH - Male
MH - *Phylogeny
MH - Species Specificity
MH - Tooth/anatomy & histology
MH - Whales/anatomy & histology/*classification/*genetics
EDAT- 2008/12/17 09:00
MHDA- 2009/02/03 09:00
CRDT- 2008/12/17 09:00
PHST- 2008/12/17 09:00 [entrez]
PHST- 2008/12/17 09:00 [pubmed]
PHST- 2009/02/03 09:00 [medline]
AID - 906592768 [pii]
AID - 10.1080/10635150802559257 [doi]
PST - ppublish
SO - Syst Biol. 2008 Dec;57(6):857-75. doi: 10.1080/10635150802559257.
PMID- 19085328
OWN - NLM
STAT- MEDLINE
DCOM- 20090202
LR - 20081216
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 6
DP - 2008 Dec
TI - The impact of reticulate evolution on genome phylogeny.
PG - 844-56
LID - 10.1080/10635150802559265 [doi]
AB - Genome phylogenies are used to build tree-like representations of evolutionary
relationships among genomes. However, in condensing the phylogenetic signals
within a set of genomes down to a single tree, these methods generally do not
explicitly take into account discordant signals arising due to lateral genetic
transfer. Because conflicting vertical and horizontal signals can produce
compromise trees that do not reflect either type of history, it is essential to
understand the sensitivity of inferred genome phylogenies to these confounding
effects. Using replicated simulations of genome evolution, we show that different
scenarios of lateral genetic transfer have significant impacts on the ability to
recover the "true" tree of genomes, even when corrections for phylogenetically
discordant signals are used.
FAU - Beiko, Robert G
AU - Beiko RG
AD - Faculty of Computer Science, Dalhousie University, Institute for Molecular
Bioscience/ARC Centre for Bioinformatics, Brisbane, Australia. beiko@cs.dal.ca
FAU - Doolittle, W Ford
AU - Doolittle WF
FAU - Charlebois, Robert L
AU - Charlebois RL
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Classification/*methods
MH - Computer Simulation
MH - *Evolution, Molecular
MH - Gene Transfer, Horizontal
MH - Genetic Speciation
MH - Genetic Variation
MH - *Genome
MH - *Phylogeny
EDAT- 2008/12/17 09:00
MHDA- 2009/02/03 09:00
CRDT- 2008/12/17 09:00
PHST- 2008/12/17 09:00 [entrez]
PHST- 2008/12/17 09:00 [pubmed]
PHST- 2009/02/03 09:00 [medline]
AID - 906593303 [pii]
AID - 10.1080/10635150802559265 [doi]
PST - ppublish
SO - Syst Biol. 2008 Dec;57(6):844-56. doi: 10.1080/10635150802559265.
PMID- 19085327
OWN - NLM
STAT- MEDLINE
DCOM- 20090202
LR - 20190302
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 6
DP - 2008 Dec
TI - Evidence for a new root of the tree of life.
PG - 835-43
LID - 10.1080/10635150802555933 [doi]
AB - Directed indels, insertions or deletions within paralogous genes, have the
potential to root the tree of life. Here we apply the top-down rooting algorithm
to indels found in PyrD (dihydroorotate dehydrogenase), a key enzyme involved in
the de novo biosynthesis of pyrimidines, and HisA
(P-ribosylformimino-AICAR-P-isomerase), an essential enzyme in the histidine
biosynthesis pathway. Through the comparison of each indel with its two
paralogous outgroups, we exclude the root of the tree of life from the clade that
encompasses the Actinobacteria, the double-membrane prokaryotes, and their last
common ancestor. In combination with previous indel rooting studies excluding the
root from a clade consisting of the Firmicutes, the Archaea, and their last
common ancestor, this provides evidence for a unique eubacterial root for the
tree of life located between the actinobacterial-double-membrane clade and the
archaeal-firmicute clade. Mapping the phylogenetic distributions of genes
involved in peptidoglycan and lipid synthesis onto this rooted tree
parsimoniously implies that the cenancestral prokaryotic population consisted of
organisms enclosed by a single, ester-linked lipid membrane, covered by a
peptidoglycan layer.
FAU - Lake, James A
AU - Lake JA
AD - Department of Molecular, Cellular, and Developmental Biology, University of
California, Los Angeles, California 90095, USA. Lake@mbi.ucla.edu
FAU - Servin, Jacqueline A
AU - Servin JA
FAU - Herbold, Craig W
AU - Herbold CW
FAU - Skophammer, Ryan G
AU - Skophammer RG
LA - eng
PT - Journal Article
PT - Research Support, N.I.H., Extramural
PT - Research Support, U.S. Gov't, Non-P.H.S.
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - EC 1.3.- (Oxidoreductases Acting on CH-CH Group Donors)
RN - EC 1.3.5.2 (dihydroorotate dehydrogenase)
RN - EC 5.- (Isomerases)
SB - IM
MH - Archaea/*classification
MH - Bacteria/*classification
MH - *Evolution, Molecular
MH - INDEL Mutation/genetics
MH - Isomerases/genetics
MH - Oxidoreductases Acting on CH-CH Group Donors/genetics
MH - *Phylogeny
EDAT- 2008/12/17 09:00
MHDA- 2009/02/03 09:00
CRDT- 2008/12/17 09:00
PHST- 2008/12/17 09:00 [entrez]
PHST- 2008/12/17 09:00 [pubmed]
PHST- 2009/02/03 09:00 [medline]
AID - 906543685 [pii]
AID - 10.1080/10635150802555933 [doi]
PST - ppublish
SO - Syst Biol. 2008 Dec;57(6):835-43. doi: 10.1080/10635150802555933.
PMID- 19085326
OWN - NLM
STAT- MEDLINE
DCOM- 20090202
LR - 20081216
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 6
DP - 2008 Dec
TI - Selecting taxa to save or sequence: desirable criteria and a greedy solution.
PG - 825-34
LID - 10.1080/10635150802552831 [doi]
AB - Three desirable properties for any method of selecting a subset of evolutionary
units (EUs) for conservation or for genomic sequencing are discussed. These
properties are spread, stability, and applicability. We are motivated by a
practical case in which the maximization of phylogenetic diversity (PD), which
has been suggested as a suitable method, appears to lead to counterintuitive
collections of EUs and does not meet these three criteria. We define a simple
greedy algorithm (GREEDYMMD) as a close approximation to choosing the subset that
maximizes the minimum pairwise distance (MMD) between EUs. GREEDYMMD satisfies
our three criteria and may be a useful alternative to PD in real-world
situations. In particular, we show that this method of selection is suitable
under a model of biodiversity in which features arise and/or disappear during
evolution. We also show that if distances between EUs satisfy the ultrametric
condition, then GREEDYMMD delivers an optimal subset of EUs that maximizes both
the minimum pairwise distance and the PD. Finally, because GREEDYMMD works with
distances and does not require a tree, it is readily applicable to many data
sets.
FAU - Bordewich, Magnus
AU - Bordewich M
AD - Department of Computer Science, Durham University, Durham, United Kingdom.
m.j.r.bordewich@durham.ac.uk
FAU - Rodrigo, Allen G
AU - Rodrigo AG
FAU - Semple, Charles
AU - Semple C
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Algorithms
MH - Animals
MH - Classification/*methods
MH - Genomics/*methods/standards
MH - *Phylogeny
EDAT- 2008/12/17 09:00
MHDA- 2009/02/03 09:00
CRDT- 2008/12/17 09:00
PHST- 2008/12/17 09:00 [entrez]
PHST- 2008/12/17 09:00 [pubmed]
PHST- 2009/02/03 09:00 [medline]
AID - 906547611 [pii]
AID - 10.1080/10635150802552831 [doi]
PST - ppublish
SO - Syst Biol. 2008 Dec;57(6):825-34. doi: 10.1080/10635150802552831.
PMID- 18853367
OWN - NLM
STAT- MEDLINE
DCOM- 20081217
LR - 20081014
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 5
DP - 2008 Oct
TI - A justification for reporting the majority-rule consensus tree in Bayesian
phylogenetics.
PG - 814-21
LID - 10.1080/10635150802422308 [doi]
FAU - Holder, Mark T
AU - Holder MT
AD - Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence,
Kansas 66045, USA. mtholder@ku.edu
FAU - Sukumaran, Jeet
AU - Sukumaran J
FAU - Lewis, Paul O
AU - Lewis PO
LA - eng
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
SB - IM
MH - Bayes Theorem
MH - Decision Theory
MH - Evolution, Molecular
MH - *Genetic Variation
MH - Models, Genetic
MH - *Phylogeny
EDAT- 2008/10/15 09:00
MHDA- 2008/12/18 09:00
CRDT- 2008/10/15 09:00
PHST- 2008/10/15 09:00 [pubmed]
PHST- 2008/12/18 09:00 [medline]
PHST- 2008/10/15 09:00 [entrez]
AID - 904008159 [pii]
AID - 10.1080/10635150802422308 [doi]
PST - ppublish
SO - Syst Biol. 2008 Oct;57(5):814-21. doi: 10.1080/10635150802422308.
PMID- 18853366
OWN - NLM
STAT- MEDLINE
DCOM- 20081217
LR - 20181201
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 5
DP - 2008 Oct
TI - The use of mean instead of smallest interspecific distances exaggerates the size
of the "barcoding gap" and leads to misidentification.
PG - 809-13
LID - 10.1080/10635150802406343 [doi]
FAU - Meier, Rudolf
AU - Meier R
AD - Department of Biological Sciences, University Scholars Programme, National
University of Singapore, Singapore, Singapore. dbsmr@nus.edu.sg
FAU - Zhang, Guanyang
AU - Zhang G
FAU - Ali, Farhan
AU - Ali F
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 9007-49-2 (DNA)
SB - IM
MH - Base Sequence
MH - DNA/*genetics
MH - Electronic Data Processing/*methods
MH - Genetic Speciation
MH - Genetic Variation/genetics
MH - Phylogeny
MH - Research Design
EDAT- 2008/10/15 09:00
MHDA- 2008/12/18 09:00
CRDT- 2008/10/15 09:00
PHST- 2008/10/15 09:00 [pubmed]
PHST- 2008/12/18 09:00 [medline]
PHST- 2008/10/15 09:00 [entrez]
AID - 904008883 [pii]
AID - 10.1080/10635150802406343 [doi]
PST - ppublish
SO - Syst Biol. 2008 Oct;57(5):809-13. doi: 10.1080/10635150802406343.
PMID- 18853365
OWN - NLM
STAT- MEDLINE
DCOM- 20081217
LR - 20081014
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 5
DP - 2008 Oct
TI - Rooting and dating maples (Acer) with an uncorrelated-rates molecular clock:
implications for north American/Asian disjunctions.
PG - 795-808
LID - 10.1080/10635150802422282 [doi]
AB - Simulations suggest that molecular clock analyses can correctly identify the root
of a tree even when the clock assumption is severely violated. Clock-based
rooting of phylogenies may be particularly useful when outgroup rooting is
problematic. Here, we explore relaxed-clock rooting in the Acer/Dipteronia clade
of Sapindaceae, which comprises genera of highly uneven species richness and
problematic mutual monophyly. Using an approach that does not presuppose rate
autocorrelation between ancestral and descendant branches and hence does not
require a rooted a priori topology, we analyzed data from up to seven chloroplast
loci for some 50 ingroup species. For comparison, we used midpoint and outgroup
rooting and dating methods that rely on rooted input trees, namely penalized
likelihood, a Bayesian autocorrelated-rates model, and a strict clock. The
chloroplast sequences used here reject a single global substitution rate, and the
assumption of autocorrelated rates was also rejected. The root was placed between
Acer and Dipteronia by all three rooting methods, albeit with low statistical
support. Analyses of Acer diversification with a lineage-through-time plot and
different survival models, although sensitive to missing data, suggest a gradual
decrease in the average diversification rate. The nine North American species of
Acer diverged from their nearest relatives at widely different times: eastern
American Acer diverged in the Oligocene and Late Miocene; western American
species in the Late Eocene and Mid Miocene; and the Acer core clade, including A.
saccharum, dates to the Miocene. Recent diversification in North America is
strikingly rare compared to diversification in eastern Asia.
FAU - Renner, Susanne S
AU - Renner SS
AD - Department of Biology, University of Munich, Munich, Germany.
renner@lrz.uni-muenchen.de
FAU - Grimm, Guido W
AU - Grimm GW
FAU - Schneeweiss, Gerald M
AU - Schneeweiss GM
FAU - Stuessy, Tod F
AU - Stuessy TF
FAU - Ricklefs, Robert E
AU - Ricklefs RE
LA - eng
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
SB - IM
MH - Acer/*genetics
MH - Asia
MH - Demography
MH - *Evolution, Molecular
MH - Fossils
MH - Models, Genetic
MH - North America
MH - Software
EDAT- 2008/10/15 09:00
MHDA- 2008/12/18 09:00
CRDT- 2008/10/15 09:00
PHST- 2008/10/15 09:00 [pubmed]
PHST- 2008/12/18 09:00 [medline]
PHST- 2008/10/15 09:00 [entrez]
AID - 904007721 [pii]
AID - 10.1080/10635150802422282 [doi]
PST - ppublish
SO - Syst Biol. 2008 Oct;57(5):795-808. doi: 10.1080/10635150802422282.
PMID- 18853364
OWN - NLM
STAT- MEDLINE
DCOM- 20081217
LR - 20081014
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 5
DP - 2008 Oct
TI - Trees of trees: an approach to comparing multiple alternative phylogenies.
PG - 785-94
LID - 10.1080/10635150802424072 [doi]
AB - Phylogenetic analysis very commonly produces several alternative trees for a
given fixed set of taxa. For example, different sets of orthologous genes may be
analyzed, or the analysis may sample from a distribution of probable trees. This
article describes an approach to comparing and visualizing multiple alternative
phylogenies via the idea of a "tree of trees" or "meta-tree." A meta-tree
clusters phylogenies with similar topologies together in the same way that a
phylogeny clusters species with similar DNA sequences. Leaf nodes on a meta-tree
correspond to the original set of phylogenies given by some analysis, whereas
interior nodes correspond to certain consensus topologies. The construction of
meta-trees is motivated by analogy with construction of a most parsimonious tree
for DNA data, but instead of using DNA letters, in a meta-tree the characters are
partitions or splits of the set of taxa. An efficient algorithm for meta-tree
construction is described that makes use of a known relationship between the
majority consensus and parsimony in terms of gain and loss of splits. To
illustrate these ideas meta-trees are constructed for two datasets: a set of gene
trees for species of yeast and trees from a bootstrap analysis of a set of gene
trees in ray-finned fish. A software tool for constructing meta-trees and
comparing alternative phylogenies is available online, and the source code can be
obtained from the author.
FAU - Nye, Tom M W
AU - Nye TM
AD - School of Mathematics and Statistics, Newcastle University, Newcastle, UK.
tom.nye@ncl.ac.uk
LA - eng
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 9007-49-2 (DNA)
SB - IM
MH - Animals
MH - Classification/methods
MH - DNA/genetics
MH - *Evolution, Molecular
MH - Fishes/genetics
MH - *Genetic Variation
MH - *Phylogeny
MH - Plants/genetics
EDAT- 2008/10/15 09:00
MHDA- 2008/12/18 09:00
CRDT- 2008/10/15 09:00
PHST- 2008/10/15 09:00 [pubmed]
PHST- 2008/12/18 09:00 [medline]
PHST- 2008/10/15 09:00 [entrez]
AID - 904007528 [pii]
AID - 10.1080/10635150802424072 [doi]
PST - ppublish
SO - Syst Biol. 2008 Oct;57(5):785-94. doi: 10.1080/10635150802424072.
PMID- 18853363
OWN - NLM
STAT- MEDLINE
DCOM- 20081217
LR - 20181113
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 5
DP - 2008 Oct
TI - Wagner and Dollo: a stochastic duet by composing two parsimonious solos.
PG - 772-84
LID - 10.1080/10635150802434394 [doi]
AB - New contributions toward generalizing evolutionary models expand greatly our
ability to analyze complex evolutionary characters and advance phylogeny
reconstruction. In this article, we extend the binary stochastic Dollo model to
allow for multi-state characters. In doing so, we align previously incompatible
Wagner and Dollo parsimony principles under a common probabilistic framework by
embedding arbitrary continuous-time Markov chains into the binary stochastic
Dollo model. This approach enables us to analyze character traits that exhibit
both Dollo and Wagner characteristics throughout their evolutionary histories.
Utilizing Bayesian inference, we apply our novel model to analyze intron
conservation patterns and the evolution of alternatively spliced exons. The
generalized framework we develop demonstrates potential in distinguishing between
phylogenetic hypotheses and providing robust estimates of evolutionary rates.
Moreover, for the two applications analyzed here, our framework is the first to
provide an adequate stochastic process for the data. We discuss possible
extensions to the framework from both theoretical and applied perspectives.
FAU - Alekseyenko, Alexander V
AU - Alekseyenko AV
AD - Department of Biomathematics, David Geffen School of Medicine at UCLA, Los
Angeles, California 90095, USA. alexander.alekseyenko@ucla.edu
FAU - Lee, Christopher J
AU - Lee CJ
FAU - Suchard, Marc A
AU - Suchard MA
LA - eng
GR - R01 GM086887/GM/NIGMS NIH HHS/United States
GR - U54-RR021813/RR/NCRR NIH HHS/United States
GR - GM008185)/GM/NIGMS NIH HHS/United States
GR - T32 GM008185/GM/NIGMS NIH HHS/United States
GR - U54 RR021813/RR/NCRR NIH HHS/United States
PT - Journal Article
PT - Research Support, N.I.H., Extramural
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
SB - IM
MH - Alternative Splicing
MH - Animals
MH - Anopheles
MH - *Biological Evolution
MH - Caenorhabditis elegans
MH - Drosophila melanogaster
MH - Exons
MH - Humans
MH - *Models, Genetic
MH - *Stochastic Processes
PMC - PMC4677801
MID - NIHMS741975
EDAT- 2008/10/15 09:00
MHDA- 2008/12/18 09:00
CRDT- 2008/10/15 09:00
PHST- 2008/10/15 09:00 [pubmed]
PHST- 2008/12/18 09:00 [medline]
PHST- 2008/10/15 09:00 [entrez]
AID - 904009007 [pii]
AID - 10.1080/10635150802434394 [doi]
PST - ppublish
SO - Syst Biol. 2008 Oct;57(5):772-84. doi: 10.1080/10635150802434394.
PMID- 18853362
OWN - NLM
STAT- MEDLINE
DCOM- 20081217
LR - 20081014
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 57
IP - 5
DP - 2008 Oct
TI - A rapid bootstrap algorithm for the RAxML Web servers.
PG - 758-71
LID - 10.1080/10635150802429642 [doi]
AB - Despite recent advances achieved by application of high-performance computing
methods and novel algorithmic techniques to maximum likelihood (ML)-based
inference programs, the major computational bottleneck still consists in the
computation of bootstrap support values. Conducting a probably insufficient
number of 100 bootstrap (BS) analyses with current ML programs on large
datasets-either with respect to the number of taxa or base pairs-can easily
require a month of run time. Therefore, we have developed, implemented, and
thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated
Maximum Likelihood) that are more than an order of magnitude faster than current
algorithms. These new heuristics can contribute to resolving the computational
bottleneck and improve current methodology in phylogenetic analyses.
Computational experiments to assess the performance and relative accuracy of
these heuristics were conducted on 22 diverse DNA and AA (amino acid), single
gene as well as multigene, real-world alignments containing 125 up to 7764
sequences. The standard BS (SBS) and rapid BS (RBS) values drawn on the
best-scoring ML tree are highly correlated and show almost identical average
support values. The weighted RF (Robinson-Foulds) distance between SBS- and
RBS-based consensus trees was smaller than 6% in all cases (average 4%). More
importantly, RBS inferences are between 8 and 20 times faster (average 14.73)
than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses
with competing programs, such as PHYML or GARLI. Moreover, this performance
improvement increases with alignment size. Finally, we have set up two freely
accessible Web servers for this significantly improved version of RAxML that
provide access to the 200-CPU cluster of the Vital-IT unit at the Swiss Institute
of Bioinformatics and the 128-CPU cluster of the CIPRES project at the San Diego
Supercomputer Center. These Web servers offer the possibility to conduct
large-scale phylogenetic inferences to a large part of the community that does
not have access to, or the expertise to use, high-performance computing
resources.
FAU - Stamatakis, Alexandros
AU - Stamatakis A
AD - Exelixis Lab, Teaching and Research Unit Bioinformatics, Department of Computer
Science, Ludwig-Maximilians-University Munich, Munich, Germany.
stamatakis@bio.ifi.lmu.de
FAU - Hoover, Paul
AU - Hoover P
FAU - Rougemont, Jacques
AU - Rougemont J
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - *Algorithms
MH - Computers
MH - Evolution, Molecular
MH - *Internet
MH - Likelihood Functions
MH - Phylogeny
MH - Plants/genetics
MH - *Software
EDAT- 2008/10/15 09:00
MHDA- 2008/12/18 09:00
CRDT- 2008/10/15 09:00
PHST- 2008/10/15 09:00 [pubmed]
PHST- 2008/12/18 09:00 [medline]
PHST- 2008/10/15 09:00 [entrez]
AID - 904007647 [pii]
AID - 10.1080/10635150802429642 [doi]
PST - ppublish
SO - Syst Biol. 2008 Oct;57(5):758-71. doi: 10.1080/10635150802429642.
PMID- 18853361
OWN - NLM
STAT- MEDLINE
DCOM- 20081217