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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- 16611605
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20081121
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Goodbye Gondwana? New Zealand biogeography, geology, and the problem of
circularity.
PG - 351-6
FAU - Waters, Jonathan M
AU - Waters JM
AD - Department of Zoology, University of Otago, PO Box 56, Dunedin, New Zealand.
jonathan.waters@stonebow.otago.ac.nz
FAU - Craw, Dave
AU - Craw D
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 - Animals
MH - Anura/genetics
MH - Fishes/genetics
MH - *Genetic Speciation
MH - *Geography
MH - Geological Phenomena
MH - *Geology
MH - New Zealand
MH - Palaeognathae/genetics
MH - Plants/genetics
MH - Reptiles/genetics
EDAT- 2006/04/14 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/04/14 09:00
PHST- 2006/04/14 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/04/14 09:00 [entrez]
AID - T0414P33V4026014 [pii]
AID - 10.1080/10635150600681659 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):351-6. doi: 10.1080/10635150600681659.
PMID- 16611604
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20061115
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Discriminating supported and unsupported relationships in supertrees using
triplets.
PG - 345-50
FAU - Cotton, James A
AU - Cotton JA
AD - Department of Zoology, The Natural History Museum, Cromwell Road, SW7 5BD,
London, UK. james.cotton@nhm.ac.uk
FAU - Slater, Claire S C
AU - Slater CS
FAU - Wilkinson, Mark
AU - Wilkinson M
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 - *Models, Biological
MH - *Phylogeny
EDAT- 2006/04/14 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/04/14 09:00
PHST- 2006/04/14 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/04/14 09:00 [entrez]
AID - W47270541844Q198 [pii]
AID - 10.1080/10635150500481556 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):345-50. doi: 10.1080/10635150500481556.
PMID- 16611603
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20171116
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Utility of nuclear allele networks for the analysis of closely related species in
the genus Carabus, subgenus Ohomopterus.
PG - 329-44
AB - Nuclear DNA sequence data for diploid organisms are potentially a rich source of
phylogenetic information for disentangling the evolutionary relationships of
closely related organisms, but present special phylogenetic problems owing to
difficulties arising from heterozygosity and recombination. We analyzed allelic
relationships for two nuclear gene regions (phosphoenolpyruvate carboxykinase and
elongation factor-1a), along with a mitochondrial gene region (NADH dehydrogenase
subunit 5), for an assemblage of closely related species of carabid beetles
(Carabus subgenus Ohomopterus). We used a network approach to examine whether the
nuclear gene sequences provide substantial phylogenetic information on species
relationships and evolutionary history. The mitochondrial gene genealogy strongly
contradicted the morphological species boundary as a result of introgression of
heterospecific mitochondria. Two nuclear gene regions showed high allelic
diversity within species, and this diversity was partially attributable to
recombination between various alleles and high variability in the intron region.
Shared nuclear alleles among species were rare and were considered to represent
shared ancestral polymorphism. Despite the presence of recombination, nuclear
allelic networks recovered species monophyly more often and presented genetic
differentiation patterns (low to high) among species more clearly. Overall,
nuclear gene networks provide clear evidence for separate biological species and
information on the phylogenetic relationships among closely related carabid
beetles.
FAU - Sota, Teiji
AU - Sota T
AD - Department of Zoology, Graduate School of Science, Kyoto University, Sakyo,
Kyoto, 606-8502, Japan. sota@terra.zool.kyoto-u.ac.jp
FAU - Sasabe, Masataka
AU - Sasabe M
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 - *Alleles
MH - Animals
MH - Coleoptera/anatomy & histology/*classification/*genetics
MH - DNA/*genetics
MH - Genetic Speciation
MH - Genetic Variation
MH - Male
MH - Phylogeny
MH - Recombination, Genetic
MH - Species Specificity
EDAT- 2006/04/14 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/04/14 09:00
PHST- 2006/04/14 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/04/14 09:00 [entrez]
AID - V0LM73750847607N [pii]
AID - 10.1080/10635150500541607 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):329-44. doi: 10.1080/10635150500541607.
PMID- 16611602
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20131210
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Multiple sequence alignment accuracy and phylogenetic inference.
PG - 314-28
AB - Phylogenies are often thought to be more dependent upon the specifics of the
sequence alignment rather than on the method of reconstruction. Simulation of
sequences containing insertion and deletion events was performed in order to
determine the role that alignment accuracy plays during phylogenetic inference.
Data sets were simulated for pectinate, balanced, and random tree shapes under
different conditions (ultrametric equal branch length, ultrametric random branch
length, nonultrametric random branch length). Comparisons between hypothesized
alignments and true alignments enabled determination of two measures of alignment
accuracy, that of the total data set and that of individual branches. In general,
our results indicate that as alignment error increases, topological accuracy
decreases. This trend was much more pronounced for data sets derived from more
pectinate topologies. In contrast, for balanced, ultrametric, equal branch length
tree shapes, alignment inaccuracy had little average effect on tree
reconstruction. These conclusions are based on average trends of many analyses
under different conditions, and any one specific analysis, independent of the
alignment accuracy, may recover very accurate or inaccurate topologies. Maximum
likelihood and Bayesian, in general, outperformed neighbor joining and maximum
parsimony in terms of tree reconstruction accuracy. Results also indicated that
as the length of the branch and of the neighboring branches increase, alignment
accuracy decreases, and the length of the neighboring branches is the major
factor in topological accuracy. Thus, multiple-sequence alignment can be an
important factor in downstream effects on topological reconstruction.
FAU - Ogden, T Heath
AU - Ogden TH
AD - Center for Evolutionary Functional Genomics, The Biodesign Institute, and the
School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501,
USA. heath_ogden@asu.edu
FAU - Rosenberg, Michael S
AU - Rosenberg MS
LA - eng
GR - R03-LM008637/LM/NLM NIH HHS/United States
PT - Journal Article
PT - Research Support, N.I.H., Extramural
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 - Evolution, Molecular
MH - Likelihood Functions
MH - Models, Biological
MH - *Phylogeny
MH - Sequence Alignment/*methods
EDAT- 2006/04/14 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/04/14 09:00
PHST- 2006/04/14 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/04/14 09:00 [entrez]
AID - P4K066N6N345N408 [pii]
AID - 10.1080/10635150500541730 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):314-28. doi: 10.1080/10635150500541730.
PMID- 16611601
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20101118
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Ancestral state reconstruction of body size in the Caniformia (Carnivora,
Mammalia): the effects of incorporating data from the fossil record.
PG - 301-13
AB - A recent molecular phylogeny of the mammalian order Carnivora implied large body
size as the ancestral condition for the caniform subclade Arctoidea using the
distribution of species mean body sizes among living taxa. "Extant taxa-only"
approaches such as these discount character state observations for fossil members
of living clades and completely ignore data from extinct lineages. To more
rigorously reconstruct body sizes of ancestral forms within the Caniformia, body
size and first appearance data were collected for 149 extant and 367 extinct
taxa. Body sizes were reconstructed for four ancestral nodes using weighted
squared-change parsimony on log-transformed body mass data. Reconstructions based
on extant taxa alone favored large body sizes (on the order of 10 to 50 kg) for
the last common ancestors of both the Caniformia and Arctoidea. In contrast,
reconstructions incorporating fossil data support small body sizes (< 5 kg) for
the ancestors of those clades. When the temporal information associated with
fossil data was discarded, body size reconstructions became ambiguous,
demonstrating that incorporating both character state and temporal information
from fossil taxa unambiguously supports a small ancestral body size, thereby
falsifying hypotheses derived from extant taxa alone. Body size reconstructions
for Caniformia, Arctoidea, and Musteloidea were not sensitive to potential errors
introduced by uncertainty in the position of extinct lineages relative to the
molecular topology, or to missing body size data for extinct members of an entire
major clade (the aquatic Pinnipedia). Incorporating character state observations
and temporal information from the fossil record into hypothesis testing has a
significant impact on the ability to reconstruct ancestral characters and
constrains the range of potential hypotheses of character evolution. Fossil data
here provide the evidence to reliably document trends of both increasing and
decreasing body size in several caniform clades. More generally, including
fossils in such analyses incorporates evidence of directional trends, thereby
yielding more reliable ancestral character state reconstructions.
FAU - Finarelli, John A
AU - Finarelli JA
AD - Committee on Evolutionary Biology, University of Chicago, Illinois 60637, USA.
johnf@uchicago.edu
FAU - Flynn, John J
AU - Flynn JJ
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 - *Body Size
MH - Carnivora/*anatomy & histology/classification
MH - *Fossils
EDAT- 2006/04/14 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/04/14 09:00
PHST- 2006/04/14 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/04/14 09:00 [entrez]
AID - R022600P902HU876 [pii]
AID - 10.1080/10635150500541698 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):301-13. doi: 10.1080/10635150500541698.
PMID- 16611600
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20070719
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Evolutionary rates, divergence dates, and the performance of mitochondrial genes
in Bayesian phylogenetic analysis.
PG - 289-300
AB - The mitochondrial genome is one of the most frequently used loci in phylogenetic
and phylogeographic analyses, and it is becoming increasingly possible to
sequence and analyze this genome in its entirety from diverse taxa. However,
sequencing the entire genome is not always desirable or feasible. Which genes
should be selected to best infer the evolutionary history of the mitochondria
within a group of organisms, and what properties of a gene determine its
phylogenetic performance? The current study addresses these questions in a
Bayesian phylogenetic framework with reference to a phylogeny of plethodontid and
related salamanders derived from 27 complete mitochondrial genomes; this topology
is corroborated by nuclear DNA and morphological data. Evolutionary rates for
each mitochondrial gene and divergence dates for all nodes in the plethodontid
mitochondrial genome phylogeny were estimated in both Bayesian and maximum
likelihood frameworks using multiple fossil calibrations, multiple data
partitions, and a clock-independent approach. Bayesian analyses of individual
genes were performed, and the resulting trees compared against the reference
topology. Ordinal logistic regression analysis of molecular evolution rate, gene
length, and the G-shape parameter a demonstrated that slower rate of evolution
and longer gene length both increased the probability that a gene would perform
well phylogenetically. Estimated rates of molecular evolution vary 84-fold among
different mitochondrial genes and different salamander lineages, and mean rates
among genes vary 15-fold. Despite having conserved amino acid sequences, cox1,
cox2, cox3, and cob have the fastest mean rates of nucleotide substitution, and
the greatest variation in rates, whereas rrnS and rrnL have the slowest rates.
Reasons underlying this rate variation are discussed, as is the extensive rate
variation in cox1 in light of its proposed role in DNA barcoding.
FAU - Mueller, Rachel Lockridge
AU - Mueller RL
AD - Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences
Building Berkeley, California 94720-3160, USA. rmueller@uchicago.edu
LA - eng
PT - Journal Article
PT - Research Support, U.S. Gov't, Non-P.H.S.
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
EIN - Syst Biol. 2007 Jun;56(3):542
MH - Animals
MH - Bayes Theorem
MH - *Evolution, Molecular
MH - Genes, Mitochondrial/*genetics
MH - Mitochondria/*genetics
MH - *Phylogeny
MH - Urodela/genetics
EDAT- 2006/04/14 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/04/14 09:00
PHST- 2006/04/14 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/04/14 09:00 [entrez]
AID - T8733337X7687241 [pii]
AID - 10.1080/10635150500541672 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):289-300. doi: 10.1080/10635150500541672.
PMID- 16611599
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20061115
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Fast computation of supertrees for compatible phylogenies with nested taxa.
PG - 270-88
AB - Typically, supertree methods combine a collection of source trees in which just
the leaves are labeled by taxa. In such methods the resulting supertree is also
leaf labeled. An underlying assumption in these methods is that across all trees
in the collection, no two of the taxa are nested; for example, "buttercups" and
"plants" are nested taxa. Motivated by Page, the first supertree algorithm for
allowing the source trees to collectively have nested taxa is called
AncestralBuild. Here, in addition to taxa labeling the leaves, the source trees
may have taxa labeling some of their interior nodes. Taxa-labeling interior nodes
are at a higher taxonomic level than that of their descendants (for example,
genera versus species). Analogous to the supertree method Build for deciding the
compatibility of a collection of source trees in which just the leaves are
labeled, AncestralBuild is a polynomial-time algorithm for deciding the
compatibility of a collection of source trees in which some of the interior nodes
are also labeled by taxa. Although a more general method, in this paper we show
that the original description of AncestralBuild can be modified so that the
running time is as fast as the current fastest running time for Build. Fast
computation for deciding compatibility is essential if one is to make use of
phylogenetic databases that contain thousands of trees on tens of thousands of
taxa. This is particularly so as AncestralBuild is incorporated as a basic tool
inside more general supertree methods (that is, methods that always output a tree
regardless of the compatibility of the source trees). We apply the method to
propose a comprehensive phylogeny of the strepsirrhines, a major group of the
primates.
FAU - Berry, Vincent
AU - Berry V
AD - Departement Informatique, L.I.R.M.M.-C.N.R.S., 161 rue Ada, 34392 Montpellier
Cedex 5, France. vberry@lirmm.fr
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 - Computer Simulation
MH - Models, Biological
MH - *Phylogeny
MH - Software
MH - Strepsirhini/classification/genetics
MH - Time Factors
EDAT- 2006/04/14 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/04/14 09:00
PHST- 2006/04/14 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/04/14 09:00 [entrez]
AID - M33725745505H733 [pii]
AID - 10.1080/10635150500541649 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):270-88. doi: 10.1080/10635150500541649.
PMID- 16551582
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20101118
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Inferring complex DNA substitution processes on phylogenies using uniformization
and data augmentation.
PG - 259-69
AB - A new method is developed for calculating sequence substitution probabilities
using Markov chain Monte Carlo (MCMC) methods. The basic strategy is to use
uniformization to transform the original continuous time Markov process into a
Poisson substitution process and a discrete Markov chain of state transitions. An
efficient MCMC algorithm for evaluating substitution probabilities by this
approach using a continuous gamma distribution to model site-specific rates is
outlined. The method is applied to the problem of inferring branch lengths and
site-specific rates from nucleotide sequences under a general time-reversible
(GTR) model and a computer program BYPASSR is developed. Simulations are used to
examine the performance of the new program relative to an existing program BASEML
that uses a discrete approximation for the gamma distributed prior on
site-specific rates. It is found that BASEML and BYPASSR are in close agreement
when inferring branch lengths, regardless of the number of rate categories used,
but that BASEML tends to underestimate high site-specific substitution rates, and
to overestimate intermediate rates, when fewer than 50 rate categories are used.
Rate estimates obtained using BASEML agree more closely with those of BYPASSR as
the number of rate categories increases. Analyses of the posterior distributions
of site-specific rates from BYPASSR suggest that a large number of taxa are
needed to obtain precise estimates of site-specific rates, especially when rates
are very high or very low. The method is applied to analyze 45 sequences of the
alpha 2B adrenergic receptor gene (A2AB) from a sample of eutherian taxa. In
general, the pattern expected for regions under negative selection is observed
with third codon positions having the highest inferred rates, followed by first
codon positions and with second codon positions having the lowest inferred rates.
Several sites show exceptionally high substitution rates at second codon
positions that may represent the effects of positive selection.
FAU - Mateiu, Ligia
AU - Mateiu L
AD - Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada.
FAU - Rannala, Bruce
AU - Rannala B
LA - eng
GR - HG01988/HG/NHGRI NIH HHS/United States
PT - Journal Article
PT - Research Support, N.I.H., Extramural
PT - Research Support, Non-U.S. Gov't
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 0 (Receptors, Adrenergic, alpha-2)
RN - 9007-49-2 (DNA)
SB - IM
MH - Algorithms
MH - Animals
MH - Base Sequence
MH - DNA/*genetics
MH - Mammals/genetics
MH - Markov Chains
MH - *Models, Biological
MH - Monte Carlo Method
MH - *Phylogeny
MH - Receptors, Adrenergic, alpha-2/genetics
MH - Software
EDAT- 2006/03/23 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/03/23 09:00
PHST- 2006/03/23 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/03/23 09:00 [entrez]
AID - R05Q3757V645376J [pii]
AID - 10.1080/10635150500541599 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):259-69. doi: 10.1080/10635150500541599.
PMID- 16551581
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20171116
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - How can third codon positions outperform first and second codon positions in
phylogenetic inference? An empirical example from the seed plants.
PG - 245-58
AB - Greater phylogenetic signal is often found in parsimony-based analyses of third
codon positions of protein-coding genes relative to their corresponding first and
second codon positions, even for early-derived ("basal") clades. We used the
Soltis et al. (2000; Bot. J. Linn. Soc. 133:381-461) data matrix of atpB and rbcL
from 567 seed plants to quantify how each of six factors (observed
character-state space, frequencies of observed character states, substitution
probabilities among nucleotides, rate heterogeneity among sites, overall rate of
evolution, and number of parsimony-informative characters) contributed to this
phenomenon. Each of these six factors was estimated from the original data matrix
for parsimony-informative third codon positions considered separately from first
and second codon positions combined. One of the most parsimonious trees found was
used as the constraint topology; branch lengths were estimated using
likelihood-based distances, and characters were simulated on this tree.
Differential frequencies of observed character states were found to be the most
limiting of the factors simulated for all three codon positions. Differential
frequencies of observed character states and differential substitution
probabilities among states were relatively advantageous for first and second
codon positions. In contrast, differential numbers of observed character states,
differential rate heterogeneity among sites, the greater number of
parsimony-informative characters, and the higher overall rate of evolution were
relatively advantageous for third codon positions. The amount of possible
synapomorphy was predictive of the overall success of resolution.
FAU - Simmons, Mark P
AU - Simmons MP
AD - Department of Biology, Colorado State University, Fort Collins, Colorado
80523-1878, USA. psimmons@lamar.colostate.edu
FAU - Zhang, Li-Bing
AU - Zhang LB
FAU - Webb, Colleen T
AU - Webb CT
FAU - Reeves, Aaron
AU - Reeves A
LA - eng
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 0 (Codon)
RN - EC 4.1.1.39 (RbcL protein, plastid)
RN - EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)
SB - IM
MH - Base Sequence
MH - Codon/*genetics
MH - Evolution, Molecular
MH - Gene Expression Regulation, Plant
MH - Magnoliopsida/*genetics
MH - Models, Biological
MH - *Phylogeny
MH - Ribulose-Bisphosphate Carboxylase/genetics
EDAT- 2006/03/23 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/03/23 09:00
PHST- 2006/03/23 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/03/23 09:00 [entrez]
AID - T382031288437360 [pii]
AID - 10.1080/10635150500481473 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):245-58. doi: 10.1080/10635150500481473.
PMID- 16551580
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20081121
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Arrival and diversification of caviomorph rodents and platyrrhine primates in
South America.
PG - 228-44
AB - Platyrrhine primates and caviomorph rodents are clades of mammals that colonized
South America during its period of isolation from the other continents, between
100 and 3 million years ago (Mya). Until now, no molecular study investigated the
timing of the South American colonization by these two lineages with the same
molecular data set. Using sequences from three nuclear genes (ADRA2B, vWF, and
IRBP, both separate and combined) from 60 species, and eight fossil calibration
constraints, we estimated the times of origin and diversification of platyrrhines
and caviomorphs via a Bayesian relaxed molecular clock approach. To account for
the possible effect of an accelerated rate of evolution of the IRBP gene along
the branch leading to the anthropoids, we performed the datings with and without
IRBP (3768 sites and 2469 sites, respectively). The time window for the
colonization of South America by primates and by rodents is demarcated by the
dates of origin (upper bound) and radiation (lower bound) of platyrrhines and
caviomorphs. According to this approach, platyrrhine primates colonized South
America between 37.0 +/- 3.0 Mya (or 38.9 +/- 4.0 Mya without IRBP) and 16.8 +/-
2.3 (or 20.1 +/- 3.3) Mya, and caviomorph rodents between 45.4 +/- 4.1 (or 43.7
+/- 4.8) Mya and 36.7 +/- 3.7 (or 35.8 +/- 4.3) Mya. Considering both the fossil
record and these molecular datings, the favored scenarios are a trans-Atlantic
migration of primates from Africa at the end of the Eocene or beginning of the
Oligocene, and a colonization of South America by rodents during the Middle or
Late Eocene. Based on our nuclear DNA data, we cannot rule out the possibility of
a concomitant arrival of primates and rodents in South America. The caviomorphs
radiated soon after their arrival, before the Oligocene glaciations, and these
early caviomorph lineages persisted until the present. By contrast, few
platyrrhine fossils are known in the Oligocene, and the present-day taxa are the
result of a quite recent, Early Miocene diversification.
FAU - Poux, Celine
AU - Poux C
AD - Laboratoire de Paleontologie, Phylogenie et Paleobiologie, CC064, Institut des
Sciences de l'Evolution (UMR 5554/CNRS), Universite Montpellier II, Place E.,
Bataillon, 34 095, Montpellier Cedex 05, France.
FAU - Chevret, Pascale
AU - Chevret P
FAU - Huchon, Dorothee
AU - Huchon D
FAU - de Jong, Wilfried W
AU - de Jong WW
FAU - Douzery, Emmanuel J P
AU - Douzery EJ
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 0 (Genetic Markers)
RN - 0 (Receptors, Adrenergic, alpha-2)
RN - 0 (Retinol-Binding Proteins)
RN - 0 (von Willebrand Factor)
SB - IM
MH - Animal Migration
MH - Animals
MH - Bayes Theorem
MH - *Evolution, Molecular
MH - Fossils
MH - Genetic Markers/genetics
MH - Genetic Variation
MH - *Phylogeny
MH - Platyrrhini/*classification/*genetics
MH - Receptors, Adrenergic, alpha-2/genetics
MH - Retinol-Binding Proteins/genetics
MH - Rodentia/*classification/*genetics
MH - South America
MH - von Willebrand Factor/genetics
EDAT- 2006/03/23 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/03/23 09:00
PHST- 2006/03/23 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/03/23 09:00 [entrez]
AID - G175KX2542585505 [pii]
AID - 10.1080/10635150500481390 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):228-44. doi: 10.1080/10635150500481390.
PMID- 16537291
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20071115
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Molecular phylogenetic analyses indicate multiple independent emergences of
parasitism in Myzostomida (Protostomia).
PG - 208-27
AB - The fossil record indicates that Myzostomida, an enigmatic group of marine worms,
traditionally considered as annelids, have exhibited a symbiotic relationship
with echinoderms, especially crinoids, for nearly 350 million years. All known
extant myzostomids are associated with echinoderms and infest their integument,
gonads, celom, or digestive system. Using nuclear (18S rDNA) and mitochondrial
(16S and COI) DNA sequence data from 37 myzostomid species representing nine
genera, we report here the first molecular phylogeny of the Myzostomida and
investigate the evolution of their various symbiotic associations. Our analyses
indicate that the two orders Proboscidea and Pharyngidea do not constitute
natural groupings. Character reconstruction analyses strongly suggest that (1)
the ancestor of all extant myzostomids was an ectocommensal that first infested
crinoids, and then asteroids and ophiuroids, and (2) parasitism in myzostomids
emerged multiple times independently.
FAU - Lanterbecq, Deborah
AU - Lanterbecq D
AD - Marine Biology Laboratory, University of Mons-Hainaut, 6 Avenue du champ de Mars,
Life Sciences building, 7000 Mons, Belgium. deborah.lanterbecq@umh.ac.be
FAU - Rouse, Greg W
AU - Rouse GW
FAU - Milinkovitch, Michel C
AU - Milinkovitch MC
FAU - Eeckhaut, Igor
AU - Eeckhaut I
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 - Animals
MH - Annelida/*genetics/*physiology/ultrastructure
MH - Echinodermata/*parasitology
MH - *Evolution, Molecular
MH - Host-Parasite Interactions
MH - *Phylogeny
MH - *Symbiosis
EDAT- 2006/03/16 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/03/16 09:00
PHST- 2006/03/16 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/03/16 09:00 [entrez]
AID - T127351LPM06186Q [pii]
AID - 10.1080/10635150500481317 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):208-27. doi: 10.1080/10635150500481317.
PMID- 16522570
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20061115
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Computing Bayes factors using thermodynamic integration.
PG - 195-207
AB - In the Bayesian paradigm, a common method for comparing two models is to compute
the Bayes factor, defined as the ratio of their respective marginal likelihoods.
In recent phylogenetic works, the numerical evaluation of marginal likelihoods
has often been performed using the harmonic mean estimation procedure. In the
present article, we propose to employ another method, based on an analogy with
statistical physics, called thermodynamic integration. We describe the method,
propose an implementation, and show on two analytical examples that this
numerical method yields reliable estimates. In contrast, the harmonic mean
estimator leads to a strong overestimation of the marginal likelihood, which is
all the more pronounced as the model is higher dimensional. As a result, the
harmonic mean estimator systematically favors more parameter-rich models, an
artefact that might explain some recent puzzling observations, based on harmonic
mean estimates, suggesting that Bayes factors tend to overscore complex models.
Finally, we apply our method to the comparison of several alternative models of
amino-acid replacement. We confirm our previous observations, indicating that
modeling pattern heterogeneity across sites tends to yield better models than
standard empirical matrices.
FAU - Lartillot, Nicolas
AU - Lartillot N
AD - Laboratoire d'Informatique, de Robotique et de Microelectronique de Montpellier
UMR 5506, CNRS-Universite, de Montpellier 2, 161, rue Ada, 34392 Montpellier
Cedex 5, France. nicolas.lartillot@lirmm.fr
FAU - Philippe, Herve
AU - Philippe H
LA - eng
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 - Amino Acid Sequence
MH - Animals
MH - *Bayes Theorem
MH - *Evolution, Molecular
MH - Likelihood Functions
MH - Models, Biological
MH - *Phylogeny
MH - Proteins/chemistry/genetics
MH - Thermodynamics
EDAT- 2006/03/09 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/03/09 09:00
PHST- 2006/03/09 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/03/09 09:00 [entrez]
AID - G44K65W276345678 [pii]
AID - 10.1080/10635150500433722 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):195-207. doi: 10.1080/10635150500433722.
PMID- 16522569
OWN - NLM
STAT- MEDLINE
DCOM- 20060613
LR - 20061115
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 2
DP - 2006 Apr
TI - Tenrec phylogeny and the noninvasive extraction of nuclear DNA.
PG - 181-94
AB - Due in part to scarcity of material, no published study has yet cladistically
addressed the systematics of living and fossil Tenrecidae (Mammalia, Afrotheria).
Using a noninvasive technique for sampling nuclear DNA from museum specimens, we
investigate the evolution of the Tenrecidae and assess the extent to which
tenrecids fit patterns of relationships proposed for other terrestrial mammals on
Madagascar. Application of several tree-reconstruction techniques on sequences of
the nuclear growth hormone receptor gene and morphological data for all
recognized tenrecid genera supports monophyly of Malagasy tenrecids to the
exclusion of the two living African genera. However, both parsimony and Bayesian
methods favor a close relationship between fossil African tenrecs and the
Malagasy Geogale, supporting the hypothesis of island paraphyly, but not
polyphyly. More generally, the noninvasive extraction technique can be applied
with minimal risk to rare/unique specimens and, by better utilizing museum
collections for genetic work, can greatly mitigate field expenses and disturbance
of natural populations.
FAU - Asher, Robert J
AU - Asher RJ
AD - Museum fur Naturkunde, D-10115, Berlin, Germany. robert.asher@museum.hu-berlin.de
FAU - Hofreiter, Michael
AU - Hofreiter M
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
RN - 9007-49-2 (DNA)
SB - IM
MH - Animals
MH - Cell Nucleus/*genetics
MH - DNA/genetics/*isolation & purification
MH - Fossils
MH - Insectivora/*classification/*genetics
MH - *Phylogeny
MH - Skull
EDAT- 2006/03/09 09:00
MHDA- 2006/06/14 09:00
CRDT- 2006/03/09 09:00
PHST- 2006/03/09 09:00 [pubmed]
PHST- 2006/06/14 09:00 [medline]
PHST- 2006/03/09 09:00 [entrez]
AID - QW77988407Q75822 [pii]
AID - 10.1080/10635150500433649 [doi]
PST - ppublish
SO - Syst Biol. 2006 Apr;55(2):181-94. doi: 10.1080/10635150500433649.
PMID- 16507535
OWN - NLM
STAT- MEDLINE
DCOM- 20060418
LR - 20060301
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 1
DP - 2006 Feb
TI - A robust distance coefficient between distribution areas incorporating geographic
distances.
PG - 170-5
FAU - Hennig, Christian
AU - Hennig C
AD - University College London, Department of Statistical Science, 1-19 Torrington
Place, London, WC1E 6BT, United Kingdom.
FAU - Hausdorf, Bernhard
AU - Hausdorf B
LA - eng
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - *Demography
MH - *Geography
MH - *Models, Biological
MH - Selection Bias
EDAT- 2006/03/02 09:00
MHDA- 2006/04/19 09:00
CRDT- 2006/03/02 09:00
PHST- 2006/03/02 09:00 [pubmed]
PHST- 2006/04/19 09:00 [medline]
PHST- 2006/03/02 09:00 [entrez]
AID - U0W687N3H61387HH [pii]
AID - 10.1080/10635150500481523 [doi]
PST - ppublish
SO - Syst Biol. 2006 Feb;55(1):170-5. doi: 10.1080/10635150500481523.
PMID- 16507534
OWN - NLM
STAT- MEDLINE
DCOM- 20060418
LR - 20071114
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 1
DP - 2006 Feb
TI - Statistical approaches for DNA barcoding.
PG - 162-9
FAU - Nielsen, Rasmus
AU - Nielsen R
AD - Department of Biological Statistics and Computational Biology, Center for
Bioinformatics, University of Copenhagen Universitetsparken 15, 2100 Copenhagen,
Denmark. rn28@cornell.edu
FAU - Matz, Mikhail
AU - Matz M
LA - eng
GR - GM066243/GM/NIGMS NIH HHS/United States
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
SB - IM
MH - Animals
MH - Anura/classification/genetics
MH - Bayes Theorem
MH - Butterflies/classification/genetics
MH - Classification/*methods
MH - Data Interpretation, Statistical
MH - Sequence Analysis, DNA
MH - Species Specificity
EDAT- 2006/03/02 09:00
MHDA- 2006/04/19 09:00
CRDT- 2006/03/02 09:00
PHST- 2006/03/02 09:00 [pubmed]
PHST- 2006/04/19 09:00 [medline]
PHST- 2006/03/02 09:00 [entrez]
AID - WVHHX8X716312020 [pii]
AID - 10.1080/10635150500431239 [doi]
PST - ppublish
SO - Syst Biol. 2006 Feb;55(1):162-9. doi: 10.1080/10635150500431239.
PMID- 16507533
OWN - NLM
STAT- MEDLINE
DCOM- 20060418
LR - 20071115
IS - 1063-5157 (Print)
IS - 1063-5157 (Linking)
VI - 55
IP - 1
DP - 2006 Feb
TI - The PhyloCode and the distinction between taxonomy and nomenclature.
PG - 160-2
FAU - Queiroz, Kevin de
AU - Queiroz Kd
AD - Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian
Institution, Washington DC 20560, USA. dequeirk@si.edu
LA - eng
PT - Journal Article
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Classification/*methods
MH - Phylogeny
MH - *Terminology as Topic
EDAT- 2006/03/02 09:00
MHDA- 2006/04/19 09:00
CRDT- 2006/03/02 09:00
PHST- 2006/03/02 09:00 [pubmed]
PHST- 2006/04/19 09:00 [medline]
PHST- 2006/03/02 09:00 [entrez]
AID - M5380H652732R858 [pii]
AID - 10.1080/10635150500431221 [doi]
PST - ppublish
SO - Syst Biol. 2006 Feb;55(1):160-2. doi: 10.1080/10635150500431221.
PMID- 16507532
OWN - NLM
STAT- MEDLINE
DCOM- 20060418