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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- 22213708
OWN - NLM
STAT- MEDLINE
DCOM- 20130401
LR - 20171116
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 61
IP - 3
DP - 2012 May
TI - Interpreting the evolutionary regression: the interplay between observational and
biological errors in phylogenetic comparative studies.
PG - 413-25
LID - 10.1093/sysbio/syr122 [doi]
AB - Regressions of biological variables across species are rarely perfect. Usually,
there are residual deviations from the estimated model relationship, and such
deviations commonly show a pattern of phylogenetic correlations indicating that
they have biological causes. We discuss the origins and effects of
phylogenetically correlated biological variation in regression studies. In
particular, we discuss the interplay of biological deviations with deviations due
to observational or measurement errors, which are also important in comparative
studies based on estimated species means. We show how bias in estimated
evolutionary regressions can arise from several sources, including phylogenetic
inertia and either observational or biological error in the predictor variables.
We show how all these biases can be estimated and corrected for in the presence
of phylogenetic correlations. We present general formulas for incorporating
measurement error in linear models with correlated data. We also show how
alternative regression models, such as major axis and reduced major axis
regression, which are often recommended when there is error in predictor
variables, are strongly biased when there is biological variation in any part of
the model. We argue that such methods should never be used to estimate
evolutionary or allometric regression slopes.
FAU - Hansen, Thomas F
AU - Hansen TF
AD - Department of Biology, Centre for Ecological and Evolutionary Synthesis,
University of Oslo, PB 1066, Blindern, N-0316 Oslo, Norway.
Thomas.Hansen@bio.uio.no
FAU - Bartoszek, Krzysztof
AU - Bartoszek K
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20120102
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Bias
MH - Linear Models
MH - *Models, Biological
MH - *Phylogeny
MH - Regression Analysis
EDAT- 2012/01/04 06:00
MHDA- 2013/04/02 06:00
CRDT- 2012/01/04 06:00
PHST- 2012/01/04 06:00 [entrez]
PHST- 2012/01/04 06:00 [pubmed]
PHST- 2013/04/02 06:00 [medline]
AID - syr122 [pii]
AID - 10.1093/sysbio/syr122 [doi]
PST - ppublish
SO - Syst Biol. 2012 May;61(3):413-25. doi: 10.1093/sysbio/syr122. Epub 2012 Jan 2.
PMID- 22201160
OWN - NLM
STAT- MEDLINE
DCOM- 20120625
LR - 20181201
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 61
IP - 2
DP - 2012 Mar
TI - The poverty of the phylocode: a reply to de Queiroz and Donoghue.
PG - 360-1
LID - 10.1093/sysbio/syr117 [doi]
FAU - Platnick, Norman I
AU - Platnick NI
AD - Division of Invertebrate Zoology, American Museum of Natural History, New York,
NY 10024, USA. platnick@amnh.org
LA - eng
PT - Journal Article
PT - Comment
DEP - 20111226
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
CON - Syst Biol. 2011 Dec;60(6):887-92. PMID: 21865335
CIN - Syst Biol. 2013 Jan 1;62(1):167-74. PMID: 22649180
CIN - Syst Biol. 2013 Jan 1;62(1):175-6. PMID: 22730418
MH - Animals
MH - Classification/*methods
MH - *Phylogeny
MH - *Terminology as Topic
EDAT- 2011/12/28 06:00
MHDA- 2012/06/26 06:00
CRDT- 2011/12/28 06:00
PHST- 2011/12/28 06:00 [entrez]
PHST- 2011/12/28 06:00 [pubmed]
PHST- 2012/06/26 06:00 [medline]
AID - syr117 [pii]
AID - 10.1093/sysbio/syr117 [doi]
PST - ppublish
SO - Syst Biol. 2012 Mar;61(2):360-1. doi: 10.1093/sysbio/syr117. Epub 2011 Dec 26.
PMID- 22201159
OWN - NLM
STAT- MEDLINE
DCOM- 20130401
LR - 20120420
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 61
IP - 3
DP - 2012 May
TI - Recurrent introgression of mitochondrial DNA among hares (Lepus spp.) revealed by
species-tree inference and coalescent simulations.
PG - 367-81
LID - 10.1093/sysbio/syr114 [doi]
AB - Understanding recent speciation history requires merging phylogenetic and
population genetics approaches, taking into account the persistence of ancestral
polymorphism and possible introgression. The emergence of a clear phylogeny of
hares (genus Lepus) has been hampered by poor genomic sampling and possible
occurrence of mitochondrial DNA (mtDNA) introgression from the arctic/boreal
Lepus timidus into several European temperate and possibly American boreal
species. However, no formal test of introgression, taking also incomplete lineage
sorting into account, has been done. Here, to clarify the yet poorly resolved
species phylogeny of hares and test hypotheses of mtDNA introgression, we
sequenced 14 nuclear DNA and 2 mtDNA fragments (8205 and 1113 bp, respectively)
in 50 specimens from 11 hare species from Eurasia, North America, and Africa. By
applying an isolation-with-migration model to the nuclear data on subsets of
species, we find evidence for very limited gene flow from L. timidus into most
temperate European species, and not into the American boreal ones. Using a
multilocus coalescent-based method, we infer the species phylogeny, which we find
highly incongruent with mtDNA phylogeny using parametric bootstrap. Simulations
of mtDNA evolution under the speciation history inferred from nuclear genes did
not support the hypothesis of mtDNA introgression from L. timidus into the
American L. townsendii but did suggest introgression from L. timidus into 4
temperate European species. One such event likely resulted in the complete
replacement of the aboriginal mtDNA of L. castroviejoi and of its sister species
L. corsicanus. It is remarkable that mtDNA introgression in hares is frequent,
extensive, and always from the same donor arctic species. We discuss possible
explanations for the phenomenon in relation to the dynamics of range expansions
and species replacements during the climatic oscillations of the Pleistocene.
FAU - Melo-Ferreira, J
AU - Melo-Ferreira J
AD - CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos,
Universidade do Porto, Campus Agrario de Vairao, 4485-661 Vairao, Portugal.
jmeloferreira@cibio.up.pt
FAU - Boursot, P
AU - Boursot P
FAU - Carneiro, M
AU - Carneiro M
FAU - Esteves, P J
AU - Esteves PJ
FAU - Farelo, L
AU - Farelo L
FAU - Alves, P C
AU - Alves PC
LA - eng
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SI - GENBANK/JN037408
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20111226
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 0 (DNA, Mitochondrial)
SB - IM
MH - Animals
MH - Computer Simulation
MH - DNA, Mitochondrial/*genetics
MH - *Gene Flow
MH - Genetic Speciation
MH - Genome, Mitochondrial
MH - Hares/*classification/*genetics
MH - Molecular Sequence Data
MH - *Phylogeny
EDAT- 2011/12/28 06:00
MHDA- 2013/04/02 06:00
CRDT- 2011/12/28 06:00
PHST- 2011/12/28 06:00 [entrez]
PHST- 2011/12/28 06:00 [pubmed]
PHST- 2013/04/02 06:00 [medline]
AID - syr114 [pii]
AID - 10.1093/sysbio/syr114 [doi]
PST - ppublish
SO - Syst Biol. 2012 May;61(3):367-81. doi: 10.1093/sysbio/syr114. Epub 2011 Dec 26.
PMID- 22201158
OWN - NLM
STAT- MEDLINE
DCOM- 20120625
LR - 20120216
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 61
IP - 2
DP - 2012 Mar
TI - Testing the impact of calibration on molecular divergence times using a
fossil-rich group: the case of Nothofagus (Fagales).
PG - 289-313
LID - 10.1093/sysbio/syr116 [doi]
AB - Although temporal calibration is widely recognized as critical for obtaining
accurate divergence-time estimates using molecular dating methods, few studies
have evaluated the variation resulting from different calibration strategies.
Depending on the information available, researchers have often used primary
calibrations from the fossil record or secondary calibrations from previous
molecular dating studies. In analyses of flowering plants, primary calibration
data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and
fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in
accuracy and precision, presenting a difficult choice when selecting appropriate
calibrations. Here, we test the impact of eight plausible calibration scenarios
for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich
and well-studied fossil record. To do so, we reviewed the phylogenetic placement
and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we
identified minimum age constraints for up to 18 nodes of the phylogeny of
Fagales. Molecular dating analyses were conducted for each scenario using maximum
likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from
six regions of the chloroplast and nuclear genomes. Using either ingroup or
outgroup constraints, or both, led to similar age estimates, except near strongly
influential calibration nodes. Using "early but risky" fossil constraints in
addition to "safe but late" constraints, or using assumptions of vicariance
instead of fossil constraints, led to older age estimates. In contrast, using
secondary calibration points yielded drastically younger age estimates. This
empirical study highlights the critical influence of calibration on molecular
dating analyses. Even in a best-case situation, with many thoroughly vetted
fossils available, substantial uncertainties can remain in the estimates of
divergence times. For example, our estimates for the crown group age of
Nothofagus varied from 13 to 113 Ma across our full range of calibration
scenarios. We suggest that increased background research should be made at all
stages of the calibration process to reduce errors wherever possible, from
verifying the geochronological data on the fossils to critical reassessment of
their phylogenetic position.
FAU - Sauquet, Herve
AU - Sauquet H
AD - Laboratoire Ecologie, Systematique, Evolution, Universite Paris-Sud, CNRS UMR
8079, 91405 Orsay, France. herve.sauquet@u-psud.fr
FAU - Ho, Simon Y W
AU - Ho SY
FAU - Gandolfo, Maria A
AU - Gandolfo MA
FAU - Jordan, Gregory J
AU - Jordan GJ
FAU - Wilf, Peter
AU - Wilf P
FAU - Cantrill, David J
AU - Cantrill DJ
FAU - Bayly, Michael J
AU - Bayly MJ
FAU - Bromham, Lindell
AU - Bromham L
FAU - Brown, Gillian K
AU - Brown GK
FAU - Carpenter, Raymond J
AU - Carpenter RJ
FAU - Lee, Daphne M
AU - Lee DM
FAU - Murphy, Daniel J
AU - Murphy DJ
FAU - Sniderman, J M Kale
AU - Sniderman JM
FAU - Udovicic, Frank
AU - Udovicic F
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 - 20111226
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 0 (DNA, Plant)
SB - IM
MH - Biodiversity
MH - Calibration
MH - Classification/methods
MH - DNA, Plant/chemistry
MH - Fagus/classification/*genetics
MH - *Fossils
MH - Genetic Variation
MH - Phylogeny
MH - Sequence Alignment
MH - Time Factors
EDAT- 2011/12/28 06:00
MHDA- 2012/06/26 06:00
CRDT- 2011/12/28 06:00
PHST- 2011/12/28 06:00 [entrez]
PHST- 2011/12/28 06:00 [pubmed]
PHST- 2012/06/26 06:00 [medline]
AID - syr116 [pii]
AID - 10.1093/sysbio/syr116 [doi]
PST - ppublish
SO - Syst Biol. 2012 Mar;61(2):289-313. doi: 10.1093/sysbio/syr116. Epub 2011 Dec 26.
PMID- 22199008
OWN - NLM
STAT- MEDLINE
DCOM- 20121018
LR - 20120618
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 61
IP - 4
DP - 2012 Jul
TI - A new global palaeobiogeographical model for the late Mesozoic and early
Tertiary.
PG - 553-66
LID - 10.1093/sysbio/syr115 [doi]
AB - Late Mesozoic palaeobiogeography has been characterized by a distinction between
the northern territories of Laurasia and the southern landmasses of Gondwana. The
repeated discovery of Gondwanan lineages in Laurasia has led to the proposal of
alternative scenarios to explain these anomalous occurrences. A new
biogeographical model for late Mesozoic terrestrial ecosystems is here proposed
in which Europe and "Gondwanan" territories possessed a common Eurogondwanan
fauna during the earliest Cretaceous. Subsequently, following the Hauterivian,
the European territories severed from Africa and then connected to Asiamerica
resulting in a faunal interchange. This model explains the presence of Gondwanan
taxa in Laurasia and the absence of Laurasian forms in the southern territories
during the Cretaceous. In order to test this new palaeobiogeographical model,
tree reconciliation analyses (TRAs) were performed based on biogeographical
signals provided by a supertree of late Mesozoic archosaurs. The TRAs found
significant evidence for the presence of an earliest Cretaceous Eurogondwanan
fauna followed by a relatively short-term Gondwana-Laurasia dichotomy. The
analysis recovered evidence for a biogeographical reconnection of the European
territories with Africa and South America-Antarctica during the Campanian to
Maastrichtian time-slice. This biogeographical scenario appears to continue
through the early Tertiary and sheds light on the trans-Atlantic disjunct
distributions of several extant plant and animal groups.
FAU - Ezcurra, Martin D
AU - Ezcurra MD
AD - Laboratorio de Anatomia Comparada y Evolucion de los Vertebrados, Museo Argentino
de Ciencias Naturales B. Rivadavia, Angel Gallardo 470 C1405DJR, Buenos Aires,
Argentina. martindezcurra@yahoo.com.ar
FAU - Agnolin, Federico L
AU - Agnolin FL
LA - eng
PT - Journal Article
DEP - 20111223
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
SB - IM
MH - Animals
MH - Biological Evolution
MH - Dinosaurs/*classification/genetics
MH - *Fossils
MH - Geography
MH - Models, Biological
MH - Paleontology
MH - Reptiles/*classification/genetics
EDAT- 2011/12/27 06:00
MHDA- 2012/10/19 06:00
CRDT- 2011/12/27 06:00
PHST- 2011/12/27 06:00 [entrez]
PHST- 2011/12/27 06:00 [pubmed]
PHST- 2012/10/19 06:00 [medline]
AID - syr115 [pii]
AID - 10.1093/sysbio/syr115 [doi]
PST - ppublish
SO - Syst Biol. 2012 Jul;61(4):553-66. doi: 10.1093/sysbio/syr115. Epub 2011 Dec 23.
PMID- 22139466
OWN - NLM
STAT- MEDLINE
DCOM- 20120406
LR - 20111222
IS - 1076-836X (Electronic)
IS - 1063-5157 (Linking)
VI - 61
IP - 1
DP - 2012 Jan
TI - SATe-II: very fast and accurate simultaneous estimation of multiple sequence
alignments and phylogenetic trees.
PG - 90-106
LID - 10.1093/sysbio/syr095 [doi]
AB - Highly accurate estimation of phylogenetic trees for large data sets is
difficult, in part because multiple sequence alignments must be accurate for
phylogeny estimation methods to be accurate. Coestimation of alignments and trees
has been attempted but currently only SATe estimates reasonably accurate trees
and alignments for large data sets in practical time frames (Liu K., Raghavan S.,
Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale
coestimation of sequence alignments and phylogenetic trees. Science.
324:1561-1564). Here, we present a modification to the original SATe algorithm
that improves upon SATe (which we now call SATe-I) in terms of speed and of
phylogenetic and alignment accuracy. SATe-II uses a different divide-and-conquer
strategy than SATe-I and so produces smaller more closely related subsets than
SATe-I; as a result, SATe-II produces more accurate alignments and trees, can
analyze larger data sets, and runs more efficiently than SATe-I. Generally, SATe
is a metamethod that takes an existing multiple sequence alignment method as an
input parameter and boosts the quality of that alignment method. SATe-II-boosted
alignment methods are significantly more accurate than their unboosted versions,
and trees based upon these improved alignments are more accurate than trees based
upon the original alignments. Because SATe-I used maximum likelihood (ML) methods
that treat gaps as missing data to estimate trees and because we found a
correlation between the quality of tree/alignment pairs and ML scores, we
explored the degree to which SATe's performance depends on using ML with gaps
treated as missing data to determine the best tree/alignment pair. We present two
lines of evidence that using ML with gaps treated as missing data to optimize the
alignment and tree produces very poor results. First, we show that the
optimization problem where a set of unaligned DNA sequences is given and the
output is the tree and alignment of those sequences that maximize likelihood
under the Jukes-Cantor model is uninformative in the worst possible sense. For
all inputs, all trees optimize the likelihood score. Second, we show that a
greedy heuristic that uses GTR+Gamma ML to optimize the alignment and the tree
can produce very poor alignments and trees. Therefore, the excellent performance
of SATe-II and SATe-I is not because ML is used as an optimization criterion for
choosing the best tree/alignment pair but rather due to the particular
divide-and-conquer realignment techniques employed.
FAU - Liu, Kevin
AU - Liu K
AD - Department of Computer Science, University of Texas at Austin, Austin, TX 78712,
USA.
FAU - Warnow, Tandy J
AU - Warnow TJ
FAU - Holder, Mark T
AU - Holder MT
FAU - Nelesen, Serita M
AU - Nelesen SM
FAU - Yu, Jiaye
AU - Yu J
FAU - Stamatakis, Alexandros P
AU - Stamatakis AP
FAU - Linder, C Randal
AU - Linder CR
LA - eng
PT - Evaluation Studies
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PT - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20111201
PL - England
TA - Syst Biol
JT - Systematic biology
JID - 9302532
RN - 9007-49-2 (DNA)
SB - IM
MH - Algorithms
MH - Automation
MH - Computer Simulation
MH - DNA
MH - Evolution, Molecular
MH - Likelihood Functions
MH - *Phylogeny
MH - Sequence Alignment/*methods
MH - *Software