Rodriguez-Ezpeleta, N., H. Brinkmann, B. Roure, N. Lartillot, B.F. Lang, and H. Philippe. 2007. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst. Biol. 56(3): 389-399.
They confirmed that higher statistical support does not necessarily lead to more accurate results because: increase in data sets = increase in systematic errors = potential for strongly supported BUT incorrect phylogeny. Hedtke et al. showed this as well but they don't reference this paper.
They list known causes of model violation:
1) across-site rate variation (I'm guessing this is the same as among-site rate variation?)
2) heterotachy (they define as the across-site rate variation through time)
-I haven't really read about this. I guess at any given time throughout history, there could be a different asrv.
3) site-interdependent evolution
-I need to read the references on this
4) compositional heterogeneity
-I think this means the proportion of A's, G's, C's and T's?
5) site-heterogeneous nucleotide/amino acid replacement
-not sure what this means, have to read the references as well.
nonphylogenetic signal = the 'apparent' signal arising from model violations
The impact of model violations on phylogenetic accuracy is greatly exaggerated when multiple substitutions occur at given sites (mutational saturation).
"Long branch attraction is a well-known case of systematic error that causes the clustering of fast-evolving species regardless of their true phylogenetic relationships." Fast-evolving can either mean the time it took to evolve or the amount of evolutionary change.
They list five ways to overcome LBA:
1) increase taxon sampling
2) improve models of sequence evolution, allowing a more efficient detection of multiple substitutions
3) remove fast-evolving species from the analyses
4) remove fast-evolving genes
5) remove fast-evolving sequence positions
I should check out the programs PhyloBayes and the MUST package.
(the must package calculates the slope of saturation curves! neat)
What are RELL bootstraps?
Wednesday, September 12, 2007
Monday, September 10, 2007
Marjanovic & Laurin 2007
Marjanovic, D. and M. Laurin. 2007. Fossils, molecules, divergence times, and the origin of Lissamphibians. Syst. Biol. 56(3): 369-388.
"..a literal interpretation of the fossil record always underestimates the date of appearance of taxa because it can only give a latest possible date of appearance, not an earliest possible date of appearance..."
At first this quote didn't make sense to me, but now I think it means that when you find a fossil and put a date on the fossil, this means that the species had to have existed during this time. Therefore the speciation event could not have happened after this date, but it could have happened before this date. Fossil records cannot give an earliest possible date of appearance of a species because new fossils can always be found that can contradict the earliest possible date.
Some divergence dating methods that the authors used:
1) Multidivtime (Thorne and Kishino 2002)
2) QDate 1.11 (Rambaut and Bromham 1998)
3) r8s 1.71 (Sanderson 2003, 2006) using the penalized likelihood method
4) PATHd8 (Anderson 2006)
They couldn't get Mdt to work, I heard QDate is a bad method, r8s is okay, and I've never heard of Pathd8 and they also said the results didn't make sense.
-neighbour-joining trees are phenograms, not cladograms
On page 383, they discuss something odd. They say that according to Kolaczkowski and Thornton 2004, parsimony does better than ML and bayesian methods because parsimony does not need an assumption on how many rate categories there are. For instance, in many real cases each nucleotide position evolves at its own speed, causing potential problems for approaches that include evoltuion models. I don't think I've heard of this argument before for parsimony and I will have to read the Kolaczkowski paper to get a better handle on this. They also state that the branch lengths of the parsimony tree fit the morphological data better than the likelihood tree. These seem like odd statements to justify using parsimony instead of ML or bayesian for molecular data. I'm surprised that the reviewers didn't catch this.
"..a literal interpretation of the fossil record always underestimates the date of appearance of taxa because it can only give a latest possible date of appearance, not an earliest possible date of appearance..."
At first this quote didn't make sense to me, but now I think it means that when you find a fossil and put a date on the fossil, this means that the species had to have existed during this time. Therefore the speciation event could not have happened after this date, but it could have happened before this date. Fossil records cannot give an earliest possible date of appearance of a species because new fossils can always be found that can contradict the earliest possible date.
Some divergence dating methods that the authors used:
1) Multidivtime (Thorne and Kishino 2002)
2) QDate 1.11 (Rambaut and Bromham 1998)
3) r8s 1.71 (Sanderson 2003, 2006) using the penalized likelihood method
4) PATHd8 (Anderson 2006)
They couldn't get Mdt to work, I heard QDate is a bad method, r8s is okay, and I've never heard of Pathd8 and they also said the results didn't make sense.
-neighbour-joining trees are phenograms, not cladograms
On page 383, they discuss something odd. They say that according to Kolaczkowski and Thornton 2004, parsimony does better than ML and bayesian methods because parsimony does not need an assumption on how many rate categories there are. For instance, in many real cases each nucleotide position evolves at its own speed, causing potential problems for approaches that include evoltuion models. I don't think I've heard of this argument before for parsimony and I will have to read the Kolaczkowski paper to get a better handle on this. They also state that the branch lengths of the parsimony tree fit the morphological data better than the likelihood tree. These seem like odd statements to justify using parsimony instead of ML or bayesian for molecular data. I'm surprised that the reviewers didn't catch this.
Thursday, May 3, 2007
Bininda-Emonds et al. 2007
Bininda-Emonds, O.R.P., M. Cardillo, K.E. Jones, R.D.E. MacPhee, R.M.D. Beck, R. Grenyer, S.A. Price, R.A. Vos, J.L. Gittleman and A. Purvis. 2007. The delayed rise of present-day mammals. Nature. 446:; 507-512.
This paper uses a species-level phylogeny of extant Mammalia to answer the question of did the end-Cretaceous mass extinction event trigger the evolutionary radiation of present day mammals. They conclude that no, it did not.
The phrase that caught my eye while reading this paper was "phylogenetic fuses". The authors define phylogenetic fuses as: where lineages persist at low diversity for some time after their initial origins before undergoing evolutionary radiations (explosions).
Long fuse model= a long time period between the Cretaceous origins of the orders and the first split among their living representatives (crown groups) immediately after the KT boundary.
vs
Short fuse model= diversity occured before the KT boundary
The long- and short fuse models are two competing hypotheses for when mammalian crown groups evolved.
Their hypothesis: there was a significant increase in the net per-lineage rate of extant mammalian diversification, r (the difference between the per-lineage speciation and extinction rates), immediately after the K/T mass extinction.
Methods: -only used extant mammals (this is probably a big problem in their study)
-2, 500 partial estimates (whatever that means)
-66 gene alignment w/ 30 calibration points
Results: They found low rates of extant mammalian diversification during the Cenozoic and little evidence for the long fuse model, indicating that the extinction of dinosaurs and other taxa had a major effect on mammalian diversification. However I noticed that their supertree is only 46.7% resolved. I wouldn't trust that tree.
This paper uses a species-level phylogeny of extant Mammalia to answer the question of did the end-Cretaceous mass extinction event trigger the evolutionary radiation of present day mammals. They conclude that no, it did not.
The phrase that caught my eye while reading this paper was "phylogenetic fuses". The authors define phylogenetic fuses as: where lineages persist at low diversity for some time after their initial origins before undergoing evolutionary radiations (explosions).
Long fuse model= a long time period between the Cretaceous origins of the orders and the first split among their living representatives (crown groups) immediately after the KT boundary.
vs
Short fuse model= diversity occured before the KT boundary
The long- and short fuse models are two competing hypotheses for when mammalian crown groups evolved.
Their hypothesis: there was a significant increase in the net per-lineage rate of extant mammalian diversification, r (the difference between the per-lineage speciation and extinction rates), immediately after the K/T mass extinction.
Methods: -only used extant mammals (this is probably a big problem in their study)
-2, 500 partial estimates (whatever that means)
-66 gene alignment w/ 30 calibration points
Results: They found low rates of extant mammalian diversification during the Cenozoic and little evidence for the long fuse model, indicating that the extinction of dinosaurs and other taxa had a major effect on mammalian diversification. However I noticed that their supertree is only 46.7% resolved. I wouldn't trust that tree.
Tuesday, May 1, 2007
Dobler & Muller 2000
Dobler, S. and J.K. Muller. 2000. Resolving phylogeny at the family level by mitochondrial Cytochrome Oxidase sequences: phylogeny of carrion beetles (Coleoptera: Silphidae).
In this paper the authors use COI, COII, and tRNA-leu to reconstruct the phylogeny of the Silphidae. Important points:
1) used 23 species from 13 genera
2) the Agyrtidae is justified as a separate family based on the phylogeny
3) the genus Silpha was not monophyletic
4) Pseudosilphites triassicus, a coleopteran fossil from the Triassic, is morphologically similar to silphids and possibly an ancestor of the Staphylinoidea (Zeuner, 1930)
5) compared parsimony and likelihood trees
This paper also briefly discusses the biogeography of the family:
-Silphidae 'apparently' originated in Palearctic because it has the most genera and highest # of species (Peck and Anderson 1985). [center of origin criteria #'s 1 and 2].
The phylogeny in this paper also agrees with a Palearctic origin.
*This is the first published phylogeny of the Silphidae.
In this paper the authors use COI, COII, and tRNA-leu to reconstruct the phylogeny of the Silphidae. Important points:
1) used 23 species from 13 genera
2) the Agyrtidae is justified as a separate family based on the phylogeny
3) the genus Silpha was not monophyletic
4) Pseudosilphites triassicus, a coleopteran fossil from the Triassic, is morphologically similar to silphids and possibly an ancestor of the Staphylinoidea (Zeuner, 1930)
5) compared parsimony and likelihood trees
This paper also briefly discusses the biogeography of the family:
-Silphidae 'apparently' originated in Palearctic because it has the most genera and highest # of species (Peck and Anderson 1985). [center of origin criteria #'s 1 and 2].
The phylogeny in this paper also agrees with a Palearctic origin.
*This is the first published phylogeny of the Silphidae.
Wednesday, April 25, 2007
Whiting et al. 2004 / Trueman et al. 2004
Whiting, M.F., S. Bradler and T. Maxwell. 2004. Loss and recovery of wings in stick insects. Nature. 421: 264-267.
This paper has been commented upon in three different reading/discussion groups that I have attended so I thought I should post some of my comments of the paper here. I will also add notes on some of the rebuttals that have been published.
Whiting et al. used phylogeny to demonstrate that the first Phasmatodea was wingless and that wings evolved secondarily and on numerous occasions in this group. They suggest that wing developmental pathways are conserved in wingless stick bugs.
Data used: 1) 18S rDNA; 2) 28S rDNA; 3) portion of Histone 3.
-sequenced 22 outgroup specimens (representing all Polyneoptera)
-sequenced 37 ingroup taxa (representing 14 out of 19 subfamily groups)
Analyses: -used bootstrap and bremer support
-used POY for optimization alignment analysis and compared this to MP, ML and bayesian methods
[Notes: Acctran = Accelerated transformation -changes are assigned as close to the root of the cladogram (where the outgroups and ingroups diverge) as possible. Favours reversals.
Deltran = Delayed transformation -puts the character change as far from the root as possible. Favours parallelisms.]
Some of the problems that I had with this paper are:
1) what about fossil phasmids that have wings?
2) why did they use POY? This seems to be very rarely used and unfortunately I have never used it so I can't really comment on this program. Why didn't they publish their ML or Bayesian trees?
Another point that seems to be important and that is a direct quote from this paper is: "re-evolution of wings in insects is thought to be impossible because functional wings require complex interactions among multiple structures, and the associated genes would be free to accumulate mutations in wingless lineages, effectively blocking the path for any future wing reacquisition."
Trueman, J.W.H., B.E. Pfeil, S.A. Kelchener and D.K. Yeates. 2004. Did stick insects really regain their wings? Systematic Entomology. 29: 138-139.
Points that the authors make in this paper are:
1) two lines of evidence are necessary for the Whiting et al. hypothesis to hold true:
1) topology of phylogenetic tree
2) distribution of wing/wingless transformations on tree
2) Whiting et al. have overstated significantly the probability of wing re-evolution in stick
insects
3) reconstruction of the phasmid ancestor is not the relevant issue
4) support for each hypothesis needs to be compared when alternative ancestral states are
assumed to be true
The authors then do some easy math to show how the ratio of lost wings to gained wings is a mere 2.5:1.
Whiting, M.F. and A.S. Whiting. 2004. Systematic Entomology. 29: 140-141.
Whiting and Whiting then published a reply to Trueman et al. I found the tone very whiny. We did this and you didn't. We had super computers and you didn't, so there. It's really not even worth commenting on.
This paper has been commented upon in three different reading/discussion groups that I have attended so I thought I should post some of my comments of the paper here. I will also add notes on some of the rebuttals that have been published.
Whiting et al. used phylogeny to demonstrate that the first Phasmatodea was wingless and that wings evolved secondarily and on numerous occasions in this group. They suggest that wing developmental pathways are conserved in wingless stick bugs.
Data used: 1) 18S rDNA; 2) 28S rDNA; 3) portion of Histone 3.
-sequenced 22 outgroup specimens (representing all Polyneoptera)
-sequenced 37 ingroup taxa (representing 14 out of 19 subfamily groups)
Analyses: -used bootstrap and bremer support
-used POY for optimization alignment analysis and compared this to MP, ML and bayesian methods
[Notes: Acctran = Accelerated transformation -changes are assigned as close to the root of the cladogram (where the outgroups and ingroups diverge) as possible. Favours reversals.
Deltran = Delayed transformation -puts the character change as far from the root as possible. Favours parallelisms.]
Some of the problems that I had with this paper are:
1) what about fossil phasmids that have wings?
2) why did they use POY? This seems to be very rarely used and unfortunately I have never used it so I can't really comment on this program. Why didn't they publish their ML or Bayesian trees?
Another point that seems to be important and that is a direct quote from this paper is: "re-evolution of wings in insects is thought to be impossible because functional wings require complex interactions among multiple structures, and the associated genes would be free to accumulate mutations in wingless lineages, effectively blocking the path for any future wing reacquisition."
Trueman, J.W.H., B.E. Pfeil, S.A. Kelchener and D.K. Yeates. 2004. Did stick insects really regain their wings? Systematic Entomology. 29: 138-139.
Points that the authors make in this paper are:
1) two lines of evidence are necessary for the Whiting et al. hypothesis to hold true:
1) topology of phylogenetic tree
2) distribution of wing/wingless transformations on tree
2) Whiting et al. have overstated significantly the probability of wing re-evolution in stick
insects
3) reconstruction of the phasmid ancestor is not the relevant issue
4) support for each hypothesis needs to be compared when alternative ancestral states are
assumed to be true
The authors then do some easy math to show how the ratio of lost wings to gained wings is a mere 2.5:1.
Whiting, M.F. and A.S. Whiting. 2004. Systematic Entomology. 29: 140-141.
Whiting and Whiting then published a reply to Trueman et al. I found the tone very whiny. We did this and you didn't. We had super computers and you didn't, so there. It's really not even worth commenting on.
Wednesday, April 18, 2007
Hanski and Niemela 1990
Hanski I, Niemelä J. 1990. Elevational distributions of dung and carrion beetles in northern Sulawesi. In: Knight WJ, Holloway JD, editors. Insects and the Rain Forests of South East Asia (Wallacea). p 145-152.
This paper is really interesting to me because I work on carrion beetles in Asia and this paper is specific to my work. In this paper, the authors attempt to document the elevational distributions for all dung and carrion beetles in northern Sulawesi (Indonesia). It was hoped that this would give insight into the processes which are important in structuring dung and carrion beetle communities in tropical forests. They state that carrion beetles are a good animal to use for transect studies because their numbers can be accurately estimated in a short period of time. They compared their transect study in Sulawesi to one previously conducted in Borneo.
Hankski and Niemila found:
1) beetle diversity was higher in Sulawesi than Borneo (apparently because of higher availability of resources-I would have to question this).
2) species richness (# of species) was the same in the two localities -but more montane species were found in Sulawesi (they state that this is probably because Sulawesi has more montane forests than Borneo).
3) no distinct elevational species assemblages were found in Sulawesi
Interestingly, they state, "detailed observations however indicated mutually exclusive ranges in Nicrophorus (two species)...". However, they then contradict themselves by stating further in the paper that, "two species [N. charon and N. distinctus] were found together at one site at 1450 m on Gn. Muajat and therefore their distributions are touching or slightly overlapping". I have also found this evidence where N. distinctus and N. charon occured at the same place at one of my sites. Unfortunately, I was not able to study the elevational ranges of these two species due to the 'problems' I encountered in Dongi Dongi and Rano Rano. In Dongi Dongi, the problem was local people conducting illegal logging and making sure no one (especially white foreigners who look like they could tell the government) was snooping around in the area. The problem in Rano Rano was that it was a 6 hour hike to get to the top and we didn't bring enough food to stay longer than 1 day.
Another interesting quip is "most dung and carrion beetles in SE Asia are attracted, to a varying degree, to both dung and carrion" (Hanski 1988). I wonder if the nepalensis group (Nicrophorus) is attracted to dung as well?
"In SE Asia, only one species occurs in one region: podagricus: Borneo; insularis: Java [also occurs on Sumatra and Bali]; nepalensis: northern Philippines [and mainland Asia], apo: Mindanao; heurni: New Guinea; insignis: Flores."
"As a rule Nicrophorus in SE Asia are restricted to montane forests, but in Solomon Islands and Sulawesi, one species occurs only in the lowlands while the other one is restricted to montane forests". I found that this is not entirely true for species on Sulawesi. Although N. charon is restricted to the highlands, N. distinctus is not restricted to the lowlands.
"Sumatra has two allopatric montane Nicrophorus species". This would be N. insularis and N. hersheli. Nicrophorus hersheli is one of the two species for which I desperately need fresh tissue sample from. It is interesting that the authors state that the two species are allopatric. What barriers on the large island of Sumatra could have caused this allopatry, if it is not one of elevational distribution (and looking at locality data I don't believe it is). I know Sumatra has had a history of partial and full submergence due to sea levels rising and falling in glacial periods, perhaps this had something to due with their ranges?
This paper is really interesting to me because I work on carrion beetles in Asia and this paper is specific to my work. In this paper, the authors attempt to document the elevational distributions for all dung and carrion beetles in northern Sulawesi (Indonesia). It was hoped that this would give insight into the processes which are important in structuring dung and carrion beetle communities in tropical forests. They state that carrion beetles are a good animal to use for transect studies because their numbers can be accurately estimated in a short period of time. They compared their transect study in Sulawesi to one previously conducted in Borneo.
Hankski and Niemila found:
1) beetle diversity was higher in Sulawesi than Borneo (apparently because of higher availability of resources-I would have to question this).
2) species richness (# of species) was the same in the two localities -but more montane species were found in Sulawesi (they state that this is probably because Sulawesi has more montane forests than Borneo).
3) no distinct elevational species assemblages were found in Sulawesi
Interestingly, they state, "detailed observations however indicated mutually exclusive ranges in Nicrophorus (two species)...". However, they then contradict themselves by stating further in the paper that, "two species [N. charon and N. distinctus] were found together at one site at 1450 m on Gn. Muajat and therefore their distributions are touching or slightly overlapping". I have also found this evidence where N. distinctus and N. charon occured at the same place at one of my sites. Unfortunately, I was not able to study the elevational ranges of these two species due to the 'problems' I encountered in Dongi Dongi and Rano Rano. In Dongi Dongi, the problem was local people conducting illegal logging and making sure no one (especially white foreigners who look like they could tell the government) was snooping around in the area. The problem in Rano Rano was that it was a 6 hour hike to get to the top and we didn't bring enough food to stay longer than 1 day.
Another interesting quip is "most dung and carrion beetles in SE Asia are attracted, to a varying degree, to both dung and carrion" (Hanski 1988). I wonder if the nepalensis group (Nicrophorus) is attracted to dung as well?
"In SE Asia, only one species occurs in one region: podagricus: Borneo; insularis: Java [also occurs on Sumatra and Bali]; nepalensis: northern Philippines [and mainland Asia], apo: Mindanao; heurni: New Guinea; insignis: Flores."
"As a rule Nicrophorus in SE Asia are restricted to montane forests, but in Solomon Islands and Sulawesi, one species occurs only in the lowlands while the other one is restricted to montane forests". I found that this is not entirely true for species on Sulawesi. Although N. charon is restricted to the highlands, N. distinctus is not restricted to the lowlands.
"Sumatra has two allopatric montane Nicrophorus species". This would be N. insularis and N. hersheli. Nicrophorus hersheli is one of the two species for which I desperately need fresh tissue sample from. It is interesting that the authors state that the two species are allopatric. What barriers on the large island of Sumatra could have caused this allopatry, if it is not one of elevational distribution (and looking at locality data I don't believe it is). I know Sumatra has had a history of partial and full submergence due to sea levels rising and falling in glacial periods, perhaps this had something to due with their ranges?
Thursday, April 5, 2007
Johnson and Black 2006.
Johnson, M.S. and R. Black. 2006. Islands increase genetic subdivision and disrupt patterns of connectivity of intertidal snails in a complex archipelago. Evolution. 60(12): 2498-2506.
Because my work involves the biogeography of the malay archipelago, my supervisor thought this paper may be important for me to read. Unfortunately it really does not relate to my work at all because Johnson and Black's research is based on marine patterns, whereas my work deals with terrestrial patterns. Nonetheless, I read the paper and these are the important bits:
1) the authors wanted to find out what local conditions might favour the isolation of populations of marine species with planktonic dispersal.
2) allozyme variation among 35 populations of the intertidal snail, Austrocochlea constricta indicated highly localized populations in the Houtman Abrolhos Islands, Australia.
3) islands are important for retention of locally produced larvae and disruption of patterns of connectivity.
4) models of gene flow in marine larval populations need to take islands into account.
This paper rated 8 out of 10 on the boring scale (but this may be because it does not relate to my work at all).
Because my work involves the biogeography of the malay archipelago, my supervisor thought this paper may be important for me to read. Unfortunately it really does not relate to my work at all because Johnson and Black's research is based on marine patterns, whereas my work deals with terrestrial patterns. Nonetheless, I read the paper and these are the important bits:
1) the authors wanted to find out what local conditions might favour the isolation of populations of marine species with planktonic dispersal.
2) allozyme variation among 35 populations of the intertidal snail, Austrocochlea constricta indicated highly localized populations in the Houtman Abrolhos Islands, Australia.
3) islands are important for retention of locally produced larvae and disruption of patterns of connectivity.
4) models of gene flow in marine larval populations need to take islands into account.
This paper rated 8 out of 10 on the boring scale (but this may be because it does not relate to my work at all).
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