Knowles, L.L. and B.C. Carstens. 2007. Delimiting species without monophyletic gene trees. Syst. Bio. 56(6): 887-895.
Most researchers who use phylogenetic analyses to delimit species would say that reciprocal monophyly is an important criterion in this endeavor. Not so! According to Knowles and Carsten, one can model the probability of the relationship between gene trees and species history and get a good answer as to what constitutes a species.
Their preliminary simulation study suggests that very recently derived species can be accurately identified long before the requisite time for reciprocal monophyly is achieved following speciation.
-species delimitation will be misled by discordance if gene lineages within a species coalesce below the species divergence (also known as the species-tree gene-tree discordance problem Maddison 1997).
*a gene tree should not be equated with a species tree*
However, gene treeS do provide information about the history of species splitting (the species tree) despite widespread incomplete lineage sorting.
Knowles and Carstens use a coalescent framework to estimate gene-tree probabilities under a particular history to evaluate the likelihood of lineage splitting (i.e. that speciation has occurred).
-focuses on the stochastic loss of gene lineages by genetic drift
Methods
-gene genealogies were simulated at different depths
-the species tree was simulated using a Yule model
-gene trees were simulated under a neutral-coalescent process without gene flow
-the product of the probabilities from the gene trees of each locus under a specific history was used to evaluate the likelihood of whether species A and B are separate species lineages
-for this the authors used the program COAL, calculated likelihoods, and likelihood-ratio tests
-used Mesquite to replicate 100 data sets
Results
-the A and B lineages were successfully delimited with the coalescent-based approach across all the different times of divergence that the authors looked at
-increased sampling of loci (genes) resulted in a decrease in false-negatives (failures to delimit the separate species)
-inferred species boundaries will only be reliable to the extent that the model used is an accurate account of the process of speciation
-the power of the test of species delimitation clearly depends on the number of sampled loci.
-the info contained in independent loci provide valuable info for delimiting species, even though the gene trees are not completely concordant -the take home message is always use more than one gene
Conclusions
-what is recognized as a species boundary is very much influenced by the method used to delimit species (Sites and Marshall 2004)
-Knowles and Carstens show that it is possible to accurately delimit species despite widespread incomplete lineage sorting and discordance among loci if one uses a probablilistic modeling approach.
Tuesday, April 29, 2008
Monday, April 21, 2008
de Queiroz 2007
de Queiroz, K. 2007. Species concepts and species delimitation. Syst. Biol. 56(6): 879-886
I've always felt that the competing species concepts had an underlying commonality to them. In this paper de Queiroz has clearly confirmed this for me - there IS a unifying species concept.
The unifying species concept is:
Species are separately evolving metapopulation lineages.
I love it! So clear, so easy. Undergrads can understand it. And it is a clearly separate issue from species delineation, as de Queiroz points out.
Here are some more clarifying definitions that de Queiroz gives:
lineage = refers to an ancestor-descendant series (Simpson 1961; Hull 1980) [not to be confused with a clade or monophyletic group which is sometimes also called a lineage!]
metapopulation = an inclusive population made up of connected subpopulations (Levins 1970, Hanski and Gaggiotti 2004)
-most of the old alternative species concepts adopt different properties of lineages as secondary defining properties
-these secondary properties (secondary species criteria) arise at different times during the process of speciation, ergo their incompatibility
-one of the great things about a unified concept is that it "clarifies the issue of species delimitation by clearly separating the conceptual problem of defining the species catagory (species conceptualization) from the methodological problem of inferring the boundaries and numbers of species (species delimitation)
-under a unified species concept, the 'old species concepts' (now appropriately called species properties), are now more appropriately viewed as lines of evidence relevant to the fundamentally different methodologies. This seems to be the trend with new systematics papers, where authors go through the old concepts and see if their species holds up to them. I like it because, as de Queiroz states:
"disagreements about species delimitation should result from disagreements or differences concerning one or more of the following issues:
1) the reliability of particular methods (i.e., for inferring lineage separation)
2) the relevance of particular data
3) temporal scale (years versus decades versus centuries, etc.)
4) prospective versus retrospective perspectives [huh?]
5) cases of incomplete lineage separation"
*the main point being that a highly corroborated hypothesis of lineage separation (separate species) requires multiple lines of evidence.
Good paper!
I've always felt that the competing species concepts had an underlying commonality to them. In this paper de Queiroz has clearly confirmed this for me - there IS a unifying species concept.
The unifying species concept is:
Species are separately evolving metapopulation lineages.
I love it! So clear, so easy. Undergrads can understand it. And it is a clearly separate issue from species delineation, as de Queiroz points out.
Here are some more clarifying definitions that de Queiroz gives:
lineage = refers to an ancestor-descendant series (Simpson 1961; Hull 1980) [not to be confused with a clade or monophyletic group which is sometimes also called a lineage!]
metapopulation = an inclusive population made up of connected subpopulations (Levins 1970, Hanski and Gaggiotti 2004)
-most of the old alternative species concepts adopt different properties of lineages as secondary defining properties
-these secondary properties (secondary species criteria) arise at different times during the process of speciation, ergo their incompatibility
-one of the great things about a unified concept is that it "clarifies the issue of species delimitation by clearly separating the conceptual problem of defining the species catagory (species conceptualization) from the methodological problem of inferring the boundaries and numbers of species (species delimitation)
-under a unified species concept, the 'old species concepts' (now appropriately called species properties), are now more appropriately viewed as lines of evidence relevant to the fundamentally different methodologies. This seems to be the trend with new systematics papers, where authors go through the old concepts and see if their species holds up to them. I like it because, as de Queiroz states:
"disagreements about species delimitation should result from disagreements or differences concerning one or more of the following issues:
1) the reliability of particular methods (i.e., for inferring lineage separation)
2) the relevance of particular data
3) temporal scale (years versus decades versus centuries, etc.)
4) prospective versus retrospective perspectives [huh?]
5) cases of incomplete lineage separation"
*the main point being that a highly corroborated hypothesis of lineage separation (separate species) requires multiple lines of evidence.
Good paper!
Wednesday, March 5, 2008
Rissler and Apodaca 2007
Rissler, L.J. and J.J. Apodaca. 2007. Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus). Syst. Biol. 56(6): 924-942.
In this paper, the authors combine ecological niche modeling, spatially explicit analyses of environmental data, and phylogenetics in species delimitation. They assess the relationships between genetic, environmental and geographic distance among populations. They use ecological niche models which take into account 11 climatic variables and point locality data. They found that patterns of genetic divergence are strongly associated with patterns of ecological niche divergence.
I think that it is great that they found a correlation but it makes me wonder if many animal species will show this. It would be interesting to find out how well this works for other animals because I have a feeling it is not so clear cut as this, but who knows.
"-environmental niche modelling = understanding how abiotic factors (e.g. temp., precip., seasonality) impact the geographic limits of lineages and species"
"-georeferenced data from specimens + environmental data + GIS = predicted presence on a map (i.e. identifies areas that are ecologically similar to regions where the point locality information was used to build the models)"
"-is the predicted region the actual or "fundamental" niche? The define fundamental niche as: the environmental space where fitness is greater than or equal to 1 in the absence of range-limiting biotic interactions and dispersal barriers. However, the ecological niche modeling is probably more equal to the "realized" niche."
"-historical biogeography and comparative phylogeography seek to explain patterns of geographic congruence in phylogenetic breaks across multiple taxa"
"-the process driving lineage divergence, speciation, and the buildup of biodiversity are many and include: 1) geographic factors
2) historical factors
3) environmental factors"
I understand factors 1 and 3, but what are some examples of 2?
"-understanding the mechanisms driving divergence can help in species delimitation"
"geographic distribution + ecological niche models + genetic information = species diagnosis"
I would be worried about environments that are known to rapidly change through time. How does this affect the ecological niche model?
The authors used the evolutionary species concept (ESC) and the general lineage species concept (GLC). I've heard of the ESC but I'm not sure I know what the GLC is. Their goal was to recognize historically distinct evolutionary lineages that are likely to remain distinct.
How can you really know if distinct lineages are "likely" to remain distinct. I'm going to create a mini theory on lineages that are kind-of distinct. I'm going to call it The Oscillating Non-Species Concept. This is based on my idea that one year a lineage may seem somewhat distinct, then the next year it is not, then the next year it is really distinct, but not distinct enough to be a species, then the next year it is somewhat distinct.....
"combining independent sets of data (ecological and genetic) = robust view of independent evolutionary lineages"
"ecological divergence is an important step in the process of speciation"
"info on ecological niche can be really important when genetic data are insufficient to determine whether the lineage in question is truly distinct". This is my problem exactly. If they are not truly genetically or morphologically distinct, only borderline, then is ecological data really going to help? It could just force the entire issue so you pick one or the other (species or not a species).
For bioclimatic modeling the authors used Maxent v. 2 to create ecological niche models.
"the extent of divergence across lineages is a result of either geographic or environmental isolation". One has to make sure that the difference in lineages is not due to clinal or ontogenetic factors.
"abiotic pressures -> natural selection -> divergence -> speciation"
"analysis of ecological divergence + phylogenetic diversity = insight into biodiversity patterns and processes"
"quantifying divergence in ecological niche should be an important part of current phylogeographic studies and useful for species delimitation"
"primary species concept = entities believed to be species,
secondary species concept = operational methods for the discovery of those entities"
All in all, I enjoyed reading this paper.
In this paper, the authors combine ecological niche modeling, spatially explicit analyses of environmental data, and phylogenetics in species delimitation. They assess the relationships between genetic, environmental and geographic distance among populations. They use ecological niche models which take into account 11 climatic variables and point locality data. They found that patterns of genetic divergence are strongly associated with patterns of ecological niche divergence.
I think that it is great that they found a correlation but it makes me wonder if many animal species will show this. It would be interesting to find out how well this works for other animals because I have a feeling it is not so clear cut as this, but who knows.
"-environmental niche modelling = understanding how abiotic factors (e.g. temp., precip., seasonality) impact the geographic limits of lineages and species"
"-georeferenced data from specimens + environmental data + GIS = predicted presence on a map (i.e. identifies areas that are ecologically similar to regions where the point locality information was used to build the models)"
"-is the predicted region the actual or "fundamental" niche? The define fundamental niche as: the environmental space where fitness is greater than or equal to 1 in the absence of range-limiting biotic interactions and dispersal barriers. However, the ecological niche modeling is probably more equal to the "realized" niche."
"-historical biogeography and comparative phylogeography seek to explain patterns of geographic congruence in phylogenetic breaks across multiple taxa"
"-the process driving lineage divergence, speciation, and the buildup of biodiversity are many and include: 1) geographic factors
2) historical factors
3) environmental factors"
I understand factors 1 and 3, but what are some examples of 2?
"-understanding the mechanisms driving divergence can help in species delimitation"
"geographic distribution + ecological niche models + genetic information = species diagnosis"
I would be worried about environments that are known to rapidly change through time. How does this affect the ecological niche model?
The authors used the evolutionary species concept (ESC) and the general lineage species concept (GLC). I've heard of the ESC but I'm not sure I know what the GLC is. Their goal was to recognize historically distinct evolutionary lineages that are likely to remain distinct.
How can you really know if distinct lineages are "likely" to remain distinct. I'm going to create a mini theory on lineages that are kind-of distinct. I'm going to call it The Oscillating Non-Species Concept. This is based on my idea that one year a lineage may seem somewhat distinct, then the next year it is not, then the next year it is really distinct, but not distinct enough to be a species, then the next year it is somewhat distinct.....
"combining independent sets of data (ecological and genetic) = robust view of independent evolutionary lineages"
"ecological divergence is an important step in the process of speciation"
"info on ecological niche can be really important when genetic data are insufficient to determine whether the lineage in question is truly distinct". This is my problem exactly. If they are not truly genetically or morphologically distinct, only borderline, then is ecological data really going to help? It could just force the entire issue so you pick one or the other (species or not a species).
For bioclimatic modeling the authors used Maxent v. 2 to create ecological niche models.
"the extent of divergence across lineages is a result of either geographic or environmental isolation". One has to make sure that the difference in lineages is not due to clinal or ontogenetic factors.
"abiotic pressures -> natural selection -> divergence -> speciation"
"analysis of ecological divergence + phylogenetic diversity = insight into biodiversity patterns and processes"
"quantifying divergence in ecological niche should be an important part of current phylogeographic studies and useful for species delimitation"
"primary species concept = entities believed to be species,
secondary species concept = operational methods for the discovery of those entities"
All in all, I enjoyed reading this paper.
Wednesday, September 12, 2007
Rodriguez-Ezpeleta et al. 2007
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?
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?
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.
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