Tuesday, April 29, 2008

Knowles & Carstens 2007

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


-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


-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


-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.

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!