Monday, March 8, 2010

Rabosky 2010

Rabosky, D.L. 2010.  Extinction rates should not be estimated from molecular phylogenies.  Evolution.  Early View Date: January 2010.

Hmm weird.  If a paper is accepted in the journal Evolution, it goes through an early viewing thing where you can download the pdf but it is not actually printed in the journal yet, so it doesn't get a volume/issue number yet.

First off, I should state that I enjoyed this paper, mainly because it confirms (using fancy-math) the obvious: that you can't infer extinction rates using phylogenies without fossils.

True, the shape of a tree can be influenced by both the net rate of lineage diversification through time as well as the ratio of the extinction rate to the speciation rate; however, this does not give us license to use living species to provide information on the historical extinction rates.  I mean, if an organism goes extinct without a trace, you really can't know for certain that it existed, right?

One thing that confused me was in the abstract when he states, "molecular phylogenies contain information about the tempo and mode of species diversification through time".  What does he mean by the 'mode'?

In the article, the author shows that when rates vary across the branches of a phylogenetic tree or among clades (as they usually do), estimators that assume rate-constancy among lineages perform poorly (as they should!).  To do this, he first took a number of diversification rates from a set of clades with known extinction rates (an avian families dataset).  He then simulated clade diversity under those rates, and finally estimated the extinction rate for each set of clades.

It is clear from the author's results that among-lineage variation in diversification rates results in messed-up or directionally biased estimates of extinction rate.  He strongly urges that fossils should be used in conjunction with molecular phylogenetic studies to generate a richer perspective on the dynamics of speciation and extinction.  Agreed.

Sunday, February 28, 2010

Graur & Martin 2004

Graur, D. and W. Martin.  2004.  Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision.  TRENDS in Genetics.  20(2): 80-86.

The purpose of this paper was to mostly make fun of some other papers (mainly by Hedges).  While I agree that the science was bad in those papers and Graur and Martin were kind of funny in their paper, I felt it was also kind of unprofessional and I think there may have been a more diplomatic way to make it clear that the science was bad.  I don't know, maybe that's just me.  Science is supposed to be objective after all, not emotional.

Here are the main points:

-the findings summarized in a Trends in Genetics review are all based on a single calibration point and tenous methodology

-the calibration point is a supposedly well-constrained fossil divergence time between the ancestor of birds (diapsid reptiles) and mammals (synapsid reptiles) at precisely 310 ma

-the first problem is that this calibration has no errors associated with it.  The second is Graur and Martin could not find the original reference to this calibration

-the authors suggest that a solution to the single-calibration conundrum would be to use multiple primary calibrations

-the use of standard errors as error bars in highly misleading, it is more appropriate to calculate the 95% or 99% confidence intervals

-the authors state that the appearance of these outlandish reviews have resulted in hundreds of citations in which such dates were accepted as factual, but they don't actually cite any.  Was it really in the hundreds? I have my doubts.

Although this paper is mostly bashing another paper(s), it does get the point across that you have to be really careful with this methodology and not base your calibrations on someone else's calibrations.  This paper is getting a bit old now and hopefully most researchers who work with divergence dating know this already and would never take calibrations from someone else's work.  I mean, seriously.  I do appreciate that the authors sate that molecular estimates of divergence times are useful when based on solid statistical methodology and multiple fossil calibrations.  See, it's not all bad! :)

Tuesday, January 6, 2009

Coleman 2009

Coleman, A.W. 2009. Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide. Molecular Phylogenetics and Evolution. 50(1): 197-203.

This paper focuses on the second Internal Transcribed Spacer of the nuclear ribosomal gene cistron (ITS2).


1) to explore information content of ITS2 region (concentration is on characteristics that accompany seperation of clades into two or more sexually isolated subclades)

2) to evaluate predictive powers of ITS2 for discriminating interbreeders

3) to derive a simplified sequence-based technique for its application to evaluate biological species

-where multiple taxonomic species/genera are capable of gamete interaction, their ITS2 sequences are extremely similar
-where one species encompasses more than one interbreeding group, their ITS2 sequences contain considerable variation
-as ITS2 differences between potential mates increase, sexual compatibility and zygote productivity decrease
-organisms that differ by even one compensatory base change in the ITS2 region are completely unable to cross. There has been no exception yet to this rule. However, this paper does not use a whole lot of animal examples in their table so there could be many exceptions. Who knows.

Wednesday, October 22, 2008

Sota and Hayashi 2007

Sota, T. and M. Hayashi. 2007. Comparative historical biogeography of Plateumaris leaf beetles (Coleoptera: Chrysomelidae) in Japan: interplay between fossil and molecular data. Journal of Biogeography. 34: 977-993.

I love this journal because they break the abstract into different subheadings such as methods, results, and main conclusions, which allows for a quicker skim to find what you are looking for.

This study uses molecular and fossil data to study the historical biogeography of five Plateumaris leaf beetles in Japan.

One word they used that I had not come across before was "conspecies". I've heard of conspecific but not conspecies. I'm assuming that it means species belonging to the same genus? I couldn't find a definition anywhere.

Another word I had to look up was haplotype. I usually read that word to mean an organism/cell with half the amount of chromosomes as a diploid one but that is not what they mean in this case. I think in this paper they are referring to haplotype as another word for an SNP (single nucleotide polymorphism). Weird.

The Mantel test is just a statistical test of the correlation between two matrices.

They state that although fossils play an essential role in the dating of molecular phylogenies, they are usually sparse for most organisms!!! So true.

An accretionary prism is a wedge-shaped mass of sediment and rock scraped off the top of a down-going plate and accreted onto the overriding plate at a convergent plate margin.

They state that the edge of the East Asian continent may have occurred in the mid-Miocene as many fragmented islands, and because of this, "most of the present terrestrial biota may have originated from colonization events from the East Asian continent, rather than vicariance". I'm not sure I am comfortable with this statement. Although it seems likely that dispersal plays a large role, how can you rule out vicariance for most of the terrestrial biota?

For their phylogeography methods they used:

1) maximum likelihood for COI data using PhyMl
2) analysis of molecular variances (AMOVAS) to look at intraspecific differences
3) Arlequin to look at intraspecific differences
4) relationship graphs between population pairwise FST and geographical difference
5) nested clade phylogeographical analyses using GEODIS

Another statement they make that I am uncomfortable with is "it was assumed that this species colonized Japan after the ancient archipelago was connected to the continent about 10 Ma. Before 10 Ma, the archipelago was a group of fragmented islands and is unlikely to have harboured donaciine beetles". How can they be really sure?

They state it is important to consider habitat conditions and life-history traits for insects crossing over large bodies of ocean. Also continuous land bridges may not be necessary for insects that can fly or raft.

They found that many insect and mammalian studies indicate that most colonization events occurred during the mid-Pleistocene for both extant and extinct terrestrial animals, probably via a land bridge or narrowed channel between western Japan and the East Asian continent at several regression periods during glacial maxima.

Another neat thing about this paper was that there data agreed with Penny 2005 in that molecular rate depends on the time span of differentiation and is likely to be higher in more recent divergences. Therefore, phylogenetic time estimation using constant sequence divergence rates will lead to over-estimation as the time span is decreased.

Monday, July 28, 2008

Peck 2001

Peck, S.B. 2001. Review of the carrion beetles of Australia and New Guinea (Coleoptera: Silphidae). Australian Journal of Entomology. 40: 93-101.

The author gives keys, distributional maps and bionomic summaries for Nicrophorus heurni, Diamesus osculans, Ptomaphila ovata, Ptomaphila lacrymosa, and Ptomaphila perlata.

World fauna of Silphidae reviewed by Portevin 1926.
Australian fauna of Silphidae reviewed by Britton 1994.

-all species of Silphidae in Australia are mostly collected less than 300 km from the coastline (author speculates that it could be too dry in the interior - this could easily be tested in the lab).

-Silphids are not known to occur on the major Pacific islands of New Zealand, Fiji, or New Caledonia (author also did field work in these places and did not find them).

-there is no evidence that any species of Nicrophorus has every crossed the climatic dry zone bordering Torres Strait from New Guinea onto the Australian continent.

Nicrophorus heurni Portevin 1926
Type locality: North-west New Guinea, Doormanpad Camp, headwaters of the Mamberamo River, 1410 m elevation.
-distributed throughout upland forests in both Irian Jaya and Papua New Guinea. Collected from 480 m to 2750 m at all months of the year. Collected from carrion, human-dung, mercury-vapour, and ultraviolet lights.

No informative characters were found on the male aedeagus of Oxelytrum or Ptomaphila species! But, several characters of the female genitalia were found to be informative, as well as various external structures.

Friday, July 25, 2008

Wolsan 2007

Wolsan, M. 2007. Naming species in phylogenetic nomenclature. Syst. Biol. 56(6): 1011-1021.

This paper opened my eyes a bit more as to the nitty gritty happenings in the world of the Phylocode and how they are trying to govern the naming of species. I was actually quite shocked at the amount of different proposals (20 different ways to name a species!).

species = an individuated segment of a metapopulation-level lineage
clade = a complete system of ancestry and descent, consisting of an ancestor and all its descendants

-species and clades are individuals that exist independently of human perception

The paper lists problems with Linnean binomen:

1. every change in generic assignment of a species necessitates changes in the name of that species (causing instability)
2. there can be people who disagree with the generic placement of species therefore some species have multiple names in use
3. unable to accommodate lack of knowledge about the genus-level relationships (i.e. someone has to assign a species to a genus even if they don't know what genus to put it in).

The paper lists desirable features of species names:

1. uniqueness
2. stability
3. distinguishability from clade names
-yes, I agree with this, but I don't think that every clade needs a name!
4. consistency of form among species names
-I think this is a good idea, but enforcing it is kind of picky.
5. consistency of form with the Linnaean Binomen
6. consistency of species names between PN and TN
7. ease of pronunciation, brevity, and simplicity of form
-same comment for number 4.
8. no need for conversion

It is nice to see that people are thinking about this a lot. Because if people do start moving towards the Phylocode, it does need to be well thought out. I don't think that will happen anytime soon, but it could in my lifetime and as someone who will be using the system, I hope the people who are creating it are doing a good job. I'm not sure if I want to be involved in creating the system, it seems a little too nit picky for me, but I definitely want to be able to give my input and I want any change to be a benefit for the user.

Tuesday, June 17, 2008

Godfray et al. 2007

Godfray, H.C.J., B.R. Clark, I.J. Kitching, S.J. Mayo, and M.J. Scoble. 2007. The web and the structure of taxonomy. Syst. Biol. 56(6): 943-955.

The main thesis of this paper is "an easily accessible taxonomic knowledge base is critically important for all biodiversity-related sciences". Yes, I agree with this but isn't an easily accessible knowledge base about anything quite handy? In this paper, the authors "review different ways in which taxonomy has already made use of the Web or may do so in the future". This paper made me think about how much work taxonomists are doing on their free time, for free, putting information on the web so that other people can have it at a click's moment. I understand that it is great to share all of our knowledge and have open access to everything, but I guess some days I feel like our capitalist society is crushing me and

Notes on the paper:

-they talk about the 'second' bioinformatics crisis being solved by making genomic sequence and other data available on the Web and developing data handling and mining tools for accessibility and analyses. So I'm wondering, do people think that crisis is over? How can we gauge when a crisis is over? Hmm..

-"a major part of being a specialist in a group is the ability to navigate [through publications scattered throughout the literature] and to understand the location of different sources of information and specimens (Scoble, 2004)". SO TRUE!

-"the absence of an up-to-date and accessible taxonomy is a serious shortcoming to an expanding user base...".

-the authors are for a 'current consensus' taxonomy with option to see competing hypotheses if user is so inclined. I can imagine some authors of taxonomic web pages with a tiny little click button at the bottom of their page with teeny tiny words "for alternative hypotheses, click here".

-the authors talk briefly about taxonomic resetting and how doing this, people could be missing out on some important "nuggets of information". Well I guess if everything was on the specific webpage for a taxonomic group, you would never have to dig through that old literature. It would be so great! I can definitely see this as a wiki sort of deal.

Types of taxonomy on the web:

1. Fundamental data
-collection lists
-specimen digital images (2- and 3-dimensions)
-specimen locality data
-catalogues of previous taxon hypotheses
-literature (pdf's)

2. Collection-level metadata
-e.g. number of specimens of a given species within a particular museum

3. Data used in phylogenetic studies
-raw sequence databases
-aligned sequence files
-character matrices
-tree databases (treebase)

4. Raw data synthesis (better called species name lists)
-Species 2000 project

5. Tools
-source of software (database, phylogenetic)
-online keys
-Globally Unique Identifier (GUI)/LifeScience Identifiers (LSID's)

6. Web Publication

7. Wikis
-e.g. Wikispecies, Citizendium

8. Mash-Ups - Federating data
-a web page produced by automatically searching the web for all information available on a certain taxa
-e.g. iSpecies

9. Unitary taxonomies
-all resources relevant to the systematics of a particular group would be present at a single site (Godfray 2002)
-definitely a lot of advantages and disadvantages to this proposal

The authors then discuss the Cate Project (Creating A Taxonomic E-scienc), which is a website with software resources used to allow new taxonomic hypotheses to be advanced within the site. It is basically a test of the unitary taxonomy idea.

They conclude by stating that a web-based, unitary taxonomy is the way to avoid possible future schisms in the field of taxonomy.