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.

Wednesday, May 21, 2008

Shaffer & Thomson 2007

Shaffer, H.B. and R.C. Thomson. 2007. Delimiting Species in Recent Radiations. Syst. Biol. 56(6): 896-906.

This paper is yet another example of how species delimitation is becoming heavily reliant upon population processes. To analyze population processes using molecular data, you really have to have quite a large sample size (at least 20 individuals per population so I've been told from the experts). Alas, I unfortunately do not have that many samples for my PhD work. Maybe in the future...

In this work, Shaffer and Thomson make use of SNP's (Single nucleotide polymorphisms) to delimit turtle species and find that they are useful. However, because the turtle case study was an example of very distantly related taxa and they only discuss how SNP's can be good for recent radiations, I think their title may be a bit misleading.

Also, I'm not too sure on what exactly a single nucleotide polymorphism is. It must be some sort of stretch of DNA because they talk about designing primers for it. They compare SNPs to microsatellite loci but say SNPs are generally biallelic and contain less info than microsats. They also compare SNPs to AFLPs and RAPDs. However, I thought I was told that AFLPs and RAPDs don't actually use evolutionary derived traits and so they should not be used in phylogenetic analyses. Well I guess this isn't a phylogenetic analysis, it is a population analysis so that could be different, and anyway, SNPs are probably completely different from the other two.

Interesting notes/quotes from the paper:

"In practice, older species have often had time to accumulate a range of features: reproductive isolation, fixed apomorphies, and gene-tree monophyly, whereas young taxa often lack these features".

"Tree-based methods [of species delimitation] tend to require demonstrable monophyly, whereas non-tree-based methods more often focus on the discovery of differentiation associated with the earliest stages of lineage diversification". Such as??? I guess I will have to see Sites and Marshall (2003, 2004) for specifics. But I'm assuming non-tree methods are derived from population genetics like the ones used in this paper.

-the authors hope that both tree-based and non-tree based methods will be used together to delimit species

-the authors give four examples of famous species radiations that lack clear evidence on actual species boundaries: 1) Darwin's finches, 2) cichlid fishes, 3) Galapagos Tortoises, and 4) Tiger salamanders.

"Under the neutral coalescent the expected time to monophyly for even a single nuclear gene is often long (Hudson and Coyne 2002) suggesting that many real species exist that have not yet achieved monophyly for even a few genes".

"This reliance on multiple markers [many genes to delimit a species] implies that species in their very earliest stages will probably not be recognized, but it is the price one pays for the taxonomic stability that follows from only recognizing comparatively well-differentiated species". Interesting quote. It makes me think about the future of taxonomy, and whether one wants to focus on the process or the pattern. If you want to focus on the pattern, you will want to work on delimiting well-differentiated species. If you want to focus on the process, you might want to research species in their early stages. Or is it better to be experienced in both? Probably.

-the authors find parametric approaches that simultaneously estimate ancestral population size, migration rate and divergence times appealing for testing species taxa

-"melding of population genetics and speciation biology" -I'm seeing this phrase everywhere!

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!

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.