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.