The purpose of this forum is to introduce notable papers and books published by you and other persons. The work can be new or old, but it should be of wide interest and high quality. A brief comment on the significance of the work should be attached. The current categories of the subjects are (1) adaptation, (2) behavioral evolution, (3) dosage compensation, (4) evo-devo, (5) gene evolution, (6) genomic evolution, (7) molecular phylogeny, (8) natural selection, (9) phenotypic evolution, (10) sensory receptors, (11) sex chromosomes, (12) sex determination, (13) speciation, (14) symbiosis and evolution, and (15) horizontal gene transfer. However, new categories can be added if necessary. Emphasis will be given on the biological work rather than on the mathematical. Any person may post a paper by sending it to one of the editors listed below. We also welcome your comments on posted work, but we moderate all the comments to control spam. This forum is primarily for scientific discussion and to construct a database for good molecular evolution papers.

Tuesday, December 4, 2012

Speciation Driven by Divergence in Heterochromatic Repeats

Contributed by: Zhenguo Lin

 Darwin used the title "On the origin of species" for his most famous book published in 1859. In this book he explained how a single species changes over time, but did not provide a proper explanation about how a species split into two or more different species. The problem of speciation has now become an important subject in evolutionary biology. From Hugo de Vries, Theodosius Dobzhansky, and Ernst Mayr to contemporary workers such as Jerry Coyne and Allen Orr, this problem has been studied extensively.

In this case it seems to be crucial to study speciation at the molecular level. In their recent review article, Nei and Nozawa (1) emphasized the importance of mutations in speciation by presenting many cases of molecular studies.  One of the mechanisms they considered is hybrid incapacity associated with heterochromatin. Specifically, they stated that hybrid sterility or inviability may occur by changes in repeat DNA elements in heterochromatin regions of the genome. Two representative examples were presented in the review article. (1) The different numbers of 359 bp repeats (zygote hybrid rescue locus, Zhr) caused hybrid inviability between Drosophila melanogaster males and D. simulans females.  (2) The localization of Odysseus homeobox (OdsH) protein to heterochromatic Y chromosome causes hybrid male sterility between D. mauritiana females and D. simulans males.  Recently conducting a comparative study of the genomic sequences from two closely related flycatcher bird species, Ellegren et al. (2) suggested that the divergence of complex genomic repeat structures (centromere and telomeres) may have generated the two species.

Figure 1 a, Male collared flycatcher. b, Male pied flycatcher. (From Ellegren et al. (2)).

 The collared flycatcher Ficedula albicollis and the pied flycatcher Ficedula hypoleuca diverged less than 2 million years ago.  They look very similar except for the presence of white collar in the former species (Figure 1). The authors from Uppsala University in Sweden have sequenced the ~1.1Gb genomic regions for 10 unrelated males in each species. By comparing these genomic regions, the author identified 50 "divergence islands", which show significantly high levels of sequence divergence between the two species. The length of an "island" ranges from 100 kb to 3 Mb, with a mean of 625kb. Interestingly, these “islands” are over-represented in the telomere or centromere regions, which are rich in repeat structures (Figure 2).  After detailed analyses of various evolutionary patterns of these "divergence islands" , such as  local mutation rates,  levels of nucleotide diversity,  allele-frequency spectra,  levels of linkage disequilibrium and shared polymorphisms,  the authors confirmed that these islands have experienced parallel selection in each species. Although no direct evidence was provided to support how these "divergence islands" contributed to the speciation, the authors believed that these observations "raise the possibility that centromeres or other heterochromatic repeats themselves are the driver of speciation" (2).


Figure 2. Distribution of divergence measured as the density of fixed differences per bp for 200-kb windows across the genome. Chromosomes are listed in numerical order and are separated by gaps. Red horizontal bars show the approximate location of centromeres in homologous chromosomes of zebra finch. Open read symbols are used to indicate that avian microchromosomes are generally acro- or telocentric. Both ends of these chromosomes are labeled as the orientation is not known. For chromosomes 4, 6 and 8, there is a lack of an in situ mapped marker 5′ of the centromere in zebra finch. (from Ellegren et al. (2)).

1. Nei, M. and Nozawa, M. (2011), 'Roles of mutation and selection in speciation: from Hugo de Vries to the modern genomic era', Genome Biol Evol, 3, 812-29.
2. Ellegren, H., et al. (2012), 'The genomic landscape of species divergence in Ficedula flycatchers', Nature. doi:10.1038/nature11584

No comments:

Post a Comment