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.

Wednesday, October 31, 2012

Evolution of Obligate Specialist Species: How Changes to a Single Gene Restricted Drosophila pachea to a Single Species of Cactus

Contributed by: Steve Schaeffer

             The hormone ecdysone regulates many developmental processes during metamorphosis in insects.  In most Drosophila species, cholesterol is the initial substrate for the pathway that synthesizes ecdysone.  A recent study by Lang et al. (2012) provides evidence that amino acid substitutions in the neverland gene are responsible for an adaptive host shift of a Drosophila species. The enzyme produced by the neverland gene converts cholesterol to 7-dehydrocholesterol in the initial step in the ecdysone pathway.  Drosophila pachea lives exclusively on senita cactus (Lophocereus schottii).  The senita cactus lacks appreciable levels of cholesterol, but does have other sterols such as lathosterol that could be used to make ecdysone.  The neverland enzyme of Drosophila pachea is unable to make 7-dehydrocholesterol from cholesterol, which results from two to four amino acid changes in residues that are strongly conserved among Drosophila species. Lang et al. (2012) used transgenic experiments in Drosophila melanogaster neverland knockdown mutants to test the activity of the D. pachea neverland extant and inferred proteins with a variety of sterols.  The ancestral neverland proteins were able to convert both cholesterol and lathosterol into 7-dehydrocholesterol while only lathosterol is used by the extant D. pachea enzyme to make 7-dehydrocholesterol.  A population genetics analysis shows that nucleotide diversity in the neverland gene region is consistent with a recent selective sweep.  This study is a nice example of an integrative study that used molecular and population genetic analysis to show how changes to a single enzyme can result in a species being an obligate specialist.  In this case, D. pachea became an obligate specialist on senita cactus.  This change may have allowed D. pachea to have fewer competitors on its new host.  While this change may currently be advantageous, if availability of the host is reduced, D. pachea could be an evolutionary deadend.


Most living species exploit a limited range of resources. However, little is known about how tight associations build up during evolution between such specialist species and the hosts they use. We examined the dependence of Drosophila pachea on its single host, the senita cactus. Several amino acid changes in the Neverland oxygenase rendered D. pachea unable to transform cholesterol into 7-dehydrocholesterol (the first reaction in the steroid hormone biosynthetic pathway in insects) and thus made D. pachea dependent on the uncommon sterols of its host plant. The neverland mutations increase survival on the cactuss unusual sterols and are in a genomic region that faced recent positive selection. This study illustrates how relatively few genetic changes in a single gene may restrict the ecological niche of a species.

Lang, M., S. Murat, A. G. Clark, G. Gouppil, C. Blais, L. M. Matzkin, É. Guittard, T. Yoshiyama-Yanagawa, H. Kataoka, R. Niwa, R Lafont, C. Dauphin-Villemant, and V. Orgogozo. 2012 Mutations in the neverland gene turned Drosophila pachea into an obligate specialist species. Science 337: 1658-1661.

Friday, October 26, 2012

Changes of the XY and ZW Chromosomal Systems in a Frog Species

            It is well known that the sex in mammals is determined by the X and Y chromosomes, the XY being male and the XX being female, whereas the sex in birds is determined by the Z and W chromosomes (ZZ males and ZW females). These XY and ZW systems have a history of about 200 million years. Therefore, the sex determination system seems to be quite stable once it is established (1).

Fig. 1. Four geographic forms of Rana rugosa, differing in the morphology of sex-determining chromosome 7. Three of these, indicated by the dotted areas, have an XX/XY sex-determining system. The fourth form, indicated by the black area, is characterized by a ZZ/ZW system. Three kinds of sex chromosome 7 can be distinguished morphologically in these four geographic forms. The Z, Y, and Hiroshima-type chromosomes are subtelocentric, the W and X chromosomes are metacentric, and the Isehara-type chromosome is more subtelocentric. S = subtelocentric; mS = more subtelocentric; M = metacentric.

            In amphibians, however, this is not the case, and the same taxonomic family may include species with both the XY and ZW systems (2). In an extreme case the same species contains both the XY and ZW systems as polymorphism. This situation is observed in the Japanese frog Rana rugosa. This species inhabits almost the entire territory of Japan, but depending on the geographical area the chromosomal system is either the XY or the ZW (see Fig. 1). The ZW system is heterogametic, and therefore the male and female can be distinguished by the chromosomal morphology. However, the XY system is either heterogametic (Hamakita areas) or homogametic (Hiroshima and Isehara areas) depending on the geographical area (3). Further studies have shown that the gene sequence arrangements of the X and Y chromosomes from Hiroshima and Isehara are different from each other (Fig. 1). How did these chromosomal systems evolve? Solution of this question may allow us to understand the general scheme of evolution of sex determination.

Fig. 2. A phylogenetic tree of the ADP/ATP translocase gene from the six kinds of sex-determining chromosome 7. The three kinds of chromosome 7 are shown on the right: S = subtelocentric; mS = more subtelocentric; M = metacentric.

            Miura et al. (3) studied the evolutionary history of these sex chromosomes by using the sex-linked gene, AP/ATP translocase gene, on the sex chromosome (chromosome 7). The phylogenetic tree constructed from this gene is presented in Fig. 2. On the basis of this phylogenetic tree, they proposed the evolutionary scenario presented in Fig. 3. This scenario suggests that the “subtelocentric chromosomes” in the Hiroshima area first generated the “more subtelocentric chromosomes” similar to the chromosomes from the Isehara area. The parental “subtelocentric chromosomes” are then hybridized with the “more subtelocentric chromosomes” to produce the “metacentric chromosomes.” Finally, these “metacentric chromosomes” and the Hiroshima “subtelocentric chromosomes” generated the XY and the ZW chromosomal systems. These evolutionary changes are believed to have occurred relatively recently.

Fig. 3. A phylogenetic pathway of the sex-determining chromosome 7 inferred from the ADP/ATP translocase gene tree. The subtelocentric chromosome is shown by a white area, the more subtelocentric by shaded area, and the metacentric by black area.

            However, there are several problems in this scenario. The first and most important one, which the authors also recognized, is the nature and the location of sex-determining genes on the sex chromosomes. The sex is determined not by chromosomes but by genes, and therefore it is essential to identify the genes that trigger the formation of testis or ovary. Chromosomal morphology can change relatively easily by inversion and translocation, but the sex-determining genes are generally more conserved, and therefore they are likely to give a more accurate pattern of evolution of sex determination. Furthermore, the morphological study of chromosomes does not give information on small gene deletions, insertions, or pseudonization. It is therefore difficult to reconstruct the evolutionary history of sex determination in the present case.
            For the above reason, the authors have not clearly distinguished between the X and Y chromosomes in the Hiroshima and Isehara areas (Fig. 1 and 3). Fig. 2, however, indicates that the X and W chromosomes and the Y and Z chromosomes are evolutionarily related, respectively. Although the phylogenetic tree was constructed by using a sex-linked gene rather than the sex determining gene, the results presented are interesting if we consider the mammalian sex determining gene, SRY, that initiates the pathway of testis formation. In this case the individual without the SRY gene becomes female as a default option. In birds, which have the ZW system, the male (ZZ) is believed to form testis because of the presence of two copies of the sex determining gene, Dmrt1, and the ZW female produces ovary as a default option (2, 4).
            At the present time we know nothing about the molecular basis of sex determination in frogs. However, if we use the sex determination in mammals and birds as guidance, the evolutionary changes of the XY and ZW systems may be studied at the molecular level.
            In this connection, Miura et al. (5) presented an interesting observation with respect to the accumulation of lethal mutations in the Y and W chromosomes. In frogs it is possible to generate the WW homozygotes by producing the ZW males with a hormone treatment and by crossing the ZW males with the normal ZW females (5). This WW homozygote did not survive well in the tadpole stage, and most of the individuals died sooner or later. When the WW homozygotes were produced from various geographical locations, it was clear that the W chromosome carries a lethal mutation but the lethal mutation varies from location to location. In other words, the W chromosome evolved independently in different locations. Therefore, when the WW was produced by using the W chromosome from different locations, the WW homozygotes could survive up to adulthood.
            The same type of experiment was done with the Y chromosome. In this case the YY individual could not survive even if the two different Y’s were derived from different locations. This suggests that the XY system evolved earlier than the ZW system.
            It has been argued that once a set of linked genes related to sex determination evolve in a chromosome the recombination value of the linked gene region tends to be reduced by modifier genes (6) or chromosomal inversions (7) and the recessive lethal mutations gradually accumulate in the region (8, 9). The rate of accumulation of lethal mutations depends on the mutation rate, population size, and evolutionary time.
            The evolutionary change between the XY and ZW systems also occurs more frequently in small populations than in large populations. Because the R. rugosa frogs generally inhabit the mountainous areas, the effective population size must be very small. Probably for these reasons, R. rugosa have undergone rather rapid changes of the sex chromosome (chromosome 7) and the genes controlling sex determination. However, the evolutionary changes of sex determining genes are poorly understood at present. It is hoped that a more detailed molecular study will be conducted for understanding the evolutionary mechanism of sex determination in the future.

2. Sarre SD, Ezaz T, and Georges A. 2011. Transitions between sex-determining systems in reptiles and amphibians. Annu Rev Genomics Hum Genet 12:391-406.
4. Smith CA, Roeszler KN, Ohnesorg T, Cummins DM, Farlie PG, Doran TJ, and & Sinclair AH. 2009. The avian Z-linked gene DMRT1 is required for male sex determination in the chicken. Nature 461:267-271.
5. Miura I, Ohtani H, and Ogata M. 2012. Independent degeneration of W and Y sex chromosomes in frog Rana rugosa.Chromosome Res 20:47-55.
6. Nei, M. 1969. Linkage modification and sex difference in recombination. Genetics 63:681-699.
7. Ohno S. 1967. Sex chromosomes and sex-linked genes. Springer-Verlag, New York.
8. Muller HJ. 1914. A gene for the fourth chromosome of Drosophila. J Exp Zool 17:325-336.