

Thursday, April 19, 2012

Evolution of Milk Casein Genes from Tooth Genes

Contributed by: Kazuhiko Kawasaki

            In most mammals, caseins are the most abundant proteins in milk. Caseins associate with calcium and stabilize it at a high concentration, which helps infants to develop bone and teeth. Despite the critical role of caseins in mammalian evolution, their origin has been unknown or highly speculative. Association of caseins with calcium is mediated by negatively charged amino acids, and no rigid 3-dimensional structure is required for this function. Mainly for this reason, caseins evolve rapidly, and hence the amino acid or nucleotide sequence similarity is not very useful for exploring their evolution. For this reason, we studied similarities in the exon-intron structure of the genes, which is more conserved during evolution (1). The results suggest that two of the three casein genes have evolved by duplication of the SCPPPQ1 gene, whereas the third casein gene originated from the FDCSP gene. In addition, the SCPPPQ1 and FDCSP genes share a common ancestral gene called ODAM. Interestingly, all these three precursor genes are expressed in dental tissues and probably encode calcium-binding proteins. We therefore argue that all casein genes arose from tooth genes and that the calcium-binding ability of caseins was inherited from their ancestor.

Figure: A likely scenario of the evolution of case in genes

[Gene symbols]
ODAM: odontogenic ameloblast-associated
SCPPPQ1: secretory calcium-binding phosphoprotein proline and glutamine rich 1
FDCSP: follicular dendritic cell secreted peptide

Caseins are among cardinal proteins that evolved in the lineage leading to mammals.  In milk, caseins and calcium phosphate (CaP) form a huge complex, called casein micelle.  By forming the micelle, milk maintains high CaP concentrations, which help altricial mammalian neonates to grow bone and teeth.  Two types of caseins are known.  Ca-sensitive caseins (as- and b-caseins) bind Ca but precipitate at high Ca concentrations, whereas Ca-insensitive casein (k-casein) does not usually interact with Ca but instead stabilizes the micelle.  Thus, it is thought that these two types of caseins are both necessary for stable micelle formation.  Both types of caseins show high substitution rates, which make it difficult to elucidate the evolution of caseins.  Yet, recent studies have revealed that all casein genes belong to the secretory calcium-binding phosphoprotein (SCPP) gene family that arose by gene duplication.  In the present study, we investigated exon-intron structures and phylogenetic distributions of casein and other SCPP genes, particularly the odontogenic ameloblast associated (ODAM) gene, the SCPP-Pro-Gln-rich 1 (SCPPPQ1) gene, and the follicular dendritic cell secreted peptide (FDCSP) gene.  The results suggest that contemporary Ca-sensitive casein genes arose from a putative common ancestor, which we refer to as CSN1/2.  The six putative exons comprising CSN1/2 are all found in SCPPPQ1, although ODAM also shares four of these exons.  By contrast, the five exons of the Ca-insensitive casein gene are all reminiscent of FDCSP.  The phylogenetic distribution of these genes suggests that both SCPPPQ1 and FDCSP arose from ODAM.  We thus argue that all casein genes evolved from ODAM via two different pathways; Ca-sensitive casein genes likely originated directly from SCPPPQ1, whereas the Ca-insensitive casein genes directly differentiated from FDCSP.  Further, expression of ODAM, SCPPPQ1, and FDCSP was detected in dental tissues, supporting the idea that both types of caseins evolved as Ca-binding proteins.  Based on these findings, we propose two alternative hypotheses for micelle formation in primitive milk.  The conserved biochemical characteristics in caseins and their immediate ancestors also suggest that many slight genetic modifications have created modern caseins, proteins vital to the sustained success of mammals. 

1. Kawasaki, K., Lafont, A.G., and Sire, J.Y. 2011. The evolution of milk casein genes from tooth genes before the origin of mammals. Mol. Biol. Evol. 28(7):2053-2061.

Monday, April 16, 2012

Parallel Adaptive Evolution and Genomic Changes in Stickleback Fish

Contributed by: Jongmin Nam

            The molecular basis of phenotypic evolution is largely unknown, and identification of exact DNA changes underlying a specific morphological, physiological, or behavioral evolution is very hard, though it is a fascinating subject. Despite these difficulties, stickleback fish have been a great model system for studying the molecular basis of adaptive evolution, because they have experienced rapid parallel adaptation from salt to freshwater life in multiple geographical locations. They are therefore good organisms for studying recurrent adaptive evolution.

             In a recent Nature paper, Jones et al. (1) sequenced the genomes of multiple, independently evolved marine-freshwater pairs of sticklebacks (see Figure 1). They then examined sequence changes that are shared by most freshwater fishes but are different from typical sequences shared by most saltwater fishes. Not only did they detect what was already known, but they also detected about 60 strong candidate genomic regions for recurrent adaptive evolution. About 40% - 80% of them had either changes in noncoding regions or synonymous substitutions in protein coding regions, and only about 17% contained changes causing amino acid substitutions. Genes within or near these protein-coding regions varied widely from differentiation genes to regulatory genes. It would be of great interest to study molecular function of these regions in relation to the changes of specific phenotypic characters.

Figure 1. Genome scans for parallel marine–freshwater divergence. Marine (red) and freshwater (blue) stickleback populations were surveyed from diverse locations.


            Conducting killer experiments to show causality of these regulatory changes to specific phenotype evolution is still challenging, partly because we do not know how these functional elements work in complex regulatory networks and partly because experimental tools for re-engineering functional elements in the genome are not yet available in most species. Nevertheless, there are at least a good number of candidate regions for studying adaptive evolution to begin with, and this is a big step forward.




Friday, April 13, 2012

Evolution of a Poison-Resistance Gene through Introgression

Contributed by: Zhenguo Lin

Warfarin is an anticoagulant that inhibits the synthesis of clotting factors. Because it causes internal bleeding in rats and mice, warfarin has been widely used a rodenticide since 1948. Warfarin decreases blood coagulation by inhibiting the vitamin K epoxide reductase (VKOR), an enzyme involved in the carboxylation of several blood coagulation proteins.

             After merely 10 years of introduction of warfarin as a rodenticide, warfarin resistant mouse or rats have been found. The resistance to warfarin of house mice (Mus musculus domesticus) was found to be due to some nonsynonymous single-nucleotide polymorphisms (SNPs) in the vitamin K epoxide reductase subcomponent 1 (vkorc1) that encodes the warfarin-sensitive component of VKOR.

Song et al. (2011) recently found that the polymorphisms of vkorc1 in resistant house mice were acquired from the Algerian mouse (Mus spretus), a species known to be naturally resistant to warfarin, through introgressive hybridization (1).

The Algerian mouse and house mouse diverged 1.5–3 million years ago and the distributions of the two species has some overlaps in Spain and northern Africa. The hybridization between the two species is not common and only some female offspring are fertile. However, it is surprising that the piece of DNA that contain warfarin resistant gene can spread quickly in the house mouse populations in a few decades. For example, the vkorc1 gene in 27 of 29 house mice examined in Spain was entirely or partly originated from Algerian mice. Similar cases were also observed in 16 of 50 house mice in Germany, where Algerian mice do not exist (1). Although it is believed that interspecific hybrids have severe disadvantages, this study suggests that hybridization can be an important way for the evolution of a specific character.

Distribution of vkorc1 genotypes in Western European M. m. domesticus. The hatched area depicts the native range of M. spretus. The house mouse (Mus musculus spp.) has become a cosmopolitan species and now is occurring across the entire area depicted and beyond. Pie charts show the frequencies of pure vkorc1 of M. m. domesticus origin (vkorc1dom) (pink, genotypes 1–6 in A), genotypes that correspond to the complete M. spretus vkorc1 allele or share parts of it in the form of heterozygosity and/or intragenic recombination (all vkorc1spr, yellow, genotypes 8–20 in A), and ambiguous genotypes (genotype 7, green). Countries sampled in this study are shaded in gray. Sampling locations (some overlapping as a result of proximity) are shown as triangles (pink, vkorc1spr absent; yellow, vkorc1spr present). From Song et al. (2011).

1. Song, Y.,  Endepols, S.,  Klemann, N., Richter, D.,  Matuschka, F.R., Shih, C.H., Nachman, M.W., and Kohn, M.H. 2011. Adaptive introgression of anticoagulant rodent poison resistance by hybridization between Old World mice. Current Biology 21:1296-1301

Wednesday, April 11, 2012

Soldier Ants and Caste Evolution











Probing the Origin of Multicellularity in a Test Tube

Contributed by: Jianzhi Zhang

The evolution of multicellularity is undoubtedly one of the most important events in the history of the Earth. Although multicellularity originated multiple times, all occurred long ago and no transitional form exists today. Thus, there is little information about the key steps that led to these transformative evolutionary events. While the origin of multicellularity may sound very complex, a recent study showed that primitive forms of multicellularity can emerge from unicellularity within a matter of weeks in test tubes, when the “environment” is right.

Ratcliff et al. (1) used gravity to select yeast cells that stick together and thus settle more quickly than separated cells. After just 60 rounds of selection, the yeast population is dominated by snowflake-like phenotypes, with a new life history characterized by reproduction via multicellular propagules, a juvenile phase, and determinate growth. However, the genetic changes responsible for the new phenotype are unknown. Given the ease of sequencing yeast genomes, it would be of great interest to identify the causal mutations, which will allow a molecular understanding of such primitive multicellularity.

            In an earlier study that is somewhat less dramatic but more elegant, Koschwanez et al. (2) studied the condition under which multicellularity is favored over unicellularity, by creating an environment in which cells need to cooperate to be able to survive and reproduce. To use sucrose as the sole carbon source, yeast expresses an enzyme called invertase in the cell wall to degrade sucrose into glucose and fructose. These monosaccharides unfortunately diffuse into the environment and need to be re-absorbed by yeast cells. One can imagine that under a low sucrose concentration, a single cell in a test tube would not be able to survive because most of the monosaccharides produced are diffused and wasted. When the cell density increases, the monosaccharide concentration in the environment rises, which may be able to support yeast growth. This was indeed demonstrated experimentally. Furthermore, the authors found mutant yeasts whose cells fail to separate after mitosis to be fitter than the wild-type yeast under certain parameters of cell density and sucrose concentration. Thus, a single mutation may initiate the path to multicellularity.   

Molecular dissections of microevolutionary changes are becoming routine, thanks to rapid progress in molecular genetics and genomics. But big, transformative changes seen in macroevolution remain largely unexplained in terms of their molecular genetic basis. The very micro evolutionary experiments in test tubes may prove instrumental in unlocking the mysteries of macroevolution.

1. Ratcliff WC, Denison RF, Borrello M, Travisano M. 2012. Experimental evolution of multicellularity. Proc Natl Acad Sci U S A. 109:1595-600.
2. Koschwanez JH, Foster KR, Murray AW. 2011. Sucrose utilization in budding yeast as a model for the origin of undifferentiated multicellularity. PLoS Biol. 9:e1001122.

Tuesday, April 10, 2012

Drosophila Self-medicates Itself against Parasitoid Wasps

Contributed by: Steve Schaeffer

           Hosts use a variety of strategies to deal with a never ending battle with its parasites.  Larvae of Drosophila species are often infected by parasitoid wasps and feeding by the wasp larvae lead to the eventual death of fly larvae.  A recent study by Milan et al. (2012) published in Current Biology shows that fly larvae take advantage of environmental alcohols to limit the infection of parasitoid wasp larvae.  The work shows that consumed alcohol leads to the death of the wasp larvae.  In addition, Drosophila larvae seek out alcohol when infected by the parasite in an effort to self-medicate itself against the invader.  How this story develops will be interesting in light of the well-known polymorphism in the alcohol dehydrogenase gene in Drosophila melanogaster.  It will be interesting to know if the different alleles of Adh change the effectiveness of the self-medication or the behavior.


Plants and fungi often produce toxic secondary metabolites that limit their consumption [1-4], but herbivores and fungivores that evolve resistance gain access to these resources and can also gain protection against nonresistant predators and parasites [3, 5-8]. Given that Drosophila melanogaster fruit fly larvae consume yeasts growing on rotting fruit and have evolved resistance to fermentation products [9, 10], we decided to test whether alcohol protects flies from one of their common natural parasites, endoparasitoid wasps [11-13]. Here, we show that exposure to ethanol reduces wasp oviposition into fruit fly larvae. Furthermore, if infected, ethanol consumption by fruit fly larvae causes increased death of wasp larvae growing in the hemocoel and increased fly survival without need of the stereotypical antiwasp immune response. This multifaceted protection afforded to fly larvae by ethanol is significantly more effective against a generalist wasp than a wasp that specializes on D. melanogaster. Finally, fly larvae seek out ethanol-containing food when infected, indicating that they use alcohol as an antiwasp medicine. Although the high resistance of D. melanogaster may make it uniquely suited to exploit curative properties of alcohol, it is possible that alcohol consumption may have similar protective effects in other organisms.


1. Milan, N.F., Kacsoh, B.Z., Schlenke, T.A. 2012. Alcohol Consumption as Self-Medication against Blood-Borne Parasites in the Fruit Fly. Current Biology 22(6):488-493.

Friday, April 6, 2012

The Phylogeny and Timing of Mammalian Evolution

Contributed by: Blair Hedges

Until the mid-1990s, our understanding of mammal phylogeny and timescale was largely guided by the fossil record. Those data told us, for example, that all mammals with hoofs, such as horses and elephants, were related, and that most ordinal splits among living placentals occurred after the dinosaurs went extinct 66 million years ago (mya). Molecular sequence evidence altered this view by showing that there are continental-scale groups of mammals (1) and deep, Cretaceous, divergences among orders (2,3). By about 10 years ago, this New View of mammal evolution began to stabilize (4).

Against this backdrop, Bininda-Emonds et al. (5) published a supertree analysis of mammal evolution in 2007 that captured people's attention because it included 99% of the 4500 species (although one-third of the species had no data, so were "interpolated"). It did not challenge the major components of the New View, including deep Cretaceous divergences among orders, but they found a curious spike in diversification during the Eocene (~50 mya) that they dubbed the "delayed rise in mammals." Recently, Meredith et al. (6), assembled the largest sequence data set so far (35,603 base pairs, in 164 taxa) and their results do not agree with those of Bininda-Emonds et al. (5). They used a supermatrix (concatenated genes) analysis, finding differences in both the tree topology and timescale (see illustration). Most notably, they did not find a "delayed rise" or as many deep, intra-ordinal splits ("short fuses").

Some would view these differences merely as "fine-tuning" of New View of mammal evolution. Nonetheless, they relate to mechanisms of diversification and therefore are of general interest. Without picking sides, I raise some questions here for discussion. Is a timed supermatrix analysis better than a timed supertree analysis? How many species can be "interpolated" in a study before the interpolation affects the results? What proportion of total lineages (e.g., species) is needed in a study before patterns of diversification can be accurately studied?


1. Springer, M.S., et al. 1997. Endemic African mammals shake the phylogenetic tree. Nature 388:61-63.
2. Hedges, S.B., et al. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-229.
3. Kumar, S. and S.B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
4. Murphy, W.J., et al. 2001. Molecular phylogenetics and the origins of placental mammals. Nature, 2001. 409(6820):614-618.
5. Bininda-Emonds, O.R.P., et al. 2007. The delayed rise of present-day mammals. Nature 446(7135):507-512.

Tuesday, April 3, 2012

Polyploidy, Incompatibility Mutations, and Speciation

            The roles of mutation and natural selection in the formation of new species have been controversial for the last 150 years. It is often stated that Charles Darwin (1) did not solve the problem of origin of new species because he did not explain how a species splits into two or more species. Darwin was aware of the hybrid sterility and inviability between different species, but he had a difficulty to explain it by natural selection. At his time some authors suggested that hybrid sterility or inviability might be enhanced by natural selection because the mixing of two incipient species by hybridization is disadvantageous for the formation of new species. Darwin rejected this idea after examination of various cases of species hybridization and concluded that “hybrid sterility is not a specially acquired or endowed quality but is incidental on other acquired differences.

            de Vries (2) proposed a very different view called the mutation theory, in which new species or elementary species (meaning incipient species) are produced by single mutational events. According to this theory, new incipient species are suddenly produced and reproductively isolated from the parental species. Because this theory was based on experimental studies conducted with the evening primrose Oenthera lamarkiana, it was accepted by many biologists when it was proposed. About two decades later, however, the mutation theory was almost abandoned mainly because O. lamarkiana was found to be a heterozygote for chromosomal complexes and the mutant forms he found were mostly caused by chromosomal rearrangements derived from this unusual parental species. At the time of de Vries the genetic cause of mutations was not known, and he regarded any heritable changes of phenotypic characters as mutations. Later studies showed that at least one of the elementary species (O. gigas) he discovered was a tetraploid, and it established itself as a new species in self-fertilizing evening primrose. Therefore, he was right in his proposal of mutation theory. In fact, recent genomic data abundantly support his theory of origin of species by polyploidization or  chromosomal changes in plants (see illustration).

Circles indicate suspected genome duplication events.

In animals, however, the formation of new species by chromosomal mutations is rare, and new species are believed to be generated by genic mutations and natural selection. The models of genic speciation are complicated, and there are many different ways of generating hybrid weakness. In these cases most investigators have emphasized the importance of natural selection rather than mutation (3). Some authors implied that positive selection for incompatibility genes is important in speeding up speciation. In my view, the crucial event of speciation is the development of reproductive barriers between species, and this is accomplished mainly by incompatibility mutations.
Recently, Masafumi Nozawa and I (4) critically examined various papers concerned with speciation by re-analyzing molecular data available. We then reached the conclusion that the hybrid inviability or sterility is cause by incompatibility genes that are manifested when two different species are hybridized. The abstract of their paper is as follows:

One of the most important problems in evolutionary biology is to understand how new species are generated in nature. In the past, it was difficult to study this problem because our lifetime is too short to observe the entire process of speciation. In recent years, however, molecular and genomic techniques have been developed for identifying and studying the genes involved in speciation. Using these techniques, many investigators have already obtained new findings. At present, however, the results obtained are complex and quite confusing. We have therefore attempted to understand these findings coherently with a historical perspective and clarify the roles of mutation and natural selection in speciation. We have first indicated that the root of the currently burgeoning field of plant genomics goes back to Hugo de Vries, who proposed the mutation theory of evolution more than a century ago and that he unknowingly found the importance of polyploidy and chromosomal rearrangements in plant speciation. We have then shown that the currently popular Dobzhansky-Muller model of evolution of reproductive isolation is only one of many possible mechanisms. Some of them are Oka's model of duplicate gene mutations, multiallelic speciation, mutation-rescue model, segregation-distorter gene model, heterochromatin-associated speciation, single-locus model, etc. The occurrence of speciation also depends on the reproductive system, population size, bottleneck effects, and environmental factors, such as temperature and day length. Some authors emphasized the importance of natural selection to speed up speciation, but mutation is crucial in speciation because reproductive barriers cannot be generated without mutations.

Our conclusion is that hybrid inviability or sterility is a mere consequence of establishment of sets of genes that are compatible within species but incompatible between species. This is similar to Darwin’s conclusion. We therefore believe that both Darwin and de Vries were correct in visualizing the mechanism of formation of new species.
I would appreciate any of the comments on the Nei-Nozawa paper or any other matter.﻿﻿﻿﻿


1.  Darwin C. 1859. On the origin of species by means of natural selection or the preservation of favoured races in the struggle for life. Murray, London.
2. de Vries H. 1909. The mutation theory: Experiments and observations on the origin of species in the vegetable kingdom. Vol. I. The origin of species by mutation. English translation by Farmer, JB and Darbishire, AD. Open Court Publishing Company, Chicago.
3. Coyne JA and Orr HA. 2004. Speciation. Sinauer Associates, Sunderland, MA.