Modern humans have gone through varied processes of genetic adaptations when their ancestors left Africa about 100,000 years ago. The environmental stresses and the social transitions (e.g., emergence of the Neolithic culture) have been acting as the major selective forces reshaping the genetic make-up of human populations. Genetic adaptations have occurred in many aspects of human life, including the adaptation to cold climate and high-altitude hypoxia, the improved ability of defending infectious diseases, and the polished strategy of utilizing new diet with the advent of agriculture. At the same time, the adaptations once developed during evolution may sometimes generate deleterious effects (e.g., susceptibility to diseases) when facing new environmental and social changes. The molecular (especially the genome-wide screening of genetic variations) studies in recent years have detected many genetic variants that show signals of Darwinian positive selection in modern human populations, which will not only provide a better understanding of human evolutionary history, but also help dissecting the genetic basis of human complex diseases.

Hong Shi

Bing Su

Molecular Adaptation of Modern Human Populations

Comparisons of gene content and orthologous protein sequence constitute a major strategy in whole-genome comparison studies. It is expected that horizontal gene transfer between phylogenetically distant organisms and lineage-specific gene loss have greater influence on gene content-based phylogenetic analysis than orthologous protein sequence-based phylogenetic analysis. To determine the evolution of the syntrophic bacterium Symbiobacterium thermophilum, we analyzed phylogenetic relationships among Clostridia on the basis of gene content and orthologous protein sequence comparisons. These comparisons revealed that these 2 phylogenetic relationships are topologically different. Our results suggest that each Clostridia has a species-specific gene content because frequent genetic exchanges or gene losses have occurred during evolution. Specifically, the phylogenetic positions of syntrophic Clostridia were different between these 2 phylogenetic analyses, suggesting that large diversity in the living environments may cause the observed species-specific gene content. S. thermophilum occupied the most distant position from the other syntrophic Clostridia in the gene content-based phylogenetic tree. We identified 32 genes (14 under relaxed selection and 18 under functional constraint) evolving under Symbiobacterium-specific selection on the basis of synonymous-to-nonsynonymous substitution ratios. Five of the 14 genes under relaxed selection are related to transcription. In contrast, none of the 18 genes under functional constraint is related to transcription.

Kenro Oshima

Kenji Ueda

Teruhiko Beppu

Hiromi Nishida

Unique Evolution of Symbiobacterium thermophilum Suggested from Gene Content and Orthologous Protein Sequence Comparisons

Although the bacterium Symbiobacterium thermophilum has a genome with a high guanine-cytosine (GC) content (69&#37;), it belongs to a low GC content bacterial group. We detected only 18 low GC content regions with 5 or more consecutive genes whose GC contents were below 65&#37; in the genome of this organism. S. thermophilum has 66 transposase genes, which are markers of transposable genetic elements, and 38 (58&#37;) of them were located in the low GC content regions, suggesting that Symbiobacterium has a similar gene silencing system as Salmonella. The top hit (best match) analyses for each Symbiobacterium protein showed that putative horizontally transferred genes and vertically inherited genes are scattered across the genome. Approximately 25&#37; of the 3338 Symbiobacterium proteins have the highest similarity with the protein of a phylogenetically distant organism. The putative horizontally transferred genes also have a high GC content, suggesting that Symbiobacterium has gained many DNA fragments from phylogenetically distant organisms during the early stage of Firmicutes evolution. After acquiring genes, Symbiobacterium increased the GC content of the horizontally transferred genes and thereby maintained a genome with a high GC content.

Choong-Soo Yun

Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum Genes

We characterized ectopic gene conversions in the genome of ten hemiascomycete yeast species. Of the ten species, three diverged prior to the whole genome duplication (WGD) event present in the yeast lineage and seven diverged after it. We analyzed gene conversions from three separate datasets: paralogs from the three pre-WGD species, paralogs from the seven post-WGD species, and common ohnologs from the seven post-WGD species. Gene conversions have similar lengths and frequency and occur between sequences having similar degrees of divergence, in paralogs from pre- and post-WGD species. However, the sequences of ohnologs are both more divergent and less frequently converted than those of paralogs. This likely reflects the fact that ohnologs are more often found on different chromosomes and are evolving under stronger selective pressures than paralogs. Our results also show that ectopic gene conversions tend to occur more frequently between closely linked genes. They also suggest that the mechanisms responsible for the loss of introns in S. cerevisiae are probably also involved in the gene 3'-end gene conversion bias observed between the paralogs of this species.

Robert T. Morris

Guy Drouin

Ectopic Gene Conversions in the Genome of Ten Hemiascomycete Yeast Species

Aspergillus fumigatus Fresenius has the capacity to degrade elastin (the principal protein of the lungs) and it is considered that elastase activity (EA) is among the most important pathogenicity factors of this mold. In particular, there is a strong correlation between EA in A. fumigatus and invasive aspergillosis. However, EA is not universal in this mold, and it is unknown whether the capacity to degrade elastin is the consequence of physiological mechanisms and/or genetic changes (putative adaptive mutations) induced after the exposure to this substrate or, on the contrary, it is due to random spontaneous mutations that occur under nonselective conditions. In order to discriminate between these possibilities, a Luria-Delbrück fluctuation analysis was carried out on an elastase-negative (<svg style="vertical-align:-0.0pt;width:29.137501px;" id="M1" height="11.6125" version="1.1" viewBox="0 0 29.137501 11.6125" width="29.137501" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg"><g transform="matrix(.017,-0,0,-.017,.062,11.55)"><path id="x45" d="M517 162l29 -4q-18 -100 -35 -158h-482v28q68 5 83.5 20t15.5 77v398q0 66 -13 80t-73 19v28h446q0 -8 8 -144l-29 -4q-11 51 -32 85q-11 17 -35 23t-78 6h-76q-23 0 -28 -5t-5 -27v-228h94q67 0 83 12t25 63h29v-191h-29q-10 54 -26 65.5t-81 11.5h-95v-189&#xA;q0 -65 24 -81q19 -13 104 -13q57 0 83 7t43 27q28 33 50 94z" /></g><g transform="matrix(.017,-0,0,-.017,9.718,11.55)"><path id="x41" d="M673 0h-245v28q47 6 58 16t1 39l-55 154h-213q-31 -87 -36 -129q-16 -47 -5 -61t68 -19v-28h-226v28q50 7 68.5 23.5t43.5 80.5l214 524l24 9l193 -536q23 -63 41.5 -79.5t68.5 -21.5v-28zM418 280l-81 255h-2q-74 -197 -101 -255h184z" /></g><g transform="matrix(.012,-0,0,-.012,21.463,3.4)"><path id="x2212" d="M535 230h-483v50h483v-50z" /></g></svg>) A. fumigatus strain, using as selective factor a culture medium containing elastin as the sole source of nitrogen. Here we show that the <svg style="vertical-align:-0.0pt;width:89.474998px;" id="M2" height="14.1125" version="1.1" viewBox="0 0 89.474998 14.1125" width="89.474998" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg"><g transform="matrix(.017,-0,0,-.017,.062,14.05)"><use xlink:href="#x45" /></g><g transform="matrix(.017,-0,0,-.017,9.718,14.05)"><use xlink:href="#x41" /></g><g transform="matrix(.012,-0,0,-.012,21.463,5.887)"><use xlink:href="#x2212" /></g><g transform="matrix(.017,-0,0,-.017,36.625,14.05)"><path id="x2192" d="M901 255q-71 -62 -185 -187l-22 15l102 147h-727v50h727l-102 147l22 15q114 -125 185 -187z" /></g><g transform="matrix(.017,-0,0,-.017,60.389,14.05)"><use xlink:href="#x45" /></g><g transform="matrix(.017,-0,0,-.017,70.045,14.05)"><use xlink:href="#x41" /></g><g transform="matrix(.012,-0,0,-.012,81.8,5.887)"><path id="x2B" d="M535 230h-212v-233h-58v233h-213v50h213v210h58v-210h212v-50z" /></g></svg> transformation in A. fumigatus appears by rare, random mutations before the exposure of the strain to selective conditions. This work represents the first experimental evidence of pathogenicity factor acquisition in mycelial fungi by preselective mutation.

Sergio Álvarez-Pérez

Jose L. Blanco

Victoria López-Rodas

Antonio Flores-Moya

Eduardo Costas

Marta E. García

Elastase Activity in Aspergillus fumigatus Can Arise by Random, Spontaneous Mutations

Although the nature of ruminant evolution is still disputed, current theory based on physiology and genetic analysis suggests that the abomasum is the evolutionarily oldest stomach compartment, the rumen evolved some time after the abomasum, and the omasum is the evolutionarily youngest stomach compartment. In addition, there is some evidence of relaxed selective constraint in the stomach-like organ and the foregut shortly after the foregut formation event. Along with the assumption of a mean, stochastic rate of evolution, analysis of differences in genetic profiles among digestive body organs can give clues to the relationships among these organs. The presence of large numbers of uniquely expressed entries in the abomasum and rumen indicates either a period of relaxed selective constraint or greater evolutionary age. Additionally, differences in expression profiles indicate that the abomasum, rumen, and intestine are more closely related to each other, while the reticulum and omasum are more closely related to the rumen. Functional analysis using Gene Ontology (GO) categories also supports the proposed evolutionary relationships by identifying shared functions, such as muscle activity and development, lipid transport, and urea metabolism, between all sections of the digestive tract investigated.

D. C. Beck

Honglin Jiang

Liqing Zhang

Elucidating the Evolutionary Relationships among Bos taurus Digestive Organs Using Unigene Expression Data

In the housefly Musca domestica, synthesis of yolk proteins (YPs) depends on the level of circulating ecdysteroid hormones. In female houseflies, the ecdysterone concentration in the hemolymph oscillates and, at high levels, is followed by expression of YP. In male houseflies, the ecdysterone titre is constantly low and no YP is produced. In some strains, which are mutant in key components of the sex-determining pathway, males express YP even though their ecdysterone titre is not significantly elevated. However, we find that these males express a substantial amount of the female variant of the Musca doublesex homologue, Md-dsx. The dsx gene is known to sex-specifically control transcription of yp genes in the fat body of Drosophila melanogaster. Our data suggest that Md-dsx also contributes to the regulation of YP expression in the housefly by modulating the responsiveness of YP-producing cells to hormonal stimuli.

Christina Siegenthaler

Peter Maroy

Monika Hediger

Andreas Dübendorfer

Daniel Bopp

Hormones and Sex-Specific Transcription Factors Jointly Control Yolk Protein Synthesis in Musca domestica

Directional asymmetry (DA), the consistent difference between a pair of morphological structures in which the same side is always larger than the other, presents an evolutionary mystery. Although many paired traits show DA, genetic variation for DA has not been unambiguously demonstrated. Artificial selection is a powerful technique for uncovering selectable genetic variation; we review and critique the limited number of previous studies that have been performed to select on DA and present the results of a novel artificial selection experiment on the DA of posterior crossvein location in Drosophila wings. Fifteen generations of selection in two genetically distinct lines were performed and none of the lines showed a significant response to selection. Our results therefore support and reconfirm previous findings; despite apparent natural variation and evolution of DA in nature, DA remains a paradoxical trait that does not respond to artificial selection.

Ashley J. R. Carter

Elizabeth Osborne

David Houle

Heritability of Directional Asymmetry in Drosophila melanogaster

Glacier ice worms, Mesenchytraeus solifugus and related species, are the largest glacially obligate metazoans. As one component of cold temperature adaptation, ice worms maintain atypically high energy levels in an apparent mechanism to offset cold temperature-induced lethargy and death. To explore this observation at a mechanistic level, we considered the putative contribution of <svg style="vertical-align:-0.1638pt;width:12.4375px;" id="M1" height="17.9125" version="1.1" viewBox="0 0 12.4375 17.9125" width="12.4375" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
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			<g transform="matrix(.012,-0,0,-.012,8.225,9.488)"><path id="x2032" d="M227 744l-123 -338l-31 15l73 368q12 3 41.5 -8t36.5 -20z" /></g>

		
	
</svg> adenosine monophosphate deaminase (AMPD), a key regulator of energy metabolism in eukaryotes. We cloned cDNAs encoding ice worm AMPD, generating a fragment encoding 543 amino acids that included a short N-terminal region and complete C-terminal catalytic domain. The predicted ice worm AMPD amino acid sequence displayed conservation with homologues from other mesophilic eukaryotes with notable exceptions. In particular, an ice worm-specific K188E substitution proximal to the AMP binding site likely alters the architecture of the active site and negatively affects the enzyme&#x27;s activity. Paradoxically, this would contribute to elevated intracellular ATP levels, which appears to be a signature of cold adapted taxa.

Roberto Marotta

Bradley R. Parry

Daniel H. Shain

Divergence of AMP Deaminase in the Ice Worm Mesenchytraeus solifugus (Annelida, Clitellata, Enchytraeidae)

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International Journal of Evolutionary Biology

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International Journal of Evolutionary Biology