The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes

It has now been established that transposable elements (TEs) make up a variable, but significant proportion of the genomes of all organisms, from Bacteria to Vertebrates. However, in addition to their quantitative importance, there is increasing evidence that TEs also play a functional role within the genome. In particular, TE regulatory regions can be viewed as a large pool of potential promoter sequences for host genes. Studying the evolution of regulatory region of TEs in different genomic contexts is therefore a fundamental aspect of understanding how a genome works. In this paper, we first briefly describe what is currently known about the regulation of TE copy number and activity in genomes, and then focus on TE regulatory regions and their evolution. We restrict ourselves to retrotransposons, which are the most abundant class of eukaryotic TEs, and analyze their evolution and the subsequent consequences for host genomes. Particular attention is paid to much-studied representatives of the Vertebrates and Invertebrates, Homo sapiens and Drosophila melanogaster, respectively, for which high quality sequenced genomes are available.     

Gamma-tubulin is present in Drosophila melanogaster and Homo sapiens and is associated with the centrosome

The mipA gene of A. nidulans encodes a newly discovered member of the tubulin superfamily of proteins, gamma-tubulin. In A. nidulans, gamma-tubulin is essential for nuclear division and microtubule assembly and is associated with the spindle pole body, the fungal microtubule organizing center. By low stringency hybridizations we have cloned cDNAs from D. melanogaster and H. sapiens, the predicted products of which share more than 66% amino acid identity with A. nidulans gamma-tubulin. gamma-Tubulin-specific antibodies stained centrosomes of Drosophila, human, and mouse cell lines. Staining was most intense in prophase through metaphase when microtubule assembly from centrosomes was maximal. These results demonstrate that gamma-tubulin genes are present and expressed in humans and flies; they suggest that gamma-tubulin may be a universal component of microtubule organizing centers; and they are consistent with an earlier hypothesis that gamma-tubulin is a minus-end nucleator of microtubule assembly.     

Population structure and the evolution of Homo sapiens in Africa

It has been proposed that a multiregional model could describe how Homo sapiens evolved in Africa beginning 300,000 years ago. Multiregionalism would require enduring morphological or behavioral differences among African regions and morphological or behavioral continuity within each. African fossils, archeology, and genetics do not comply with either requirement and are unlikely to, because climatic change periodically disrupted continuity and reshuffled populations. As an alternative to multiregionalism, I suggest that reshuffling produced novel gene constellations, including one in which the additive or cumulative effect of newly associated genes enhanced cognitive or communicative potential. Eventual fixation of such a constellation in the lineage leading to modern H. sapiens would explain the abrupt appearance of the African Later Stone Age 50–45 thousand years ago, its nearly simultaneous expansion to Eurasia in the form of the Upper Paleolithic, and the ability of fully modern Upper Paleolithic people to swamp or replace non‐modern Eurasians.     

Morphological relationship between the cranial and supraorbital regions in Homo sapiens

Although some hypotheses that attempt to explain the variation in supraorbital region morphology in modern humans have been proposed, this issue is still not well understood. In this study, the craniofacial size and spatial models were tested using a sample of modern human crania from geographically diverse populations, and the co‐occurrence of the degrees of glabella (GL) and superciliary arch (ST) expression were analyzed. The two supraorbital structures were examined by visual assessment, and eight quantitative variables were included in the three‐way ANOVA, canonical variates analysis and partial rank correlation. The influences of sex and the region of origin of the cranial samples on the relationships between the examined variables and the degrees of supraorbital structures expression were also considered. The results only partially supported the craniofacial size and spatial models and suggested that GL and ST experienced separate influences during development. In the sample of all crania, the neurocranial size more strongly influenced the morphological variation of the ST than of the GL, and sex influenced both of these structures the most. The results suggest that sex may be the main factor (having an influence independent of the other traits) on the morphological variation of the GL and ST. Am J Phys Anthropol 156:110–124, 2015 © 2014 Wiley Periodicals, Inc.     

Enamel thickness of deciduous and permanent molars in modern Homo sapiens

This study presents data on the enamel thickness of deciduous (dm2) and permanent (M1-M3) molars for a geographically diverse sample of modern humans. Measurements were recorded from sections through the mesial cusps of unworn teeth. Enamel is significantly thinner on deciduous than on permanent molars, and there is a distinct trend for enamel to increase in relative thickness from M1 to M3. The relatively thicker enamel of M2s and especially M3s can be related to the overall reduction in size of more distal molar crowns, which has been attained through a differential loss of the dentine component. Enamel tends to be thicker on the protocone than on the paracone, and thicker on the protoconid than on the metaconid, but its distribution is not wholly concordant with models that predict increased thickness as a means by which to counter heavier attritional loss on these "functional" cusps. Indeed, the thickness of enamel tends to be more variable on cusp tips and occlusal surfaces than over the lateral aspects of cusps. The proportionately thicker enamel over the lateral aspects of the protocone and protoconid more likely serves as a means to prolong functional crown life by preventing cusp fracture, rather than being an adaptation to increase the attritional longevity of wear facets. The present data suggest that the human dentition is not predisposed to develop a helicoidal wear plane through the disposition of molar enamel thickness.     

The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes

Background  

Several studies have shown that genomes contain a mixture of transposable elements, some of which are still active and others ancient relics that have degenerated. This is true for the non-LTR retrotransposon Helena, of which only degenerate sequences have been shown to be present in some species (Drosophila melanogaster), whereas putatively active sequences are present in others (D. simulans). Combining experimental and population analyses with the sequence analysis of the 12 Drosophila genomes, we have investigated the evolution of Helena, and propose a possible scenario for the evolution of this element.     

The Exploitation of Ungulate Bones in Homo neanderthalensis and Homo sapiens

Analysis of ungulate bones recovered from a number of Upper and Middle Palaeolithic sites in southern Italy revealed differences in the presence of anatomical elements. There is a lack of clear evidence of carnivore activities, and differences can be attributed to human activity. Indeed, these differences were probably due to different patterns of skeletal exploitation between Homo neanderthalensis and H. sapiens. Small limb bones (carpals, tarsals, sesamoids, long bone epiphyses and especially phalanges) are rarely found in Middle Palaeolithic deposits, but are abundant in the Upper Palaeolithic. The observation of unidentified bone fragments at these sites indicates that during the middle Palaeolithic, marrow extraction regarded essentially the treatment of long bones. First and second phalanges were not frequently used for this practice, but they were often fragmented by H. sapiens. Lack of these bones among the remains of meals of Neanderthal suggests that these bones were probably destroyed by their utilisation as fuel.     

Evolutionary pattern of the gtwin retrotransposon in the Drosophila melanogaster subgroup

The gtwin retrotransposon was recently discovered in the Drosophila melanogaster genome and it is evolutionarily closer to gypsy endogenous retrovirus. This study has identified gtwin homologous sequences in the genome of D. simulans, D. sechellia, D. erecta and D. yakuba by performing homology searches against the public genome database of Drosophila species. The phylogenetic analyses of the gtwin env gene sequences of these species have shown some incongruities with the host species phylogeny, suggesting some horizontal transfer events for this retroelement. Moreover, we reported the existence of DNA sequences putatively encoding full-length Env proteins in the genomes of Drosophila species other than D. melanogaster. The results suggest that the gtwin element may be an infectious retrovirus able to invade the genome of new species, supporting the gtwin evolutionary picture shown in this work.     

Five Drosophila genomes reveal nonneutral evolution and the signature of host specialization in the chemoreceptor superfamily

The insect chemoreceptor superfamily comprises the olfactory receptor (Or) and gustatory receptor (Gr) multigene families. These families give insects the ability to smell and taste chemicals in the environment and are thus rich resources for linking molecular evolutionary and ecological processes. Although dramatic differences in family size among distant species and high divergence among paralogs have led to the belief that the two families evolve rapidly, a lack of evolutionary data over short time scales has frustrated efforts to identify the major forces shaping this evolution. Here, we investigate patterns of gene loss/gain, divergence, and polymorphism in the entire repertoire of approximately 130 chemoreceptor genes from five closely related species of Drosophila that share a common ancestor within the past 12 million years. We demonstrate that the overall evolution of the Or and Gr families is nonneutral. We also show that selection regimes differ both between the two families as wholes and within each family among groups of genes with varying functions, patterns of expression, and phylogenetic histories. Finally, we find that the independent evolution of host specialization in Drosophila sechellia and D. erecta is associated with a fivefold acceleration of gene loss and increased rates of amino acid evolution at receptors that remain intact. Gene loss appears to primarily affect Grs that respond to bitter compounds while elevated Ka/Ks is most pronounced in the subset of Ors that are expressed in larvae. Our results provide strong evidence that the observed phenomena result from the invasion of a novel ecological niche and present a unique synthesis of molecular evolutionary analyses with ecological data.     

LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR’s divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.     

现代人起源问题的新争论

现代人在分类学上称为晚期智人。他们是怎样起源的?长期来有两种理论,一种叫直接演化说(Direct evolution hypothesis)或系统说,也叫多地区起源说。这种理论认为现代人是由当地的早期智人以至猿人演化而来的,各人种在很久以前即已分歧,各自平行发展,演化成现代人,但长时期来互相有基因的交流。例如欧洲的白种人是由当地的尼安德特人逐渐演变来的;亚洲的黄种人是由当地的早期智人和猿人演变来的。另一种理论叫入侵论(Invasion hypothesis),也叫迁徙说或代替说,这种理论认为欧洲是典型尼人的家乡, 而解剖结构上的现代人是在欧洲以外地区演化出来, 然后侵人欧洲的尼人区域, 消灭了土著的尼人而形成的;侵人亚洲的也一样, 形成现代的黄种人。这种单一地区起源说过去一般认为亚洲西部是现代人最早形成的地区, 近年来有人提出非洲南部才是现代人最早形成的地区, 然后迁徙到世界各地。     

Distribution of the bilbo non-LTR retrotransposon in Drosophilidae and its evolution in the Drosophila obscura species group

The bilbo element is a non-LTR retrotransposon isolated from Drosophila subobscura. We conducted a distribution survey by Southern blot for 52 species of the family Drosophilidae, mainly from the obscura and melanogaster groups. Most of the analyzed species bear sequences homologous to bilbo from D. subobscura. In the obscura group, species from the same species subgroup also share similar Southern blot patterns. To investigate the phylogenetic relationship among these elements, we analyzed eight copies of a short sequence of the element from several species of the obscura group. The obtained phylogram agrees with the phylogeny of the species, which suggests vertical transmission of the element.     

Interactions of Polycomb and trithorax with cis regulatory regions of Ultrabithorax during the development of Drosophila melanogaster.

The activity of the Ultrabithorax gene is continuously required during imaginal development to maintain the morphogenetic identity of the third thoracic segment of Drosophila. The spatial pattern of Ultrabithorax gene expression depends on certain cis regulatory regions and several trans regulatory genes. Amongst the latter the Polycomb gene is necessary to maintain Ultrabithorax repressed in cells where it was not initially activated and the trithorax gene is required for maintaining the expression of the gene where initially active. We have studied genetic interactions between several Ultrabithorax mutations in coding and cis regulatory regions in combination with Polycomb and trithorax mutations. Our results suggest that Polycomb and trithorax gene products do not interact with Ultrabithorax protein products but interact (directly or indirectly) with specific and discrete cis regulatory regions such as those where anterobithorax and postbithorax but not bithorax mutations map. We discuss possible mechanisms of these interactions.     

我国三地区黑腹果蝇中Wolbachia的系统发育关系及其对宿主生殖的影响

【目的】Wolbachia 是广泛存在于节肢动物和丝状线虫体内的一类共生菌, 能够以多种方式对宿主产生影响。精卵细胞质不亲和（CI）是其引起的最普遍的表型, 即感染Wolbachia的雄性宿主与未感染或感染不同品系的雌性宿主交配后, 不能产生后代或后代极少, 而感染同品系Wolbachia的雌雄宿主交配后则能正常产生后代。我们前期研究发现, 湖北武汉、 云南六库和天津3个地区黑腹果蝇Drosophila melanogaster被Wolbachia感染。本研究旨在明确这3个地区黑腹果蝇中Wolbachia的系统发育关系及其对宿主生殖的影响。【方法】利用Clustal X软件对Wolbachia的wsp基因序列进行比对, 利用MEGA软件构建系统发育树。采用多位点序列分型（MLST）的方法对Wolbachia进行分型。通过区内交配和区之间杂交的方式研究不同地区黑腹果蝇体内Wolbachia 的关系及其对果蝇生殖的影响。【结果】湖北武汉、 云南六库和天津3个地区黑腹果蝇中感染的Wolbachia都是属于A大组的Mel亚群。这3个地区果蝇感染的Wolbachia的序列类型（ST）不同, Wolbachia之间存在一定的差异。湖北武汉和天津果蝇中的Wolbachia能引起强烈的CI表型, 而云南六库果蝇中的Wolbachia引起的CI强度相对较弱。武汉果蝇中Wolbachia不能完全挽救天津果蝇中Wolbachia引起的CI表型, 而天津果蝇中Wolbachia也不能完全挽救武汉果蝇中Wolbachia引起的CI表型。【结论】武汉和天津地区黑腹果蝇中的Wolbachia可能距离较远。Wolbachia的长期共生可能对黑腹果蝇的进化产生了一定的影响, 湖北武汉与云南六库的黑腹果蝇中感染的Wolbachia属于不同的序列类型, 这2个地区的黑腹果蝇已发生了一定的分歧, 产生了一定的生殖隔离。