Same-Sex Twin Pair Phenotypic Correlations are Consistent with Human <Emphasis Type="Italic">Y</Emphasis> Chromosome Promoting Phenotypic Heterogeneity

Junk DNA has been long appreciated as an evolutionary facilitator because it can participate in the causation of genetic variation such as chromosome rearrangements and can be exapted into coding or regulatory elements. Recently, it has been proposed that junk DNA variation within natural populations indirectly causes a phenotypic heterogeneity that subsequently promotes genetic capacitance, i.e., the random fluctuation of genetic variation. Junk DNA role as capacitor might drive population traits such as sexual dimorphism, spatiotemporal dynamics, or genetic diversification leading into speciation. Whether the human species also showed junk DNA-based capacitance manifested as a junk DNA-dependent phenotypic heterogeneity that contributed to the etiology and expression of diseases or the evolutionary history of human populations is intriguing. Because the human Y chromosome is highly enriched in junk DNA, humans are sexually dimorphic for the genomic content in junk DNA. Thus, it would be expected that junk DNA-based capacitance in humans were manifested as a sexual dimorphism for phenotypic heterogeneity. Here, I gather supporting evidence for the existence of a sexual dimorphism for putative junk DNA-based phenotypic heterogeneity by analyzing same-sex twin pairs phenotypic concordance.     

Geographic structuring into vicariant species-pairs in a wide-ranging,high-dispersal plant–insect mutualism: the case of <Emphasis Type="Italic">Ficus racemosa</Emphasis> and its pollinating wasps

Ficus and their mutualistic pollinating wasps provide a unique model to investigate joint diversification in a high dispersal system. We investigate genetic structuring in an extremely wide-ranging Ficus species, Ficus racemosa, and its pollinating wasp throughout their range, which extends from India to Australia. Our samples were structured into four large, vicariant populations of figs and wasps which may correspond to distinct (sub)species, located in India, China-Thailand, Borneo, and Australia. However, the genetically most divergent group was the Indian population for the figs and the China-Thailand population for the wasps, suggesting different evolutionary histories of populations. Molecular dating for the wasps shows that diversification of the pollinator clade is surprisingly old, beginning about 13.6 Ma. Data on both the host fig species and its pollinating wasps suggest that strong genetic flow within biogeographic groups over several hundreds of kilometers has limited genetic and morphological differentiation and, potentially, local adaptation. This is probably due to long-distance dispersal of pollinating wasps. The genetic clustering into large geographic units observed in F. racemosa and its pollinators is reminiscent of what can be observed in some other high-dispersal organisms characterized by morphology that varies little over huge distances. The implications of strong gene flow for diversification processes and adaptation to different ecological conditions in Ficus and their pollinating wasps are just beginning to emerge.     

Significant patterns of fine-scale spatial genetic structure in a narrow endemic wind-dispersed tree species, <Emphasis Type="Italic">Cedrus brevifolia</Emphasis> Henry

Cedrus brevifolia is a narrowly distributed conifer species, currently limited to a single mountain in Cyprus, growing in restricted habitats on sites of different densities and sizes. This study assessed the influence of seed and pollen dispersal, as well as the effect of demographic and genetic features on the magnitude of fine-scale spatial genetic structure (SGS). Sampling was performed in 11 plots where 50 neighboring adult trees were sampled from each plot, while biparentally and paternally inherited genomes were used for analysis with microsatellites. Fine-scale SGS was significant but showed contrasting patterns among plots. Although the magnitude of SGS in C. brevifolia mainly results from restricted seed dispersal, short-distance pollen dispersal could also explain fine-scale SGS in some plots, which is rather uncommon in wind-pollinated conifer species. The lack of a general and consistent trend of SGS among plots and between genomes indicates that pollen and seed dispersal varies at plot level. The complex SGS patterns in C. brevifolia may result from the unequal ratio of male and female strobilies of trees within the same plots, at different reproductive periods. Demographic features such as habitat fragmentation did not influence the magnitude of SGS in C. brevifolia, whereas low tree aggregation reduced it. Further, the significant correlation observed between linkage disequilibrium (LD) and plots with significant SGS supports the assumption that under specific conditions, LD is likely to be caused by the magnitude of SGS.     

Looking beneath the tip of the iceberg: diversification of the genus <Emphasis Type="Italic">Epimeria</Emphasis> on the Antarctic shelf (Crustacea,Amphipoda)

The amphipod genus Epimeria is very speciose in Antarctic waters. Although their brooding biology, massive and heavily calcified body predict low dispersal capabilities, many Epimeria species are documented to have circum-Antarctic distributions. However, these distribution records are inevitably dependent on the morphological species definition. Yet, recent DNA evidence suggests that some of these Epimeria species may be complexes of species with restricted distributions. Mitochondrial COI and nuclear 28S rDNA sequence data were used to infer evolutionary relationships among 16 nominal Epimeria species from the Antarctic Peninsula, the eastern Weddell Sea and the Adélie Coast. Based on this phylogenetic framework, we used morphology and the DNA-based methods GMYC, bPTP and BPP to investigate species boundaries, in order to revise the diversity and distribution patterns within the genus. Most of the studied species appeared to be complexes of pseudocryptic species, presenting small and previously overlooked morphological differences. Altogether, 25 lineages were identified as putative new species, increasing twofold the actual number of Antarctic Epimeria species. Whereas most of the species may be geographically restricted to one of the three studied regions, some still have very wide distribution ranges, hence suggesting a potential for large-scale dispersal.     

Forms of natural selection controlling the genomic evolution in nodule bacteria

The role of different forms of natural selection in the evolution of genomes in root nodule bacteria (rhizobia) is analyzed for the first time. In these nitrogen-fixing symbionts of leguminous plants, two types of genome organization are revealed: (i) unitary type, where over 95% of genetic information is encoded by chromosomes (5.3–5.5 Mb in Azorhizobium, 7.0–7.8 Mb in Mesorhizobium, 7.3–10.1 Mb in Bradyrhizobium); (ii) multipartite type, where up to 50% of genetic information is allocated to plasmids or chromids which may exceed 2 Mb in size and usually control the symbiotic properties (pSyms) in fast-growing rhizobia (Rhizobium, Sinorhizobium, Neorhizobium). Emergence of fast-growing species with narrow host ranges are correlated to the extension of extrachromosomal parts of genomes, including the increase in pSyms sizes (in Sinorhizobium). An important role in this evolution is implemented by diversifying selection since the genomic diversity evolved in rhizobia owing to symbiotic interactions with highly divergent legumes. However, analysis of polymorphism in nod genes (encoding synthesis of lipo-chitooligosaccharide signaling Nod factors) suggests that the impacts of diversifying selection are restricted to the bacterial divergence for host specificity and do not influence the overall genome organization. Since the extension of rhizobia genome diversity results from the horizontal sym gene transfer occurring with low frequencies, we suggest that this extension is due to the frequency-dependent selection anchoring the rare genotypes in bacterial populations. It is implemented during the rhizobia competition for nodulation encoded by the functionally diverse cmp genes. Their location in different parts of bacterial genomes may be considered as an important factor of their adaptive diversification implemented in the host-associated microbial communities.     

Development of the St/J and V Genome Specific Molecular Marker Based on 5s rDNA Polymorphism in <Emphasis Type="Italic">Thinopyrum bessarabicum</Emphasis>, <Emphasis Type="Italic">Pseudoroegneria spicata</Emphasis>, and <Emphasis Type="Italic">Dasypyrum villosum</Emphasis>

Nontranscribed spacers (NTS) of 5S rDNA are often polymorphic in closely related species and even in the same genome. The polymorphism of 5S rDNA NTS was shown between genomes St, J, and V of Triticeae species Thinopyrum bessarabicum, Pseudoroegneria spicata, and Dasypyrum villosum, respectively. A molecular genetic marker was designed based on the 5S rDNA NTS polymorphism that allows identification of the St, J, and V genomes. We designed a pair of primers that correspond to the conserved regions of 5S rDNA NTS between the genomes studied. The PCR amplicon length is 158 bp, 171 bp, and 172 bp for V, St, and J genomes, respectively. The fragment of the St genome is characterized by the SmiM I restriction site that enables its differentiation from the J genome fragment that lacks this site. The developed marker showed its efficiency for verification of germplasm accessions and the study of allopolyploids.     

Evolution of root nodule bacteria: Reconstruction of the speciation processes resulting from genomic rearrangements in a symbiotic system

The processes of speciation and macroevolution of root nodule bacteria (rhizobia), based on deep rearrangements of their genomes and occurring in the N₂-fixing symbiotic system, are reconstructed. At the first stage of rhizobial evolution, transformation of free-living diazotrophs (related to Rhodopseudomonas) to symbiotic N₂-fixers (Bradyrhizobium) occurred due to the acquisition of the fix gene system, which is responsible for providing nitrogenase with electrons and redox potentials, as well as for oxygen-dependent regulation of nitrogenase synthesis in planta, and then of the nod genes responsible for the synthesis of the lipo-chitooligosaccharide Nod factors, which induce root nodule development. The subsequent rearrangements of bacterial genomes included (1) increased volume of hereditary information supported by species, genera (pangenome), and individual strains; (2) transition from the unitary genome to a multicomponent one; and (3) enhanced levels of bacterial genetic plasticity and horizontal gene transfer, resulting in formation of new genera—of which Mesorhizobium, Rhizobium, and Sinorhizobium are the largest—and of over 100 species. Rhizobial evolution caused by development and diversification of the Nod factor-synthesizing systems may result in either relaxed host specificity range (transition of Bradyrhizobium from autotrophic to symbiotrophic carbon metabolism in interaction with a broad spectrum of legumes) or narrowed host specificity range (transition of Rhizobium and Sinorhizobium to “altruistic” interaction with legumes of the galegoid clade). Reconstruction of the evolutionary pathway from symbiotic N₂-fixers to their free-living ancestors makes it possible to initiate the studies based on up-to-date genome screening technologies and aimed at the issues of genetic integration of organisms into supraspecies complexes, ratios of the macro- and microevolutionary mechanisms, and development of cooperative adaptations based on altruistic interaction between the symbiotic partners.     

Characterization of the complete mitochondrial genome of flower-breeding <Emphasis Type="Italic">Drosophila incompta</Emphasis> (Diptera,Drosophilidae)

Drosophila incompta belongs to the flavopilosa group of Drosophila, and has a restricted ecology, being adapted to flowers of Cestrum as feeding and oviposition sites. We sequenced, assembled, and characterized the complete mitochondrial genome (mtDNA) of D. incompta. In addition, we performed phylogenomic and polymorphism analyses to assess evolutionary diversification of this species. Our results suggest that this genome is syntenic with the other published mtDNA of Drosophila. This molecule contains 15,641 bp and encompasses two rRNA, 22 tRNA and 13 protein-coding genes. Regarding nucleotide composition, we found a high A?T bias (76.6 %). The recovered phylogenies indicate D. incompta in the virilis–repleta radiation, as sister to the virilis or repleta groups. The most interesting result is the high degree of polymorphism found throughout the D. incompta mitogenome, revealing pronounced intrapopulational variation. Furthermore, intraspecific nucleotide diversity levels varied between different regions of the genome, thus allowing the use of different mitochondrial molecular markers for analysis of population structure of this species.     

Genome-wide analysis of long,exact DNA repeats in rhizobia

The rhizobia are a group of bacteria widely studied for their capacity to form intimate symbiotic relationships with leguminous plants. However, they are also interesting for containing a remarkable abundance of repetitive genetic elements, such as long DNA repeats. In this study we deeply analyzed long, exact DNA repeats in five representative rhizobial genomes; Rhizobium etli, Rhizobium leguminosarum, Bradyrhizobium japonicum, Sinorhizobium meliloti and Mesorhizobium loti. The results suggest that a huge proportion of repeats can be located in either plasmid or chromosome replicons, except in B. japonicum, which lacks plasmids, but contains the largest number, and longest repeat elements of the genomes analyzed here. Interestingly, we detected a slight correlation between the density of repeats (either number or length) and genome size. As expected, the highest percentage of DNA repeats code for mobile genetic elements, including insertion sequences, recombinases, and transposases. Some repeats corresponded to non-coding or intergenic regions, while in genomes like that of R. etli, a significant percentage of large repeats, mainly located in plasmids, were strongly associated with symbiotic and nitrogen fixation activities. In conclusion, our analysis shows that rhizobial genomes contain a high density of long DNA repeats, which might facilitate recombination events and genome rearrangements, functioning in adaption and persistence during saprophytic or symbiotic life.     

Evolutionary and ecological implications of genome size in the North American endemic sagebrushes and allies (Artemisia, Asteraceae)

The genome size of 51 populations of 20 species of the North American endemic sagebrushes (subgenus Tridentatae ), related species, and some hybrid taxa were assessed by flow cytometry, and were analysed in a phylogenetic framework. Results were similar for most Tridentatae species, with the exception of three taxonomically conflictive species:  Artemisia bigelovii Gray,  Artemisia pygmaea Gray, and  Artemisia rigida Gray. Genome size homogeneity (together with the high morphological, chemical, and karyological affinities, as well as low DNA sequence divergence) could support a recent diversification process in this geographically restricted group, thought to be built upon a reticulate evolutionary framework. The Tridentatae and the other North American endemic Artemisia show a significantly higher genome size compared with the other subgenera. Our comparative analyses including genome size results, together with different kinds of ecological and morphological traits, suggest an evolutionary change in lifestyle strategy linked to genome expansion, in which junk or selfish DNA accumulation might be involved. Conversely, weed or invasive behaviour in Artemisia is coupled with lower genome sizes. Data for both homoploid and polyploid hybrids were also assessed. Genome sizes are close to the expected mean of parental species for homoploid hybrids, but are lower than expected in the allopolyploids, a phenomenon previously documented to be related with polyploidy.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 631–649.     

Evolutionary relationships between Saccharomyces cerevisiae and other fungal species as determined from genome comparisons

The increasing number of fungal genomes whose sequence has been completed permits their comparison both at the nucleotide and protein levels. The information thus obtained improves our knowledge on evolutionary relationships between fungi. Comparison of the Saccharomyces cerevisiae genome with other Hemiascomycetes genomes confirms that a whole-genome duplication occurred before the diversification between Candida glabrata and the Saccharomyces sensu stricto species and after separation from the branch leading to the other Hemiascomycetes. Duplication was followed by individual gene losses and rearrangements affecting extensive DNA regions. Although S. cerevisiae and C. glabrata are two closely related yeast species at an evolutionary scale, their different habitats and life styles correlate with specific gene differences and with more extensive gene loses having occurred in the parasitic C. glabrata. At a closer evolutive scale, diversification among the sensu stricto species began with nucleotide changes at the intergenic regions affecting sequences that are not relevant for gene regulation, together with more extensive genome rearrangements involving transposons and telomeric regions. One important characteristic of fungal genomes that is shared with other eukaryotes is the fusion of gene sequences coding for separate protein modules into a single open reading frame. This allows diversification of protein functions while saving gene information.     

Research on meiotic chromosome pairing in <Emphasis Type="Italic">Roegneria sinica</Emphasis> var. <Emphasis Type="Italic">media</Emphasis> evaluated using genomic in situ hybridization

The analysis of chromosome pairing during meiosis is important for understanding the relationships between different genomes. To evaluate the diversity of chromosome pairing behavior in the wild species of Roegneria sinica var. media Keng with St and H genomes in Triticeae (Poaceae), differences and similarities in the meiotic chromosome pairing behaviors of the two genomes in two populations of R. sinica var. media, were analyzed using genomic in situ hybridization. Chromosome pairing at meiotic metaphase I in the two populations of R. sinica var. media mainly formed bivalents, although several univalents, trivalents and quadrivalents also occurred. Chromosome pairings occurred mainly between homologous chromosomes. However, some non-homologous pairings were observed under natural conditions. No significant differences in karyotype were found between the St and H genomes. Chromosome pairing behaviors differed between and within the two populations. Genetic variation occurred mainly within populations (94.04 %), and variation was more abundant in one population than the other. The genomes St and H differed, but there was some relationship between the two genomes. These findings suggest that homoeologous pairing of chromosomes or exchanges occurred between different genomes of the wild species in Triticeae during evolution. The findings also provide conclusive cytological evidence for genetic variation within the wild species, which forms the basis of their genetic diversity.     

Surviving in isolation: genetic variation,bottlenecks and reproductive strategies in the Canarian endemic <Emphasis Type="Italic">Limonium macrophyllum</Emphasis> (Plumbaginaceae)

Oceanic archipelagos are typically rich in endemic taxa, because they offer ideal conditions for diversification and speciation in isolation. One of the most remarkable evolutionary radiations on the Canary Islands comprises the 16 species included in Limonium subsection Nobiles, all of which are subject to diverse threats, and legally protected. Since many of them are single-island endemics limited to one or a few populations, there exists a risk that a loss of genetic variation might limit their long-term survival. In this study, we used eight newly developed microsatellite markers to characterize the levels of genetic variation and inbreeding in L. macrophyllum, a species endemic to the North-east of Tenerife that belongs to Limonium subsection Nobiles. We detected generally low levels of genetic variation over all populations (H _T = 0.363), and substantial differentiation among populations (F _ST = 0.188; R _ST = 0.186) coupled with a negligible degree of inbreeding (F?=?0.042). Obligate outcrossing may have maintained L. macrophyllum relatively unaffected by inbreeding despite the species’ limited dispersal ability and the genetic bottlenecks likely caused by a prolonged history of grazing. Although several factors still constitute a risk for the conservation of L. macrophyllum, the lack of inbreeding and the recent positive demographic trends observed in the populations of this species are factors that favour its future persistence.     

Comparative study on mitogenomes of green tide algae

Since 2007, the annual green tide disaster in the Yellow Sea has brought serious economic losses to China. There is no research on the genetic similarities of four constituent species of green tide algae at the genomic level. We previously determined the mitochondrial genomes of Ulva prolifera, Ulva linza and Ulva flexuosa. In the present work, the mitochondrial genome of another green tide (Ulva compressa) was sequenced and analyzed. With the length of 62,311 bp, it contained 29 encoding genes, 26 tRNAs and 10 open reading frames. By comparing these four mitochondrial genomes, we found that U. compressa was quite different from the other three types of Ulva species. However, there were similarities between U. prolifera and U. linza in the number, distribution and homology of open reading frames, evolutionary and codon variation of tRNA, evolutionary relationship and selection pressure of coding genes. Repetitive sequence analysis of simple sequence repeats, tandem repeat and forward repeats further supposed that they have evolved from the same origin. In addition, we directly analyzed gene homologies and translocation of four green tide algae by Mauve alignment. There were gene order rearrangements among them. With fast-evolving genomes, these four green algal mitochondria have both conservatism and variation, thus opening another window for the understanding of origin and evolution of Ulva.     

What transposable elements tell us about genome organization and evolution: the case of Drosophila

Transposable elements (TEs) have been identified in every organism in which they have been looked for. The sequencing of large genomes, such as the human genome and those of Drosophila, Arabidopsis, Caenorhabditis, has also shown that they are a major constituent of these genomes, accounting for 15% of the genome of Drosophila, 45% of the human genome, and more than 70% in some plants and amphibians. Compared with the 1% of genomic DNA dedicated to protein-coding sequences in the human genome, this has prompted various researchers to suggest that the TEs and the other repetitive sequences that constitute the so-called "noncoding DNA", are where the most stimulating discoveries will be made in the future (Bromham, 2002). We are therefore getting further and further from the original idea that this DNA was simply "junk DNA", that owed its presence in the genome entirely to its capacity for selfish transposition. Our understanding of the structures of TEs, their distribution along the genomes, their sequence and insertion polymorphisms within genomes, and within and between populations and species, their impact on genes and on the regulatory mechanisms of genetic expression, their effects on exon shuffling and other phenomena that reshape the genome, and their impact on genome size has increased dramatically in recent years. This leads to a more general picture of the impact of TEs on genomes, though many copies are still mainly selfish or junk DNA. In this review we focus mainly on discoveries made in Drosophila, but we also use information about other genomes when this helps to elucidate the general processes involved in the organization, plasticity, and evolution of genomes.     

Autopolyploidy leads to rapid genomic changes in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Polyploidy is a widespread feature of plant genomes. As a typical model of polyploidy, autopolyploidy has been postulated evolutionary dead ends and received little attention compared with allopolyploidy. For the limited data available so far, the evolutionary outcome of genome diversity in autopolyploids remains controversial in comparison with its diploid ancestors. In the present study, the effects of autopolyploidy on genome diversity were revealed at a genome-wide scale by comparative analyses of polymorphism between Arabidopsis autopolyploids (autotetraploids and autotriploids) and related diploids within the first ten successive inbred generations using amplified fragment length polymorphism. The results showed that in contrast with diploids, the rapid genomic changes (including gain and loss of DNA sequences) in autopolyploids were definitely found within the first generations after autopolyploidization, but slow down and probably stabilized in the higher generations as a source of genetic diversity in the long term. The sequencing of these DNA fragments indicated that these changes occurred both on genic and inter-genic (or intronic) regions, and quantitative PCR showed that the expression of some corresponding genes in the genic regions was obviously affected (including upregulation, downregulation and silencing) in autopolyploids. Therefore, this study demonstrated that autopolyploidy could lead to rapid genomic changes and probably influence expression and function of certain genes within the first generations, giving rising to genetic diversification after polyploidization.     

An evolutionary correlate of genome size change in plethodontid salamanders

Variation in the amount of nuclear DNA, the C-value, does not correlate with differences in morphological complexity. There are two classes of explanations for this observation, which is known as the ''C-value paradox''. The quantity of DNA may serve a ''nucleotypic'' function that is positively selected. Alternatively, large genomes may consist of junk DNA, which increases until it negatively affects fitness. Attempts to resolve the C-value paradox focus on the link between genome size and fitness. This link is usually sought in life history traits, particularly developmental rates. I examined the relationship among two life history traits, egg size and embryonic developmental time and genome size, in 15 species of plethodontid salamanders. Surprisingly, there is no correlation between egg size and developmental time, a relationship included in models of life history evolution. However, genome size is positively correlated with embryonic developmental time, a result that is robust with respect to many sources of variation in the data. Without information on the targets of natural selection it is not possible with these data to distinguish between nucleotypic and junk DNA explanations for the C-value paradox.     

Variability of DNA Content in Individual Cells of <Emphasis Type="Italic">Bacillus</Emphasis>

THE average content of DNA in Bacillus spores is unaffected by the growth medium and is constant for each species¹. Within the Bacillus group, however, the average amount of DNA per spore varies from species to species¹. A cell of B. cereus contains on average twice as much DNA as the spore and during sporulation this DNA is divided equally between the spore and the sporangium². Estimates^3–5 of genome size vary from 1.3 × 10⁹ to 10 × 10⁹ daltons and the number of genomes per cell from 2 to 4^4–8. Some of these variations may be associated with differences within the cells rather than differences of methodolqgy; spores within a population vary not only in size and shape, but also in their content of stainable chromatin⁹. Moreover, in ‘Renografm’ density gradients¹⁰, spores band within a range of densities. If spores are taken from a narrow part of this range, regrown and rebanded, the original pattern of dispersal occurs, suggesting that spores in the same population normally show variation in density as well as in size (A. I. Aronson, personal communication).