Bounds to parapatric speciation: A Dobzhansky–Muller incompatibility model involving autosomes,X chromosomes,and mitochondria

We investigate the conditions for the origin and maintenance of postzygotic isolation barriers, so called (Bateson‐)Dobzhansky–Muller incompatibilities or DMIs, among populations that are connected by gene flow. Specifically, we compare the relative stability of pairwise DMIs among autosomes, X chromosomes, and mitochondrial genes. In an analytical approach based on a continent‐island framework, we determine how the maximum permissible migration rates depend on the genomic architecture of the DMI, on sex bias in migration rates, and on sex‐dependence of allelic and epistatic effects, such as dosage compensation. Our results show that X‐linkage of DMIs can enlarge the migration bounds relative to autosomal DMIs or autosome‐mitochondrial DMIs, in particular in the presence of dosage compensation. The effect is further strengthened with male‐biased migration. This mechanism might contribute to a higher density of DMIs on the X chromosome (large X‐effect) that has been observed in several species clades. Furthermore, our results agree with empirical findings of higher introgression rates of autosomal compared to X‐linked loci.     

Satellite DNA and chromosomes in Neotropical fishes: methods,applications and perspectives

Constitutive heterochromatin represents a substantial portion of the eukaryote genome, and it is mainly composed of tandemly repeated DNA sequences, such as satellite DNAs, which are also enriched by other dispersed repeated elements, including transposons. Studies on the organization, structure, composition and in situ localization of satellite DNAs have led to consistent advances in the understanding of the genome evolution of species, with a particular focus on heterochromatic domains, the diversification of heteromorphic sex chromosomes and the origin and maintenance of B chromosomes. Satellite DNAs can be chromosome specific or species specific, or they can characterize different species from a genus, family or even representatives of a given order. In some cases, the presence of these repeated elements in members of a single clade has enabled inferences of a phylogenetic nature. Genomic DNA restriction, using specific enzymes, is the most frequently used method for isolating satellite DNAs. Recent methods such as C₀t–1 DNA and chromosome microdissection, however, have proven to be efficient alternatives for the study of this class of DNA. Neotropical ichthyofauna is extremely rich and diverse enabling multiple approaches with regard to the differentiation and evolution of the genome. Genome components of some species and genera have been isolated, mapped and correlated with possible functions and structures of the chromosomes. The 5SHindIII‐DNA satellite DNA, which is specific to Hoplias malabaricus of the Erythrinidae family, has an exclusively centromeric location. The As51 satellite DNA, which is closely correlated with the genome diversification of some species from the genus Astyanax, has also been used to infer relationships between species. In the Prochilodontidae family, two repetitive DNA sequences were mapped on the chromosomes, and the SATH 1 satellite DNA is associated with the origin of heterochromatic B chromosomes in Prochilodus lineatus. Among species of the genus Characidium and the Parodontidae family, amplifications of satellite DNAs have demonstrated that these sequences are related to the differentiation of heteromorphic sex chromosomes. The possible elimination of satellite DNA units could explain the genome compaction that occurs among some species of Neotropical Tetraodontiformes. These topics are discussed in the present review, showing the importance of satellite DNA analysis in the differentiation and karyotype evolution of Actinopterygii.     

Mammalian X Chromosome Dosage Compensation: Perspectives From the Germ Line

Sex chromosomes are advantageous to mammals, allowing them to adopt a genetic rather than environmental sex determination system. However, sex chromosome evolution also carries a burden, because it results in an imbalance in gene dosage between females (XX) and males (XY). This imbalance is resolved by X dosage compensation, which comprises both X chromosome inactivation and X chromosome upregulation. X dosage compensation has been well characterized in the soma, but not in the germ line. Germ cells face a special challenge, because genome wide reprogramming erases epigenetic marks responsible for maintaining the X dosage compensated state. Here we explain how evolution has influenced the gene content and germ line specialization of the mammalian sex chromosomes. We discuss new research uncovering unusual X dosage compensation states in germ cells, which we postulate influence sexual dimorphisms in germ line development and cause infertility in individuals with sex chromosome aneuploidy.     

Genome size and chromosomes in marine sponges [Suberites domuncula,Geodia cydonium]

The genome size of the marine sponges Suberites domuncula and Geodia cydonium has been determined by flow cytofluorometric analysis using diamidino-phenylindole [DAPI]. Using human lymphocytes as reference the amount of DNA in cells from S. domuncula has been determined to be 3.7 pg and that of G. cydonium 3.3 pg. While no chromosomes could be identified in G. cydonium, the karyotype of the Suberites domuncula is 32 chromsomes in the diploid state. The size of the chromosomes was between 0.25 and 1.0 μm. No pronounced banding pattern was visible.     

Babesia bovis: Genome size, number of chromosomes and telomeric probe hybridisation

Pulsed field gel electrophoresis of intact chromosomes of Babesia bovis revealed four chromosomes in the haploid genome. A telomere probe, derived from Plasmodium berghei, hybridised to eight SfiI restriction fragments of genomic B. bovis DNA digests indicating the presence of four chromosomes. A small subunit (18S) ribosomal RNA gene probe hybridised to the third chromsome only. The genome size of B. bovis is estimated to be 9.4 million base pairs. The sizes of chromosomes 1, 2, 3 and 4 are estimated to be 1.4, 2.0, 2.8 and 3.2 million base pairs, respectively.     

Genome size and GC content evolution of Festuca: ancestral expansion and subsequent reduction

Background and Aims: Plant evolution is well known to be frequently associated withremarkable changes in genome size and composition; however,the knowledge of long-term evolutionary dynamics of these processesstill remains very limited. Here a study is made of the finedynamics of quantitative genome evolution in Festuca (fescue),the largest genus in Poaceae (grasses). Methods: Using flow cytometry (PI, DAPI), measurements were made of DNAcontent (2C-value), monoploid genome size (Cx-value), averagechromosome size (C/n-value) and cytosine + guanine (GC) contentof 101 Festuca taxa and 14 of their close relatives. The resultswere compared with the existing phylogeny based on ITS and trnL-Fsequences. Key Results: The divergence of the fescue lineage from related Poeae waspredated by about a 2-fold monoploid genome and chromosome sizeenlargement, and apparent GC content enrichment. The backwardreduction of these parameters, running parallel in both mainevolutionary lineages of fine-leaved and broad-leaved fescues,appears to diverge among the existing species groups. The mostdramatic reductions are associated with the most recently andrapidly evolving groups which, in combination with recent intraspecificgenome size variability, indicate that the reduction processis probably ongoing and evolutionarily young. This dynamicsmay be a consequence of GC-rich retrotransposon proliferationand removal. Polyploids derived from parents with a large genomesize and high GC content (mostly allopolyploids) had smallerCx- and C/n-values and only slightly deviated from parentalGC content, whereas polyploids derived from parents with smallgenome and low GC content (mostly autopolyploids) generallyhad a markedly increased GC content and slightly higher Cx-and C/n-values. Conclusions: The present study indicates the high potential of general quantitativecharacters of the genome for understanding the long-term processesof genome evolution, testing evolutionary hypotheses and theirusefulness for large-scale genomic projects. Taken together,the results suggest that there is an evolutionary advantagefor small genomes in Festuca.     

Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA

Many cells in the thorax of Drosophila were found to stall during replication, a phenomenon known as underreplication. Unlike underreplication in nuclei of salivary and follicle cells, this stall occurs with less than one complete round of replication. This stall point allows precise estimations of early-replicating euchromatin and late-replicating heterochromatin regions, providing a powerful tool to investigate the dynamics of structural change across the genome. We measure underreplication in 132 species across the Drosophila genus and leverage these data to propose a model for estimating the rate at which additional DNA is accumulated as heterochromatin and euchromatin and also predict the minimum genome size for Drosophila. According to comparative phylogenetic approaches, the rates of change of heterochromatin differ strikingly between Drosophila subgenera. Although these subgenera differ in karyotype, there were no differences by chromosome number, suggesting other structural changes may influence accumulation of heterochromatin. Measurements were taken for both sexes, allowing the visualization of genome size and heterochromatin changes for the hypothetical path of XY sex chromosome differentiation. Additionally, the model presented here estimates a minimum genome size in Sophophora remarkably close to the smallest insect genome measured to date, in a species over 200 million years diverged from Drosophila.     

Quantifying the relative contributions of the X chromosome,autosomes, and mitochondrial genome to local adaptation*

During local adaptation with gene flow, some regions of the genome are inherently more responsive to selection than others. Recent theory predicts that X‐linked genes should disproportionately contribute to local adaptation relative to other genomic regions, yet this prediction remains to be tested. We carried out a multigeneration crossing scheme, using two cline‐end populations of Drosophila melanogaster, to estimate the relative contributions of the X chromosome, autosomes, and mitochondrial genome to divergence in four traits involved in local adaptation (wing size, resistance to heat, desiccation, and starvation stresses). We found that the mitochondrial genome and autosomes contributed significantly to clinal divergence in three of the four traits. In contrast, the X made no significant contribution to divergence in these traits. Given the small size of the mitochondrial genome, our results indicate that it plays a surprisingly large role in clinal adaptation. In contrast, the X, which represents roughly 20% of the Drosophila genome, contributes negligibly—a pattern that conflicts with theoretical predictions. These patterns reinforce recent work implying a central role of mitochondria in climatic adaptation, and suggest that different genomic regions may play fundamentally different roles in processes of divergence with gene flow.     

Chromosome numbers and DNA content in Bromeliaceae: additional data and critical review

For the large Neotropical plant family Bromeliaceae, we provide new data on chromosome numbers, cytological features and genome size estimations, and combine them with data available in the literature. Root‐tip chromosome counts for 46 species representing four subfamilies and a literature review of previously published data were carried out. Propidium iodide staining and flow cytometry were used to estimate absolute genome sizes in five subfamilies of Bromeliaceae, sampling 28 species. Most species were diploid with 2n = 50 in Bromelioideae, Puyoideae and Pitcairnioideae, followed by 2n = 48 observed mainly in Tillandsioideae. Individual chromosome sizes varied more than tenfold, with the largest chromosomes observed in Tillandsioideae and the smallest in Bromelioideae. Genome sizes (2C‐values) varied from 0.85 to 2.23 pg, with the largest genomes in Tillandsioideae. Genome evolution in Bromeliaceae relies on two main mechanisms: polyploidy and dysploidy. With the exception of Tillandsioideae, polyploidy is positively correlated with genome size. Dysploidy is suggested as the mechanism responsible for the generation of the derived chromosome numbers, such as 2n = 32/34 or 2n = 48. The occurrence of B chromosomes in the dysploid genus Cryptanthus suggests ongoing speciation processes closely associated with chromosome rearrangements. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 349–368.     

Intervening sequences in paralogous genes: a comparative genomic approach to study the evolution of X chromosome introns

The enlargement of the genome size and the decrease in genome compactness with increase in the number and size of introns is a general pattern during the evolution of eukaryotes. Among the possible mechanisms for modifying intron size, it has been suggested that the insertion of transposable elements might have an important role in driving intron evolution. The analysis of large portions of the human genome demonstrated that a relatively recent (50 to 100 MYA) accumulation of transposable elements appears to be biased, favoring a preferential insertion of LINE1 transposons into sex chromosomes rather than into autosomes. In the present work, the effect of chromosomal location on the increase in size of introns was evaluated with a comparative analysis performed on pairs of human paralogous genes, one located on the X chromosome and the second on an autosome. A phylogenetic analysis was also performed on the X-encoded proteins and their paralogs to confirm orthology-paralogy and to approximately estimate the time of gene duplication. Statistical analysis of total intron length for each pair of paralogous genes provided no evidence for a larger size of introns in the gene copies located on the X chromosome. On the opposite, introns of autosomal genes were found to be significantly longer than introns of their X-linked paralogs. Likewise, LINE1 elements were not significantly more frequent in X-chromosome introns, whereas the frequency of SINE elements showed a marginally significant bias toward autosomal introns.     

Genome size and numerical polymorphism for the B chromosome in races of maize (Zea mays ssp. mays, Poaceae)

Twenty-one native populations (1120 individuals) of maize from Northern Argentina were studied. These populations, which belong to 13 native races, were cultivated at different altitudes (80-3620 m). Nineteen of the populations analyzed showed B chromosome (Bs) numerical polymorphism. The frequency of individuals with Bs varied from 0 to 94%. The number of Bs per plant varied from 0 to 8 Bs, with the predominant doses being 0, 1, 2, and 3. Those populations with varying number of Bs showed a positive and statistically significant correlation of mean number of Bs with altitude. The DNA content, in plants without Bs (A-DNA)(2n = 20), of 17 populations of the 21 studied was determined. A 36% variation (5.0-6.8 pg) in A-DNA content was found. A significant negative correlation between A-DNA content and altitude of cultivation and between A-DNA content and mean number of Bs was found. This indicates that there is a close interrelationship between the DNA content of A chromosomes and doses of Bs. These results suggest that there is a maximum limit to the mass of nuclear DNA so that Bs are tolerated as long as this maximum limit is not exceeded.     

Smallest angiosperm genomes found in lentibulariaceae, with chromosomes of bacterial size

Nuclear holoploid genome sizes (C-values) have been estimated to vary about 800-fold in angiosperms, with the smallest established 1C-value of 157 Mbp recorded in Arabidopsis thaliana. In the highly specialized carnivorous family Lentibulariaceae now three taxa have been found that exhibit significantly lower values: Genlisea margaretae with 63 Mbp, G. aurea with 64 Mbp, and Utricularia gibba with 88 Mbp. The smallest mitotic anaphase chromatids in G. aurea have 2.1 Mbp and are thus of bacterial size (NB: E. coli has ca. 4 Mbp). Several Utricularia species range somewhat lower than A. thaliana or are similar in genome size. The highest 1C-value known from species of Lentibulariaceae was found in Genlisea hispidula with 1510 Mbp, and results in about 24-fold variation for Genlisea and the Lentibulariaceae. Taking into account these new measurements, genome size variation in angiosperms is now almost 2000-fold. Genlisea and Utricularia are plants with terminal positions in the phylogeny of the eudicots, so that the findings are relevant for the understanding of genome miniaturization. Moreover, the Genlisea-Utricularia clade exhibits one of the highest mutational rates in several genomic regions in angiosperms, what may be linked to specialized patterns of genome evolution. Ultrasmall genomes have not been found in Pinguicula, which is the sister group of the Genlisea-Utricularia clade, and which does not show accelerated mutational rates. C-values in Pinguicula varied only 1.7-fold from 487 to 829 Mbp.     

The origin and evolution of sex chromosomes,revealed by sequencing of the Silene latifolia female genome

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DNA Damage Checkpoint, Damage Repair, and Genome Stability

Genomic DNA is under constant attack from both endogenous and exogenous sources of DNA damaging agents. Without proper care, the ensuing DNA damages would lead to alteration of genomic structure thus affecting the faithful transmission of genetic information. During the process of evolution, organisms have acquired a series of mechanisms responding to and repairing DNA damage, thus assuring the maintenance of genome stability and faithful transmission of genetic information. DNA damage checkpoint is one such important mechanism by which, in the face of DNA damage, a cell can respond to amplified damage signals, either by actively halting the cell cycle until it ensures that critical processes such as DNA replication or mitosis are complete or by initiating apoptosis as a last resort. Over the last decade, complex hierarchical interactions between the key components like ATM/ATR in the checkpoint pathway and various other mediators, effectors including DNA damage repair proteins have begun to emerge. In the meantime, an intimate relationship between mechanisms of damage checkpoint pathway, DNA damage repair, and genome stability was also uncovered. Reviewed hereinare the recent findings on both the mechanisms of activation of checkpoint pathways and their coordination with DNA damage repair machinery as well as their effect on genomic integrity.     

De novo DNA methylation independent establishment of maternal imprint on X chromosome in mouse oocytes

In female mouse embryos, the paternal X chromosome (Xp) is preferentially inactivated during preimplantation development and trophoblast differentiation. This imprinted X-chromosome inactivation (XCI) is partly due to an activating imprint on the maternal X chromosome (Xm), which is set during oocyte growth. However, the nature of this imprint is unknown. DNA methylation is one candidate, and therefore we examined whether disruptions of the two de novo DNA methyltransferases in growing oocytes affect imprinted XCI. We found that accumulation of histone H3 lysine-27 trimethylation, a hallmark of XCI, occurs normally on the Xp, and not on the Xm, in female blastocysts developed from the mutant oocytes. Furthermore, the allelic expression patterns of X-linked genes including Xist and Tsix were unchanged in preimplantation embryos and also in the trophoblast. These results show that a maternal disruption of the DNA methyltransferases has no effect on imprinted XCI and argue that de novo DNA methylation is dispensable for Xm imprinting. This underscores the difference between imprinted XCI and autosomal imprinting.     

Mammalian chromosomes contain cis-acting elements that control replication timing, mitotic condensation, and stability of entire chromosomes

Recent studies indicate that mammalian chromosomes contain discrete cis-acting loci that control replication timing, mitotic condensation, and stability of entire chromosomes. Disruption of the large non-coding RNA gene ASAR6 results in late replication, an under-condensed appearance during mitosis, and structural instability of human chromosome 6. Similarly, disruption of the mouse Xist gene in adult somatic cells results in a late replication and instability phenotype on the X chromosome. ASAR6 shares many characteristics with Xist, including random mono-allelic expression and asynchronous replication timing. Additional "chromosome engineering" studies indicate that certain chromosome rearrangements affecting many different chromosomes display this abnormal replication and instability phenotype. These observations suggest that all mammalian chromosomes contain "inactivation/stability centers" that control proper replication, condensation, and stability of individual chromosomes. Therefore, mammalian chromosomes contain four types of cis-acting elements, origins, telomeres, centromeres, and "inactivation/stability centers", all functioning to ensure proper replication, condensation, segregation, and stability of individual chromosomes.     

海三棱藨草及其近缘种基因组大小的测定

基因组大小是物种基因组的重要特征,通常用DNA C值来衡量,能够用于快速判断基因组倍性,并为分类学与进化生物学提供重要依据。海三棱藨草(Scirpus mariqueter)是长江口和杭州湾具有重要生态意义的标志性物种,被认为是扁秆藨草(S. planiculmis)和藨草(S. triqueter)的杂交种,因染色体小而难以准确确定倍性。近年来,部分研究者指出该物种的分类和命名存在疑点。该研究通过基因组Survey分析检测海三棱藨草样本CJ1的基因组特征,测序深度约为120 ×,并以绿豆(Vigna radiata)为参考标准,利用流式细胞术测定了海三棱藨草及其同域近缘种扁秆藨草和藨草以及海三棱藨草和扁秆藨草的杂交F1共13个样本的DNA C值和相对倍性。结果表明:(1)基因组Survey分析测得CJ1的基因组大小为244.12 Mbp,杂合率为0.68%,重复序列比例为42.38%,GC含量为37.25%。(2)流式细胞术测得来自不同区域的海三棱藨草各样本的基因组倍性相同,1C值在234.87 ～ 242.5 Mbp之间,其中CJ1的基因组大小与基因组Survey检测结果高度一致。(3)扁秆藨草的1C值在251.77 ～ 264.13 Mbp之间,藨草1C值为537.33 Mbp。根据上述基因组大小,认为海三棱藨草不可能是这两者的杂交种。该研究补充了海三棱藨草及其近缘种的基因组特征,为后续全基因组测序奠定基础,同时也否定了海三棱藨草起源于扁杆藨草和藨草杂交的假说。