Concerted Evolution

The major histocompatibility complex (MHC) hosts the most polymorphic genes ever described in vertebrates. The MHC triggers the adaptive branch of the immune response, and its extraordinary variability is considered an evolutionary consequence of pathogen pressure. The last few years have witnessed the characterization of the MHC multigene family in a large diversity of bird species, unraveling important differences in its polymorphism, complexity, and evolution. Here, we characterize the first MHC class II B sequences isolated from a Rallidae species, the Eurasian Coot Fulica atra. A next-generation sequencing approach revealed up to 265 alleles that translated into 251 different amino acid sequences (b chain, exon 2) in 902 individuals. Bayesian inference identified up to 19 codons within the presumptive peptide-binding region showing pervasive evidence of positive, diversifying selection. Our analyses also detected a significant excess of high-frequency segregating sites (average Tajima's D = 2.36, P < 0.05), indicative of balancing selection. We found one to six different alleles per individual, consistent with the occurrence of at least three MHC class II B gene duplicates. However, the genotypes comprised of three alleles were by far the most abundant in the population investigated (49.4%), followed by those with two (29.6%) and four (17.5%) alleles. We suggest that these proportions are in agreement with the segregation of MHC haplotypes differing in gene copy number. The most widespread segregating haplotypes, according to our findings, would contain one single gene or two genes. The MHC class II of the Eurasian Coot is a valuable system to investigate the evolutionary implications of gene copy variation and extensive variability, the greatest ever found, to the best of our knowledge, in a wild population of a non-passerine bird.

viii to Ribosomal RNA in Species of the Genus Nicotiana 33 II. The Relationship Between Haploid Chromosome Complements and Per Cents of rDNAgo in Nicotiana Species 35 III. Taxonomic and Cytogenetic Data for the Genus Nicotiana 36 IV. The Proportions of Two Nicotiana Species Leaf and Seed DNAs Complementary to Ribosomal RNAs 51 V. Per Cent of Brassica pekinensis Seed and Leaf DNAs Which Hybridize to Ribosomal RNA 58 vii ABSTRACT One way of assessing the degree of relatedness of organisms is to compare the biochemical properties of their genetic material, deoxyribonucleic acid (DNA). The DNAs of 10 members of the genus Nicotiana (tobacco) and of a phylogenetically well separated species, Brassica pekinensis (chinese cabbage), were examined for their proportions of nucleotide sequences complementary to the ribosomal ribonucleic acids (rRNAs) of 80s, cytoplasmic, and 70s, chloroplastic, ribosomes. RNAs from leaves, which contain both 80s and 70s ribosomes, were hybridized with DNA to determine the proportion of DNA which is sequence comple mentary to the rRNA species found in 80s and 70s ribosomes. The rRNA from roots, which contain only 80s ribosomes, was used to determine the proportion of complementarity to cytoplasmic rRNA. The proportion of DNA complementary to chloroplastic rRNA was determined as the difference between leaf and root rRNA hybridization values. The per cent of DNA which is complementary to RNA of 80s plus 70s ribosomes (the per cent of total rDNA) differs among species of Nicotiana. Five species contain low and nearly equal percentages of total rDNA (0.27% to 0.33%) and five species contain higher and more variable percentages of total rDNA (0.43% to 0.90%). The per cent of viii rDNA complementary only to RNA of 80s ribosomes (per cent rDNAg0) may be used to distinguish the same two groups with the exception that N. occidentalis (total rDNA = 0.43%) is now in the low hybridizing group. Six species contain various low percentages of rDNAgg (0.13% to 0.20%) and four species contain a higher percentage of rDNAg^ (0.25% to 0.27%). Species with low percentages of rDNAgg (N. rustica. N. occidentalis. N. tabacum. N. qlauca. N. biqelovii. and N. benthamiana) are tetraploids (n = 24) and species with high percentages of rDNAgQ (N. qlutinosa. N. acuminata. N. paniculata. and N. sylvestris) are diploids (n = 12). The percentage of the DNA of each species represented as total rDNA or as rDNAgg was found not to correlate to numbers of nucleoli, chromosomal morphology, or to taxonomy in the genus. All Nicotiana species DNAs studied contain a major DNA fraction with a buoyant density of 1.693 to 1.696 g/cc when analyzed by isopycnic centrifugation in CsCl. In addition, DNAs with over 0.5% of rDNA contain a dense satellite DNA fraction (1.704 _+ 0.001 g/cc) which, in the case of N. sylvestris. was shown to contain the rDNA comple ment plus other kinds of DNA. The DNAs of seed and leaf tissues of N. tabacum and of N. paniculata were examined for possible differences in the percentage of total rDNA. In both species, seed DNA contains a lower percentage of total rDNA than does leaf tissue DNA; N. tabacum seed DNA contains 0.15% rDNA compared to 0.30% rDNA for leaf DNA, and N. paniculata seed DNA is composed of 0.43% rDNA while leaf DNA contains 0.73% rDNA. Comparable examination of B. pekinensis showed that leaf and seed DNAs of this plant contain the same percentages of total rDNA (1.8%).

Modes of reproduction vary considerably in the genus Taraxacum. In particular, the extent and distribution of sexuality are decisive criteria for the evaluation of variation and the taxonomic conclusions in this complicated genus. Taraxacum sect. Borealia is widespread in the Arctic and Subarctic regions of the Asiatic part of Russia, but sexual reproduction has not been known to occur there, unlike T. sect. Arctica with a number of sexually reproducing species in the continental Far East. A detailed analysis of the herbarium material of Taraxacum kolymense Khokhryakov, using pollen size analysis and achene set examination, revealed sexuality in this distinctive member of T. sect. Borealia. The lectotype is selected for T. kolymense from a rich type gathering consisting of seven herbarium specimens, and a new consolidated description was compiled.

Phylogenetic relationships among 50 Phytophthora species and between Phytophthora and other oomycetes were examined on the basis of the ITS sequences of genomic rDNA. Phytophthora grouped with Pythium, Peronospora, and Halophytophthora, distant from genera in the Saprolegniales. Albugo was intermediate between these two groups. Unlike Pythium, Phytophthora was essentially monophyletic, all but three species forming a cluster of eight clades. Two clades contained only species with nonpapillate sporangia. The other six clades included either papillate and semipapillate, or semipapillate and nonpapillate types, transcending traditional morphological groupings, which are evidently not natural assemblages. Peronospora was related to P. megakarya and P. palmivora and appears to be derived from a Phytophthora that has both lost the ability to produce zoospores and become an obligate biotroph. Three other Phytophthoras located some distance from the main Phytophthora-Peronospora cluster probably represent one or more additional genera.

We quantified C-band size variations of the No. 2 chromosomes in the Japanese house mice, Mus musculus, including wild-caught mice and their F1 offsprings produced by crosses between them. The sizes of C-bands were expressed by their relative lengths as a positively stained region / a negatively stained region by Cbanding in each of the No. 2 homologue. In 11 of the 16 mice examined by one-way ANOVA, the relative lengths of the C-bands were statistically polymorphic in the No. 2 homologue with variable C-band sizes at p= 0.05. On the other hand, the remaining five individuals carried slightly different relative lengths without significance, which is considered as a homomorphism. Usually, heterochromatin is thought to be evolutionally neutral without strong selections, and it is considered that the polymorphic state is a frequent phenomenon of the Japanese house mice without any cytogenetically deleterious effects. In addition, the mean of the difference between the relative lengths in the No. 2 homologue ranged from 0.046 to 0.210 in the 11 individuals showing polymorphic state and from 0.032 to 0.044 in the five showing homomorphic state. Thus, a mean index of approximately 0.045 is considered to be the boundary dividing polymorphic and homomorphic states.

To evaluate the colonization histories of the Japanese house mice (Mus musculus), phenotypic and genotypic admixtures of the subspecific traits were studied by evaluation of external body characteristics and mitochondrial gene elements. We analyzed mitochondrial Cytb gene and coat colorations and body dimensions as subspecific characteristics in mice from four areas of the Japanese Islands, the Sorachi, Ishikari and Iburi areas of Hokkaido, the Hidaka area of Hokkaido, and northeastern and central Honshu. Three occurrence patterns of the subspecific haplotypes of Cytb-the castaneus type only, the musculus type only, and the castaneus, musculus, and domesticus types together-were observed in the study areas. In central Honshu, the properties of haplotypes were in accord with the external characteristics as reported in previous findings. In contrast, complicated external characteristics were observed in the Hidaka area, where mice showed multiple haplotype properties. In addition, in northeastern Honshu, coat colorations were not in accord with haplotype properties and such discordance was also observed in most mice in the Sorachi, Ishikari and Iburi areas of Hokkaido. These complexities and discordances suggest that the genetic and phenotypic properties have been caused by different processes, not only through founder effects by migrations and subsequent subspecific hybridizations but also through differentiation in each study area.

Background: Extrachomosomal circular DNA (eccDNA) is ubiquitous in eukaryotic organisms and was detected in every organism tested, including in humans. A two-dimensional gel electrophoresis facilitates the detection of eccDNA in preparations of genomic DNA. Using this technique we have previously demonstrated that most of eccDNA consists of exact multiples of chromosomal tandemly repeated DNA, including both coding genes and satellite DNA. Results: Here we report the occurrence of eccDNA in every tested human cell line. It has heterogeneous mass ranging from less than 2 kb to over 20 kb. We describe eccDNA homologous to human alpha satellite and the SstI mega satellite. Moreover, we show, for the first time, circular multimers of the human 5S ribosomal DNA (rDNA), similar to previous findings in Drosophila and plants. We further demonstrate structures that correspond to intermediates of rolling circle replication, which emerge from the circular multimers of 5S rDNA and SstI satellite. Conclusions: These findings, and previous reports, support the general notion that every chromosomal tandem repeat is prone to generate eccDNA in eukryoric organisms including humans. They suggest the possible involvement of eccDNA in the length variability observed in arrays of tandem repeats. The implications of eccDNA on genome biology may include mechanisms of centromere evolution, concerted evolution and homogenization of tandem repeats and genomic plasticity.

The monogenean Gyrodactylus salaris Malmberg, 1957 is an economically important parasite on Atlantic salmon whereas the morphologically very similar G. thymalli Z ˇitn ˇan, 1960 on grayling is considered harmless. Even molecular markers cannot unambiguously discriminate both species. The nuclear internal transcribed spacer (ITS) sequences are identical in both species, and although mitochondrial cytochrome oxidase I (COI) sequences show substantial variation, no support for monophyly of either species is found. Analysis of nucleotide sequences of the intergenic spacer (IGS) have, however, been interpreted as support for 2 species. Here, IGS and COI sequences from 81 G. salaris and G. thymalli specimens of 39 populations across the species' distribution range were determined. Mitochondrial diversity was not reflected in the nuclear marker. Since various 23 bp IGS repeat types usually differ by just one nucleotide and sequences primarily differ in the number and order of repeat types, alignments may be biased and arbitrary, impeding meaningful phylogenetic analyses. The hypothesis that parasites on rainbow trout represent hybrids of both species is rejected. The presence or absence of particular repeat types is not considered informative. We interpret the IGS data as support for G. salaris and G. thymalli being a single species.

Eleven normal families with at least four children were studied cytogenetically using the C-band technique to identify polymorphisms in the constitutive heterochromatin of chromosomes 1, 9 and 16. Thirteen individuals showed one or more variants in such chromosomes. The analysis of the segregation ratios in the 35 offspring of these 13 individuals showed that these marker chromosomes generally segregated according to the expected 50:50. However, one of these variants, chromosome no. 9 with an increased heterochromatin block in the secondary constriction, has an apparently preferential segregation, when the findings from this study are combined with those of other authors.

We have found that human and ape ribosomal genes undergo concerted evolution involving genetic exchanges among nucleolus organizers on nonhomologous chromosomes. This conclusion is based upon restriction enzyme analysis of the ribosomal gene families in man and five ape species. Certain structural features were found to differ among (but not within) species even though the ribosomal genes have a multichromosomal distribution. Genetic exchanges among nucleolus organizer regions may be related to the well-known phenomenon of acrocentric chromosome associations observed in man and apes. Length variation in a region of the nontranscribed spacer was found in both chimpanzee species we examined. The nature of this length variation was found to be identical to that previously described in man. The origin of the length variation and its polymorphism within these three species might be explained by unequal alignment and unequal cross-over among the ribosomal genes. An especially surprising f...

The vertebrate brain is composed of several interconnected, functionally distinct structures and much debate has surrounded the basic question of how these structures evolve. On the one hand, according to the 'mosaic evolution hypothesis', because of the elevated metabolic cost of brain tissue, selection is expected to target specific structures mediating the cognitive abilities which are being favored. On the other hand, the 'concerted evolution hypothesis' argues that developmental constraints limit such mosaic evolution and instead the size of the entire brain varies in response to selection on any of its constituent parts. To date, analyses of these hypotheses of brain evolution have been limited to mammals and birds; excluding Actinopterygii, the basal and most diverse class of vertebrates. Using a combination of recently developed phylogenetic multivariate allometry analyses and comparative methods that can identify distinct rates of evolution, even in highly correlated traits, we studied brain structure evolution in a highly variable clade of ray-finned fishes; the Tanganyikan cichlids. Results: Total brain size explained 86% of the variance in brain structure volume in cichlids, a lower proportion than what has previously been reported for mammals. Brain structures showed variation in pair-wise allometry suggesting some degree of independence in evolutionary changes in size. This result is supported by variation among structures on the strength of their loadings on the principal size axis of the allometric analysis. The rate of evolution analyses generally supported the results of the multivariate allometry analyses, showing variation among several structures in their evolutionary patterns. The olfactory bulbs and hypothalamus were found to evolve faster than other structures while the dorsal medulla presented the slowest evolutionary rate. Our results favor a mosaic model of brain evolution, as certain structures are evolving in a modular fashion, with a small but non-negligible influence of concerted evolution in cichlid fishes. Interestingly, one of the structures presenting distinct evolutionary patterns within cichlids, the olfactory bulbs, has also been shown to evolve differently from other structures in mammals. Hence, our results for a basal vertebrate clade also point towards a conserved developmental plan for all vertebrates.

Plant pollen has diverse morphological characteristics that can be consistently passed down from generation to generation. Information on pollen morphology is thus immensely important for plant classification and identification. In the genus Gossypium, however, in-depth research on pollen morphology is lacking, with only few reports on limited cotton species. To evaluate the diversity of pollen in Gossypium, we therefore conducted a comprehensive analysis of the pollen morphology of 33 cotton species and varieties using scanning electron microscopy.
The 33 analyzed cotton samples exhibited common pollen morphological features, including spherical shapes, radial symmetry, echination, panporation, and operculation, while the pollen size, spine shape, spine density and length showed distinctive features. Pollen size varied significantly among species, with diameters ranging from 62.43 μm in G. harknessii to 103.41 μm in G. barbadense. The exine had an echinate sculptural texture, and spines were mostly conical or sharply conical but occasionally rod-like. Spine density varied from 173 in G. incanum to 54 in G. gossypioides, while spine length ranged from 3.53 μm in G. herbaceum to 9.47 μm in G. barbadense. In addition, the 33 cotton species and varieties were grouped at a genetic distance of 3.83 into three clusters. Cluster I comprised five allotetraploid AD-genome cotton species, four D-genome species, and one K-genome species. Cluster II included 13 diploid species from A, B, D, E, and G genomes, whereas Cluster III only consisted one E-genome species G. incanum.
Although pollen characteristics alone are not enough to resolve taxonomic and systematic relationships within the genus Gossypium, our results add to knowledge on palynomorphology and contribute to phenological information on these taxa. Our findings should aid future systematic and phylogenetic studies of the Gossypium genus.

Background SINEs (Short INterspersed Elements) are homoplasy-free and co-dominant genetic markers which are considered to represent useful tools for population genetic studies, and could help clarifying the speciation processes ongoing within the major malaria vector in Africa, Anopheles gambiae s.s. Here, we report the results of the analysis of the insertion polymorphism of a nearly 200 bp-long SINE (SINE200) within genome areas of high differentiation (i.e. &quot;speciation islands&quot;) of M and S A. gambiae molecular forms. Methods A SINE-PCR approach was carried out on thirteen SINE200 insertions in M and S females collected along the whole range of distribution of A. gambiae s.s. in sub-Saharan Africa. Ten specimens each for Anopheles arabiensis, Anopheles melas, Anopheles quadriannulatus A and 15 M/S hybrids from laboratory crosses were also analysed. Results Eight loci were successfully amplified and were found to be specific for A. gambiae s.s.: 5 on 2L chromosome and one...

Bat genomes are characterised by an A-T richness and by a small C-value compared with other mammalian groups. It has been suggested that the small C-value is mainly due to the lack of repetitive DNA sequences. However, little information about repetitive DNA sequences in this mammalian group is available at the molecular level. Here we describe a PstI family of repetitive DNA sequences present in three species of the genus Pteropus. These repetitive sequences

C4 and CYPZl are two adjacent, but functionally unrelated genes residing in the middle of the mammalian major histocompatibility complex (Mhc). T h e C4 gene codes for the fourth component of the complement cascade, whereas the CYP2l gene specifies an enzyme (cytochrome P450c21) of the glucocorticoid and mineralocorticoid pathways. T h e genes occur frequently in multiple copies on a single chromosome arranged in the order C4 . . . CYPPl . . . C 4 . . . CYP21. The unit of duplication (a module) is the C4-CYP21 gene pair. We sequenced the flanking regions of the C4-CYP21 modules and the intermodular regions of the chimpanzee, gorilla, and orangutan, as well as the intermodular region of an Old World monkey, the pigtail macaque. By aligning the sequences, we could identify the duplication breakpoints in these species. T h e breakpoint turned out to be at exactly the same position as that found previously in humans. T h e sequences flanking paralogous genes in the same species were found to be more similar to one another than sequences flanking orthologous genes in different species. We interpret these results as indicating that the original (primigenial) duplication occurred before the separation of apes from Old World monkeys more than 23 million years ago. The nature of the sequence at the breakpoint suggests that the duplication occurred by nonhomologous recombination. Since then, the C4-CYP21 haplotypes have been expanding and contracting by homologous crossing over which has homogenized the sequences in each species. We speculate that the reason for the concerted evolution of the primate C4-CYP21 region may be a requirement for the coevolution of certain components of the complement pathway, including the C4 component. We contrast the evolution of the C4-CYP21 region with that of other Mhc regions. C OMPLEMENT component 4, C4, is one of more than 20 proteins constituting the complement cascade, which is involved in defense of vertebrate bodies against pathogens. Activation of the cascade by antigen-antibody complexes or by other means leads ultimately to the assembly of lytic complexes on the cell surface, perforation of the plasma membrane, and killing of the cell (Ross 1986). Some of the activated components of the cascade are also involved in a variety of other biological functions. Cytochrome P450c2 1 (2 1-hydroxylase), CYP2 1, is an enzyme participating in the conversion of cholesterol to aldosterone or cortisol in the cortex of the vertebrate adrenal gland (MILLER 1988). In mammals, complement component 4 and cytochrome P450c21 are encoded in adjacent genes, C4 and CYP21, respectively, residing in the middle of the major histocompatibility complex, Mhc . The per haplotype number of C4 and CYP21 copies varies from species to species and also among individuals of certain species. Single C4-CYP21 haplotypes have been found in humans and others),

Interlocus gene conversion is a major evolutionary force that drives the concerted evolution of duplicated genomic regions. Theoretical models successfully have addressed the effects of interlocus gene conversion and the importance of crossover in the evolutionary fate of gene families and duplications but have not considered complex recombination scenarios, such as the presence of hotspots. To study the interplay between interlocus gene conversion and crossover, we have developed a forward-time simulator that allows the exploration of a wide range of interlocus gene conversion rates under different crossover models. Using it, we have analyzed patterns of nucleotide variation and linkage disequilibrium within and between duplicate regions, focusing on a neutral scenario with constant population size and validating our results with the existing theoretical models. We show that the interaction of gene conversion and crossover is nontrivial and that the location of crossover junctions ...

Members of cytochrome P450 subfamily 1A (CYP1As) are involved in detoxification and bioactivation of common environmental pollutants. Understanding the functional evolution of these genes is essential to predicting and interpreting species differences in sensitivity to toxicity by such chemicals. The CYP1A gene subfamily comprises a single ancestral representative in most fish species and two paralogs in higher vertebrates, including birds and mammals. Phylogenetic analysis of complete coding sequences suggests that mammalian and bird paralog pairs (CYP1A1/2 and CYP1A4/5, respectively) are the result of independent gene duplication events. However, comparison of vertebrate genome sequences revealed that CYP1A genes lie within an extended region of conserved fine-scale synteny, suggesting that avian and mammalian CYP1A paralogs share a common genomic history. Algorithms designed to detect recombination between nucleotide sequences indicate that gene conversion has homogenized most of the length of the chicken CYP1A genes, as well as the 5' end of mammalian CYP1As. Together, these data indicate that avian and mammalian CYP1A paralog pairs resulted from a single gene duplication event and that extensive gene conversion is responsible for the exceptionally high degree of sequence similarity between CYP1A4 and CYP1A5. Elevated nonsynonymous/synonymous substitution ratios within a putatively unconverted stretch of ~250 bp suggests that positive selection may have reduced the effective rate of gene conversion in this region, which contains two substrate recognition sites. This work significantly alters our understanding of functional evolution in the CYP1A subfamily, suggesting that gene conversion and positive selection have been the dominant processes of sequence evolution.

The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the presence of SSR in plastomes is specific for simple thalloid species. Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae and partially congruent with previous studies, due to dataset-dependent results of Dumortiera-Reboulia relationships. Despite the lower evolutionary rate of Marchantiales plastomes, significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species. The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species.

The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the p...

Simplified DNA sequence acquisition has provided many new data sets that are useful for phylogenetic reconstruction, including single-and multiple-copy nuclear and organellar genes. Although transcribed regions receive much attention, nontranscribed regions have recently been added to the repertoire of sequences suitable for phylogenetic studies, especially for closely related taxa. We evaluated the efficacy of a small portion of the histone repeat for phylogenetic reconstruction among Drosophila species. Histone repeats in invertebrates offer distinct advantages similar to those of widely used ribosomal repeats. First, the units are tandemly repeated and undergo concerted evolution. Second, histone repeats include both highly conserved coding and variable intergenic regions. This composition facilitates application of ''universal'' primers spanning potentially informative sites. We examined a small region of the histone repeat, including the intergenic spacer segments of coding regions from the divergently transcribed H2A and H2B histone genes. The spacer (about 230 bp) exists as a mosaic with highly conserved functional motifs interspersed with rapidly diverging regions; the former aid in alignment of the spacer. There are no ambiguities in alignment of coding regions. Coding and noncoding regions were analyzed together and separately for phylogenetic information. Parsimony, distance, and maximum-likelihood methods successfully retrieve the corroborated phylogeny for the taxa examined. This study demonstrates the resolving power of a small histone region which may now be added to the growing collection of phylogenetically useful DNA sequences.

Genomic plasticity of human chromosome 8p23.1 region is highly influenced by two groups of complex segmental duplications (SDs), termed REPD and REPP, that mediate different kinds of rearrangements. Part of the difficulty to explain the wide range of phenotypes associated with 8p23.1 rearrangements is that REPP and REPD are not yet well characterized, probably due to their polymorphic status. Here, we describe a novel primate-specific gene family, named FAM90A (family with sequence similarity 90), found within these SDs. According to the current human reference sequence assembly, the FAM90A family includes 24 members along 8p23.1 region plus a single member on chromosome 12p13.31, showing copy number variation (CNV) between individuals. These genes can be classified into subfamilies I and II, which differ in their upstream and 5 0 -untranslated region sequences, but both share the same open reading frame and are ubiquitously expressed. Sequence analysis and comparative fluorescence in situ hybridization studies showed that FAM90A subfamily II suffered a big expansion in the hominoid lineage, whereas subfamily I members were likely generated sometime around the divergence of orangutan and African great apes by a fusion process. In addition, the analysis of the Ka/Ks ratios provides evidence of functional constraint of some FAM90A genes in all species. The characterization of the FAM90A gene family contributes to a better understanding of the structural polymorphism of the human 8p23.1 region and constitutes a good example of how SDs, CNVs and rearrangements within themselves can promote the formation of new gene sequences with potential functional consequences.

The nanovirus Banana bunchy top virus (BBTV) has six standard components in its genome and occasionally contains components encoding additional Rep (replication initiation protein) genes. Phylogenetic network analysis of coding sequences of DNA 1 and 3 confirmed the two major groups of BBTV, a Pacific and an Asian group, but show evidence of web-like phylogenies for some genes. Phylogenetic analysis of 102 major common regions (CR-Ms) from all six components showed a possible concerted evolution within the Pacific group, which is likely due to recombination in this region. The CR-M of additional Rep genes is close to that of DNA 1 and 2. Comparison of tree topologies constructed with DNA 1 and DNA 3 coding sequences of 14 BBTV isolates showed distinct phylogenetic histories based on Kishino-Hasegawa and Shimodaira-Hasegawa tests. The results of principal component analysis of amino acid and codon usages indicate that DNA 1 and 3 have a codon bias different from that of all other genes of nanoviruses, including all currently known additional Rep genes of BBTV, which suggests a possible ancient genome reassortment event between distinctive nanoviruses.

ABSTRACTThe nanovirusBanana bunchy top virus(BBTV) has six standard components in its genome and occasionally contains components encoding additional Rep (replication initiation protein) genes. Phylogenetic network analysis of coding sequences of DNA 1 and 3 confirmed the two major groups of BBTV, a Pacific and an Asian group, but show evidence of web-like phylogenies for some genes. Phylogenetic analysis of 102 major common regions (CR-Ms) from all six components showed a possible concerted evolution within the Pacific group, which is likely due to recombination in this region. The CR-M of additional Rep genes is close to that of DNA 1 and 2. Comparison of tree topologies constructed with DNA 1 and DNA 3 coding sequences of 14 BBTV isolates showed distinct phylogenetic histories based on Kishino-Hasegawa and Shimodaira-Hasegawa tests. The results of principal component analysis of amino acid and codon usages indicate that DNA 1 and 3 have a codon bias different from that of all oth...

Conmmunicated by M.Radmran Circular heteroduplex DNAs of bacteriophage fX174 have been constructed carrying either a G:T (Eam+lEam3) or a G:A (Bam+lBarn16) mismatch and containing either two, one or no GATC sequences. MIismatches w'ere efficiently repaired in wild-type Escherichia coli transfected with OX174 heteroduplexes only when two unmethylated GATC sequences were present in oX174 DNA. The requirements for GATC sequences in substrate DNA and for the E. coli MutH function in E. coli mismatch repair can be alleviated by the presence of a persistent nick (transfection with nicked heteroduplex DNA in ligase temperature-sensitive mutant at 40°C). A persistent nick in the GATC sequence is as effective in stimulating mutL-and mutS-dependent mismatch repair as a nick distant from the GATC sequence and from the mismatch. These observations suggest that the MutH protein participates in methyl-directed mismatch repair by recognizing unmethylated DNA GATC sequences and/or stimulating the nicking of unmethylated strands.

In this study, we determined the complete nucleotide sequence of the mitochondrial genome of the Japanese pond frog Rana nigromaculata. The length of the sequence of the frog was 17,804 bp, though this was not absolute due to length variation caused by differing numbers of repetitive units in the control regions of individual frogs. The gene content, base composition, and codon usage of the Japanese pond frog conformed to those of typical vertebrate patterns. However, the comparison of gene organization between three amphibian species (Rana, Xenopus and caecilian) provided evidence that the gene arrangement of Rana differs by four tRNA gene positions from that of Xenopus or caecilian, a common gene arrangement in vertebrates. These gene rearrangements are presumed to have occurred by the tandem duplication of a gene region followed by multiple deletions of redundant genes. It is probable that the rearrangements start and end at tRNA genes involved in the initial production of a tandemly duplicated gene region. Putative secondary structures for the 22 tRNAs and the origin of the L-strand replication (OL) are described. Evolutionary relationships were estimated from the concatenated sequences of the 12 proteins encoded in the H-strand of mtDNA among 37 vertebrate species. A quartet-puzzling tree showed that three amphibian species form a monophyletic clade and that the caecilian is a sister group of the monophyletic Anura.

The internal transcribed spacers (ITS) exhibit concerted evolution by the fast homogenization of these sequences at the intragenomic level. However, the rate and extension of this process are unclear and might be conditioned by the number and divergence of the different ITS copies. In some cases, such as hybrid species and polyploids, ITS sequence homogenization appears incomplete, resulting in multiple haplotypes within the same organism. Here, we studied the dynamics of concerted evolution in 85 individuals of seven plant species of the genus Erysimum (Brassicaceae) with multiple ploidy levels. We estimated the rate of concerted evolution and the degree of sequence homogenization separately for ITS1 and ITS2 and whether these varied with ploidy. Our results showed incomplete sequence homogenization, especially for polyploid samples, indicating a lack of concerted evolution in these taxa. Homogenization was usually higher in ITS2 than in ITS1, suggesting that concerted evolution operates more efficiently on the former. Furthermore, the hybrid origin of several species appears to contribute to the maintenance of high haplotype diversity, regardless of the level of ploidy. These findings indicate that sequence homogenization of ITS is a dynamic and complex process that might result in varying intra-and inter-genomic diversity levels. Concerted evolution is an evolutionary process by which sequences from the same gene family show higher sequence similarity to each other than to orthologous genes in related species 1,2 . Hence, genes evolved in a concerted manner present low polymorphism in their sequences, i.e., the sequences are homogenized. Concerted evolution is particularly notable in multicopy nuclear genes, where homogenization is mainly achieved by unequal crossing over and gene conversion . One of the best characterized multicopy gene families is the 45S nuclear ribosomal DNA (nrDNA) 5 . It appears arranged as tandem repeated units with hundreds to thousands of copies in one or several loci per genome. These units are composed of the 18S rDNA, internal transcribed spacer 1 (ITS1), 5.8 S rDNA, internal transcribed spacer 2 (ITS2), and 26S rDNA, separated by longer nontranscribed intergenic spacers 6 . Among all these units, the internal transcribed spacers (ITS1 and ITS2) are the best-characterized nrDNA sequences 7 partly because ITS sequences show characteristics advantageous for phylogenetic studies, such as biparental inheritance, short length, and high evolution rate . ITS sequences usually present fast concerted evolution with low levels of intra-genomic sequence variation and very few polymorphic positions . However, in some animals (e.g., ) and especially in plants , sequence homogenization remains incomplete across ITS sequences, resulting in relatively high intra-genomic polymorphism. This ITS diversity is often linked to hybridization events . Different ITS sequences may meet after hybridization and become homogenized after a time, but this homogenization may not be consistent among descendant lineages 23 . As concerted evolution tends to homogenize sequences rapidly 8 , evidence of nonconcerted evolution is mostly expected in recently-formed hybrid species, where both parental ITS sequences may still be present. This phenomenon should be particularly conspicuous in recent allopolyploid species, where the occurrence of different ITS sequences located in distinct chromosomes tends to delay this homogenization 24 .

The full catalogue of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago. We found that about one-third of their satDNA families (near 60 in every species) showed sequence homology, and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH pattern at both intra-and interspecific levels. We defined indices of homogenization and degeneration, and quantified the level of incomplete library sorting between species. Our analyses revealed that satDNA degenerates through point mutation and rejuvenates through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification, degeneration, and rejuvenation, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split. .

The internal transcribed spacers (ITS) exhibit concerted evolution by the fast homogenization of these sequences at the intragenomic level. However, the rate and extension of this process are unclear and might be conditioned by the number and divergence of the different ITS copies. In some cases, such as hybrid species and polyploids, ITS sequence homogenization appears incomplete, resulting in multiple haplotypes within the same organism. Here, we studied the dynamics of concerted evolution in 85 individuals of seven plant species of the genus Erysimum (Brassicaceae) with multiple ploidy levels. We estimated the rate of concerted evolution and the degree of sequence homogenization separately for ITS1 and ITS2 and whether these varied with ploidy. Our results showed incomplete sequence homogenization, especially for polyploid samples, indicating a lack of concerted evolution in these taxa. Homogenization was usually higher in ITS2 than in ITS1, suggesting that concerted evolution operates more efficiently on the former. Furthermore, the hybrid origin of several species appears to contribute to the maintenance of high haplotype diversity, regardless of the level of ploidy. These findings indicate that sequence homogenization of ITS is a dynamic and complex process that might result in varying intra-and inter-genomic diversity levels.

The internal transcribed spacers (ITS) exhibit concerted evolution by the fast homogenization of these sequences at the intragenomic level. However, the rate and extension of this process are unclear and might be conditioned by the number and divergence of the different ITS copies. In some cases, such as hybrid species and polyploids, ITS sequence homogenization appears incomplete, resulting in multiple haplotypes within the same organism. Here, we studied the dynamics of concerted evolution in 85 individuals of seven plant species of the genus Erysimum (Brassicaceae) with multiple ploidy levels. We estimated the rate of concerted evolution and the degree of sequence homogenization separately for ITS1 and ITS2 and whether these varied with ploidy. Our results showed incomplete sequence homogenization, especially for polyploid samples, indicating a lack of concerted evolution in these taxa. Homogenization was usually higher in ITS2 than in ITS1, suggesting that concerted evolution op...

The pinyon pines (Pinus subsection Cembroides), distributed in semiarid regions of the western United States and Mexico, include a mixture of relictual and more recently evolved taxa. To investigate relationships among the pinyons, we screened and partially sequenced 3000-bp clones of the nuclear ribosomal DNA internal transcribed spacer (ITS) region for 16 taxa from subsect. Cembroides and nine representatives from four other subsections of subgenus Strobus. Restriction digests of clones reveal within-individual heterogeneity, suggesting that concerted evolution is operating slowly on the ITS in pine species. Two ITS clones were identified as pseudogenes. Tandem subrepeats in the ITS1 form stem loops comparable to those in other genera of Pinaceae and may be promoting recombination between rDNA repeats, resulting in ITS1 chimeras. Within the pinyon clade, phylogenetic structure is present, but different clones from the same (or different) individuals of a species are polyphyletic, indicating that coalescence of ITS copies within individual genomes predates evolutionary divergence in the group. At the level of subsection and above, the ITS region corresponds well with morphological and cpDNA evidence. Except for P. nelsonii, the pinyons are monophyletic, with both subsect. Cembroides and P. nelsonii forming a clade with the foxtail and bristlecone pines (subsect. Balfourianae) of western North America.

Repetitive DNA sequences are a major component of eukaryotic genomes and may account for up to 90% of the genome size. They can be divided into minisatellite, microsatellite and satellite sequences. Satellite DNA sequences are considered to be a fast-evolving component of eukaryotic genomes, comprising tandemly-arrayed, highly-repetitive and highly-conserved monomer sequences. The monomer unit of satellite DNA is 150-400 base pairs (bp) in length. Repetitive sequences may be species-or genus-specific, and may be centromeric or subtelomeric in nature. They exhibit cohesive and concerted evolution caused by molecular drive, leading to high sequence homogeneity. Repetitive sequences accumulate variations in sequence and copy number during evolution, hence they are important tools for taxonomic and phylogenetic studies, and are known as ''tuning knobs'' in the evolution. Therefore, knowledge of repetitive sequences assists our understanding of the organization, evolution and behavior of eukaryotic genomes. Repetitive sequences have cytoplasmic, cellular and developmental effects and play a role in chromosomal recombination. In the post-genomics era, with the introduction of next-generation sequencing technology, it is possible to evaluate complex genomes for analyzing repetitive sequences and deciphering the yet unknown functional potential of repetitive sequences.

5S rDNA sequences present an intense dynamism and have proved to be valuable as genetic markers to distinguish closed related species and also in the understanding of the evolutionary dynamic of repetitive sequences in the genomes. In order to identify patterns of 5S rDNA organization and their evolution in the genome of fish species, such genomic segment was investigated in the tilapias Oreochromis niloticus and Tilapia rendalli, and in the hybrid O. urolepis hornorum  O. mossambicus. A dual 5S rDNA system was identified in the three analyzed tilapia samples. Although each 5S rDNA class was conserved among the three samples, a distinct 5S rDNA genome organization pattern could be evidenced for each sample. The presence of a dual 5S rDNA system seems to be a general trait among non-related teleost fish orders, suggesting that evolutionary events of duplication have occurred before the divergence of the main groups of teleost fishes.

A new class of human interspersed repeated sequences distinct from the AluI family was found by screening a hunan gene library with a mouse ribosomal gene non-transcribed spacer probe (rDNA NTS). A member of this sequence family was localized to a 251 bp segment between the human 6 and a globin genes: a region previously judged to be devoid of repeated DNA. The complete nucleotide sequence of this segment revealed a tandem block of 17 TG dinucleotides, a feature hypothesized by others to be a reconbination hot spot responsible for gene conversion in the y globin locus region. When the genomes of Xenopus, pigeon, slime mold and yeast were examined, reiterated sequences homologous to both the mouse rDNA NTS and human globin repeat were found in every case. The discovery of this extraordinarily conserved repeated sequence family appears to have depended upon not using salmon sperm DNA during hybridization. The use of eucaryotic carrier DNA may bias the search for repeated sequences against any which may be highly conserved during eucaryotic evolution. INTRODIUCTION Analysis of cloned fragments of mouse ribosomal gene non-transcribed spacer (rDNA NTS) has shown that homologous sequences are reiterated and interspersed throughout the mouse genome (1). This interspersed sequence family appears to be distinct from other known mouse interspersed repeated sequences (2-5). When the mouse rDNA NTS probe was found to hybridize to a human rDNA clone carrying NTS sequences (Krystal and Arnheim, unpublished data), it raised the possibility that sequences homologous to the mouse rDNA NTS were also scattered throughout the human genome. Our results have confirmed this supposition and further studies localized one member of the family in the human a globin gene complex. When the study was extended to other species, including additional higher as well as lower eucaryotes homologous reiterated sequences were found in every case.

Genomic plasticity of human chromosome 8p23.1 region is highly influenced by two groups of complex segmental duplications (SDs), termed REPD and REPP, that mediate different kinds of rearrangements. Part of the difficulty to explain the wide range of phenotypes associated with 8p23.1 rearrangements is that REPP and REPD are not yet well characterized, probably due to their polymorphic status. Here, we describe a novel primate-specific gene family, named FAM90A (family with sequence similarity 90), found within these SDs. According to the current human reference sequence assembly, the FAM90A family includes 24 members along 8p23.1 region plus a single member on chromosome 12p13.31, showing copy number variation (CNV) between individuals. These genes can be classified into subfamilies I and II, which differ in their upstream and 5 0-untranslated region sequences, but both share the same open reading frame and are ubiquitously expressed. Sequence analysis and comparative fluorescence in situ hybridization studies showed that FAM90A subfamily II suffered a big expansion in the hominoid lineage, whereas subfamily I members were likely generated sometime around the divergence of orangutan and African great apes by a fusion process. In addition, the analysis of the Ka/Ks ratios provides evidence of functional constraint of some FAM90A genes in all species. The characterization of the FAM90A gene family contributes to a better understanding of the structural polymorphism of the human 8p23.1 region and constitutes a good example of how SDs, CNVs and rearrangements within themselves can promote the formation of new gene sequences with potential functional consequences.

Origin and rearrangement of ribosomal DNA repeats in natural allotetraploid Nicotiana tabacum are described. Comparative sequence analysis of the intergenic spacer (IGS) regions of Nicotiana tomentosiformis (the paternal diploid progenitor) and Nicotiana sylvestris (the maternal diploid progenitor) showed species-specific molecular features. These markers allowed us to trace the molecular evolution of parental rDNA in the allopolyploid genome of N. tabacum; at least the majority of tobacco rDNA repeats originated from N. tomentosiformis, which endured reconstruction of subrepeated regions in the IGS. We infer that after hybridization of the parental diploid species, rDNA with a longer IGS, donated by N. tomentosiformis, dominated over the rDNA with a shorter IGS from N. sylvestris; the latter was then eliminated from the allopolyploid genome. Thus, repeated sequences in allopolyploid genomes are targets for molecular rearrangement, demonstrating the dynamic nature of allopolyploid genomes.

Hsp70 molecular chaperones are ubiquitous. By preventing aggregation, promoting folding, and regulating degradation, Hsp70s are major factors in the ability of cells to maintain proteostasis. Despite a wealth of functional information, little is understood about the evolutionary dynamics of Hsp70s. We undertook an analysis of Hsp70s in the fungal clade Ascomycota. Using the well-characterized 14 Hsp70s of Saccharomyces cerevisiae, we identified 491 orthologs from 53 genomes. Saccharomyces cerevisiae Hsp70s fall into seven subfamilies: four canonical-type Hsp70 chaperones (SSA, SSB, KAR, and SSC) and three atypical Hsp70s (SSE, SSZ, and LHS) that play regulatory roles, modulating the activity of canonical Hsp70 partners. Each of the 53 surveyed genomes harbored at least one member of each subfamily, and thus establishing these seven Hsp70s as units of function and evolution. Genomes of some species contained only one member of each subfamily that is only seven Hsp70s. Overall, members of each subfamily formed a monophyletic group, suggesting that each diversified from their corresponding ancestral gene present in the common ancestor of all surveyed species. However, the pattern of evolution varied across subfamilies. At one extreme, members of the SSB subfamily evolved under concerted evolution. At the other extreme, SSA and SSC subfamilies exhibited a high degree of copy number dynamics, consistent with a birth-death mode of evolution. KAR, SSE, SSZ, and LHS subfamilies evolved in a simple divergent mode with little copy number dynamics. Together, our data revealed that the evolutionary history of this highly conserved and ubiquitous protein family was surprising complex and dynamic.

A phylogenetic tree comprising clades with high bootstrap values or other strong measures of statistical support is usually interpreted as providing a good estimate of the true phylogeny. Convergent evolution acting on groups of characters in concert, however, can lead to highly supported but erroneous phylogenies. Identifying such groups of phylogenetically misleading characters is obviously desirable. Here we present a procedure that uses an independent data source to identify sets of characters that have undergone concerted convergent evolution. We examine the problematic case of the cormorants and shags, for which trees constructed using osteological and molecular characters both have strong statistical support and yet are fundamentally incongruent. We find that the osteological characters can be separated into those that fit the phylogenetic history implied by the molecular data set and those that do not. Moreover, these latter nonfitting osteological characters are internally consistent and form groups of mutually compatible characters or "cliques," which are significantly larger than cliques of shuffled characters. We suggest, therefore, that these cliques of characters are the result of similar selective pressures and are a signature of concerted convergence.

The human Y chromosome consists of ampliconic genes, which are located in palindromes and undergo frequent gene conversion, and single-copy genes including the primary sex-determining locus, SRY. Here, we demonstrate that SRY is duplicated in a large palindrome in the European rabbit (Oryctolagus cuniculus). Furthermore, we show through comparative sequencing that orthologous palindrome arms have diverged 0.40% between rabbit subspecies over at least 2 My, but paralogous palindrome arms have remained nearly identical. This provides clear evidence of gene conversion on the rabbit Y chromosome. Together with previous observations in humans, these results suggest that gene conversion is a general feature of the evolution of the mammalian Y chromosome.

Wolbachia are among the most abundant symbiotic microbes on earth; they are present in about 66% of all insect species, some spiders, mites and crustaceans, and most filarial nematode species. Infected filarial nematodes, including many pathogens of medical and veterinary importance, depend on Wolbachia for proper development and survival. The mechanisms behind this interdependence are not understood. Interestingly, a minority of filarial species examined to date are naturally Wolbachia-free. We used 454 pyrosequencing to survey the genomes of two distantly related Wolbachia-free filarial species, Acanthocheilonema viteae and Onchocerca flexuosa. This screen identified 49 Wolbachia-like DNA sequences in A. viteae and 114 in O. flexuosa. qRT-PCR reactions detected expression of 30 Wolbachia-like sequences in A. viteae and 56 in O. flexuosa. Approximately half of these appear to be transcribed from pseudogenes. In situ hybridization showed that two of these pseudogene transcripts were...

Background: The full catalog of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago. Results: We found that about one third of their satDNA families (near 60 in every species) showed sequence homology and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH patterns at both intra-and interspecific levels. We defined indices of homogenization and degeneration and quantified the level of incomplete library sorting between species. Conclusions: Our analyses revealed that satDNA degenerates through point mutation and homogenizes through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification and degeneration, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split.

The PIGSFEAST (PF) exon of the Drosophila dumpy gene is undergoing concerted evolution by the process of unequal crossing over. We have developed a long-range PCR-based assay to amplify the approximately 12 kb long exon which contains variable numbers of 303 or 306 nt long repeats in a tandem array. We applied this procedure to mutation accumulation lines of Drosophila melanogaster established by M. Wayne and L. Higgins. Nine new repeat length variants were found in these lines allowing us to measure the rate of unequal crossing over in the PF exon. The rate, which for several reasons is an underestimate, is 7.05 9 10 -4 exchanges per generation.

Mosquito vectors-borne infectious diseases are enormous burden on human health and development worldwide. Disease-transmitting mosquito vector species use a reproductive strategy termed anautogeny that requires a blood meal to initiate egg maturation or oogenesis. Understanding the molecular basis of the regulation of egg development following a blood meal is essential to recognize the developmental biology and life cycle of mosquitoes and pinpoint important targets for control interventions. Vitellogenin (Vtg) is the major yolk protein synthesized during oogenesis and widely characterized in many mosquito species, mainly Culex pipiens complex mosquitoes. In this study, we report the differential stage and temporal expression of vtg genes in anautogenous Cx pipiens complex mosquitoes collected from Egypt following the ingestion of a blood meal using quantative real-time PCR (qRT-PCR) analysis. qRT-PCR analysis of the transcriptional pattern was performed in adult females at differen...

Interspecific hybridization is one of the major factors leading to phylogenetic incongruence among loci, but the knowledge is still limited about the potential of each locus to introgress between species. By directly sequencing three DNA regions: chloroplast DNAs (matK gene and trnL-F noncoding region), the nuclear ribosomal external transcribed spacer (ETS) region, and internal transcribed spacer (ITS) regions, we construct three phylogenetic trees of Asian species of Mitella (Saxifragaceae), a genus of perennials in which natural hybrids are commonly observed. Within this genus, there is a significant topological conflict between chloroplast and nuclear phylogenies and also between the ETS and the ITS, which can be attributed to frequent hybridization within the lineage. Chloroplast DNAs show the most extensive introgression pattern, ITS regions show a moderate pattern, and the ETS region shows no evidence of introgression. Nonuniform concerted evolution best explains the difference in the introgression patterns between the ETS region and ITS regions, as the sequence heterogeneity of the ITS region within an individual genome is estimated to be twice that of an ETS in this lineage. Significant gene conversion patterns between two hybridizing taxa were observed in contiguous arrays of cloned ETS-ITS sequences, further confirming that only ITS regions have introgressed bidirectionally. The relatively slow concerted evolution in the ITS regions probably allows the coexistence of multiple alleles within a genome, whereas the strong concerted evolution in the ETS region rapidly eliminates heterogeneous alleles derived from other species, resulting in species delimitations highly concordant with those based on morphology. This finding indicates that the use of multiple molecular tools has the potential to reveal detailed organismal evolution processes involving interspecific hybridization, as an individual locus varies greatly in its potential to introgress between species.

Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the Mediterranean Region. The species also has the ability to form interspecific hybrids with the human parasite S. haematobium with natural hybridisation observed in West Africa, presenting possible zoonotic transmission. Additionally, this exchange of alleles between species may dramatically influence disease dynamics and parasite evolution. We have generated a 374 Mb assembly of the S. bovis genome using Illumina and PacBio-based technologies. Despite infecting different hosts and organs, the genome sequences of S. bovis and S. haematobium appeared strikingly similar with 97% sequence identity. The two species share 98% of protein-coding genes, with an average sequence identity of 97.3% at the amino acid level. Genome comparison identified large continuous parts of the genome (up to several 100 kb) showing almost 100% sequence identity between S. bovis and S. haematobium. It is unlikely that this is a result of genome conservation and provides further evidence of natural interspecific hybridization between S. bovis and S. haematobium. Our results suggest that foreign DNA obtained by interspecific hybridization was maintained in the population through multiple meiosis cycles and that hybrids were sexually reproductive, producing viable offspring. The S. bovis genome assembly forms a highly valuable resource for studying schistosome evolution and exploring genetic regions that are associated with species-specific phenotypic traits.

Phosphodiesterase 6 (PDE6) is a protein complex that hydrolyses cGMP and acts as the effector of the vertebrate phototransduction cascade. The PDE6 holoenzyme consists of catalytic and inhibitory subunits belonging to two unrelated gene families. Rods and cones express distinct genes from both families: PDE6A and PDE6B code for the catalytic and PDE6G the inhibitory subunits in rods while PDE6C codes for the catalytic and PDE6H the inhibitory subunits in cones. We performed phylogenetic and comparative synteny analyses for both gene families in genomes from a broad range of animals. Furthermore, gene expression was investigated in zebrafish. We found that both gene families expanded from one to three members in the two rounds of genome doubling (2R) that occurred at the base of vertebrate evolution. The PDE6 inhibitory subunit gene family appears to be unique to vertebrates and expanded further after the teleost-specific genome doubling (3R). We also describe a new family member tha...