Low Levels Of Recombination Research Articles

Development of DNA Barcoding for the Rapid Assessment of Biodiversity: 2024 Benjamin Franklin Medal in Earth and Environmental Science presented to Paul D. N. Hebert, Ph.D., FRSC, O.C.

The total number of species on Earth ranges from at least one billion to as many as six billion with the number of animal species likely being between 10 and 150 million and the number of plant species about 340,000. Yet, taxonomists have identified only about 2.2 million species, and naming and identifying new species by traditional methods is a slow process. In 1998, Professor Paul Hebert experienced an epiphany and realized a short length of DNA could be used as a “barcode” for every species. Hebert decided a short sequence from subunit 1 of the mitochondrial gene cytochrome c oxidase (COI) would be the ideal barcode for species identification. He was well aware of the advantage of using a mitochondrial gene, which lacks introns, has low levels of recombination, and has a haploid mode of inheritance. In particular, COI has sufficient sequence variation to distinguish among species, and in the early 1990s, there were good universal primers for COI. In 2003, Hebert and his colleagues published their demonstration of the utility of COI as a barcode in the Proceedings of the Royal Society B: Biological Sciences. Their paper remains the most highly cited paper ever to be published in this journal.Interest in Hebert's vision for barcoding all of life was well-known prior to the publication of the 2003 paper, and the Sloan Foundation in conjunction with Cold Spring Harbor Laboratory sponsored two meetings in 2003 to bring together molecular evolutionary biologists such as Hebert, museum-based systematists, and other researchers to discuss the prospects of using DNA barcoding for rapid identification of species. This led to the establishment of the Consortium for the Barcode of Life (CBOL) in 2004 and then the data platform to support the infrastructure of managing barcode information—BOLD: Barcode of Life Data Systems. As of March 2024, the BOLD platform has almost 16 million barcodes with 255,000 linked to a named animal species and 72,000 linked to a named plant species.The ease of barcoding has led to its use in a variety of ways including environmental monitoring of invasive species, detection of trafficking in exotic and protected species, quality assurance of food, and a broadening of involvement of non-scientists in assessing biodiversity. It is also now possible to extract DNA from environmental DNA (eDNA), and eDNA can be used to detect hard-to-find species. The utility of barcodes will continue to expand because of Hebert's original vision and his ongoing efforts to make barcoding cheap and widely available. The possibilities are only limited by our imagination.

The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes.

Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we report a complex and previously hidden landscape of structural divergence between the genomes of Drosophila persimilis and D. pseudoobscura, two classic species in speciation research, and study the relationships among structural variants, transposable elements, and gene expression divergence. The new assemblies confirm the already known fixed inversion differences between these species. Consistent with previous studies showing higher levels of nucleotide divergence between fixed inversions relative to collinear regions of the genome, we also find a significant overrepresentation of INDELs inside the inversions. We find that transposable elements accumulate in regions with low levels of recombination, and spatial correlation analyses reveal a strong association between transposable elements and structural variants. We also report a strong association between differentially expressed (DE) genes and structural variants and an overrepresentation of DE genes inside the fixed chromosomal inversions that separate this species pair. Interestingly, species-specific structural variants are overrepresented in DE genes involved in neural development, spermatogenesis, and oocyte-to-embryo transition. Overall, our results highlight the association of transposable elements with structural variants and their importance in driving evolutionary divergence.

Extreme variation in recombination rate and genetic diversity along the Sylvioidea neo-sex chromosome.

Recombination strongly impacts sequence evolution by affecting the extent of linkage and the efficiency of selection. Here, we study recombination over the Z chromosome in great reed warblers (Acrocephalus arundinaceus) using pedigree‐based linkage mapping. This species has extended Z and W chromosomes (“neo‐sex chromosomes”) formed by a fusion between a part of chromosome 4A and the ancestral sex chromosomes, which provides a unique opportunity to assess recombination and sequence evolution in sex‐linked regions of different ages. We assembled an 87.54 Mbp and 90.19 cM large Z with a small pseudoautosomal region (0.89 Mbp) at one end and the fused Chr4A‐part at the other end of the chromosome. A prominent feature in our data was an extreme variation in male recombination rate along Z with high values at both chromosome ends, but an apparent lack of recombination over a substantial central section, covering 78% of the chromosome. The nonrecombining region showed a drastic loss of genetic diversity and accumulation of repeats compared to the recombining parts. Thus, our data emphasize a key role of recombination in affecting local levels of polymorphism. Nonetheless, the evolutionary rate of genes (dN/dS) did not differ between high and low recombining regions, suggesting that the efficiency of selection on protein‐coding sequences can be maintained also at very low levels of recombination. Finally, the Chr4A‐derived part showed a similar recombination rate as the part of the ancestral Z that did recombine, but its sequence characteristics reflected both its previous autosomal, and current Z‐linked, recombination patterns.

Conditional loss of IKK\u03b1 in Osterix\u2009+\u2009cells has no effect on bone but leads to age-related loss of peripheral fat

NF-κB has been reported to both promote and inhibit bone formation. To explore its role in osteolineage cells, we conditionally deleted IKKα, an upstream kinase required for non-canonical NF-κB activation, using Osterix (Osx)-Cre. Surprisingly, we found no effect on either cancellous or cortical bone, even following mechanical loading. However, we noted that IKKα conditional knockout (cKO) mice began to lose body weight after 6 months of age with severe reductions in fat mass and lower adipocyte size in geriatric animals. qPCR analysis of adipogenic markers in fat pads of cKO mice indicated no difference in early differentiation, but instead markedly lower leptin with age. We challenged young mice with a high fat diet finding that cKO mice gained less weight and showed improved glucose metabolism. Low levels of recombination at the IKKα locus were detected in fat pads isolated from old cKO mice. To determine whether recombination occurs in adipocytes, we examined fat pads in Osx-Cre;TdT reporter mice; these showed increasing Osx-Cre-mediated expression in peripheral adipocytes from 6 weeks to 18 months. Since Osx-Cre drives recombination in peripheral adipocytes with age, we conclude that fat loss in cKO mice is most likely caused by progressive deficits of IKKα in adipocytes.

Charge Transfer in Mixed-Phase TiO2 Photoelectrodes for Perovskite Solar Cells

In mesoscopic perovskite solar cells (PSCs) the recombination processes within the TiO2 photoelectrode and at the TiO2/perovskite interface limit power conversion efficiency. To overcome this challenge, we investigated the effect of TiO2 phase composition on the electronic structure of TiO2 photoelectrodes, as well as on PSCs performance. For this, a set of PSCs based on TiO2 thin films with different content of anatase and rutile particles was fabricated under ambient conditions. X-ray diffraction, optical spectroscopy and scanning electron microscopy were used to study the structural, morphological and optical characteristics of TiO2 powders and TiO2-based thin films. X-ray photoelectron spectroscopy (XPS) analysis of anatase revealed a cliff conduction band alignment of 0.2 eV with respect to the rutile. Energy band alignment at the anatase/rutile/perovskite interfaces deduced from the XPS data provides the possibility for interparticle electron transport from the rutile to anatase phase and the efficient blocking of electron recombination at the TiO2/perovskite interface, leading to efficient electron-hole separation in PSCs based on mixed-phase TiO2 photoelectrodes. PSCs based on TiO2 layers with 60/40 anatase/rutile ratio were characterized by optimized charge extraction and low level of recombination at the perovskite/TiO2 interface and showed the best energy conversion efficiency of 13.4% among the studied PSCs. Obtained results provide a simple and effective approach towards the development of the next generation high efficiency PSCs.

Development of mouse models of angiosarcoma driven by p53.

ABSTRACTAngiosarcomas are a rare group of tumours which have poor prognosis and limited treatment options. The development of new therapies has been hampered by a lack of good preclinical models. Here, we describe the development of an autochthonous mouse model of angiosarcoma driven by loss of p53 in VE-cadherin-expressing endothelial cells. Using Cdh5-Cre to drive recombination in adult endothelial cells, mice developed angiosarcomas with 100% penetrance upon homozygous deletion of Trp53 with a median lifespan of 325 days. In contrast, expression of the R172H mutant p53 resulted in formation of thymic lymphomas with a more rapid onset (median lifespan 151 days). We also used Pdgfrb-Cre-expressing mice, allowing us to target predominantly pericytes, as these have been reported as the cell of origin for a number of soft tissue sarcomas. Pdgfrb-Cre also results in low levels of recombination in venous blood endothelial cells in multiple tissues during development. Upon deletion of Trp53 in Pdgfrb-Cre-expressing mice (Pdgfrb-Cre, Trp53fl/fl mice), 65% developed lymphomas and 21% developed pleomorphic undifferentiated soft tissue sarcomas. None developed angiosarcomas. In contrast, 75% of Pdgfrb-Cre, Trp53R172H/R172H mice developed angiosarcomas, with 60% of these mice also developing lymphomas. The median lifespan of the Pdgfrb-Cre, Trp53R172H/R172H mice was 151 days. Re-implantation of angiosarcoma tumour fragments from Cdh5-Cre, Trp53fl/fl mice provided a more consistent and rapid model of angiosarcoma than the two spontaneous models. The ability to passage tumour fragments through the mouse provides a novel model which is amenable to preclinical studies and will help the development of potential new therapies for angiosarcoma.

Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance

BackgroundContinuing evolution of the Mycobacterium tuberculosis (Mtb) complex genomes associated with resistance to anti-tuberculosis drugs is threatening tuberculosis disease control efforts. Both multi- and extensively drug resistant Mtb (MDR and XDR, respectively) are increasing in prevalence, but the full set of Mtb genes involved are not known. There is a need for increased sensitivity of genome-wide approaches in order to elucidate the genetic basis of anti-microbial drug resistance and gain a more detailed understanding of Mtb genome evolution in a context of widespread antimicrobial therapy. Population structure within the Mtb complex, due to clonal expansion, lack of lateral gene transfer and low levels of recombination between lineages, may be reducing statistical power to detect drug resistance associated variants.ResultsTo investigate the effect of lineage-specific effects on the identification of drug resistance associations, we applied genome-wide association study (GWAS) and convergence-based (PhyC) methods to multiple drug resistance phenotypes of a global dataset of Mtb lineages 2 and 4, using both lineage-wise and combined approaches. We identify both well-established drug resistance variants and novel associations; uniquely identifying associations for both lineage-specific and -combined GWAS analyses. We report 17 potential novel associations between antimicrobial resistance phenotypes and Mtb genomic variants.ConclusionsFor GWAS, both lineage-specific and -combined analyses are useful, whereas PhyC may perform better in contexts of greater diversity. Unique associations with XDR in lineage-specific analyses provide evidence of diverging evolutionary trajectories between lineages 2 and 4 in response to antimicrobial drug therapy.

Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter

Horizontal gene transfer accelerates bacterial adaptation to novel environments, allowing selection to act on genes that have evolved in multiple genetic backgrounds. This can lead to ecological specialization. However, little is known about how zoonotic bacteria maintain the ability to colonize multiple hosts whilst competing with specialists in the same niche. Here we develop a stochastic evolutionary model and show how genetic transfer of host segregating alleles, distributed as predicted for niche specifying genes, and the opportunity for host transition could interact to promote the emergence of host generalist lineages of the zoonotic bacterium Campylobacter. Using a modelling approach we show that increasing levels of homologous recombination enhance the efficiency with which selection can fix combinations of beneficial alleles, speeding adaptation. We then show how these predictions change in a multi-host system, with low levels of recombination, consistent with real r/m estimates, increasing the standing variation in the population, allowing a more effective response to changes in the selective landscape. Our analysis explains how observed gradients of host specialism and generalism can evolve in a multihost system through the transfer of ecologically important loci among coexisting strains.

Transition from Environmental to Partial Genetic Sex Determination in Daphnia through the Evolution of a Female-Determining Incipient W Chromosome.

Sex chromosomes can evolve during the evolution of genetic sex determination (GSD) from environmental sex determination (ESD). Despite theoretical attention, early mechanisms involved in the transition from ESD to GSD have yet to be studied in nature. No mixed ESD-GSD animal species have been reported, except for some species of Daphnia, small freshwater crustaceans in which sex is usually determined solely by the environment, but in which a dominant female sex-determining locus is present in some populations. This locus follows Mendelian single-locus inheritance, but has otherwise not been characterized genetically. We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations of D. magna, and spans 3.6 Mb. Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium among the 36 associated SNPs. The region carries numerous genes involved in sex differentiation in other taxa, including transformer2 and sox9. Taken together, the region determining the genetic females shows characteristics of a sex-related supergene, suggesting that LG3 is potentially an incipient W chromosome despite the lack of significant additional restriction of recombination between Z and W. The occurrence of the female-determining locus in a pre-existing low recombining region illustrates one possible form of recombination suppression in sex chromosomes. D. magna is a promising model for studying the evolutionary transitions from ESD to GSD and early sex chromosome evolution.

Genetic diversity of NBS–LRR class disease-resistance gene analogs in cultivated and wild eggplants

The genes encoding the nucleotide-binding site (NBS) and leucine-rich repeat (LRR) motifs constitute a large gene family in plants and have attracted much interest, because most of the plant disease-resistance genes that have been cloned are from this gene family. In this study, degenerate oligonucleotide primers, designed on the basis of conserved regions of the NBS domains from known plant resistance genes, were used to isolate resistance gene analogs (RGAs) from cultivated and wild eggplants, i.e., S. melongena, S. aethiopicum gr. Gilo, S. linnaeanum, S. integrifolium, S. sisymbriifolium, and S. khasianum. Sequence analysis indicated that the cloned eggplant RGAs belong to the non-TIR–NBS–LRR type, which are very similar to the R genes or the RGAs identified in other plant species, especially Solanaceae plants, suggesting the existence of common ancestors. Wide genetic diversity of eggplant RGAs was observed both in interspecific and intraspecific sequences, and eight distinct families of eggplant RGAs were identified. Further studies revealed a high average ratio of synonymous to non-synonymous substitution and a low level of recombination. These results suggest that NBS-encoding sequences of RGAs in cultivated and wild eggplants are subject to gradual accumulation of mutations leading to purifying selection. This is the first report of NBS–LRR class RGAs in eggplants.

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus.

BackgroundNext-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bayesian approach, BRATNextGen, for detecting recombination on an expanded NGS dataset of the globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clone ST239.ResultsThe data confirm strong geographical clustering at continental, national and city scales and demonstrate that the rate of recombination varies significantly between phylogeographic sub-groups representing independent introductions from Europe. These differences are most striking when mobile non-core genes are included, but remain apparent even when only considering the stable core genome. The monophyletic ST239 sub-group corresponding to isolates from South America shows heightened recombination, the sub-group predominantly from Asia shows an intermediate level, and a very low level of recombination is noted in a third sub-group representing a large collection from Turkey.ConclusionsWe show that the rapid global dissemination of a single pathogenic bacterial clone results in local variation in measured recombination rates. Possible explanatory variables include the size and time since emergence of each defined sub-population (as determined by the sampling frame), variation in transmission dynamics due to host movement, and changes in the bacterial genome affecting the propensity for recombination.

RAPDs distinguish the lichens Xanthoria aureola and X. parietina in a mixed seashore rock population

Morphological characters can vary to an extent that makes it difficult to separate the two morphologically and chemically similar species Xanthoria aureola and X. parietina for an inexperienced field biologist. They occur frequently in mixed stands on seashore rocks on the western coast of Norway. We examined (1) whether a simple method like RAPD-PCR could confirm the distinction between the two species previously reported on the basis of DNA sequences, and (2) whether infraspecific DNA and RAPD data from X. parietina were congruent. We also checked whether the RAPD band scoring procedure could affect the results. Results show that (1) RAPD distance matrices based on band scorings performed independently by the two authors were always congruent and differences never affected conclusions, (2) RAPD clearly distinguishes between X. parietina and X. aureola in a way that is fully congruent with a classification based on DNA sequence data, and (3) there was no significant congruence between infraspecific distances based on DNA sequences and RAPD data in X. parietina. The latter observation may be taken as support for a previously published report of low levels of recombination in X. parietina, which stands in contrast to statements of obligate homothallism in that species.

Molecular mapping of the suppressor gene Igc1 to the gametocidal gene Gc3-C1 in common wheat

Several species of the genus Aegilops, wild relatives of wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) carry gametocidal (Gc) genes. Gc genes kill the gametes without themselves by causing chromosomal breakage during post-meiotic cell divisions, and therefore are strong segregation distorters. The Gc gene Gc3-C1 derived from chromosome 3C of Ae. triuncialis (2n = 4x = 28, CCUU) induces chromosomal breakage in wheat cultivar 'Chinese Spring' (CS) but not in cultivar 'Norin 26' (N26). This cultivar-specific inhibition of Gc function is caused by a suppressor gene Igc1 located on chromosome 3B of N26. Igc1 is presumed to be a modified Gc gene without breakage function because of its homoeology to Gc3-C1. Here we report the results of linkage and physical mapping of Igc1 to help elucidate the molecular mechanisms underlying Gc action. Segregation analysis of the phenotypic data in BC(1)F(1) mapping population of the cross between (CSxN26)F(1) and CS + 3C" showed a 1:1 segregation ratio indicating that Igc1 is a dominant gene. In the linkage analysis, three molecular marker loci Xgwm285, Xgwm376, and Xcfp1886 cosegregated with the Igc1 locus. Bin mapping assigned the loci Xgwm285 and Xcfp1886 to bin C-3BS1-0.33 and Xgwm376 to bin C-3BL2-0.22. Physical mapping using Gc-induced chromosomal deletion lines of chromosome 3B of N26 revealed that the Igc1 locus resides in 52.0% or 2.1% of bins C-3BS1-0.33 and C-3BL2-0.22, respectively. Pericentromeric localization of Igc1 in chromosome 3B of N26 may have a positive effect to keep the two-component system of the Gc action. Map-based cloning approach to isolate the Igc1 may be difficult because recombination is depleted in the pericentromeric region. As is shown in this study, the combination of genetic and physical mapping offers high efficiency to identify the regions where genes are located especially in regions with low levels of recombination.

CHROMOSOMAL INVERSIONS AND SPECIES DIFFERENCES: WHEN ARE GENES AFFECTING ADAPTIVE DIVERGENCE AND REPRODUCTIVE ISOLATION EXPECTED TO RESIDE WITHIN INVERSIONS?

Many factors can promote speciation, and one which has received much attention is chromosomal inversions. A number of models propose that the recombination suppressing effects of inversions facilitate the maintenance of differences between interbreeding populations in genes affecting adaptive divergence and reproductive isolation. These models predict that such genes will disproportionately reside within inversions, rather than in collinear regions. This hypothesis has received some support, but exceptions exist. Additionally, the effects of known low levels of recombination within inversions on these models are uninvestigated. Here, simulations are used to compare the maintenance of genetic differences between populations following secondary contact and hybridization in different inversion models. We compare regions with no recombination within them to regions with low recombination and to collinear regions with free recombination. Our most general finding is that the low levels of recombination within an inversion often result in the loss of accentuated divergence in inverted regions compared to collinear ones. We conclude that inversions can facilitate the maintenance of species differences under some conditions, but that large or qualitative differences between inverted and collinear regions need not occur. We also find that strong selection facilitates maintenance of divergence in a manner analogous to inversions.

Effective population size and tests of neutrality at cytoplasmic genes inArabidopsis

Cytoplasmic genomes typically lack recombination, implying that genetic hitch-hiking could be a predominant force structuring nucleotide polymorphism in the chloroplast and mitochondria. We test this hypothesis by analysing nucleotide polymorphism data at 28 loci across the chloroplast and mitochondria of the outcrossing plant Arabidopsis lyrata, and compare patterns with multiple nuclear loci, and the highly selfing Arabidopsis thaliana. The maximum likelihood estimate of the ratio of effective population size at cytoplasmic relative to nuclear genes in A. lyrata does not depart from the neutral expectation of 0.5. Similarly, the ratio of effective size in A. thaliana is close to unity, the neutral expectation for a highly selfing species. The results are thus consistent with neutral organelle polymorphism in these species or with comparable effects of hitch-hiking in both cytoplasmic and nuclear genes, in contrast to the results of recent studies on gynodioecious taxa. The four-gamete test and composite likelihood estimation provide evidence for very low levels of recombination in the organelles of A. lyrata, although permutation tests do not suggest that adjacent polymorphic sites are more closely linked than more distant sites across the two genomes, suggesting that mutation hotspots or very low rates of gene conversion could explain the data.

A microsatellite-based, physically anchored linkage map for the gray, short-tailed Opossum (Monodelphis domestica)

The genome of the gray, short-tailed opossum, Monodelphis domestica, will be the first of any marsupial to be fully sequenced. The utility of this sequence will be greatly enhanced by construction and integration of detailed genetic and physical maps. Therefore, it is important to verify the unusual recombinational characteristics that were suggested by the 'first-generation' M. domestica linkage map; specifically, very low levels of recombination and severely reduced female recombination, both of which are contrary to patterns in other vertebrates. We constructed a new linkage map based on a different genetic cross, using a new and much larger set of map markers, and physically anchored and oriented the linkage groups onto chromosomes via fluorescence in-situ hybridization mapping. This map includes 150 loci in eight autosomal linkage groups corresponding to the eight autosome pairs, and spans 86-89% of the autosomal genome. The sex-averaged autosomal map covers 715 cM, with a full-length estimate of 866 cM; the shortest full-length linkage map reported for any vertebrate. The sex-specific maps confirmed severely reduced female recombination in all linkage groups, and an overall F/M map ratio = 0.54. These results greatly extend earlier findings, and provide an improved microsatellite-based linkage map for this species.

Interference among deleterious mutations favours sex and recombination in finite populations

Sex and recombination are widespread, but explaining these phenomena has been one of the most difficult problems in evolutionary biology. Recombination is advantageous when different individuals in a population carry different advantageous alleles. By bringing together advantageous alleles onto the same chromosome, recombination speeds up the process of adaptation and opposes the fixation of harmful mutations by means of Muller's ratchet. Nevertheless, adaptive substitutions favour sex and recombination only if the rate of adaptive mutation is high, and Muller's ratchet operates only in small or asexual populations. Here, by tracking the fate of modifier alleles that alter the frequency of sex and recombination, we show that background selection against deleterious mutant alleles provides a stochastic advantage to sex and recombination that increases with population size. The advantage arises because, with low levels of recombination, selection at other loci severely reduces the effective population size and genetic variance in fitness at a focal locus (the Hill-Robertson effect), making a population less able to respond to selection and to rid itself of deleterious mutations. Sex and recombination reveal the hidden genetic variance in fitness by combining chromosomes of intermediate fitness to create chromosomes that are relatively free of (or are loaded with) deleterious mutations. This increase in genetic variance within finite populations improves the response to selection and generates a substantial advantage to sex and recombination that is fairly insensitive to the form of epistatic interactions between deleterious alleles. The mechanism supported by our results offers a robust and broadly applicable explanation for the evolutionary advantage of recombination and can explain the spread of costly sex.

Genetic features of Khoton Mongolians revealed by SNP analysis of the X chromosome

The Khoton Mongolian population is a small and relatively isolated ethnic group residing predominantly in the northwestern part of Mongolia. A recent genetic study of the Y chromosome revealed that the major Mongolian ethnic groups have a relatively close genetic affinity to populations in the northern part of East Asia, while the Khoton population reflected an apparent genetic differentiation from the other Mongolian populations. To further investigate the genetic features of the Khoton and the other Mongolian populations, we analyzed the single nucleotide polymorphisms (SNPs) in the Xq13.3 region, which is thought to have an extremely low level of recombination in the human X chromosome. We found that the frequency distribution of Xq13.3 haplotypes in the Khoton population was substantially different from those in three other Mongolian populations (Khalkh, Uriankhai, and Zakhchin). The same relationship was also revealed by the results from the population tree and principal-component (PC) analysis based on the allele frequencies. These results are largely consistent with the hypothesis that the Khoton population descended from a nomadic tribe of Turkish origin, which has been supported by previous anthropological, historical, and Y-chromosome studies. However, the population structure analysis produced an additional finding, namely, that the Khoton population is likely to be an admixed population.

The lack of recombination drives the fixation of transposable elements on the fourth chromosome of Drosophila melanogaster.

In regions of suppressed recombination, where selection is expected to be less efficient in removing slightly deleterious mutations, transposable element (TE) insertions should be more likely to drift to higher frequencies, and even to reach fixation. In the absence of excision events, once a TE is fixed it cannot be eliminated from the population, and accumulation of elements thus should become an irreversible process. In the long term, this can drive the degeneration of large non-recombining fractions of the genomes. Chromosome 4 of Drosophila melanogaster has very low levels of recombination, if any, and this could be causing its degeneration. Here we report the results of a PCR-based analysis of the population frequencies of TE insertions in a sample from three African natural populations. We investigated 27 insertions from 12 TE families, located in regions of either suppressed or free recombination. Our results suggest that TE insertions tend to be fixed in the non-recombining regions, particularly on the fourth chromosome. We have also found that this involves all types of elements, and that fixed insertions are significantly shorter and more divergent from the canonical sequence than those segregating in the sample (28.1% vs 86.3% of the canonical length, and average nucleotide divergence (D(XY)) = 0.082 vs 0.008, respectively). Finally, DNA-based elements seem to show a greater tendency to reach fixation than retrotransposons. Implications of these findings for the population dynamics of TEs, and the evolutionary forces that shape the patterns of genetic variation in regions of reduced recombination, are discussed.

Evolution of the core genome of Pseudomonas syringae, a highly clonal, endemic plant pathogen.

Pseudomonas syringae is a common foliar bacterium responsible for many important plant diseases. We studied the population structure and dynamics of the core genome of P. syringae via multilocus sequencing typing (MLST) of 60 strains, representing 21 pathovars and 2 nonpathogens, isolated from a variety of plant hosts. Seven housekeeping genes, dispersed around the P. syringae genome, were sequenced to obtain 400 to 500 nucleotides per gene. Forty unique sequence types were identified, with most strains falling into one of four major clades. Phylogenetic and maximum-likelihood analyses revealed a remarkable degree of congruence among the seven genes, indicating a common evolutionary history for the seven loci. MLST and population genetic analyses also found a very low level of recombination. Overall, mutation was found to be approximately four times more likely than recombination to change any single nucleotide. A skyline plot was used to study the demographic history of P. syringae. The species was found to have maintained a constant population size over time. Strains were also found to remain genetically homogeneous over many years, and when isolated from sites as widespread as the United States and Japan. An analysis of molecular variance found that host association explains only a small proportion of the total genetic variation in the sample. These analyses reveal that with respect to the core genome, P. syringae is a highly clonal and stable species that is endemic within plant populations, yet the genetic variation seen in these genes only weakly predicts host association.