Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse

Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Structural variants (SVs) (i.e., deletions, insertions, duplications, and inversions) are now known to play an important role in phenotypic variation, and consequently in processes such as disease determination or adaptation to a new environment. However, single-nucleotide variants receive much more attention than SVs, probably because they are easier to detect, and their phenotypic effects are easier to predict. The development of short- and long-read deep sequencing technologies have strongly improved the detection of SVs, but the quantification of their frequency from pooled sequencing (poolseq) data is still technically complex and expensive. Here, we present a rather simple and inexpensive method, which allows researchers to follow the dynamics of SV allele frequency. As an example of application, we follow the frequency of an insertion sequence (IS) insertion in experimental evolution populations of bacteria. This method is based on the design of triplets of primers around the structural variant borders, such that the amplicons produced by amplification of the wild-type (WT) and derived alleles differ in size by at least 5%, and that their amplification efficiency is similar. The quantity of each amplicon is then determined by parallel capillary electrophoresis and normalized to a calibration curve. This method can be easily extended to the quantification of the frequency of other structural variants (deletions, duplications, and inversions) and to pool-seq approaches of natural populations, including within-patient pathogen populations.

Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.)

The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.

Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.)

Abstract

Background

In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosine methylation in the red blood cells (RBCs) of challenged European sea bass (Dicentrarchus labrax), a species widely studied in both natural and farmed environments.

Results

We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appeared to manifest after the challenge test and a family-effect was detected. Only fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-challenge individuals. Thirty-seven of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. While further investigation remains necessary, few DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear relevant to integrate a centrally produced stress response in RBCs.

Conclusion

Our modified epiGBS protocol was powerful to analyze patterns of cytosine methylation in RBCs of D. labrax and to evaluate the impact of a challenge using minimally invasive blood samples. This study is the first approximation to identify epigenetic biomarkers of exposure to stress in fish.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07420-9.

Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms

The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.

Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

Understanding the evolutionary consequences of human-mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make-up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double-digested restriction site-associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data.

Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations

A genome-wide assessment of diversity is provided for wild Mediterranean brown trout Salmo trutta populations from headwater tributaries of the Orb River and from Atlantic and Mediterranean hatchery-reared strains that have been used for stocking. Double-digest restriction-site-associated DNA sequencing (dd-RADseq) was performed and the efficiency of de novo and reference-mapping approaches to obtain individual genotypes was compared. Large numbers of single nucleotide polymorphism (SNP) markers with similar genome-wide distributions were discovered using both approaches (196 639 v. 121 016 SNPs, respectively), with c. 80% of the loci detected de novo being also found with reference mapping, using the Atlantic salmon Salmo salar genome as a reference. Lower mapping density but larger nucleotide diversity (π) was generally observed near extremities of linkage groups, consistent with regions of residual tetrasomic inheritance observed in salmonids. Genome-wide diversity estimates revealed reduced polymorphism in hatchery strains (π = 0·0040 and π = 0·0029 in Atlantic and Mediterranean strains, respectively) compared to wild populations (π = 0·0049), a pattern that was congruent with allelic richness estimated from microsatellite markers. Finally, pronounced heterozygote deficiency was found in hatchery strains (Atlantic F_IS = 0·18; Mediterranean F_IS = 0·42), indicating that stocking practices may affect the genetic diversity in wild populations. These new genomic resources will provide important tools to define better conservation strategies in S. trutta.

Physiological mechanisms underlying individual variation in tolerance of food deprivation in juvenile European sea bass, Dicentrarchus labrax

Although food deprivation is a major ecological pressure in fishes, there is wide individual variation in tolerance of fasting, whose mechanistic bases are poorly understood. Two thousand individually tagged juvenile European sea bass were submitted to two 'fasting/feeding' cycles each comprising 3 weeks of food deprivation followed by 3 weeks of ad libitum feeding at 25°C. Rates of mass loss during the two fasting periods were averaged for each individual to calculate a population mean. Extreme fasting tolerant (FT) and sensitive (FS) phenotypes were identified that were at least one and a half standard deviations, on opposing sides, from this mean. Respirometry was used to investigate two main hypotheses: (1) tolerance of food deprivation reflects lower mass-corrected routine metabolic rate (RMR) in FT phenotypes when fasting, and (2) tolerance reflects differences in substrate utilisation; FT phenotypes use relatively less proteins as metabolic fuels during fasting, measured as their ammonia quotient (AQ), the simultaneous ratio of ammonia excretion to RMR. There was no difference in mean RMR between FT and FS over 7 days fasting, being 6.70±0.24 mmol h(-1) fish(-1) (mean ± s.e.m., N=18) versus 6.76±0.22 mmol h(-1) fish(-1) (N=17), respectively, when corrected to a body mass of 130 g. For any given RMR, however, the FT lost mass at a significantly lower rate than FS, overall 7-day average being 0.72±0.05 versus 0.90±0.05 g day(-1) fish(-1), respectively (P<0.01, t-test). At 20 h after receiving a ration equivalent to 2% body mass as food pellets, ammonia excretion and simultaneous RMR were elevated and similar in FT and FS, with AQs of 0.105±0.009 and 0.089±0.007, respectively. At the end of the period of fasting, ammonia excretion and RMR had fallen in both phenotypes, but AQ was significantly lower in FT than FS, being 0.038±0.004 versus 0.061±0.005, respectively (P<0.001, t-test). There was a direct linear relationship between individual fasted AQ and rate of mass loss, with FT and FS individuals distributed at opposing lower and upper extremities, respectively. Thus the difference between the phenotypes in their tolerance of food deprivation did not depend upon their routine energy use when fasting. Rather, it depended upon their relative use of tissue proteins as metabolic fuels when fasting, which was significantly lower in FT phenotypes.

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation.

The European sea bass is an economically important fish species, which is subject to intense selective breeding. Here, the authors sequence the genome of the European sea bass and highlight gene family expansions underlying adaptation to salinity change, as well as the genomic architecture of speciation between two divergent sea bass lineages.

Evolution of the structure and composition of house mouse satellite DNA sequences in the subgenus Mus (Rodentia: Muridea): a cytogenomic approach

The composition and orientation of the house mouse satellite DNA sequences (minor, major, TLC) were investigated by a FISH and CO-FISH approach in 11 taxa belonging to three clades of the subgenus Mus. Using a phylogenetic framework, our results highlighted two distribution patterns. The TLC satellite, the most recently discovered satellite, was present in all clades but varied quantitatively among species. This distribution supported its appearance in the ancestor of the subgenus followed by independent evolution in species of each clade. In contrast, the minor and major satellites occurred in only two clades of the subgenus indicating the simultaneous and recent amplification of these sequences. In addition, although qualitative differences in the composition and orientation of the satellite sequences were observed among the taxa, none of the features studied were unique to the house mouse and could account for the extensive chromosomal plasticity evidenced in Mus musculus domesticus.

Gene flow at major transitional areas in sea bass (Dicentrarchus labrax) and the possible emergence of a hybrid swarm

The population genetic structure of sea bass (Dicentrarchus labrax) along a transect from the Atlantic Ocean (AO) to the Eastern Mediterranean (EM) Sea differs from that of most other marine taxa in this area. Three populations (AO, Western Mediterranean [WM], EM) are recognized today, which were originally two allopatric populations. How two ancestral genetic units have evolved into three distinct units has not been addressed yet. Therefore, to investigate mechanisms that lead to the emergence of the central WM population, its current status, and its connectivity with the two parental populations, we applied 20 nuclear loci that were either gene associated or gene independent. Results confirmed the existence of three distinct gene pools, with higher differentiation at two transitional areas, the Almeria-Oran Front (AOF) and of the Siculo-Tunisian Strait (STS), than within any population. Significant linkage disequilibrium and heterozygote excess indicated that the STS is probably another tension zone, as already described for the AOF. Neutrality tests fail to reveal marker loci that could be driven by selection within or among metapopulations, except for locus DLA0068. Collectively, results support that the central WM population arose by trapping two tensions zones at distinct geographic locations of limited connectivity. Population assignment further revealed that WM individuals were more introgressed than individuals from the other two metapopulations. This suggests that this population might result from hybrid swarming, and was or is still seeded by genes received through the filter of each tension zone.

SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing

Summary: Characterizing genetic diversity through genotyping short amplicons is central to evolutionary biology. Next-generation sequencing (NGS) technologies changed the scale at which these type of data are acquired. SESAME is a web application package that assists genotyping of multiplexed individuals for several markers based on NGS amplicon sequencing. It automatically assigns reads to loci and individuals, corrects reads if standard samples are available and provides an intuitive graphical user interface (GUI) for allele validation based on the sequences and associated decision-making tools. The aim of SESAME is to help allele identification among a large number of sequences.

Availability: SESAME and its documentation are freely available under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Licence for Windows and Linux from http://www1.montpellier.inra.fr/CBGP/NGS/ or http://tinyurl.com/ngs-sesame.

Contact:emese.meglecz@univ-provence.fr

Supplementary information:Supplementary data are available at Bioinformatics online.

Disseminated Histoplasma capsulatum infection presenting with panniculitis and focal myositis in rheumatoid arthritis treated with etanercept

We report the case of a patient with rheumatoid arthritis (RA) on etanercept who presented with panniculitis and focal myositis as manifestations of disseminated histoplasmosis. Systematic search of the literature showed 11 additional case reports of disseminated histoplasmosis with tumour necrosis factor-alpha (TNFalpha) blockade therapy (infliximab, n = 8; etanercept, n = 3). Although disseminated histoplasmosis may manifest with classical symptoms of fever and respiratory complaints, it may also present atypically, such as with panniculitis and focal myositis. This review illustrates and emphasizes the importance of being highly suspicious for infection, including by opportunistic organisms, and to exclude such process in patients treated with a TNFalpha inhibitor when faced with unusual complications, even when an alternative aetiology appears plausible.

Molecular diversity of antimicrobial effectors in the oyster Crassostrea gigas

Background

To gain insight into the molecular diversity of antimicrobial peptides and proteins in the oyster Crassostrea gigas, we characterized and compared the sequence polymorphism of the antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline Rich peptide (Cg-Prp), and of the bactericidal permeability increasing protein, Cg-BPI. For that, we analyzed genomic and transcript sequences obtained by specific PCR amplification and in silico searches.

Results

High diversification among the three antimicrobial effectors was evidenced by this polymorphism survey. On the basis of sequence phylogenies, each AMP aggregates into clearly defined groups of variants and is the product of a multigenic family displaying a variety of gene structures. In contrast, Cg-bpi forms a single group and is encoded by a single gene copy. Moreover, we identified for both AMPs several genetic mechanisms of diversification such as recombination, parallel mutations leading to phylogenetic homoplasy and indel events. In addition, the non synonymous to synonymous substitutions ratio by codon (dN/dS) revealed several negatively and positively selected sites for both AMPs, suggesting that directional selection pressures have shaped their sequence variations.

Conclusions

This study shows for the first time in a mollusc that antimicrobial peptides and proteins have been subject to distinct patterns of diversification and we evidence the existence of different evolutionary routes leading to such sequence variability.

Evidence from population genetics that the ectomycorrhizal basidiomycete Laccaria amethystina is an actual multihost symbiont

It is commonly assumed that ectomycorrhizal (ECM) fungi associated with temperate forest tree roots are not host-specific. Because this assumption relies on species delineations based on fruitbodies morphology or ribosomal DNA sequences, host-specific, cryptic biological species cannot be ruled out. To demonstrate that Laccaria amethystina has true generalist abilities, we sampled 510 fruitbodies on three French sites situated 150-450 km away from each other. At each site, populations from monospecific stands (Abies alba, Castanea europea and Fagus sylvatica) or mixed stands (F. sylvatica + Quercus robur or Q. robur +Carpinus betulus) were sampled. Three different sets of markers were used for genotyping: (i) five microsatellite loci plus the ribosomal DNA intergenic spacer, (ii) the mitochondrial large ribosomal DNA subunit, and (iii) direct amplification of length polymorphism (DALP), a new method for fungi providing dominant markers. Evidence for allogamous populations (with possible inbreeding at local scale) and possibly for biparental mitochondrial inheritance was found. All markers congruently demonstrated that L. amethystina populations show little structure at this geographical scale, indicating high gene flow (as many as 50% of founding spores in all populations being of external origin). Our results also showed that host species contributed even less to population differentiation, and there was no evidence for cryptic biological species. This first in situ demonstration of a true multihost ability in an ECM species is discussed in terms of ecology and evolutionary biology.

Local mutagenic impact of insertions of LTR retrotransposons on the mouse genome

Solitary LTR loci are the predominant form of LTR retrotransposons in most eukaryotic genomes. They originate from recombination between the two LTRs of an ancestral retrovirus and are therefore incapable of transposition. Despite this inactivity, they appear to have a substantial impact on the host genome. Here we use the murine RMER10 LTR family as an example to describe how such elements can reshape regions of the genome through multiple mutations on an evolutionary time scale. Specifically, we use phylogenetic analysis of multiple copies of RMER10 in rodent species, as well as comparisons of orthologous pairs in mouse and rat, to argue that insertions of members of this family have locally induced the emergence of tandem repeat loci as well as many indels. Analysis of structural aspects of these sequences (secondary structures and transcription factors signals) may explain why RMER10 can become endogenous "mutagenic" factors through induction of replication fork blockages and/or error-prone repair of aberrant DNA structures. This hypothesis is also consistent with features of other interspersed repeated elements.

Phylogenetic relationships among monogenean gill parasites (Dactylogyridea, Ancyrocephalidae) infesting tilapiine hosts (Cichlidae): systematic and evolutionary implications

We studied the systematics of 14 species of monogenean (Ancyrocephalidae) gill parasites from West African tilapiine hosts (Cichlidae) using both morphological and genetic data. With these tools, we were able to: (i) confirm the validity of the previously described morphological parasite species and of the genus Scutogyrus; (ii) propose that some stenoxenous species (i.e., parasite species with more than one host) may be composed of sister species (e.g., Cichlidogyrus tilapiae); (iii) state that the use of the morphology of the haptoral sclerites is more suitable to infer phylogenetic relationships than the morphology of the genitalia (which seems to be more useful to resolve species-level identifications, presumably because of its faster rate of change). These results imply that: (i) the specificity of these monogenean parasites is greater than initially supposed (what were thought to be stenoxenous species may be assemblages of oïoxenous sister species); (ii) related species groups (i.e., "tilapiae," "halli," and "tiberianus") have to be, as genus Scutogyrus, validated within the 54 ancyrocephalid species described from 18 species of tilapiine hosts in West Africa, (iii) the group "tilapiae," due to its morphology and host range, have to be considered as being the most primitive; (iv) the occurrence of lateral transfers and parallel speciation processes are necessary to describe the repartition of the newly described parasite groups on the three host genera studied (Tilapia, Oreochromis, and Sarotherodon).

Characterization of a centromeric marker on mouse Chromosome 11 and its introgression in a domesticus/musculus hybrid zone

It has been proposed that the distribution of Robertsonian chromosome fusions and the Chromosome 11 Nucleolar Organizer Region (NOR) in the Danish hybrid zone between M. m. musculus and M. m. domesticus stems from centromeric incompatibilities between the two subspecies. To test this hypothesis, we identified and characterized a diagnostic subspecific marker closely linked to the centromere on mouse Chromosome 11. Using an allele-specific PCR assay, we investigated the introgression pattern of this centromere in a large sample of mice from a North-South transect of the hybrid zone in Jutland. Domesticus alleles were found to introgress far away from the center of the zone on the musculus side. These results suggest there is no incompatibility between the domesticus centromere of Chromosome 11 in the musculus genomic background.

Mouse biodiversity in the genomic era

Comparative genomics has developed by comparison of distantly related genomes, for which the link between the reported evolutionary changes and species development/physiology/ecology is not obvious. It is argued that the mouse (genus Mus) is an optimal model for microevolutionary genomics in vertebrates. This is because the mouse genome sequence, physical and genetic map have been completed, because mouse genetics, morpho-anatomy, pathology, behavior and ecology are well-studied, and because the Mus genus is a diverse, well- documented taxon, allowing comparative studies at the level of individual, population, subspecies, and species. The potential of the interaction between mouse genome and mouse biodiversity is illustrated by recent studies of speciation in the house mouse Mus musculus, and studies about the evolution of isochores, the peculiar pattern of GC-content variation across mammalian genomes.

Molecular evolution of plant haemoglobin: two haemoglobin genes in Nymphaeaceae Euryale ferox

We isolated and sequenced two haemoglobin genes from the early-branching angiosperm Euryale ferox (Nymphaeaceae). The two genes belong to the two known classes of plant haemoglobin. Their existence in Nymphaeaceae supports the theory that class 1 haemoglobin was ancestrally present in all angiosperms, and is evidence for class 2 haemoglobin being widely distributed. These sequences allowed us to unambiguously root the angiosperm haemoglobin phylogeny, and to corroborate the hypothesis that the class 1/class 2 duplication event occurred before the divergence between monocots and eudicots. We addressed the molecular evolution of plant haemoglobin by comparing the synonymous and nonsynonymous substitution rates in various groups of genes. Class 2 haemoglobin genes of legumes (functionally involved in a symbiosis with nitrogen-fixing bacteria) show a higher nonsynonymous substitution rate than class 1 (nonsymbiotic) haemoglobin genes. This suggests that a change in the selective forces applying to plant haemoglobins has occurred during the evolutionary history of this gene family, potentially in relation with the evolution of symbiosis.

Combined mapping of DALP and AFLP markers in cultivated sunflower using F9 recombinant inbred lines

A genetic map was constructed with specific PCRs, DALPs and AFLPs using F8-generation sunflower recombinant inbred lines. RI lines generated from a F2 population of one cross between the two cultivated inbred lines HA89 (maintainer for Pet1 CMS) and LR4 (restorer for Pet1 CMS) were used. A total of 305 markers were located using seven sPCR, 64 DALP and 301 AFLP loci. They were generated with one, seven and 14 primer pairs, respectively. The map construction consisted of a two-step strategy using 6 and 3.1 LOD scores revealed by a simulation file. Mapped markers were assembled into 18 linkage groups covering 2,168.6 cM with an average of 6.1 cM. The distribution of DALPs and AFLPs revealed that both markers tagged different regions to enable covering most of the sunflower genome. This leads to the longest map published so far for sunflower.

Polymerase chain reaction-single strand conformation polymorphism analyses of nuclear and chloroplast DNA provide evidence for recombination, multiple introductions and nascent speciation in the Caulerpa taxifolia complex

Independent lines of evidence support an Australian origin for the Mediterranean populations of the tropical alga Caulerpa taxifolia. To complement previous biogeographical studies based on nuclear rDNA internal transcribed spacer (ITS), a new chloroplast marker was developed--the cp 16S rDNA intron-2. Sequence variability for both nuclear and chloroplast markers were assessed in 110 individuals using single strand conformation polymorphism. Comparison of intrapopulation genetic diversity between invasive Mediterranean and 'native' Australian populations revealed the occurrence of two divergent and widespread clades. The first clade grouped nontropical invasive populations with inshore-mainland populations from Australia, while the second clustered all offshore-island populations studied so far. Despite our finding of nine distinct nuclear and five distinct chloroplast profiles, a single nucleocytoplasmic combination was characteristic of the invasive populations and sexual reproduction was found to be very rare. C. taxifolia is clearly a complex of genetically and ecologically differentiated sibling species or subspecies.

Is the Octomacridae the sister family of the Diplozodae?

Diplozoidae and Octomacridae are usually considered as sister families. Essentially this is because they are the only polyopisthocotyleans parasitising primary freshwater teleosts. Because of the lack of phylogenetically informative morphological characters to explore the pattern of colonisation of the primary continental freshwater teleosts and in order to understand the appearance of the "natural parabiosis" of Diplozoidae, a molecular phylogeny was inferred by comparing newly obtained partial 28S and 18S rDNA gene sequences of Eudiplozoon nipponicum and Diplozoon homoion with other already available sequences. The phylogenetic analysis seems to show that Diplozoidae and Octomacridae are not sister groups. Thus, the colonisation of primary freshwater teleosts by these two families could be independent.

[Molecular characterization of Diplozoidae populations on 5 species of Cyprinidae: new data on parasite specificity]

The genus Diplozoon (Platyhelminth) exhibits one of the most striking modes of reproduction. Adults reproduce after the permanent fusion of two larval hermaphrodites, which play a symmetrical role. The Diplozoidae are also exceptional among the Monogenea Polyopisthocotylea for two other reasons. They represent the only group really diversified on continental freshwater fishes; however, this diversification is difficult to evaluate since few morphoanatomical criteria are available to distinguish species and their host specificity is atypically variable among the Monogenea. For the first time in the Diplozoidae, the problems of species definition and of host specificity are examined using molecular tools. Two ribosomal markers (ITS2 and 28S rDNA (D1)) have been sequenced in five Diplozoidae, interacting with five Cyprinidae host species: the corresponding parasite-host systems have been well characterised, revealing some contrasting situations in the relations between Diplozoidae and Cyprinidae. Some species are effectively strictly host specific, but Diplozoon scardinii initially considered as a specific species on Scardinius erythrophtalmus and D. homoion on Rutilus rutilus are proposed to be a single species on the basis of their identical ITS2 and 28S rDNA sequences. On the same basis we proposed that D. paradoxum is able to parasitize two fish species, Abramis brama and Blicca bjoerkna, despite the morphological differences observed between the two xenopopulations. Phylogenetic relationships among Diplozoidae species were estimated with ITS2 sequences while cytochrome b sequences were used for their fish hosts. Finally, the comparison between these two molecular phylogenies seems to exhibit the phenomenon of cospeciation.

Derivation of a simple microsatellite locus from a compound ancestor in the genus Mus

Many microsatellite loci contain more than a single repeat motif. These compound microsatellites are perhaps most easily explained as arising from simple ancestors. We have uncovered a contrary example in mice of the genus Mus. Sequence analysis of the locus D1MIT29 in most of the members of the genus Mus reveals that this locus is compound in all species except M. musculus, in which it is simple. Moreover, phylogenetic analyses of base substitutions in the non-repetitive flanking region gives trees which are consistent with the previously accepted phylogenetic hypothesis that M. musculus is nested within the subgenus Mus. This confirms that the history of this locus is similar to that of molecular markers previously used in phylogenetic studies of this group and, therefore, demonstrates that the simple state in this lineage is derived from a compound ancestor. We also demonstrate the utility of this type of nuclear sequence variation for phylogeographic studies in the genus Mus. Finally, our sequences reveal homoplasy for size, reemphasizing the danger of using microsatellite size variation alone when the individuals under study are not closely related.

Slow rate of evolution in the mitochondrial control region of gulls (Aves: Laridae)

We sequenced part of the mitochondrial control region and the cytochrome b gene in 72 specimens from 32 gull species (Laridae, Larini) and 2 outgroup representatives (terns: Laridae, Sternini). Our control region segment spanned the conserved central domain II and the usually hypervariable 3' domain III. Apart from some heteroplasmy at the 3' end of the control region, domain III was not more variable than domain II or the cytochrome b gene. Furthermore, variation in the tempo of evolution of domain III was apparent between phyletic species groups. The lack of variation of the gull control region could not be explained by an increase in the proportion of conserved sequences in these birds, and the gull control region showed an organization similar to those of other avian control regions studied to date. A novel invariant direct repeat was identified in domain II of gulls, and in domain III, two to three inverted, sometimes imperfect, repeats are able to form a significantly stable stem-and-loop structure. These putative secondary structures have not been reported before, and a comparison between species groups showed that they are more stable in the group with the more conserved control region. The unusually slow rate of evolution of control region part III of the gulls could thus be partly explained by the existence of secondary structures in domain III of these species.

Isolation and characterization by direct amplification of length polymorphisms (DALP) of codominant genetic markers with Mendelian inheritance in Neoseiulus californicus (Acari: Phytoseiidae)

We report the first application of a new method designed to isolate polymorphic loci in any organism, the direct amplification of length polymorphism. Five polymorphic loci were readily isolated in the predatory mite Neoseiulus californicus (Acari: Phytoseiidae). Two to five alleles were identified among 46 isofemale lines based on fragment size variation due to micro-deletions/insertions. Genotyping F1 and F2 progenies from controlled heterogametic crosses and backcrosses allowed to establish the Mendelian inheritance of these alleles, their codominance, and pairwise recombination rates. Nucleotidic sequence divergence due to single base substitution was also found in the flanking regions of the polymorphism. We discuss the usefulness of these markers in studies of reproductive systems as well as population genetics, in particular, in mite species where the amount of DNA or richness in microsatellites could be limiting factors in the isolation of polymorphic loci.

Direct amplification of length polymorphisms (DALP), or how to get and characterize new genetic markers in many species

Direct amplification of length polymorphisms (DALP) uses an arbitrarily primed PCR (AP-PCR) to produce genomic fingerprints and to enable sequencing of DNA polymorphisms in virtually any species. Oligonucleotide pairs were designed to each produce a specific multi-banded pattern and all the fragments thus generated can be directly sequenced with the same two universal M13 sequencing primers. This strategy combines the advantages of a high resolution fingerprint technique and the possibility of characterizing the polymorphisms. The use of family members as templates in the multi-locus detection step allows a direct test of allele transmission, as well as early mapping of the markers or selection of loci associated with some traits or diseases. We used this method to detect micro-deletions/insertions and microsatellite DNA loci useful in population genetics studies, but it could be applied in many other fields of biology, such as genome mapping for definition of polymorphic sequence tagged sites, directly localized on a genetic map.

Does polyploidy lead to fewer and shorter microsatellites in Barbus (Teleostei:Cyprinidae)?

Screening of a hybrid Barbus barbus-B. meridionalis genome was performed for CA, GA, TAT, TCT, TAG, TGT, TATT, TACT, ATCT motifs, and simultaneously on another fish species, tilapia S. melanotheron. Sequences of positive clones were obtained for Barbus and revealed that repetitive structure significantly depends on the motif: most TAT and TATT repeats contain small numbers of repeats, and these repeats are highly heterogeneous, whereas other motifs (we mainly obtained CA and GATA repeats) form longer and much more homogeneous arrays. Polymorphism data from five loci in two different species of barbel show that perfectly repetitive loci are much more variable than imperfect loci (TAT and TATT). We compared the frequency of positive clones for different repeat motifs between barbel and tilapia. For dinucleotide repeats (CA and GA), the comparison was extended to additional fish species, trout and sea bass, which were screened in nearly identical conditions for these motifs. The most salient feature of these comparisons reveals that arrays of dinucleotide motifs are significantly under-represented and shorter in Barbus than in other fish species. We propose an explanation that can account for most features of microsatellites characterizing the genome of barbel. A bias toward deletion affecting slipped-strand mispairing events would lead to shortening and loss of microsatellite loci. Such a bias would represent an efficient way of eliminating useless DNA from polyploidized species with an excessive amount of DNA.

DNA polymorphisms in linkage disequilibrium at the 3' end of the human APO AII gene: relationships with lipids, apolipoproteins and coronary heart disease

Two investigations were undertaken to analyze the 3' region of the apolipoprotein AII (Apo AII) gene in patients with myocardial infarction (MI) and controls. Previous studies have suggested that a MspI polymorphism in this gene may be associated with hypertriglyceridaemia, high levels of HDL cholesterol and Apo AII. To verify this hypothesis, the distribution of MspI genotypes and their possible associations with several plasma lipid variables were studied in 882 subjects (411 cases with MI and 471 controls) from the ECTIM study. There were no differences in genotype and allele frequencies between cases and controls, and no differences in lipid variable levels in controls carrying the less frequent MspI allele vs other controls. Using single-strand conformation polymorphism (SSCP) analysis, we detected a new polymorphism which caused by a C-to-T transition located in the third intron near the splice junction site (acceptor). This polymorphism modifies a Bst N1 restriction site. The ECTIM population was screened for this new marker, and no significant associations with MI and plasma lipid levels were found. Our results suggest that these two variants located in the coding region of the Apo AII gene are unlikely to contribute significantly to the level of plasma lipid variables and the risk of coronary heart disease (CHD) in the European population.

Structural analysis of the minisatellite present at the 3' end of the human apolipoprotein B gene: new definition of the alleles and evolutionary implications

The internal structure of different alleles of the minisatellite present at the 3' end of the apolipoprotein B (ApoB) gene has been analysed by different approaches including sequencing. The repeat unit arrangements of the minisatellite on 570 chromosomes belonging to European and African populations were thus determined. It was possible to group the alleles using this structural criterion much more clearly than by the number of repeat units which can in some cases be misleading in case-control genetic epidemiological studies using such DNA sequences as markers. We were thus able to define five types (a to e) of alleles and their subtypes and to recognize clearly those which are, respectively, specific of the African and Caucasian populations. A phylogeny of the different alleles found in all human populations could also be deduced by this approach. The different putative mutational events leading from one type, or subtype, to the other were simply determined as point mutations, expansion/contraction and conversion events. Sequencing of one chimpanzee's allele suggested that the ApoB minisatellite was present before divergence between great apes and humans. It was determined also that a particular ApoB gene haplotype was in linkage disequilibrium with the minisatellite (a) type of alleles. This and the observation that the potential scaffold attachment regions (SAR) and topoisomerase II binding sites present in this minisatellite have a different distribution between the Caucasian and the African specific alleles suggest that the minisatellite could be involved in the epidemiology of coronary diseases.

Identification and inheritance of (GA/TC)n and (AC/GT)n repeats in the European flat oyster Ostrea edulis (L.)

Twelve microsatellites were isolated from a partial genomic library of Ostrea edulis using (GA/TC)n and (AC/GT)n probes and were subsequently sequenced. We estimate that, on average, 12,700 (GA/TC)n and 3900 (AC/GT)n microsatellites could be found in the genome assuming a random distribution. These estimates are high enough for the construction of a saturated genetic map. Primers were designed for three microsatellite loci, and analyses of polymorphism in a wild cohort revealed that one was suitable for population genetics studies (5 alleles), while the other two were highly polymorphic (between 17 and 48 alleles) and thus were more useful for paternity testing. Mendelian inheritance was tested on two full-sib families, and significant distortions of genotypic frequencies were found, although the gametic distributions seemed to be in agreement with Mendelian expectations. We interpret this as evidence for zygotic selection.

Polymorphism at VNTR locus 3 to the apolipoprotein B gene in a Tunisian population: difference from other ethnic groups

The Hypervariable region (HVR) detected at the 3' end of the apolipoprotein B (Apo B) locus has been the subject of numerous studies. As for many VNTR (variable number of tandem repeat), this locus is highly polymorphic and until now about 20 alleles have been described. The genotype distribution in all populations follows the Hardy-Weinberg predictions. A bimodal pattern of allele frequency distribution is apparent in all Caucasoid populations. We have analyzed the frequencies of different alleles in a Tunisian population (123 individuals) by the polymerase chain reaction technique and compared our results to those obtained in several ethnic groups. It appears that the distributions of the allele frequencies are very different: for Caucasoid populations, there are two peaks of frequencies for alleles with 36 and 48 repeats, but alleles of intermediate lengths are more frequent. Hixson et al. [(1993) Hum Genet 91:475-479] have shown a similar difference between black and white American populations. We found the same results in a black African group. Some of the repeat units of this HVR contain a Ssp I restriction site and digestion of the PCR products by this enzyme gives different patterns on gradient acrylamide gel [Desmarais et al., 1993, Nucleic Acids Res 21:2179-2184.] The DNA of African individuals (42) has been analyzed to discover the origin of this new allele. Preliminary results indicate that these particular alleles probably arose by introgression from the African population into the Tunisian one.

Variant mapping of the Apo(B) AT rich minisatellite. Dependence on nucleotide sequence of the copy number variations. Instability of the non-canonical alleles

Because of its variations in length, the AT rich Hyper-Variable Region (HVR) of the 3' end of the Apolipoprotein B gene is used as a polymorphic maker in genetic studies. It contains a SspI site in its repeated motif and we used this feature to precisely analyse the internal structure of the different alleles found at this locus in a Caucasian population. We performed total digestion on 194 alleles as well as Minisatellite Variant Repeat mapping (MVR mapping: partial digestion) on 54. The results show that the level of length variability (in copy number) of the 5' end of this locus is at least two times higher than that of the 3' end. This could be correlated with the difference in nucleotide sequence between the two parts of the HVR and suggests the dependence on the primary structure of the mechanism that produces length variability. A molecular model is proposed to explain this result. Moreover, the sharp analysis of the minisatellite structure by the distribution of SspI sites reveals differences between long and short alleles, indicating that in most cases, no recombination occurs between alleles of different sizes. Finally the rare alleles exhibit a non-canonical structure. These important points could explain the bimodal distribution of the frequencies of the alleles in the population.

The polymorphism ApoB/4311 in patients with myocardial infarction and controls: the ECTIM Study

The polymorphism affecting codon 4311 of the apolipoprotein B gene (ApoB/4311) was investigated in a large case-control study in two French and one Northern Irish geographically defined populations. Cases were recruited 3 to 9 months after a myocardial infarction (MI) and controls were randomly selected from the population. The polymorphism was assessed using allele-specific oligonucleotides (ASO). The genotype frequencies of the ApoB/4311 polymorphism did not differ in Northern Ireland and France and were in Hardy-Weinberg equilibrium in all groups; strong associations with three other polymorphisms of the ApoB gene (XbaI, EcoRI, VNTR(34 repeats)) were observed and it was possible to identify highly sensitive and specific markers of the ApoB/4311 rare variant. Homozygotes for the ApoB 4311 rare variant were slightly less frequent in cases than in controls: 22 (4.4%) and 35 (6.7%) respectively (population adjusted chi 2 = 3.3 P less than 0.07), especially in Belfast: 6 (3.1%) and 12 (7.6%), respectively (P less than 0.06). Several lipid and lipoprotein parameters were measured. Consistently among control groups, rare homozygotes had lower mean levels of ApoB (P less than 0.02), triglycerides (P less than 0.02), and lipoprotein particles containing ApoE and ApoB (LpE:B; P less than 0.001) and a higher mean level of lipoprotein particles containing ApoAI and not ApoAII (LpAI; P less than 0.02) than heterozygotes and frequent homozygotes combined. The strong association between the ApoB/4311 polymorphism and LpE:B was also observed in patients with MI. When present in the homozygous form, the ApoB/4311 Asn----Ser variant is associated with a lipoprotein profile that is apparently favourable.

Concerted evolution of light satellite DNA in genus Mus implies amplification and homogenization of large blocks of repeats

Light satellite DNA components present in species belonging to the genus Mus and to related murids were studied using the Southern blot technique. The results show species variations in both the amount and periodic structure of the repeating units, which suggests that families of related higher-order repeats developed in a common ancestor and were then amplified and/or deleted to different extents during the subsequent evolutionary period. Although the patterns generated by a series of type B enzymes (restriction enzymes that possess sites in a limited number of segments making up the total satellite DNA) in the species closely related to the M. musculus complex were very similar, sequence analysis of cloned unit repeats in two of these species (M. musculus domesticus and M. spretoides) showed near fixation of species-diagnostic variant nucleotides. This suggests that the important amplification and homogenization events that occurred after the divergence of M. spretus must have involved large blocks of sequences.