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PubMed2003

Genetic variation in the endangered wild apple (Malus sylvestris (L.) Mill.) in Belgium as revealed by amplified fragment length polymorphism and microsatellite markers.

The genetic variation within and between wild apple samples (Malus sylvestris) and cultivated apple trees was investigated with amplified fragment length polymorphisms (AFLP) and microsatellite markers to develop a conservation genetics programme for the endangered wild apple in Belgium. In total, 76 putative wild apples (originating from Belgium and Germany), six presumed hybrids and 39 cultivars were typed at 12 simple sequence repeats (SSR) and 139 amplified fragment length polymorphism (AFLP) loci. Principal co-ordinate analysis and a model-based clustering method classified the apples into three major gene pools: wild Malus sylvestris genotypes, edible cultivars and ornamental cultivars. All presumed hybrids and two individuals (one Belgian, one German) sampled as M. sylvestris were assigned completely to the edible cultivar gene pool, revealing that cultivated genotypes are present in the wild. However, gene flow between wild and cultivated gene pools is shown to be almost absent, with only three genotypes that showed evidence of admixture between the wild and edible cultivar gene pools. Wild apples sampled in Belgium and Germany constitute gene pools that are clearly differentiated from cultivars and although some geographical pattern of genetic differentiation among wild apple populations exists, most variation is concentrated within samples. Concordant conclusions were obtained from AFLP and SSR markers, which showed highly significant correlations in both among-genotypes and among-samples genetic distances.

Belgium↗

PubMed1998

Somitogenesis: segmenting a vertebrate.

The partitioning of the vertebrate body into a repetitive series of segments, or somites, requires the spatially and temporally co-ordinated behaviour of mesodermal cells. To date, it remains unknown how applicable our knowledge of the genetic mechanisms governing Drosophila segmentation will be to that of vertebrates, though recent results indicate some degree of conservation. Genetic studies in the mouse point to a major role for the Notch-Delta signalling pathway in somite formation. Furthermore, a molecular clock may be 'ticking' in the presomitic mesoderm.

Animals↗

PubMed1997

Effective size and F-statistics of subdivided populations. II. Dioecious species.

For a dioecious diploid population subdivided into an arbitrary number of subpopulations, we have derived recurrence equations for the inbreeding coefficient and coancestries between individuals within and among subpopulations and formulas for effective size and F-statistics. Stable population size and structure, discrete generations, autosomal inheritance, and the island migration model are assumed, and arbitrary distributions of the numbers of male and female progeny per family, different numbers and variable migration rates of males and females are incorporated in our derivation. Some published equations for effective size and F-statistics for a subdivided population are shown to be incorrect because several incorrect probabilities are used in the derivation. A more general equation for effective size is obtained by finding eigenvalue solutions to the recurrence equations for inbreeding coefficient and coancestry in this article, which reduces to the simple and familiar expressions derived by previous authors for the special case of a single unsubdivided population. Our general expressions for F-statistics also reduce to the classical results of WRIGHT's infinite island model and its extensions. It is shown that population structure is important in determining effective size and F-statistics and should be recognized and incorporated into programs for genetic conservation and evolution.

Biological Evolution↗

PubMed2006

Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine-scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation-based approach, we investigated how comparative and single-point methods, traditionally used in a Wright-Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex 'quartet' of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.

Alleles↗

PubMed2025

A telomere-to-telomere gap-free genome assembly of the endangered humphead wrasse (Cheilinus undulatus).

Humphead wrasse, Cheilinus undulatus, is an endangered fish species with high economic and ecological value as well as natural sex change from female to male, while sexual selection occurs in breeding aggregations. In our present study, we constructed the first gap-free telomere-to-telomere (T2T) genome assembly for humphead wrasse, by integration of PacBio HiFi, ONT Ultra-long and Hi-C sequencing techniques. With 99% of the entire sequences anchored into 24 chromosomes, this haplotypic genome assembly spans approximately 1.25 Gb and presents a complete set of 48 telomeres and 24 centromeres. In terms of correctness (quality value QV: 53.447) and completeness (BUSCO score: 99.3%), this chromosome-scale assembly is indeed of high quality. We predicted 658.03 Mb of repetitive sequences and annotated 26,609 protein-coding genes in the assembled genome. This high-quality T2T genome assembly not only facilitates the genetic conservation of humphead wrasse, but also offers fundamental genomic data for supporting in-depth investigations on functional genomics, genetic diversity, and selective breeding for this economically important teleost.

Animals↗

PubMed2003

The taxonomic status of Digramma (Pseudophyllidea: Ligulidae) inferred from DNA sequences.

The traditional classification of the ligulid tapeworms into 2 genera, Ligula Bloch, 1782 and Digramma Cholodkovsky, 1914, remains controversial. Molecular data of sequences for the 5' end of the nuclear 28S ribosomal ribonucleic acid (rRNA) gene, the mitochondrial cytochrome c oxidase subunit I (COI) gene, and the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene, as well as the first internal transcribed spacer (ITS1) of the nuclear ribosomal deoxyribonucleic acid (DNA), were used to characterize Digramma and to investigate its relationship with Ligula. Digramma spp. exhibited identical sequences with Ligula intestinalis both in the 28S rRNA and the COI gene and differed from L. intestinalis by 0.7% in the ITS1 region and 7.4% in the ND1 gene, respectively. A high degree of genetic conservation within 28S ribosomal DNA, COI, ITS1, and even ND1 genes, was found in Ligula and Digramma. The low genetic divergence in the 4 genes between Ligula and Digramma indicates that Digramma is probably not an independent genus. Therefore, it is proposed that Ligula and Digramma should be considered as 2 species within the genus Ligula and the tapeworms of Digramma collected from diverse localities in China belong to the same species. The present study also suggests that ITS1 and ND1 sequences can act as useful genetic markers to distinguish Ligula and Digramma.

Animals↗

PubMed2026

Systems genetics approaches model the heritable architecture of polyendocrine metabolic ovarian syndrome.

Polyendocrine metabolic ovarian syndrome (PMOS), formerly known as polycystic ovary syndrome (PCOS), is the most common endocrine disorder in women and is closely associated with complex diseases such as cardiovascular disease and type 2 diabetes. However, the mechanistic links between PMOS and its comorbidities remain poorly understood. Here, we present an integrative systems genetics platform that leverages genetic diversity in both mice and humans to dissect the drivers of PMOS and its associated complications. This framework uncovered conserved genetic and environmental factors underlying PMOS, identified susceptible cell types and organs, and elucidated mechanisms linking PMOS to subsequent pathologies. For instance, we showed that increased ovarian area contributes to both PMOS susceptibility and ovarian cancer progression, while specific ovary-heart signaling circuits modulate cardiac function with aging. We further identified ovarian SF3B1-mediated alternative splicing as a key mechanistic link between PMOS and metabolic traits. Pharmacologic inhibition of SF3B1 in mice reduced circulating testosterone, insulin, and glucose levels as well as fat mass expansion. Transcriptomics analysis of ovaries from mice and experiments using human cell lines localized these effects to exon skipping events in granulosa cells. Together, this study offers a mechanistic framework for modeling the diversity of PMOS pathologies and uncovers SF3B1-mediated splicing as a link between ovary function and systemic metabolism.

Female↗

PubMed2002

Perspective: purging the genetic load: a review of the experimental evidence.

Inbreeding depression, the reduction in fitness that accompanies inbreeding, is one of the most important topics of research in evolutionary and conservation genetics. In the recent literature, much attention has been paid to the possibility of purging the genetic load. If inbreeding depression is due to deleterious alleles, whose effect on fitness are negative when in a homozygous state, then successive generations of inbreeding may result in a rebound in fitness due to the selective decrease in frequency of deleterious alleles. Here we examine the experimental evidence for purging of the genetic load by collating empirical tests of rebounds in fitness-related traits with inbreeding in animals and plants. We gathered data from 28 studies including five mammal, three insect, one mollusc, and 13 plant species. We tested for purging by examining three measures of fitness-component variation with serial generations of inbreeding: (1) changes in inbreeding depression, (2) changes in fitness components of inbred lines relative to the original outbred line, and (3) purged population (outcrossed inbred lines) trait means as a function of ancestral outbred trait means. Frequent and substantial purging was found using all three measures, but was particularly pronounced when tracking changes in inbreeding depression. Despite this, we found little correspondence between the three measures of purging within individual studies, indicating that the manner in which a researcher chooses to estimate purging will affect interpretation of the results obtained. The discrepancy suggests an alternative hypothesis: rebounds in fitness with inbreeding may have resulted from adaptation to laboratory conditions and not to purging when using outcrossed inbred lines. However, the pronounced reduction in inbreeding depression for a number of studies provides evidence for purging, as the measure is likely less affected by selection for laboratory conditions. Unlike other taxon-specific reviews on this topic, our results provide support for the purging hypothesis, but firm predictions about the situations in which purging is likely or the magnitude of fitness rebound possible when populations are inbred remain difficult. Further research is required to resolve the discrepancy between the results obtained using different experimental approaches.

Animals↗

PubMed2000

[Structural and functional diversity of homeodomain genes of the orthodenticle and empty spiracles classes in Craniata].

Despite extensively divergent morphologies, the patterning of the embryonic brain is controlled by highly conserved genetic networks. Orthodenticle and empty spiracles-related homeodomain genes, which are expressed in insects as in vertebrates in anteriormost neuromeres of the embryonic brain, provide examples of such conservations. In gnathostomes, they form small multigene families, each containing three well-characterised orthology classes. In mice, paralogous genes play very different roles in the development of cephalic regions. Some of these roles are probably ancient and conserved in all chordates, while others, like the morphogenesis of gnathostomespecific characters, correspond to much more diversified functions. Genetic analyses in mice together with comparative analyses in a broad range of vertebrates provide new possibilities to investigate the molecular mechanisms which underlie these functional diversifications.

Animals↗

PubMed2000

Whole-genome characterization of embryonic stage inbreeding depression in a selfed loblolly pine family.

Inbreeding depression is important in the evolution of plant populations and mating systems. Previous studies have suggested that early-acting inbreeding depression in plants is primarily due to lethal alleles and possibly epistatic interactions. Recent advances in molecular markers now make genetic mapping a powerful tool to study the genetic architecture of inbreeding depression. We describe a genome-wide evaluation of embryonic viability loci in a selfed family of loblolly pine (Pinus taeda L.), using data from AFLP markers from an essentially complete genome map. Locus positions and effects were estimated from segregation ratios using a maximum-likelihood interval mapping procedure. We identified 19 loci showing moderately deleterious to lethal embryonic effects. These loci account for >13 lethal equivalents, greater than the average of 8.5 lethal equivalents reported for loblolly pine. Viability alleles show predominantly recessive action, although potential overdominance occurs at 3 loci. We found no evidence for epistasis in the distribution of pairwise marker correlations or in the regression of fitness on the number of markers linked to deleterious alleles. The predominant role of semilethal alleles in embryonic inbreeding depression has implications for the evolution of isolated populations and for genetic conservation and breeding programs in conifers.

Crosses, Genetic↗

PubMedDate not supplied

Entamoeba histolytica: sequence conservation of the Gal/GalNAc lectin from clinical isolates.

The Gal/GalNAc lectin gene of Entamoeba histolytica is a major amebic virulence protein responsible for interaction with host tissues. We investigated sequence differences in the Gal/GalNAc lectin heavy subunit in three isolates from Bangladesh and one isolate from Georgia, each of which was determined to be genetically distinct by SREHP AluI digestion. Interestingly, we observed only slight genetic diversity in the lectin gene as compared with the HM1:IMSS laboratory strain, originally a clinical isolate from Mexico. Genetic conservation of the Gal/GalNAc lectin between isolates may reflect that the lectin is under strong functional selection or possibly, that E. histolytica is a clonal population. Sequence conservation of the lectin indicates that immune responses against it should be cross-protective.

Amino Acid Sequence↗

PubMed2001

Transcriptional analysis and regulation of the sigma-E gene of Streptomyces antibioticus.

We report here the mapping of the transcriptional start point and identification of the promoter for the sigE gene of Streptomyces antibioticus. Sequence analysis revealed a conserved genetic organization of five genes encompassing sigE in S. antibioticus and S. coelicolor. Upstream of sigE a number of direct repeats, while conserved in both species, are arranged differently. Gel shift analysis demonstrated binding of a component of both S. antibioticus and S. coelicolor crude protein extracts to a 30 bp sequence encompassing one repeat, the A-rich box. Deletion analysis in promoter probes showed that maximal activity of the S. antibioticus promoter depends upon the presence of the sequence surrounding the A-rich box, as well as the region further upstream carrying other direct repeats.

Bacterial Proteins↗

PubMed1994

Rare alleles, MHC and captive breeding.

In recent years, more detailed genetic information has become available for individuals of endangered species in captive breeding programs. There have been suggestions that this information be used to identify rare alleles, particularly those at the MHC, that can be subsequently selected for captive breeding programs. First, we summarize the current information on the MHC relevant to conservation genetics, so that such a possible breeding program is seen in a proper perspective. For example, very few specific alleles at the MHC have been identified as selectively advantageous, even though there has been substantial effort to find such alleles in humans and a few other organisms. Further, many of the balancing selection models suggested for MHC variation are based on heterozygotes in general having a higher fitness than homozygotes and not on specific selectively advantageous alleles. Because there is no detailed data on MHC variability in captive populations, we used transferrin data in Przewalski's horses to evaluate a breeding program to select for rare alleles. In this species, one individual, 1060, has been identified to have the transferrin allele J. We determine the effect on founder contribution of multiply mating 1060 to increase the number of copies of this allele. Since there were 485 individuals in the population at this time, this extra mating had little detrimental effect on the distribution of founder contributions and the number of founder equivalents. We then selected 65, an ancestor of 1060, which had a high likelihood of being the individual that passed on the J allele in the lineage of 1060. We examined the effect of increasing the number of copies of alleles of 65 at a time when the population had only 22 other individuals. In this case, even though the founder contributions were changed more, there was also little effect on the founder contributions and the number of founder equivalents. Overall, it appears that selection that results in a limited change in the number of copies of rare alleles may not always have an overall detrimental effect. However, because other pedigrees may have very different properties, it is essential to perform a detailed pedigree analysis of any such selective breeding program to determine its effect before such a selection program is implemented.

Alleles↗

PubMed2000

Genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) germplasm from Ethiopia assessed by random amplified polymorphic DNA (RAPD).

The extent and distribution of genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) collected from five different geographical regions in Ethiopia were analyzed using random amplified polymorphic DNA (RAPD) markers for 93 individuals representing 11 populations. Nine decamer primers generated a total of 83 polymorphic bands with 8-12 bands per primer and a mean of 9 bands across the 93 individuals. The amount of genetic variation among the populations (H = 0.37) and among the geographical region (H = 0.44) was low to moderate, despite the high degree of polymorphic bands per primer. Similarly, the mean genetic distance (0.08) among populations as well as among regions of origin (0.04) of the population was found to be low. The low genetic variation may be due to the reduced population size of the wild sorghum in Ethiopia because of habitat change. Partitioning of the genetic variation into between and within the population as well as between and within the regions of origin revealed that 75% and 88% of the variation was found within the populations and within the regions, respectively. Cluster analysis of genetic distance estimates further confirmed low level of differentiation of wild sorghum populations both on population and regional bases. The implications of the results for genetic conservation purposes are discussed.

DNA, Plant↗

PubMed2006

Polymorphisms and haplotypes of the regulator of G protein signaling-2 gene in normotensives and hypertensives.

Regulator of G protein signaling (RGS) proteins stimulate the GTPase activity of Galpha subunits of heterotrimeric G proteins, thereby negatively regulating G protein-coupled receptor signaling. RGS2, which preferentially alters Galphaq-mediated signaling, may be important for cardiovascular health, because knockout of RGS2 in mice is associated with altered smooth muscle relaxation and hypertension. In this study, we determined genetic variation in the human RGS2 gene by sequencing DNA in normotensive and hypertensive populations of whites (n=128) and blacks (n=122). We identified 14 single nucleotide polymorphisms and 2 two-base insertion/deletions (in/del; 1891 to 1892 TC and 2138 to 2139 AA). Although most of the genetic variants were found at low allelic frequency, in particular in coding regions, the 1891 to 1892 TC and 2138 to 2139 AA intronic in/del were in linkage disequilibrium and were associated with hypertension in blacks (P<0.05). We defined several haplotypes for the RGS2 gene, certain of which showed striking differences between whites and blacks. Additionally, 2 haplotypes had significantly different frequencies between hypertensive and normotensive black groups (P<0.05). We conclude that RGS2 is genetically conserved within coding regions but that the intronic in/del define ethnicity-specific haplotypes. Moreover, certain RGS2 variants that occur at greater frequency in hypertensive blacks may serve as ethnicity-specific genetic variants for this disease.

Adult↗

PubMed1994

Cytochrome b and 16S rRNA sequence variation in the Salmo trutta (Salmonidae, Teleostei) species complex.

PCR amplification and direct sequencing of regions of the cytochrome b and 16S rRNA mitochondrial genes was carried out on Italian and Irish populations of the brown trout (Salmo trutta) species complex. These included S. t. marmoratus, S. t. macrostigma, Salmo carpio, and Salmo fibreni collected in Italy, and S. t. trutta morpha fario, from both Italy and Ireland. Samples of Atlantic salmon (Salmo salar) were also examined and used as an outgroup in the phylogenetic analysis. Results based on 592 bp indicated differentiation between fario morphs from Italy and Ireland. Despite the large phenotypic differences within Italian salmonids, very low genetic variation was found. On the basis of the mtDNA sequences studied, S. carpio and S. fibreni, which have been described as good species, are genetically undifferentiated from the other Italian taxa. The finding of a haplotype from Ireland in the Brenta River in Italy stresses the importance of conservation genetics studies aimed at identifying and preserving native genotypes.

Animals↗

PubMed2001

Patterns of genetic architecture for life-history traits and molecular markers in a subdivided species.

Understanding the utility and limitations of molecular markers for predicting the evolutionary potential of natural populations is important for both evolutionary and conservation genetics. To address this issue, the distribution of genetic variation for quantitative traits and molecular markers is estimated within and among 14 permanent lake populations of Daphnia pulicaria representing two regional groups from Oregon. Estimates of population subdivision for molecular and quantitative traits are concordant, with QST generally exceeding GST. There is no evidence that microsatellites loci are less informative about subdivision for quantitative traits than are allozyme loci. Character-specific comparison of QST and GST support divergent selection pressures among populations for the majority of life-history traits in both coast and mountain regions. The level of within-population variation for molecular markers is uninformative as to the genetic variation maintained for quantitative traits. In D. pulicaria, regional differences in the frequency of sex may contribute to variation in the maintenance of expressed within-population quantitative-genetic variation without substantially impacting diversity at the genic level. These data are compared to an identical dataset for 17 populations of the temporary-pond species, D. pulex.

Animals↗

PubMedDate not supplied

H-2-linked low-molecular weight polypeptide antigens assemble into an unusual macromolecular complex.

The major histocompatibility complex (MHC) is a cluster of tightly linked genes whose products are of central importance in the functioning of the immune system. Class I and II MHC antigens are integral membrane proteins which regulate cell-surface interactions between T cells and their targets, while class III antigens are components of the complement system of serum proteins. All available evidence indicates that the structure and function of the MHC and its gene products are highly conserved among species (for review, see ref.5). We recently reported the existence in murine cells of a fourth class of MHC-linked polypeptides which are biochemically and genetically distinct from previously identified MHC gene products: BALB.B anti-BALB/c (anti-H-2d) antiserum immunoprecipitates a set of 16 cytoplasmic low-molecular weight polypeptides (LMP) from BALB/c spleen cells and from the WEHI-3 cell line. The production of these peptides is coordinately regulated (by immune interferon) with the production of the class I and II MHC antigens, suggesting that they too are functionally relevant to the immune system. We demonstrate here that these 16 polypeptides are associated with one another in vivo as a very large (580,000-molecular weight, Mr) noncovalent complex. The unusual nature of this complex has allowed the non-immunochemical identification of similar complexes from (serologically negative) H-2b murine cells and from a human cell line. Thus, LMP antigens display two properties in common with other MHC antigens: they are both polymorphic and genetically conserved across species.

Animals↗