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An introgression approach to mapping differences in mating success and sperm competitive ability in Drosophila simulans and D. sechellia.

The progeny of Drosophila females doubly-mated to males from the same and a closely related species are mostly sired by conspecific males. We examined the genetic basis for conspecific mating preference and sperm precedence by using 186 Drosophila lines in which random chromosomal fragments of D. sechellia were introgressed into D. simulans. Sperm competition was measured for each of these lines by crossing ebony D. simulans female with ebony D. simulans males followed by wild-type males from the introgressed lines. Variation in sperm competition (proportion of progeny sired by the second male), mating discrimination (proportion of introgressed males that failed to remate), and male fecundity (proportion of progeny sired by introgressed males) were scored. The introgressed lines exhibited highly significant heterogeneity in the three phenotypes scored, motivating an analysis to locate quantitative trait loci (QTLs) responsible for the differences. Applying composite interval mapping, we found eight QTLs that explain a significant level of variation among introgressed lines in the phenotypes scored. Cytological position overlapped among some QTLs suggesting possible pleiotropic effects. Analysis of the joint effects of simulans/sechellia genetic composition at different QTLs and markers suggests that complex interactions among alleles are partially responsible for interspecific differences in sexual traits.

Animals↗

A polymorphism in randomly amplified DNA that differentiates the Y chromosomes of Bos indicus and Bos taurus.

A small number of west African Bos taurus cattle breeds, including the N'Dama, constitute a valuable genetic resource by virtue of their ability to remain productive under trypanosomiasis challenge. However, introgression of Bos indicus genes into the trypanotolerant breeds, particularly by introduction of zebu bulls, is a threat to this resource. This work describes the characterization and cloning of a bovine randomly amplified polymorphic DNA (RAPD) that is generated in polymorphic DNA (RAPD) that is generated in polymerase chain reaction (PCR) with the 10 base primer ILO1065 from Bos indicus male templates, but not from B. taurus male templates or female templates of either type. Male-specific sequences with homology to the RAPD also occur in B. taurus breeds. This suggests that the polymorphism may be due to base substitution(s) in an ILO1065 priming site, or insertion/deletion events either affecting priming sites or occurring between sites on the cattle Y chromosome. We have shown that cattle, whether of B. indicus or B. taurus phenotype, which possess a typically B. indicus metaphase Y chromosome on the basis of QFQ banding, have a B. indicus ILO1065-generated genotype. The ILO1065-primed RAPD can be used in a simple dot blot assay as a probe of RAPD-PCR products, to provide a convenient, reliable and effective means of detecting introgression of zebu genes in B. taurus cattle populations.

Africa, Western↗

[Structural organization and evolution of t-complex in Mus genus].

Modern data on the structure and evolution of the t complex are discussed. The t complex is a series of inversions in the proximal region of murine chromosome 17; it contains a set of genes that determine its predominant transmission to the offspring of heterozygous males. Variants of structural organization of this genetic system (t haplotypes) have been found in wild populations of four species of genus Mus (M. domesticus, M. musculus, M. molossinus, and M. castaneus), but not in representatives of other, evolutionarily remote species of this genus. The so-called vertical, horizontal, and introgressive hypotheses are discussed of the origin and evolution of the t complex. Based on population genetic studies and molecular analysis a new hypothesis on the origin of the t-complex is put forward. This hypothesis is a synthesis between the vertical and horizontal models and assumes that all known t haplotypes had a common ancestral chromosome 17 carrying a proximal inversion.

Animals↗

Hybridization and introgression between Callicarpa japonica and C. mollis (Verbenaceae) in central Japan, as inferred from nuclear and chloroplast DNA sequences.

Callicarpa x shirasawana is a natural hybrid between C. japonica and C. mollis, and has a morphology that is intermediate between those of the parent species. Characterization of natural Callicarpa populations in the Atsumi Peninsula of central Japan, which all three of the above species inhabit sympatrically, revealed hybrids with various morphologies. Molecular analysis revealed a high occurrence of introgression of the C. japonica genome into that of C. mollis. Moreover, all individuals examined with morphology similar to that of C. mollis had genetic traces of hybridization with C. japonica. Molecular analysis of individual C. mollis and C. japonica from five other areas of Japan showed that introgression of C. japonica into C. mollis occurs widely. Molecular data also strongly suggested that the previously recognized C. x shirasawana individuals with intermediate morphology are not F1 hybrids between C. japonica and C. mollis, but instead are progeny of C. x shirasawana backcrossed with C. japonica. Moreover, it was revealed that individuals with F1-type genotypes are indistinguishable morphologically from pure C. mollis. The results of the present study point to the need for re-evaluation of natural populations of C. mollis and C. x shirasawana.

Base Sequence↗

Genetic evidence for three species within Pseudoterranova decipiens (Nematoda, Ascaridida, Ascaridoidea) in the North Atlantic and Norwegian and Barents Seas.

Genetic variation of 1017 specimens of codworm, Pseudoterranova decipiens, collected from fish and seals at 23 sampling locations in the North Atlantic and Norwegian and Barents Seas, was analysed on the basis of 16 enzyme loci. Three reproductively isolated species, provisionally designated P. decipiens A, B and C, were detected, showing distinct alleles at the following loci: Mdh-1, 6Pgdh, Np, Pgm, Est-2 (between species A and B); Mdh-3, 6Pgdh, Np, Sod-1, Adk, Pgm, Est-2, Mpi (between A and C); Mdh-1, Mdh-3, Sod-1, Adk, Pgm, Est-2, Mpi (between B and C). One F1 hybrid was observed between P. decipiens A and B, but this apparently does not lead to any gene exchange between the two species, which do not show any evidence of introgression. No hybrids or introgressed individuals were observed between P. decipiens C and either A or B. Genetic distances among conspecific populations were low (average Nei's D 0.001-0.005), even though they were collected thousands of kilometres apart, indicating high levels of gene flow within each of the three species. The values of Nei's index D were 0.44 between P. decipiens A and B, 0.57 between B and C, and 0.79 between A and C. Estimated evolutionary divergence times, using Nei's formula, range from 2 to 4 million years. Differences between P. decipiens A, B and C were also found with respect to genetic variability, morphology, geographical distribution and hosts. Mean heterozygosity values of 0.08, 0.05 and 0.02 were obtained for P. decipiens A, B and C, respectively. Preliminary morphological examination of adult males, previously identified by multilocus electrophoresis, revealed differences in the relative size and pattern of caudal papillae. P. decipiens B is widespread in the study area, whereas P. decipiens A was found only in the North-East Atlantic and Norwegian Sea. In this area P. decipiens A is most common in the grey seal, Halichoerus grypus, while the common seal, Phoca vitulina, is the main host for P. decipiens B. In Canadian Atlantic waters, where P. decipiens A is apparently absent, P. decipiens B infects both grey and common seals; a few specimens were also found in the hooded seal, Cystophora cristata. The only definitive host so far identified for P. decipiens C is the bearded seal, Erignathus barbatus; P. decipiens C appears to be widespread, occurring in both the North-West Atlantic and Barents Sea.

Animals↗

Ancestors of white clover ( Trifolium repens L.), as revealed by isozyme polymorphisms.

Isozymes were used to study the putative ancestors of white clover ( Trifolium repens L.). Ten enzymes were examined, and 18 loci were resolved via starch-gel electrophoresis for accessions representing T. repens, Trifolium isthmocarpum, Trifolium nigrescens, Trifolium occidentale and Trifolium uniflorum, in addition to two more distantly related species, Trifolium alpinum and Trifolium purseglovei. Nei's genetic identities indicate that T. uniflorum and T. nigrescens are the closest relatives of T. repens. The isozyme data thus support a hypothesis that the two genomes of the tetraploid T. repens could have been derived from hybridization between T. nigrescens and T. uniflorum. This conclusion is further supported by shared alleles between T. repens, T. nigrescens and T. uniflorum. However, the origin of T. repens is somewhat obscured by the presence of shared alleles between T. repens and both T. occidentale and T. isthmocarpum, suggesting that introgression of genes from the latter two species into T. repens may also have taken place. High values of genetic identity are shared between T. occidentale with T. nigrescens and T. uniflorum, also indicative of introgression. Alternatively the presence of shared alleles among the five species may reflect their recent common ancestry.

Evolution, Molecular↗

Identification of barley genome segments introgressed into wheat using PCR markers.

Barley has several important traits that might be used in the genetic improvement of wheat. For this report, we have produced wheat-barley recombinants involving barley chromosomes 4 (4H) and 7 (5H). Wheat-barley disomic addition lines were crossed with 'Chinese Spring' wheat carrying the phlb mutation to promote homoeologous pairing. Selection was performed using polymerase chain reaction (PCR) markers to identify lines with the barley chromosome in the ph1b background. These lines were self pollinated, and recombinants were identified using sequence-tagged-site (STS) primer sets that allowed differentiation between barley and wheat chromosomes. Several recombinant lines were isolated that involved different STS-PCR markers. Recombination was confirmed by allowing the lines to self pollinate and rescreening the progeny via STS-PCR. Progeny testing confirmed 9 recombinants involving barley chromosome 4 (4H) and 11 recombinants involving barley chromosome 7 (5H). Some recombinants were observed cytologically to eliminate the possibility of broken chromosomes. Since transmission of the recombinant chromosomes was lower than expected and since seed set was reduced in recombinant lines, the utility of producing recombinants with this method is uncertain.

DNA, Plant↗

Microarray analysis of rat chromosome 2 congenic strains.

Human essential hypertension is a complex polygenic trait with underlying genetic components that remain unknown. The stroke-prone spontaneously hypertensive rat (SHRSP) is a model of human essential hypertension, and a number of reproducible blood pressure regulation quantitative trait loci have been found to map to rat chromosome 2. The SP.WKYGla2c* congenic strain was produced by introgressing a region of rat chromosome 2 from the normotensive Wistar Kyoto (WKY) strain into the genetic background of the SHRSP. Systolic and diastolic blood pressures were significantly reduced in the SP.WKYGla2c* compared with the SHRSP parental strain (198/134+/-6.1/3.3 versus 172/120+/-3.8/3.4 mm Hg; F=15.8/8.1, P=0.0009/0.013). Genome-wide microarray expression profiling was undertaken to identify differentially expressed genes among the parental SHRSP, WKY, and congenic strain. We identified a significant reduction in expression of glutathione S-transferase mu-type 2, a gene involved in the defense against oxidative stress. Quantitative reverse transcription-polymerase chain reaction relative to a beta-actin standard confirmed the microarray results with SHRSP mRNA at 8.56 x 10(-4) +/-1.6 x 10(-4) compared with SP.WKYGla2c* 3.67 x 10(-3)+/-2.8 x 10(-4) (95% CI -3.9 x 10(-3) to -1.8 x 10(-3); P=0.0034) and WKY 4.03 x 10(-3)+/-5.1 x 10(-4); (95% CI -5.4 x 10(-3) to -8.9 x 10(-4); P=0.027). We also identified regions of conserved synteny, each containing the Gstm2 gene, on mouse chromosome 3 and human chromosome 1.

Animals↗

Geographic differences in species boundaries among members of the Montastraea annularis complex based on molecular and morphological markers.

The three members of the Montastraea annularis complex (M. annularis, M. franksi, and M. faveolata) are dominant reef builders in the western Atlantic whose species status has been controversial for over a decade. Although differences in colony morphology and reproductive characteristics exist, interspecific fertilizations are possible in the laboratory and genetic differentiation is slight. Here we compare the three taxa genetically and morphologically in Panama and the Bahamas, widely separated locations spanning most of their geographic ranges. In Panama, analyses of three AFLP loci, a noncoding region of the mitochondrial genome, and ITS sequences reveal that M. faveolata is strongly differentiated genetically. Discriminant function analysis also indicates no overlap with the other two species in the fine structure of the corallites that comprise the colony. Genetic analyses of larvae from interspecific crosses between M. faveolata and the other two taxa confirmed the hybrid status of the larvae, but no examples of the most probable F1 genotype were observed in the field. Although M. annularis and M. franksi were more similar, they also exhibited strong frequency differences at two AFLP loci and in the mitochondrial noncoding region, as well as distinct corallite structure. In the Bahamas, in contrast, the three taxa exhibited overlapping morphologies. Montastraeafranksi and M. annularis were indistinguishable genetically, and M. faveolata was distinct at fewer genetic loci. Once again, however, the most probable F1 genotype involving M. faveolata was not observed. Geographic differences between Panama and the Bahamas explain why past studies have come to different conclusions concerning the status of the three species. In general, the genetic and morphological data suggest a north to south hybridization gradient, with evidence for introgression strongest in the north. However, reproductive data show no such trend, with intrinsic barriers to gene flow comparable or stronger in the north.

Animals↗

Molecular phylogeography of western Mediterranean dusky grouper Epinephelus marginatus.

Intraspecific sequence variation in a portion of the gene coding for cytochrome b in the dusky grouper (Epinephelus marginatus Lowe 1834), an endangered fish species in various regions of the Mediterranean sea, was examined in 29 individuals from the western Mediterranean sea. Sixty-four phylogenetically informative nucleotide positions were present in a 353-base pair cytochrome b sequence, amplified using the polymerase chain reaction. Statistical analysis of the sequence data using a variety of tree-building algorithms separated the taxa into one group of dusky groupers corresponding to some of the Algerian individuals and another regrouped set of fishes originating in France, Tunisia and the remaining Algerian specimens. Although, on the basis of their morphology, E. marginatus are now considered as a single species, our results suggest that a subgroup of the Algerian dusky grouper constitutes a cryptic (undescribed) species. These results suggest that morphological and genetic evolution may be uncoupled in dusky grouper, resulting in morphological similarity between species despite extensive genetic divergence. In addition, we cannot rule out the possibility of gene introgression with other species of grouper. A more in depth phylogenetic analysis (i.e. between and within the different Epinephelus species) would likely affect many conservation management decisions about this assemblage of groupers.

Animals↗

Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement.

Tomato represents an important source of fiber and nutrients in the human diet and is a central model for the study of fruit biology. To identify components of fruit metabolic composition, here we have phenotyped tomato introgression lines (ILs) containing chromosome segments of a wild species in the genetic background of a cultivated variety. Using this high-diversity population, we identify 889 quantitative fruit metabolic loci and 326 loci that modify yield-associated traits. The mapping analysis indicates that at least 50% of the metabolic loci are associated with quantitative trait loci (QTLs) that modify whole-plant yield-associated traits. We generate a cartographic network based on correlation analysis that reveals whole-plant phenotype associated and independent metabolic associations, including links with metabolites of nutritional and organoleptic importance. The results of our genomic survey illustrate the power of genome-wide metabolic profiling and detailed morphological analysis for uncovering traits with potential for crop breeding.

Computer Simulation↗

Evolution in Darwin's finches: a review of a study on Isla Daphne Major in the Galápagos archipelago.

This paper reviews research pertaining to the problem of speciation of the finches on the Galápagos archipelago carried out by assistants, several colleagues, Peter Grant and myself. I give a brief history of the radiation, examine the process of divergence by natural selection over time, and then consider the nature of the reproductive barrier to gene flow between closely related species. Fluctuating climatic conditions have produced a continuously changing ecological landscape and altered feeding conditions for the finches over the last 30 years. Finch populations tracked these changes by natural selection and evolutionary responses to the main events. At each event significant morphological change occurred from one generation to the next generation. As a consequence of these accumulated changes, the mean bill shape and body size of the Geospiza fortis and G. scandens populations differed markedly from 1973 to 2002. Song, a learned culturally transmitted trait, acted as a barrier to reproduction between these species. Rare incidences of misimprinting on song led to hybridization and introgression. Low levels of gene flow from one species to another increased genetic variation on which selection acted. Although the major driving force of diversification was ecological change, the process of diversification involved a subtle interplay between ecology, genetic evolution and learned culturally transmitted traits. An important message for conservation is that neither the environment nor species are fixed entities, therefore a wise strategy for conserving endangered species should keep them capable of further change.

Journal Article↗

Pervasive context-dependent effects in the genetic architecture of complex and quantitative traits revealed by a powerful multiparent mapping population in yeast.

The genetic dissection of complex traits remains a major challenge in basic and biomedical research, but is essential for understanding the molecular pathways that shape phenotypic variation and for developing predictive models of trait and disease susceptibility. Here, we leverage a novel multiparent mapping population of budding yeast, CYClones, comprising 9,344 haploid strains derived from eight genetically diverse founders (~270,000 SNVs, ~ 1 per 44 bp, capturing 56% of common variants and 32% of all variants with a minor allele frequency greater than 0.005 in the global population), to identify quantitative trait loci (QTL) and systematically investigate the genetic architecture of growth rates across ten environmental conditions. In total, we identified 349 QTL (ranging from 18 to 49 QTL per growth condition) that explained between 60% and 100% of narrow sense heritability across traits. The high power and resolution of CYClones revealed that growth traits exhibited distinct, condition-specific genetic architectures with extensive allelic heterogeneity, where a QTL was the result of multiple tightly linked causal variants. We also observed pleiotropy among QTL with complex, trait-dependent allele effects that are also consistent with allelic heterogeneity. Genetic complexity varied widely, with some traits showing nearly Mendelian architectures, while others were highly polygenic. Introgressed loci played a prominent role in the landscape of growth rate QTL, including a QTL localized to a 2.4 kb interval in the PCA1 cadmium transporter that explains 72% of variation in cadmium resistance and is largely driven by an introgression, and a non-additive interaction between the GAL3 regulator and introgressed GAL1/7/10 alleles, extending a previously described three-locus GAL-pathway incompatibility to a four-locus interaction. In both cadmium and galactose conditions, we show that allelic variation at a small number of loci stratifies the population into regulatory or physiological subgroups, each with distinct genetic architectures, a specific manifestation of epistasis we term allele-dependent stratification. Collectively, our results provide novel insights into the genetics of growth rates in budding yeast, the architectural features of genetic complexity, and demonstrate that CYClones is a powerful platform for revealing the molecular basis of complex trait variation.

Quantitative Trait Loci↗

Effects of chromosome-specific introgression in upland cotton on fiber and agronomic traits.

Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic "noise" from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. barbadense L. substituted into G. hirsutum and chromosome-specific F2 families. Boll size, lint percentage, micronaire, 2.5% span length, elongation, strength, and yield were measured by replicated field experiments in five diverse environments and analyzed under an additive-dominance (AD) genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except 2.5% span length. CS-B25 had additive effects increasing fiber strength and fiber length and decreasing micronaire. CS-B16 and CS-B18 had additive effects related to reduced yields. The results point toward specific chromosomes of G. barbadense 3-79 as the probable locations of the genes that significantly affect quantitative traits of importance. Our results provided a scope to analyze individual chromosomes of the genome in homozygous and heterozygous conditions and thus detected novel effects of alleles controlling important QTL.

Chromosomes, Plant↗

Detecting adaptive trait introgression between Iris fulva and I. brevicaulis in highly selective field conditions.

The idea that natural hybridization has served as an important force in evolutionary and adaptive diversification has gained considerable momentum in recent years. By combining genome analyses with a highly selective field experiment, we provide evidence for adaptive trait introgression between two naturally hybridizing Louisiana Iris species, flood-tolerant Iris fulva and dry-adapted I. brevicaulis. We planted reciprocal backcross (BC1) hybrids along with pure-species plants into natural settings that, due to a flooding event, favored I. fulva. As expected, I. fulva plants survived at much higher rates than I. brevicaulis plants. Backcross hybrids toward I. fulva (BCIF) also survived at significantly higher rates than the reciprocal backcross toward I. brevicaulis (BCIB). Survivorship of BCIB hybrids was strongly influenced by the presence of a number of introgressed I. fulva alleles located throughout the genome, while survivorship in the reciprocal BCIF hybrids was heavily influenced by two epistatically acting QTL of opposite effects. These results demonstrate the potential for adaptive trait introgression between these two species and may help to explain patterns of genetic variation observed in naturally occurring hybrid zones.

Chimera↗

Selection and dispersal in a multispecies oak hybrid zone.

The four western North American red oak species (Quercus wislizeni, Q. parvula, Q. agrifolia, and Q. kelloggii) are known to produce hybrid products in all interspecific combinations. However, it is unknown whether hybrids are transitory resulting from interspecific gene flow or whether they are maintained through extrinsic selection. Here, we examine cryptic hybrid structure in Q. wislizeni through a broad region including contact and isolation from three other western North American red oaks using amplified fragment length polymorphism molecular markers. All four species were simultaneously detected in the genetic background of individuals morphologically assigned to Q. wislizeni, although the contribution of Q. kelloggii was minor. In some cases, introgression was detected well outside the region of sympatry with one of the parental species. Molecular structure at the individual level indicated this was due to long-distance pollen dispersal and not to local extinction of parental species. Species admixture proportions were correlated with climatic variables and greater proportions of Q. agrifolia and Q. parvula were present in the genetic background of Q. wislizeni in sites with cooler and more humid summers, corresponding with habitat preferences of the parental species. Partial Mantel tests indicated that climate was more important than distance from pollen source in this association. Despite high levels of introgression, species integrity was maintained in some populations in close proximity to the other species, providing further support to environmental selection in determining population genetic structure. Thus, the contribution of species mixtures to population genetic structure varies across the landscape according to availability of pollen, but more importantly to varying environmental selection pressures that produce a complex pattern of hybrid and pure gene pools.

California↗

Genetic mapping of a cross between Gossypium hirsutum (cotton) and the Hawaiian endemic, Gossypium tomentosum.

The existence of five tetraploid species that derive from a common polyploidization event about 1 million years ago makes Gossypium (cotton) an attractive genus in which to study polyploid evolution and offers opportunities for crop improvement through introgression. To date, only crosses (HB) between the cultivated tetraploid cottons Gossypium hirsutum and G. barbadense have been genetically mapped. Genetic analysis of a cross (HT) between G. hirsutum and the Hawaiian endemic G. tomentosum is reported here. Overall, chromosomal lengths are closely correlated between the HB and HT maps, although there is generally more recombination in HT, consistent with a closer relationship between the two species. Interspecific differences in local recombination rates are observed, perhaps involving a number of possible factors. Our data corroborate cytogenetic evidence that chromosome arm translocations have not played a role in the divergence of polyploid cottons. However, one terminal inversion on chromosome (chr.) 3 does appear to differentiate G. tomentosum from G. barbadense; a few other apparent differences in marker order fall near gaps in the HT map and/or lack the suppression of recombination expected of inversions, and thus remain uncertain. Genetic analysis of a discrete trait that is characteristic of G. tomentosum, nectarilessness, mapped not to the classically reported location on chr. 12 but to the homoeologous location on chr. 26. We propose some hypotheses for further study to explore this incongruity. Preliminary quantitative trait locus (QTL) analysis of this small population, albeit with a high probability of false negatives, suggests a different genetic control of leaf morphology in HT than in HB, which also warrants further investigation.

Chromosome Mapping↗

Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers.

Evolutionary history of Muscicapidae flycatchers is inferred from nuclear and mitochondrial DNA (mtDNA) sequence comparisons and population genetic analysis of nuclear and mtDNA markers. Phylogenetic reconstruction based on sequences from the two genomes yielded similar trees with respect to the order at which the species split off. However, the genetic distances fitted a nonlinear, polynomial model reflecting diminishing divergence rate of the mtDNA sequences compared to the nuclear DNA sequences. This could be explained by Haldane's rule because genetic isolation might evolve more rapidly on the mitochondrial rather than the nuclear genome in birds. This is because hybrid sterility of the heterogametic sex (females) would predate that of the homogametic sex (males), leading to sex biased introgression of nuclear genes. Analyses of present hybrid zones of pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) may indicate a slight sexual bias in rate of introgression, but the introgression rates were too low to allow proper statistical analyses. It is suggested, however, that the observed deviation from linearity can be explained by a more rapid mutational saturation of the mtDNA sequences than of the nuclear DNA sequences, as supported by analyses of third codon position transversions at two protein coding mtDNA genes. A phylogeographic scenario for the black and white flycatcher species is suggested based on interpretation of the genetic data obtained. Four species appear to have diverged from a common ancestor relatively simultaneously during the Pleistocene. After the last glaciation period, pied and collared flycatchers expanded their breeding ranges and eventually came into secondary contact in Central and Eastern Europe and on the Baltic Isles.

Animals↗