An analysis of population genetic differentiation and genotype–phenotype association across the hybrid zone of carrion and hooded crows using microsatellites and MC1R

The all black carrion crow ( Corvus corone corone ) and the grey and black hooded crow ( Corvus   corone cornix ) meet in a narrow hybrid zone across Europe. To evaluate the degree of genetic differentiation over the hybrid zone, we genotyped crows from the centre and edges of the zone, and from allopatric populations in northern (Scotland–Denmark–Sweden) and southern Europe (western–central northern Italy), at 18 microsatellites and at a plumage candidate gene, the MC1R gene. Allopatric and edge populations were significantly differentiated on microsatellites, and populations were isolated by distance over the hybrid zone in Italy. Single-locus analyses showed that one locus, CmeH9, differentiated populations on different sides of the zone at the same time as showing only weak separation of populations on the same side of the zone. Within the hybrid zone there was no differentiation of phenotypes at CmeH9 or at the set of microsatellites, no excess of heterozygotes among hybrids and low levels of linkage disequilibrium between markers. We did not detect any association between phenotypes and nucleotide variation at MC1R , and the two most common haplotypes occurred in very similar frequencies in carrion and hooded crows. That we found a similar degree of genetic differentiation between allopatric and edge populations irrespectively of their location in relation to the hybrid zone, no differentiation between phenotypes within the hybrid zone, and neither heterozygote excess nor consistent linkage disequilibrium in the hybrid zone, is striking considering that carrion and hooded crows are phenotypically distinct and sometimes recognised as separate species.     

Homoploid hybrid speciation in animals

Among animals, evidence for homoploid hybrid speciation (HHS, i.e. the creation of a hybrid lineage without a change in chromosome number) was limited until recently to the virgin chub, Gila seminuda, and some controversial data in support of hybrid status for the red wolf, Canis rufus. This scarcity of evidence, together with pessimistic attitudes among zoologists about the evolutionary importance of hybridisation, prompted the view that HHS is extremely rare among animals, especially as compared with plants. However, in recent years, the literature on animal HHS has expanded to include several new putative examples in butterflies, ants, flies and fishes. We argue that this evidence suggests that HHS is far more common than previously thought and use it to provide insights into some of the genetic and ecological aspects associated with this type of speciation among animals.     

A genetic approach to the species problem in wild potato

Wild potatoes are native to the Americas, where they present very wide geographical and ecological distribution. Most are diploid, obligate out-crossers due to a multiallelic gametophytic self-incompatibility (S) locus that prevents self-fertilisation and crossing between individuals carrying identical S-alleles. They have two alternative modes of reproduction: sexual (by seeds) and asexual (by stolons and tubers), which provide, respectively, for genetic flexibility in changing environments and high fitness of adapted genotypes under stable conditions. Since the early twentieth century, their taxonomic classification has been mostly based on morphological phenotypes (Taxonomic Species Concept). More recently, attempts have been made to establish phylogenetic relationships, applying molecular tools in samples of populations (accessions) with a previously assigned specific category. However, neither the reproductive biology and breeding relations among spontaneous populations nor the morphological and genetic variability expected in obligate allogamous populations are considered when the taxonomic species concept is applied. In nature, wild potato populations are isolated through external and internal hybridisation barriers; the latter, which are genetically determined, can be either pre-zygotic (pollen-pistil incompatibility) or post-zygotic (abortion of embryo, endosperm or both tissues, sterility, and hybrid weakness and breakdown in segregating generations). The internal barriers, however, can be incomplete, providing opportunities for hybridisation and introgression within and between populations and ploidy levels in areas of overlap. The widespread occurrence of spontaneous hybrids in nature was recognised in the mid-twentieth century. Using genetic approaches, results have been obtained that provide strong support to the assertion that populations are at different stages of genetic divergence and are not at the end of the evolutionary process, as presupposed by the Taxonomic Species Concept. Furthermore, since wild potatoes have uniparental and biparental overlapping generations, the Biological Species Concept - developed for sexually reproducing biparental organisms - cannot be applied to them. In this paper, morphological, genetic, molecular and taxonomic studies in wild potato are reviewed, considering the genetic consequences of their reproductive biology, in an attempt to shed light on the species problem, because of its relevance in germplasm conservation and breeding.     

Genetic differentiation, behavioural reproductive isolation and mixis cues in three sibling species of monogonont rotifers

Many aquatic species usually considered to be 'cosmopolitan' have been identified as cryptic species complexes, based on deep genetic differentiation. However, reproductive isolation among sibling cryptic species has rarely been studied, and interspecific hybridization is common in some taxa.We investigated isolation mechanisms and possible introgression among three cyclical parthenogenetic rotifer species in the Epiphanes senta complex that are found in very different freshwater habitats: temperate floodplains, subtropical desert rock pools and a tropical alpine lake. Whereas Epiphanes ukera is reproductively isolated from E. chihuahuaensis and E. hawaiiensis, the latter hybridize under laboratory conditions.While reproductive isolation is incomplete, RAPD profiles indicated unique genetic signatures and showed no evidence for introgression, indicating that these three species are diverging and have independent evolutionary trajectories.Testing cues for sexual reproduction in these cyclic parthenogens demonstrated that mixis in E. chihuahuaensis and E. ukera is influenced by population density, whereas E. hawaiiensis females rarely produce mictic offspring regardless of density. Different mixis cues are likely to separate sexual periods and effectively cause reproductive isolation between the species. Epiphanes ukera and E. chihuahuaensis males display mate guarding behaviour, and E. ukera males distinguish between conspecific and heterospecific females in mate choice experiments. Geographic isolation, along with different cues for mixis induction and mate recognition, act as reproductive barriers among these sibling species.     

Life history patterns of parental and hybrid Daphnia differ between lakes

1. We investigated whether Daphnia galeata × hyalina hybrids of Lake Constance and Lake Greifensee show the same pattern of life history parameters as previously reported for D. galeata × cucullata hybrids and whether such a pattern is consistent between Daphnia populations from those two lakes. 2. Hybrids in Lake Constance were intermediate in size compared with the parental species. Hybrids in Lake Greifensee were smaller than D. galeata. The intrinsic growth rate (r) of hybrids from Lake Constance was not significantly different from the faster growing parental taxon D. galeata. However, r of hybrids from Lake Greifensee was significantly lower than that of D. galeata. 3. The observed juvenile body length differences between the taxa varied with the clutch number. The first clutch juvenile lengths of the three taxa did not differ for Lake Constance. First clutch juveniles of Lake Greifensee D. galeata were smaller than hybrid first clutch juveniles. The third clutch juvenile length did not differ between taxa from Lake Greifensee, but D. galeata juveniles from Lake Constance were bigger than those of D. hyalina. 4. The life history pattern found in Lake Constance corresponds to previous findings from other studies. The hybrids in this lake combine the faster population growth of one parental species with a relatively small size. In the case of Lake Greifensee hybrids, the relatively large size of first clutch juveniles and the small size of the adults could be interpreted as dual adaptations to invertebrate and fish predation. We speculate that the lower population growth rate of the hybrids is a trade‐off for this twofold protection.     

Extensive Introgression of Mitochondrial DNA Found between two Genetically Divergent Forms of Threespine Stickleback, Gasterosteus Aculeatus, around Japan

The genetic structure and phylogenetic relationships of Gasterosteus aculeatus around Japan were investigated for 15 populations of the Japan Sea and Pacific Ocean forms previously detected by allozyme analyses. PCR-RFLP analysis of mtDNA ND5/6 gene indicated two major divergent clades: (1) Alaskan population and (2) Russian and Japanese populations. Japanese populations were clearly subdivided into G. aculeatus populations and hariyo (G. aculeatus leiurus). However, the relationships among Japanese G. aculeatus populations did not support the genetic divergence between Japan Sea and Pacific Ocean forms shown by allozyme analyses. This suggests that mtDNA genetype similarity between the two forms could have resulted from complete replacement of mtDNA from one form to the other. MtDNA introgression is possible in two direction: from Japan Sea form to Pacific Ocean form and the reverse. The haplotype composition of each population observed in the present study suggests that the second direction is more likely. The migrant number of females per generation (Nm) between populations of the two forms was remarkablely large (9.083–infinite), suggesting that gene flow is taking place between the populations at the present time or might have occurred until recent years.     

Introgression in the genus Salmo via allotriploids

Hybridization between sympatric species is not uncommon in the wild. Wild allotriploids (individuals with two chromosome sets from a species + one chromosome set from another species) are generally the result of a backcross between interspecific hybrids that produce unreduced gametes and one of the parental species. In animals, allotriploids are commonly sterile, except for some vertebrate species complexes in which allotriploids reproduce by parthenogenesis, gynogenesis and/or hybridogenesis, producing generally clonal or hemiclonal gametes; nuclear DNA introgression between hybridizing species is considered to be extremely rare. Employing species-specific molecular markers, we show genetic introgression between the chromosomally well-differentiated salmonids Atlantic salmon (2n = 58) and brown trout (2n = 80) through spontaneous bisexual reproduction of allotriploids leading to salmon-like offspring bearing some brown trout genes. Although introgression between these Salmo species can occur via allotriploids, we hypothesize that extinction of parental species can be discarded based on very low survival of allotriploid offspring.     

Embryo rescue and plant regeneration in vitro of selfed chickpea (Cicer arietinum L.) and its wild annual relatives

The main constraint to the transfer of desired traits into cultivated chickpea from wild Cicer relatives is the presence of post-zygotic barriers which result in abortion of the immature embryo following interspecific hybridisation. Rescue of hybrid embryos in vitro and regeneration of hybrid plantlets could allow chickpea breeders to transfer desirable traits from wild relatives of chickpea. The development of embryo rescue techniques using selfed chickpea and selfed wild relatives is being used as a first step to protocols for wide hybrids. Optical microscopy studies of embryogenesis, in both selfs and hybrids, identified deleterious changes in the fertilised hybrid seed as early as 2–4 days after pollination in some crosses. These observations suggest that the appropriate time to rescue chickpea × C. bijugum hybrids is at the early globular stage of embryogenesis (2–7 days old), which requires the development of a complex tissue culture medium. In contrast hybrids between chickpea × C. pinnatifidum abort later (up to 15–20 days old) at the heart-shaped or torpedo stages, and are easier to rescue in vitro. Genotype also plays a significant role in the ability of immature selfed ovules to germinate in vitro. In this paper we report on the optimisation of␣protocols for rescueing immature embryos using selfed chickpea and its wild relatives in ovule, and subsequently to regenerate plantlets.     

Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation

Although the sexual transfer of genetic material between species (i.e. introgression) has been documented in many groups of plants and animals, genome‐wide patterns of introgression are poorly understood. Is most of the genome permeable to interspecific gene flow, or is introgression typically restricted to a handful of genomic regions? Here, we assess the genomic extent and direction of introgression between three sunflowers from the south‐central USA: the common sunflower, Helianthus annuus ssp. annuus; a near‐endemic to Texas, Helianthus debilis ssp. cucumerifolius; and their putative hybrid derivative, thought to have recently colonized Texas, H. annuus ssp. texanus. Analyses of variation at 88 genetically mapped microsatellite loci revealed that long‐term migration rates were high, genome‐wide and asymmetric, with higher migration rates from H. annuus texanus into the two parental taxa than vice versa. These results imply a longer history of intermittent contact between H. debilis and H. annuus than previously believed, and that H. annuus texanus may serve as a bridge for the transfer of alleles between its parental taxa. They also contradict recent theory suggesting that introgression should predominantly be in the direction of the colonizing species. As in previous studies of hybridizing sunflower species, regions of genetic differentiation appear small, whether estimated in terms of F_ST or unidirectional migration rates. Estimates of recent immigration and admixture were inconsistent, depending on the type of analysis. At the individual locus level, one marker showed striking asymmetry in migration rates, a pattern consistent with tight linkage to a Bateson–Dobzhansky–Muller incompatibility.     

MOLECULAR EVIDENCE FOR HOMOPLOID RETICULATE EVOLUTION AMONG AUSTRALIAN SPECIES OF GOSSYPIUM

Interspecific hybridization and introgression are important evolutionary processes in plants, but their full significance with respect to speciation at the diploid level remains unresolved. In this study, molecular markers from the plastid and nuclear genomes were used to document an unusual evolutionary history of Gossypium bickii Prokh. (Malvaceae). This species is one of three morphologically similar Australian cottons (along with G. austrate F. Muell. and G. nelsonii Fryx.) in section Hibiscoidea. In contrast to expectations based on previous morphological data, cladistic analysis of maternally inherited cpDNA restriction site mutations unites G. bickii with G. sturtianum J. H. Willis, a morphologically distant species in a different taxonomic section (Sturtia). Few restriction site mutations distinguish the plastomes of G. bickii and G. sturtianum, but these two cpDNAs are differentiated from those of G. australe and G. nelsonii by a minimum of 33 mutations (out of 640 sites scored). These two highly distinct clades are not supported by phylogenetic analyses of allozyme markers (from 58 populations) and restriction site mutations in nuclear ribosomal DNAs. Rather, phylogenies based on 83 nuclear markers indicate that G. bickii shares a more recent common ancestor with G. australe and G. nelsonii than it does with G. sturtianum. We suggest that the striking discrepancy between independent molecular phylogenies from two different genomes indicates a biphyletic ancestry of G. bickii. Our preferred hypothesis involves an ancient hybridization, in which G. sturtianum, or a similar species, served as the maternal parent with a paternal donor from the lineage leading to G. australe and G. nelsonii. Because we detected no G. sturtianum nuclear genes in G. bickii, we suggest that the nuclear genomic contribution of the maternal parent was subsequently eliminated from the hybrid or its descendent maternal lineage. Several possible mechanisms of cytoplasm transfer are suggested, including repeated backcrossing of the hybrid, as female, into the paternal donor lineage, selection against recombinant nuclear genomes and a form of apomixis known as semigamy. This example, and several others in Gossypium as well as other genera, attest to the evolutionary possibility of interspecific cytoplasmic transfer, and perhaps the origin of diploid species via reticulate speciation. In addition, this study offers an example of natural cytoplasmic introgression without long-term survival of nuclear genes from the maternal progenitor.     

外源绿原酸处理对设施番茄果实品质的影响

目的 番茄在栽培过程中;常存在着色不均、色泽差等问题;导致番茄口感差、出售难;而绿原酸是植物界中广泛存在的一种酚酸类物质;探究其对设施番茄果实品质的影响;为提高果实品质及深入探究绿原酸作用机理提供基础。 方法 以设施番茄‘京彩8号’（Solanum lycopersicum. ‘Jingcai No 8’）为实验材料;对其进行外源绿原酸（chlorogenic acid, CGA）处理后;检测相关果实品质指标;并通过RT-qPCR对番茄中成熟相关基因进行表达量的分析。 结果 外施绿原酸提高了番茄红素含量和类胡萝卜素含量;降低了叶绿素含量;促进了番茄果实的着色;能够增加番茄果实的单果重;降低番茄果实的硬度;提高番茄果实的可溶性糖含量和糖酸比;及果实的可溶性固形物含量和维生素C含量;促进番茄果实的生长和成熟;提升了番茄果实的风味和营养物质含量。对成熟相关基因表达量检测的结果表明;外施绿原酸可以诱导番茄中成熟相关转录因子、乙烯合成酶基因高表达。 结论 推测外源绿原酸能通过调控乙烯合成通路促进番茄果实着色和成熟;提高其品质。     

Hybrid swarms: catalysts for multiple evolutionary events in Senecio in the British Isles

Background: Introgressive hybridisation is an evolutionary catalyst producing novel variants able to explore new ecological niches and evolve as new hybrid taxa. However, the role of ‘hybrid swarms’ – highly variable populations produced following interspecific hybridisation – in generating this evolutionary novelty has been poorly studied.

Aims: We examine the alternative origins of tetraploid hybrid derivatives of Senecio vulgaris and S. squalidus, via local polytopic formation or long-distance dispersal from a single perennial hybrid swarm around Cork, Ireland.

Methods: Morphometric, isozyme and chloroplast DNA analysis.

Results: The Cork hybrid swarm and UK hybrid swarms exhibited a broad range of morphological variation and contained individuals similar to the stable tetraploid hybrid derivatives; S. eboracensis and S. vulgaris var. hibernicus. Chloroplast DNA analysis shows that S. eboracensis did not evolve from the Cork hybrid swarm. However, UK S. vulgaris var. hibernicus populations exhibit a broad range of variation for both chloroplast and isozyme markers, but were not distinguishable from Cork material.

Conclusions: Our study confirms that S. eboracensis did not evolve from the Cork hybrid swarm, and while our analyses could not demonstrate this conclusively for S. vulgaris var. hibernicus the ease with which hybrid swarms have been generated in the past makes a polytopic origin for S. vulgaris var. hibernicus the most likely scenario.     

Effect of parental genotypes, cross direction and temperature on the crossability of bread wheat with triticale and on the viability of f1 embryos

The relevant importance of parental crossability genes, cross direction and ambient temperature in bread wheat/triticale hybridisation were evaluated. Crossability genes were found to be useful but not essential. The use of triticale as the female gave significantly fewer embryos, but these embryos were symmetrically shaped and normal. The use of bread wheat as the female gave a seed set generally above 30% and sometimes as high as 86%, but embryo necrosis resulted in rapid death in vivo or non-regeneration in vitro . By keeping the plants at 14 °C during pollination and in vivo embryo growth, necrosis was partly eliminated, so that in one case the rate of plant production in crossing bread wheat/triticale became about as good as for the triticale/bread wheat cross direction. Crossing at 14°C could be useful when a bread wheat cytoplasm is desired by the breeder.     

Bioremediation of DDT in soil by genetically improved strains of soil fungus Fusarium solani

Bioremediation of DDT in soil by genetically improved recombinants of the soil fungus Fusarium solani was studied. The parent strains were isolated from soil enriched with DDD or DDE (immediate anaerobic and aerobic degradation products of DDT), as further degradation of these products are slow processes compared to the parent compound. These naturally occurring strains isolated from soil, however, are poor degraders of DDT and differed in their capability to degrade its metabolites such as DDD, DDE, DDOH and DBP and other organochlorine pesticides viz. kelthane and lindane. Synergistic effect was shown by some of these strains, when grown together in the medium containing DDD and kelthane under mixed culture condition. No synergism in DDE degradation was observed with the strains isolated from enriched soil. DDD-induced proteins extracted from individual culture filtrate (exo-enzyme) when subjected to SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) showed complementary polypeptide bands in these strains i.e., each strain produced distinct DDD degrading polypeptide bands and the recombinant or hybrid strains produced all of the bands of the two parents and degraded DDD better than the parental strains. Recombinant hybrid strains with improved dehalogenase activity were raised by parasexual hybridisation of two such complementary isolates viz. isolate 1(P-1) and 4(P-2) showing highest complementation and are compatible for hyphal fusion inducing heterokaryosis. These strains are genetically characterised as Kel⁺Ben^RDBP^-Lin^- and Kel^-Ben^rDBP⁺Lin⁺ respectively.Recombinants with mixed genotype, i.e., Kel⁺Ben^RDBP⁺Lin⁺ showing superior degradation quality for DDT were selected for bioremediation study. Recombination was confirmed by polypeptide band analysis of DDD induced exo-proteins from culture filtrate usingSDS-Polyacrylamide Gel Electrophoresis (PAGE) and RAPD (Random Amplified Polymorphic DNA) of genomic DNA using PCR (Polymerase Chain Reaction) technique. SDS-PAGE showed combination of DDD induced polypeptide bands characteristic of both the parents in the recombinants or the hybrids. PCR study showed the parent specific bands in the recombinant strains confirming gene transformation.     

Assessment of UK hops for the occurrence of hop latent and hop stunt viroids

The occurrences and distributions of hop stunt (HSVd) and hop latent (HLVd) viroids were assessed by a nucleic acid hybridisation assay, using samples from 476 commercial hop plantings in the UK. These samples represented about half of the UK production.
HLVd was detected in c. 17% of the samples, with infection in different cultivars ranging from 0% to 89%. This viroid was found in all cultivars sensitive to Verticillium wilt except cv. Sunshine, an old cultivar grown on only one farm in the UK. Two minor wilt-tolerant cultivars were also found to be infected at low frequencies, but the main commercially-important wilt-tolerant cultivars were all uninfected. A high proportion of the nuclear stock mother plants in the "A +" house at the Institute of Horticultural Research Dept of Hops Research, Wye College were infected. Circumstantial evidence, based on the planting dates of infected gardens, suggests that infection became established in the hop propagation system during the late 1970s and that there was a major increase in the prevalence of HLVd as a result. Whether this contamination of propagating material arose because of spread from long-standing infections or because the viroid was newly introduced into the UK, is not known.
All samples were also tested for HSVd but this viroid was not detected in any UK hop material.