Massive Hybridization Research Articles

Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

BackgroundHybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental characteristics were acquired both naturally and through artificially hybridizing species with heterozygous genomes. Therefore, the genome of hybrid flowering Prunus presents important challenges both in plant genomics and evolutionary biology.ResultsWe use long reads to sequence and analyze the highly heterozygous genome of wild Prunus yedoensis. The genome assembly covers > 93% of the gene space; annotation identified 41,294 protein-coding genes. Comparative analysis of the genome with 16 accessions of six related taxa shows that 41% of the genes were assigned into the maternal or paternal state. This indicates that wild P. yedoensis is an F1 hybrid originating from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura, and it can be clearly distinguished from its confusing taxon, Yoshino cherry. A focused analysis of the S-locus haplotypes of closely related taxa distributed in a sympatric natural habitat suggests that reduced restriction of inter-specific hybridization due to strong gametophytic self-incompatibility is likely to promote complex hybridization of wild Prunus species and the development of a hybrid swarm.ConclusionsWe report the draft genome assembly of a natural hybrid Prunus species using long-read sequencing and sequence phasing. Based on a comprehensive comparative genome analysis with related taxa, it appears that cross-species hybridization in sympatric habitats is an ongoing process that facilitates the diversification of flowering Prunus.

Van der Waals Interaction Activated Strong Electronic Coupling at the Interface between Chloro Boron-Subphthalocyanine and Cu(111).

In this article, we investigate the interface between shuttlecock-shaped chloro boron-subphthalocyanine molecules and the Cu(111) surface. We highlight how molecular planarization induced by van der Waals forces can fundamentally alter the interface properties and how it can enable a particularly strong hybridization between molecular and metal states. In our simulations, we start from a situation in which we disregard van der Waals forces and then introduce them gradually by rescaling the interaction parameter, thereby “pulling” the molecule toward the surface. This reveals two adsorption regimes with significantly different adsorption distances, molecular conformations, and adsorbate-induced changes of the work function. Notably, the above-mentioned massive hybridization of electronic states, also observed in photoelectron spectroscopy, is obtained solely for one of the regimes. We show that this regime is accessible only as a consequence of the planarization of the molecular backbone resulting from the van der Waals attraction between the molecule and the surface. The results of this study indicate that for certain metal–molecule combinations unusually strong interfacial electronic interactions can be triggered by van der Waals forces creating a situation that differs from the usually described cases of physisorptive and chemisorptive interactions.

Hybrid 'superswarm' leads to rapid divergence and establishment of populations during a biological invasion.

Understanding the genetic background of invading species can be crucial information clarifying why they become invasive. Intraspecific genetic admixture among lineages separated in the native ranges may promote the rate and extent of an invasion by substantially increasing standing genetic variation. Here, we examined the genetic relationships among threespine stickleback that recently colonized Switzerland. This invasion results from several distinct genetic lineages that colonized multiple locations and have since undergone range expansions, where they coexist and admix in parts of their range. Using 17 microsatellites genotyped for 634 individuals collected from 17 Swiss and two non-Swiss European sites, we reconstruct the invasion of stickleback and investigate the potential and extent of admixture and hybridization among the colonizing lineages from a population genetic perspective. Specifically, we test for an increase in standing genetic variation in populations where multiple lineages coexist. We find strong evidence of massive hybridization early on, followed by what appears to be recent increased genetic isolation and the formation of several new genetically distinguishable populations, consistent with a hybrid 'superswarm'. This massive hybridization and population formation event(s) occurred over approximately 140years and likely fuelled the successful invasion of a diverse range of habitats. The implications are that multiple colonizations coupled with hybridization can lead to the formation of new stable genetic populations potentially kick-starting speciation and adaptive radiation over a very short timescale.

Cultural Encounters in Québec Cinema. Identity and Otherness in Denis Chouinard's Tar Angel 1

Over the course of its history, Québec cinema displayed an interest in outsiders and intercultural exchanges. The opening up to the outside world, which characterized Québec society's evolution, resulted in a renewed consciousness of its own diversity. The quest for and affirmation of the self now proceeds by a recognition that engages in dialogue with the Other—a sign of a profound maturity. Beyond the vision of an identity founded on the heritage of the majority Francophone group, there emerges a new vision with unifying aspirations founded on the necessary inclusion of other ethnic communities. This dynamic is potentially enriching, since a society cannot open itself to others, to difference, without being transformed in return. This contact, however, can also provoke feelings of suspicion and violence. In 1997, Denis Chouinard and Nicholas Wadimoff direct Clandestins, a film of astounding originality and dramatic density: six refugees originating from Maghreb, Russia and Eastern Europe, confined in a container, desperately attempt to cross the Atlantic on a cargo ship en route to Montreal's harbour. Only two children successfully reach their destination. A glimmer of hope resonates in the film's final images, which depict the children on the steamship's bow, prolonging, in a sense, the desire of their parents for a new life. But how would the country of arrival welcome these refugees? It is in attempting to answer these questions that Chouinard directs Tar Angel in 2001. This article aims to demonstrate how the latter film, which presents itself as a social drama espousing a road-movie aesthetic, is constructed through a system of opposing exotic tones that evoke the difficult fusion of heritage and newly adopted culture in this era of massive population displacement, hybridization and plural identities.

A rapid method for species identification and interspecies introgression based on a PCR–RFLP: application to the closely related Neotropical toads Rhinella marina and R. schneideri (Anura: Bufonidae)

Toad species Rhinella marina and R. schneideri (Bufonidae, Anura) are widely distributed in Amazon and Cerrado/Caatinga, respectively. Recent data has hypothesized that these two toad species share a history of a massive introgressive hybridization. Therefore, the aim of the present work was the precise identification of organisms with signs of past introgression or actual ongoing hybridization. In this paper we conducted a method based on polymerase chain reaction–restriction fragment length polymorphism, through the use of the CfoI enzyme. The individuals of R. marina have two specific digested bands, which is not digested in R. schneideri, possessing the hybrids three bands. The method was very efficient and allowed fast identification of these species.

Good species despite massive hybridization: genetic research on the contact zone between the watersnakesNerodia sipedonandN. fasciatain the Carolinas, USA

Genomic markers generated with the amplified fragment length polymorphism method revealed extensive, panmictic-like hybridization along the narrow contact zone between the water snakes Nerodia sipedon and Nerodia fasciata in the Carolinas, USA. However, asymmetric distributions of diagnostic markers between both species and low frequencies of backcrossed hybrids with a high value of interspecific mixture infer selection against certain genotypes. This is consistent with a pronounced genetic and morphological preponderance of N. fasciata characters in the hybrid zone. Despite massive hybridization within the contact zone, the existence of nearly fixed genetic markers and the potential inferiority of certain hybrid genotypes support the species status of the two taxa and corroborate known, but nondiagnostic differences in morphology and ecology. This study stretches the applicability of species concepts to cases, where the genetic compatibility between two closely related species is very high, yet, they still evolve and persist as independent entities.

Patterns of cryptic hybridization revealed using an integrative approach: a case study on genets (Carnivora, Viverridae, Genetta spp.) from the southern African subregion

Recent years have seen the development of molecular-based methodologies to investigate hybridization and its impact on the evolutionary process. However, morphological characterization of hybrid zones has only scantily been considered, especially in zootaxa. Thus, the level of congruence between molecular and morphological characters when attempting to detect hybrids remains a poorly tackled area. The genets (genus Genetta) provide an ideal case study for further investigation of the respective contribution of morphology and DNA in hybrid zone characterization because (1) their morphology has recently been exhaustively explored and (2) the existence of hybrid zones in southern Africa was proposed in the literature. We assessed levels of hybridization among the southern African genets, and questioned the role of ecological factors on the hybridization patterns detected. We used an integrative approach involving nine discrete morphological characters and a diagnostic discriminant function, geometric morphometrics and sequences of cytochrome b including collection specimens. The combination of independent materials allowed us to accurately reassess the level of hybridization in southern African genets, and revealed cryptic, interspecific gene flows. Morphology unambiguously detected a low number of G. maculata × G. tigrina hybrids and rejected the hypothesis of a large intergradation zone in KwaZulu-Natal, thus supporting the species status of the two genets. Cytochrome b analyses revealed: (1) cryptic, massive hybridization between G. tigrina and the sympatric G. felina, and (2) a trace of reticulation (one sequence) between G. tigrina and the allopatric G. genetta. The type specimen of G. mossambica Matschie, 1902 is considered to be a morphological hybrid between G. maculata and G. angolensis. Remarkably, the morphological approaches (discrete characters and morphometrics) proved complementary to conclusions derived from cytochrome b sequences. Whilst morphometrics was generally unable to accurately identify all putative hybrids, this approach revealed diagnostic cranial shape differences between recognized species as well as the cryptic G. ‘letabae’ (included in the super-species G. maculata). Morphometrics also confirmed the diagnostic value and age dependency of discrete characters. Our integrative approach appeared necessary to the detection of cryptic hybridizations and to the comprehensive characterization of hybrid zones. The recurrent detection of hybrids exhibiting tigrina-like coat patterns may suggest (1) asymmetric hybridization of G. tigrina males to females of other species and (2) positive selection for tigrina-like phenotype in South African habitats, but these hypotheses will have to be further tested using other sources of evidence. Despite the precise mosaic of hybrid zones identified in southern African genets, the environmental factors that shape patterns of distribution of hybrids remain unclear. Nevertheless, in the light of our range reassessment, it appears that seasonality of precipitation and periods of annual frost may play stringent roles in the distribution of genets. The complementarity of our results based on morphology and molecules is regarded as encouraging for the further development of integrative approaches in order to better understand the complex phenomena that underlie hybridization processes.

The Africanization of honeybees (Apis mellifera L.) of the Yucatan: a study of a massive hybridization event across time.

Until recently, African and European subspecies of the honeybee (Apis mellifera L.) had been geographically separated for around 10,000 years. However, human-assisted introductions have caused the mixing of large populations of African and European subspecies in South and Central America, permitting an unprecedented opportunity to study a large-scale hybridization event using molecular analyses. We obtained reference populations from Europe, Africa, and South America and used these to provide baseline information for a microsatellite and mitochondrial analysis of the process of Africanization of the bees of the Yucatan Peninsula, Mexico. The genetic structure of the Yucatecan population has changed dramatically over time. The pre-Africanized Yucatecan population (1985) comprised bees that were most similar to samples from southeastern Europe and northern and western Europe. Three years after the arrival of Africanized bees (1989), substantial paternal gene flow had occurred from feral Africanized drones into the resident European population, but maternal gene flow from the invading Africanized population into the local population was negligible. However by 1998, there was a radical shift with both African nuclear alleles (65%) and African-derived mitochondria (61%) dominating the genomes of domestic colonies. We suggest that although European mitochondria may eventually be driven to extinction in the feral population, stable introgression of European nuclear alleles has occurred.

Sexual selection, reproductive isolation and the genic view of speciation

Sexual selection, reproductive isolation and the genic view of speciation

DNA sequence recognition by hybridization to short oligomers.

A format 1 technology for performing massive hybridization experiments has been developed as part of the sequencing by hybridization (SBH) project. Arrays of tens of thousands of clones are interrogated with short oligomer probes to determine sets of oligomers that are present in individual clones. SBH requires highly discriminative hybridizations with a large number of probes. One of the main uses of a reconstructed DNA sequence is in a similarity search against databases of known DNA. We argue that sequence reconstruction, even partial, should not be performed for this particular purpose; we provide an information-theoretic proof that the oligomer lists obtained from hybridization experiments should be used directly for similarity searches. We propose a similarity search method that takes full advantage of the subword structure of positively identified oligomers within a clone. The method tolerates error in hybridization experiments, requires fewer probes than necessary for sequencing, and is computationally efficient. To enable direct sequence recognition, we apply the recently developed method of sequence comparison that is based on minimal length encoding and algorithimic mutual information. The method has been tested on both real and simulated data and has led to a correct identification of clones based on hybridizations with 109 short oligomer probes. The method is applicable to hybridization data that comes from both format 1 and format 2 (sequencing chip) hybridization experiments. The sequence recognition method can provide targeting information for large-scale DNA sequencing by gel-based methods or by hybridization.

A natural hybrid of Leuciscus cephalus macedonicus X Chalcalburnus chalcoides macedonicus (Pisces, Cyprinidae) from Lake Volvi (Macedonia, Greece)

A massive hybridization between Leuciscus cephalus macedonicus and Chalcalburnus chalcoides macedonicus has been recognized and studied by examining 67 specimens from Lake Volvi (Macedonia, Greece). The majority of meristic and other characters present an intermediate position in the hybrid (total hybrid index Vh= 38.37). Nevertheless, the best expression of intermediacy is shown most clearly by the numbers of anal fin soft rays, lateral line scales and gill rakers, and also by the height of the dorsal fin and the length of the base of anal fin. Of the examined hybrid specimens. 92.5% were females. It seems that hybridization takes place during the reproduction period in the main streams flowing into the lake under special conditions which hinder the migration of the majority of the population of C. chalcoides from the lake to the breeding sites. It is suggested that individuals of C. chalcoides, which manage to arrive in these sites, mate with L. cephalus, the normal inhabitant of the streams, thus producing the hybrid.

Biochemical Genetic Variation in Pink and Chum Salmon: Inheritance of intraspecies variation and apparent absence of interspecies introgression following massive hybridization of hatchery stocks

Biochemical Genetic Variation in Pink and Chum Salmon: Inheritance of intraspecies variation and apparent absence of interspecies introgression following massive hybridization of hatchery stocks

The Taxonomic Status of Wild Canis in Arkansas

Gipson, Philip S., John A. Sealander (Department of Zoology, University of Arkansas, Fayetteville) and James E. Dunn (Department of Mathematics, University of Arkansas, Fayetteville) 1974. The Taxonomic Status of Wild Canis in Arkansas. Syst. Zool. 23:1-11.Skulls from 284 wild canids collected in Arkansas from July, 1968 through March, 1971 approximately one year old or older and of known sex and capture locality were analyzed taxonomically. Each skull was compared to six target populations of skulls from known canids (coyotes, coyote x dog hybrids, dogs, red wolves, northeastern forest gray wolves, and plains gray wolves) for identification. The 165 male unknowns were identified as: coyote, 117; coyote x dog intermediate, 26; dog, 3; red wolf, 2; coyote X red wolf intermediate, 16; dog X red wolf intermediate, 1. The 119 female unknowns were identified as: coyote, 91; coyote X dog intermediate, 12; dog, 5; coyote X red wolf intermediate, 11. Coyotes occur in all counties of the state and are the predominant wild canid in most areas. Local pockets of coyote x dog intermediates are randomly distributed but fairly common. Wild dogs have become established in some areas, especially in east-central Arkansas. A strong red wolf influence still exists in the canid population on the Gulf Coastal Plain of southern Arkansas. Occasional pockets of red wolf influence are found in the Ouachita and Ozark Mountains and Delta. [Canis; hybridization.] Three species of the genus Canis, coyotes (C. latrans), gray wolves (C. lupus), and dogs (C. familiaris), are generally recognized in North America. The taxonomic status of a fourth canid, the red wolf (C. rufus) has been debated for about 10 years. Pimlott and Joslin (1968) and Nowak (1970) have reviewed the taxonomic arguments. Recently Lawrence and Bossert (1967:230) concluded that . . from central Louisiana east to Florida the large canids hitherto called C. niger [now rufus] and niger gregoryi are no more than subspecifically distinct from Canis Paradiso (1968: 529) stated that massive hybridization was possibly occurring between red wolves and coyotes in eastern Texas. According to him: Possibly this interbreeding should be regarded merely as intergradation, which would imply only subspecific differentiation of red wolf and coyote. Subsequently Atkins and Dillon (1971:104) presented evidence based on morphology of the brain which they feel . . firmly supports the recognition of C. rufus as a distinct species. Paradiso and Nowak (1972) wrote that C. 1 Programs used in this analysis are available for loan on request. rufus is a valid species, and summarized characters which distinguish C. rufus from C. latrans and C. lupus. Increasing numbers of wild canids that cannot be positively identified as coyote, wolf or dog are being taken in areas formerly occupied by wolves and recently invaded by coyotes (McCarley, 1962; Lawrence and Bossert 1967, 1969; Paradiso, 1968; Silver and Silver, 1969; Nowak, 1970; Standfield, 1970; Kolenosky, 1971). Hybridization has usually been suggested as the factor responsible for this breakdown of species identity (McCarley, 1962; Standfield, 1970). Considerable confusion has resulted since it is often desirable to assign species names to individuals from such areas. The problem is most acute in the former range of the red wolf, C. rufus, in the south-central United States where wuild canids with characteristics ranging frc typical coyote to red wolf and dog havt been taken. Our first objective was to identify with respect to species wild canids captured in Arkansas from July, 1968, through March, 1971. Since coyotes, dogs, red wolves, northeastern forest gray wolves, and plains gray wolves occurred in or adjacent to

Hybridization in the Darters Etheostoma spectabile and Etheostoma radiosum cyanorum

The authors analyze statistically the first-known example of massive hybridization in darters of the genus Etheostoma. The population was discovered in a disturbed habitat in southern Oklahoma (Blue River: Red River System). Some of the characteristics analyzed were: distance from the union of the gill membranes vs the number of unpored lateralline scales, number of scale rows below the lateral line vs number of scales above the lateral line, distance from union of gill membranes to pelvic fins vs length of the pelvic fin, and color patterns. The aggregate hybrid index was 42.9, and most of the characteristics tended strongly toward E. spectabile in the hybrids.