Evolutionary Genomics of Weedy Rice in the USA

Red rice is an interfertiie, weedy form of cultivated rice (Oryza sativa L.) that competes aggressively with the cropin the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America andthe weed has been proposed to have evolved through multiple mechanisms, including "de-domestication" of UScrop cultivars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedyOryza strains. The phenotype of US red rice ranges from "crop mimics", which share some domestication traitswith the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity haveindicated that many weed strains are closely related to Asian taxa (including indica and aus rice varieties, whichhave never been cultivated in the US, and the Asian crop progenitor O. rufipogon), whereas others show geneticsimilarity to the tropical japonica varieties cultivated in the southern US. Herein, we review what is known aboutthe evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to furthercharacterize the evolutionary genomics of this aggressive weed.     

Population studies in Artemisia tridentata ssp. vaseyana: Chromosome numbers and sesquiterpene lactone races

The sesquiterpene lactones and chromosome numbers for three chemical races of Artemisia tridentata ssp. vaseyana have been examined from four populations in western Montana. TLC analysis of the sesquiterpene lactones in the seeds and seed producing parents demonstrated that genetic exchange does occur between sympatric sesquiterpene lactone chemical races. However, other evidence suggests that introgression between these races is restricted to zones of sympatry. There appears to be no correlation between chromosome numbers and sesquiterpene lactone races.     

Minimal evidence of interspecific hybridisation between the Yellow-billed Duck and introduced Mallard in central and northwestern South Africa

Hybridisation is the interbreeding of genetically distinct groups that can lead to introgression – an exchange of genetic material between species. Hybridisation is of conservation concern when an alien invasive species is involved, as it can lead to a loss of local genetic adaptations and genetic diversity. Hybridisation is a significant threat for many dabbling ducks where interbreeding with the closely related invasive Mallard Anas platyrhynchos is extremely common. Phenotypic evidence suggests that Mallard populations in South Africa hybridise with the indigenous Yellow-billed Duck Anas undulata. The aim of this study was to determine the incidence of hybridisation between Yellow-billed Ducks, occurring in central and northwestern South Africa, and introduced Mallards. Genetic variation between Mallards, Yellow-billed Ducks, and their inferred hybrids was assessed using mitochondrial and microsatellite DNA markers. All samples inferred to be hybrids based on the phenotype were found to have Yellowbilled Duck mitochondrial DNA and showed minimal evidence of admixture across the microsatellite markers. Thus, these results do not support the notion that hybridisation between Mallards and Yellow-billed Ducks is prevalent in central and northwestern South Africa. However, hybridisation could be occurring where Mallards are found in higher abundance, such as in the Western Cape Province. Therefore, continued monitoring of this potential hybridisation should be performed frequently and throughout South Africa.     

Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae,Allioideae) as inferred from nrDNA ITS,cpDNA rps16 and trnL–F sequences

Allium is a particularly species rich (more than 800 species) and economically important genus, with numerous taxonomic problems at all levels of classification. In this study, we try to uncover the phylogenetic relationships of the common leek Allium ampeloprasum based on selected samples of this species and its putative relatives in A. sect. Allium from Iran. The silica‐dried leaf samples of 56 accessions representing 23 species of Allium were sequenced; 53 sequences of nrDNA ITS, 35 sequences of plastid rps16 and 52 sequences of trnL–F were generated and additional accessions were extracted from GenBank in order to cover all recognized main lineages in the genus. Maximum Parsimony and Bayesian Inference generated similar trees, but the placement of A. ampeloprasum and its relatives differed slightly between the nuclear and the plastid phylogenies. In the nrITS tree, A. ampeloprasum is retrieved as a highly supported clade with A. iranicum, while in the combined plastid tree A. ampeloprasum formed a highly supported clade with A. vineale. This supports the hypothesis of a possible hybrid origin of A. ampeloprasum. Allium iranicum formed a clade in the plastid tree, but was resolved as paraphyletic in the nrITS tree, probably due to presence of multiple non‐concerted copies of nrITS. Close relationships are suggested between the following species: A. aznavense and A. wendelboi with A. talyschense, A. erubescens and A. rotundum with A. scorodoprasum and A. abbasii with A. phanerantherum.     

Evolution of insect-plant relationships: chemical constraints, coadaptation, and concordance of insect/plant traits

Co-adaptations, co-evolution, and co-speciation between herbivores and their host plants have been topics of interest for several decades. Difficulties in deciphering these relationships as well as physiological, biochemical, and ecological adaptations of herbivorous insects themselves are discussed here in relation to biotic and abiotic environmental factors that create temporal as well as spatial mosaics of genetic variation. Hybridization was shown in swallowtail butterflies (Papilio) (Lepidoptera: Papilionidae) to produce some trait concordance, but mostly independent geographic trait clines (physiological, biochemical, and morphological). Strong and extensive genetic introgression of Liriodendron tulipifera detoxification abilities was documented northward across the hybrid zone, presumably as a result of regional climate warming only during the last 3–4 years. These and other genetic novelties produced by hybridization may be important in speciation processes, and they also emphasize the difficulties identifying appropriate taxonomic classifications for discussing any species concept. Host plant detoxification abilities (as `key innovations') are shown capable of rapid movement between different polyphagous herbivore species independently of the host plant availability and well beyond the insect species geographical range distribution. Part of the difficulty associated with ecologically categorizing herbivore species and identifying affiliated adaptations for host plant use may be related to independent movement of various `species-diagnostic' traits. Climate-driven local selection regimes could help generate the dynamic variation observed for co-adapted, co-evolved, or non-adapted genotypes, and may produce the confusing and changing patterns of geographic mosaics seen within and among closely related herbivores. Experimental analyses of several factors that could explain the asymmetrical shapes of trait clines across the hybrid zone for tiger swallowtail butterflies are discussed.     

Y-Chromosome and Mitochondrial Markers in Macaca fascicularis Indicate Introgression with Indochinese M. mulatta and a Biogeographic Barrier in the Isthmus of Kra

This is the first report of Y-chromosome introgression between primate species. We sequenced 3.1 Kb of Y-chromosome DNA and 1.5 Kb of mtDNA for 27 macaques of Fooden's (Folia Primatol. [1976] 25: 225–236) fascicularis species group and 5 outgroup taxa (Macaca sylvanus, Papio hamadryas, Theropithecus gelada, Allenopithecus nigroviridis, and Cercopithecus mona). Phylogenies constructed separately for the paternal and maternal data sets show a Y-chromosome paraphyly among lineages of Macacafascicularis, but a mitochondrial monophyly for the same individuals. The Y-chromosome topology depicts Indochinese Macaca fascicularis haplotypes joining with those of M. mulatta, followed by M. cyclopis and M. fuscata, before clustering with a clade of lineages of M. fascicularis from peninsular Malaysia, Indonesia, and the Philippines. These contrasting patterns of mitochondrial and Y-chromosome DNA, evaluated in the context of the evolutionary consequences of macaque sex-biased dispersal, present strong evidence for contemporary hybridization between Macaca fascicularis and M. mulatta in Indochina and a biogeographic barrier in the Isthmus of Kra.     

Cytosine Methylation Changes in Rice Centromeric and Telomeric Sequences Induced by Foreign DNA Introgression

Cytosine methylation changes (hyper- or hypomethylation) in centromeric and telomeric sequences were observed in all three studied rice introgression lines containing DNA from wild rice, Zizania latifolia Griseb. The changed genomic Southern hybridization patterns were complex and non-concordant between a pair of isoschizomers (HpaII/MspI) digests, indicating methylation modifications at both the inner and outer cytosines of the CCGG sites. The changed patterns were inherited through generations. Possible mechanism for the methylation changes and their potential implications for the phenotypic variation and genome organization are discussed.     

Does genetic distance between parental species influence outcomes of hybridization among coral reef butterflyfishes?

Christmas Island is located at the overlap of the Indian and Pacific Ocean marine provinces and is a hot spot for marine hybridization. Here, we evaluate the ecological framework and genetic consequences of hybridization between butterflyfishes Chaetodon guttatissimus and Chaetodon punctatofasciatus. Further, we compare our current findings to those from a previous study of hybridization between Chaetodon trifasciatus and Chaetodon lunulatus. For both species groups, habitat and dietary overlap between parental species facilitate frequent heterospecific encounters. Low abundance of potential mates promotes heterospecific pair formation and the breakdown of assortative mating. Despite similarities in ecological frameworks, the population genetic signatures of hybridization differ between the species groups. Mitochondrial and nuclear data from C. guttatissimus × C. punctatofasciatus (1% divergence at cyt b) show bidirectional maternal contributions and relatively high levels of introgression, both inside and outside the Christmas Island hybrid zone. In contrast, C. trifasciatus × C. lunulatus (5% cyt b divergence) exhibit unidirectional mitochondrial inheritance and almost no introgression. Back‐crossing of hybrid C. guttatissimus × C. punctatofasciatus and parental genotypes may eventually confound species‐specific signals within the hybrid zone. In contrast, hybrids of C. trifasciatus and C. lunulatus may coexist with and remain genetically distinct from the parents. Our results, and comparisons with hybridization studies in other reef fish families, indicate that genetic distance between hybridizing species may be a factor influencing outcomes of hybridization in reef fish, which is consistent with predictions from terrestrially derived hybridization theory.     

Hybrid speciation through sorting of parental incompatibilities in Italian sparrows

Speciation by hybridization is emerging as a significant contributor to biological diversification. Yet, little is known about the relative contributions of (i) evolutionary novelty and (ii) sorting of pre‐existing parental incompatibilities to the build‐up of reproductive isolation under this mode of speciation. Few studies have addressed empirically whether hybrid animal taxa are intrinsically isolated from their parents, and no study has so far investigated by which of the two aforementioned routes intrinsic barriers evolve. Here, we show that sorting of pre‐existing parental incompatibilities contributes to intrinsic isolation of a hybrid animal taxon. Using a genomic cline framework, we demonstrate that the sex‐linked and mitonuclear incompatibilities isolating the homoploid hybrid Italian sparrow at its two geographically separated hybrid–parent boundaries represent a subset of those contributing to reproductive isolation between its parent species, house and Spanish sparrows. Should such a sorting mechanism prove to be pervasive, the circumstances promoting homoploid hybrid speciation may be broader than currently thought, and indeed, there may be many cryptic hybrid taxa separated from their parent species by sorted, inherited incompatibilities.