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Of the many threats to species' survival, genetic threats such as hybridisation and introgression are often overlooked. Threatened or range‐restricted species that hybridise with more abundant and widespread relatives can be particularly vulnerable to declines or extinction via demographic or genetic swamping. Conservation of these species requires detection of hybridisation, but this can be difficult when hybrids are morphologically indistinguishable from parental species (i.e., cryptic). We used single nucleotide polymorphism data to examine hybridisation and introgression between the endangered Booroolong frog (Litoria booroolongensis) and the more abundant eastern stony creek frog (Litoria wilcoxii), two Australian stream frog species not previously reported to hybridise. To assess whether hybrids and parental individuals could be identified by phenotype, we compared morphological and genotypic classifications of individuals. Genotyping revealed relatively high rates of hybridisation and introgression (19% (24/126) were F1 or F2 hybrids, or backcrosses) in the New South Wales Central Tablelands. Hybrids were present in all sites where the species were syntopic (five of seven sites), suggesting that hybridisation is constrained primarily by a lack of opportunity. Within these sites, the median rate of hybridisation was 31.8% (range: 5.3–100%). Based on the likely extent of syntopy, hybridisation is plausible across more than 70% of the geographic range of L. booroolongensis, with potentially negative consequences for the species' persistence. Concerningly, only 42% of hybrids were correctly identified by morphology. Our results emphasise the need for genetic data to accurately distinguish hybrids and suggest that hybridisation could be occurring undetected between many related species, representing a potentially insidious threat to threatened and range‐restricted species. Conservation policies will need to consider the possibility of hybridisation and evaluate its consequences to appropriately manage and prevent further declines of threatened species. We used single nucleotide polymorphism data and morphological assessment to investigate hybridisation and introgression between two Australian frog species not previously reported to hybridise, the endangered Booroolong frog (Litoria booroolongensis) and its abundant congener, the eastern stony creek frog (Litoria wilcoxii). Hybrids could not be reliably identified by phenotype, but genotyping revealed relatively high rates of hybridisation and introgression. Our results emphasise the need for genetic tools to detect cryptic hybrids and suggest that hybridisation could be occurring undetected between many related species, representing a potentially insidious threat to threatened and range‐restricted species.

The article presents the data of physiological and cytological studies on the study of the features of the process of fertilization, the formation of the embryo and endosperm in the distant interspecific hybridization of cotton. Normally, the influx of hormones that regulate the division of the endosperm occurs in the opposite direction of the movement of phloem and xylem nutrient flows, which cause the movement of division waves and end by the 8th-9th day with the cell formation of the nuclear endosperm, which occurs by delimiting the cytoplasm around the nuclei through the formation of chains of vesicles emerging cell walls, followed by the formation of cell walls. And in the process of formation of a distant interspecific endosperm, a massive multiple formation of abnormal nuclei occurs, which remain viable due to the total metabolism and only in the common cytoplasm of a multinuclear cenocyte. It was revealed that the imbalance of the chromosomal composition of the nuclei in the common nuclear coenocyte leads to the death of its nuclei before the stage of cell formation and, therefore, when interspecific embryos switch to endosperm nutrition, they lose it, which blocks further growth and development of interspecific embryos inside the forming seed.

Determining the potential for hybridisation between transgenic crops and their relatives is a major component of risk assessment. Recent assessments of the extent of reproductive compatibility between crops and their relatives draw heavily on existing data from experimental crosses to infer the likelihood of hybridisation and introgression. Since the literature in this area continues to grow at a rapid pace, it is essential that such analyses can be easily updated. We used a database approach to assemble data on reproductive compatibility for eight crop species in Brassica, Raphanus and Sinapis, using data from hand pollination, spontaneous (unassisted) pollination and trials using in vitro techniques (e.g. embryo rescue), incorporating 326 studies and 216 species combinations. We found many reports for major crop species (B. juncea, B. napus, B. oleracea and B. rapa), but fewer for minor crops (B. carinata, B. nigra, Raphanus sativus and Sinapis alba). Many species combinations remain untested, and we highlight these information gaps. While reproductively incompatible species can be discounted as targets for transgene escape, compatible species must be evaluated further in the particular context where transgenic crops are grown. Because the data is retained in a database in a relatively unmodified form, multiple views of the data can be generated; this review represents one possible view of this data. Our approach also allows new data to be easily incorporated into future reanalyses and can be extended to other crop groups, and as such is a useful method of assembling, analysing and sharing data for risk assessment.

The narrow genetic base of elite Upland cotton (Gossypium hirsutum L.) germplasm has been a significant impediment to sustained progress in the development of cotton cultivars to meet the needs of growers and industry in recent years. The prospect of widening the genetic base of Upland cotton by accessing the genetic diversity and fiber quality of Pima cotton (Gossypium barbadense L.) has encouraged interspecific hybridization and introgression efforts for the past century. However, success is limited due mainly to genetic barriers between the two species in the forms of divergent gene regulatory systems, accumulated gene mutations, gene order rearrangements and cryptic chromosomal structure differences that have resulted in hybrid breakdown, hybrid sterility and selective elimination of genes. The objective of this paper is to provide a mini-review in interspecific hybridization between Upland and Pima cotton relevant to breeding under the following sections: (1) qualitative genetics; (2) cytogenetic stocks; (3) quantitative genetics; (4) heterosis, and (5) introgression breeding. Case studies of successful examples are provided.

The use of crop wild relatives (CWR) genes to improve crop performance is well established with important examples dating back more than 60 years. In this paper, we review available information on the presence of genes from CWR in released cultivars of 16 mandate crops of the CGIAR institutes, and some selected additional crops, focusing on the past 20 years--the period since a comprehensive review by Robert and Christine Prescott-Allen in 1986. It appears that there has been a steady increase in the rate of release of cultivars containing genes from CWR. While there continues to be a strong emphasis on using pest and disease resistance genes, a wider range of characteristics are being introduced than in the past. Those crops whose wild relatives have traditionally been used as sources of useful traits (e.g., wheat, tomato) continue to be most likely to include new genes from their wild relatives. CWR are continually gaining in importance and prevalence, but, we argue, their contributions to the development of new cultivars remain less than might have been expected given improved procedures for intercrossing species from different gene pools, advances in molecular methods for managing backcrossing programes, increased numbers of wild species accessions in gene banks, and the substantial literature on beneficial traits associated with wild relatives.

Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. thatwas previously supported bymorphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes 9 of the top 10 most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0%, 34.8%, and 21.4% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

The degree of clonality, interspecific hybridisation and inbreeding in rare species will have significant implications for maintenance of genetic diversity and resilience to environmental change, with related implications for immediate conservation management. Using microsatellites, we detected extensive clonality within the rare mallee, Eucalyptus absita, from a highly disturbed agricultural habitat in southwestern Australia. A total of just 16 unique genets, plus five putative hybrids with E. loxophleba, were detected across the known species range and these genets were estimated to be of considerable age. Each location possessed a unique genotype and overall diversity was moderate (H E = 0.547). The outcrossing rate in seedling progeny was low (t ₘ = 0.281), reflecting a rarity of intraspecific sires and minimal inbreeding depression prior to seed dispersal. Of all seedling progeny, up to 19 % were putative hybrids. Our findings indicate that despite rarity and clonality, moderate levels of genetic diversity and the capacity to produce outcrossed seeds is maintained. However, the ongoing maintenance of E. absita genetic diversity is significantly compromised by a high rate of selfing and potential hybridisation in seedling progeny. Seeds collected for long-term storage or rehabilitation should be screened for inbreeding and hybridisation rates to improve conservation outcomes. All existing adults represent a unique portion of the genepool for conservation.

The Campanula genus comprises several economically important ornamental plants species. Wide hybridisation is a method to increase phenotypic variability, but is limited due to interspecies hybridisation barriers. In this study we investigated whether ovule culture could be used to increase the success rate of interspecific hybridisation between C. portenschlagiana  ×  C. poscharskyana and C. medium  ×  C. formanekiana . The effect of different ovule isolation times on ovule germination in vitro was examined. In general, the number of collectible ovules and ovule germination was low. Interspecific hybrids between C. medium and C. formanekiana exhibited an increased number of viable ovules with later isolation time, but with different ovule germination rates. A parent-of-origin effect on both the number of collectible ovules and ovule germination was observed for C. medium  ×  C. formanekiana . Histological analysis of embryo and endosperm development in collectible ovules isolated at different time points from interspecific crosses showed that the vast majority of ovules did not contain an embryo. When present, embryo development only progressed with ovule collection time in the C. medium and C. formanekiana crosses. The occurrence of miscoloured seedlings in interspecific crosses indicated incompatibilities between the parental lines that could not be prevented by reciprocal crossing. The low number of collectible ovules and germination rates might be inhibited due to fertilisation barriers. With this study, a protocol for ovule culture was established and the usefulness of ovule culture to obtain interspecific hybrids of selected Campanula species was demonstrated.