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The Indian spot-billed duck, Anas poecilorhyncha is a large dabbling and non-migratory breeding bird. The identification and phylogenetic relationship of A. poecilorhyncha remain uncertain due to the presence of overlapping meristic characters and hybridization with closely related species. Molecular data aids when there are challenges in morphological identification. However, genetic characterization of A. poecilorhyncha has been paid less attention. Apart from their functional and physiological role, mitochondrial genome can also be used for various purposes, including species identification, phylogenetic analysis, understanding the domestication history of species etc. Therefore, the present study aimed to sequence the mitochondrial genome of A. poecilorhyncha and its closely related domestic species A. platyrhynchos (mallard duck) to understand their mitochondrial genome structure and phylogenetic relationships. The length of mitochondrial genome of A. poecilorhyncha and A. platyrhynchos was 16,608 and 16,604 bp respectively. Mitochondrial genome contained 37 genes and a non-coding control region. Overall, the characteristics of mitochondrial genome of both species were found to be conserved. The phylogenetic tree exhibited seven major clades (A to G) with a high bootstrap support. Notably, the Indian A. poecilorhyncha population formed a distinct clade (C) whereas the A. poecilorhyncha that were probably sampled from China grouped along with A. zonorhyncha (clade B). Besides, one of the A. poecilorhyncha probably sampled from China was placed in the clade A, which predominantly consisted of A. platyrhynchos. It suggests that Indian A. poecilorhyncha population is genetically different from Chinese A. poecilorhyncha population. Further, it sheds light on the importance of conducting a comprehensive phylogenetic study on these species. The newly sequenced mitochondrial genome of A. poecilorhyncha and A. platyrhynchos would be useful not only to have a better understanding of the phylogeny and evolution of Anas species but also to help in the conservation of A. poecilorhyncha which is under constant threat from rapid urbanization, interspecific hybridization and other human activities. [ABSTRACT FROM AUTHOR]

Theropithecus gelada, the last surviving species of this genus, occupy a unique and highly specialised ecological niche in the Ethiopian highlands. A subdivision into three geographically defined populations (Northern, Central and Southern) has been tentatively proposed for this species on the basis of genetic analyses, but genomic data have been investigated only for two of these groups (Northern and Central). Here we combined newly generated whole genome sequences of individuals sampled from the population living south of the East Africa Great Rift Valley with available data from the other two gelada populations to reconstruct the evolutionary history of the species. Integrating genomic and paleoclimatic data we found that gene‐flow across populations and with Papio species tracked past climate changes. The isolation and climatic conditions experienced by Southern geladas during the Holocene shaped local diversity and generated diet‐related genomic signatures. [ABSTRACT FROM AUTHOR]

Hybridization plays a pivotal role in evolution, influencing local adaptation and speciation. However, it can also reduce biodiversity, which is especially damaging when native and non‐native species meet. Hybridization can threaten native species via competition (with vigorous hybrids), reproductive resource wastage and gene introgression. The latter, in particular, could result in increased fitness in invasive species, decreased fitness of natives and compromise reintroduction or recovery conservation practices. In this study, we use a combination of RAD sequencing and microsatellites for a range‐wide sample set of 1366 fish to evaluate the potential for hybridization and introgression between native crucian carp (Carassius carassius) and three non‐native taxa (Carassius auratus auratus, Carassius auratus gibelio and Cyprinus carpio) in European water bodies. We found hybridization between native and non‐native taxa in 82% of populations with non‐natives present, highlighting the potential for substantial ecological impacts from hybrids on crucian carp populations. However, despite such high rates of hybridization, we could find no evidence of introgression between these taxa. The presence of triploid backcrosses in at least two populations suggests that the lack of introgression among these taxa is likely due to meiotic dysfunction in hybrids, leading to the production of polyploid offspring which are unable to reproduce sexually. This result is promising for crucian reintroduction programs, as it implies limited risk to the genetic integrity of source populations. Future research should investigate the reproductive potential of triploid hybrids and the ecological pressures hybrids impose on C. carassius. [ABSTRACT FROM AUTHOR]

Summary Hybridization is increasingly recognized as an important evolutionary process across the tree of life. In many clades, phylogenomic approaches have permitted unparalleled insight into the extent and frequency of hybridization. However, we continue to lack a deep understanding of the factors that limit and shape patterns of hybridization, especially in evolutionary radiations. In this study, we characterized patterns of introgression across Costus (Costaceae), a young evolutionary radiation of tropical understory plants that maintain widespread interfertility despite exhibiting strong prezygotic reproductive isolation. We analyzed a phylogenomic dataset of 756 genes from 54 Costus species using multiple complementary approaches – D‐statistics, gene‐tree‐based tests, and phylogenetic network analyses – to detect and characterize introgression events throughout the evolutionary history of the radiation. Our results identified a moderate number of introgression events, including a particularly ancient, well‐supported event spanning one of the deepest divergences in the clade. Most introgression events occurred between taxa or ancestral lineages that shared the same pollination syndrome (bee‐pollinated or hummingbird‐pollinated). These findings suggest that prezygotic barriers, including pollinator specialization, have been key to the balance between introgression and reproductive isolation in Costus. [ABSTRACT FROM AUTHOR]

Oxford ragwort (Senecio squalidus) is one of only two homoploid hybrid species known to have originated very recently, so it is a unique model for determining genomic changes and stabilization following homoploid hybrid speciation. Here, we provide a chromosome-level genome assembly of S. squalidus with 95% of the assembly contained in the 10 longest scaffolds, corresponding to its haploid chromosome number. We annotated 30,249 protein-coding genes and estimated that ∼62% of the genome consists of repetitive elements. We then characterized genome-wide patterns of linkage disequilibrium, polymorphism, and divergence in S. squalidus and its two parental species, finding that (1) linkage disequilibrium is highly heterogeneous, with a region on chromosome 4 showing increased values across all three species but especially in S. squalidus ; (2) regions harboring genetic incompatibilities between the two parental species tend to be large, show reduced recombination, and have lower polymorphism in S. squalidus ; (3) the two parental species have an unequal contribution (70:30) to the genome of S. squalidus , with long blocks of parent-specific ancestry supporting a very rapid stabilization of the hybrid lineage after hybrid formation; and (4) genomic regions with major parent ancestry exhibit an overrepresentation of loci with evidence for divergent selection occurring between the two parental species on Mount Etna. Our results show that both genetic incompatibilities and natural selection play a role in determining genome-wide reorganization following hybrid speciation and that patterns associated with homoploid hybrid speciation—typically seen in much older systems—can evolve very quickly following hybridization. • The genome of S. squalidus , a recent homoploid hybrid species, is presented • Sorting of parental alleles is associated with presence of genetic incompatibilities • Fixed alleles from the major parent are associated with divergent natural selection • Typical patterns of hybrid speciation appear <300 generations after speciation Nevado et al. report genomic reorganization following hybrid speciation. They find that the typical genomic signatures of homoploid hybrid species are well established ∼300 generations after hybridization and that both pre-existing genetic incompatibilities and divergent natural selection play an important role following hybrid speciation. [ABSTRACT FROM AUTHOR]

Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a "worst‐case" scenario for species delimitation within vertebrates: the Ctenotus inornatus species group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation‐by‐distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that "taxonomic disaster zones" like the C. inornatus species group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization. [ABSTRACT FROM AUTHOR]

Despite large differences in morphology, behavior and lek-mating strategies the birds-of-paradise are known to hybridize occasionally, even across different genera. Many of these bird-of-paradise hybrids were originally described as distinct species based on large morphological differences when compared to recognized species. Nowadays, these specimens are generally recognized as hybrids based on morphological assessments. Having fascinated naturalists for centuries, hybrid specimens of birds-of-paradise have been collected and the specimens kept in Natural History Collections. In the present study, we utilize this remarkable resource in a museomics framework and evaluate the genomic composition of most described intergeneric hybrids and some intrageneric hybrids. We show that the majority of investigated specimens are first-generation hybrids and that the parental species, in most cases, are in line with prior morphological assessments. We also identify two specimens that are the result of introgressive hybridization between different genera. Additionally, two specimens exhibit hybrid morphologies but have no identifiable signals of hybridization, which may indicate that minor levels of introgression can have large morphological effects. Our findings provide direct evidence of contemporary introgressive hybridization taking place between genera of birds-of-paradise in nature, despite markedly different morphologies and lek-mating behaviors. [ABSTRACT FROM AUTHOR]

Lines separating native and invasive plant species can be thin due to close relatedness, obscured by cryptic invasions, or breached by hybridization. Past work suggests these phenomena are especially prevalent in aquatic systems. This could arise from strong filters imposed by aquatic environments magnifying the importance of 'preadaptation'—non‐native species succeeding where closely related native species occur due to shared traits. If so, there should be stronger signals of preadaptation in aquatic than terrestrial plant invasions, with implications for management.I tested for stronger influence of preadaptation in aquatic than terrestrial invasions by comparing relatedness of invasive and native species in aquatic versus terrestrial flora of the Midwestern USA using herbarium records and taxonomic and phylogenetic analyses. I predicted that aquatic species would constitute an evolutionarily distinct subset of plants; aquatic invaders would be more closely related, taxonomically and phylogenetically, to native aquatic plants than terrestrial invaders are to their native counterparts; and aquatic invaders from the Midwest's primary donor region (the Palearctic) would be more closely related to Midwestern species than are Palearctic aquatic plants that are not invasive in the Midwest.Findings supported the evolutionary legacy of adaptation to aquatic environments being reflected in thin lines separating invasive and native aquatic plants. Aquatic species constituted an evolutionarily distinct subset of plants, and invasive aquatic plants were more closely related to native aquatic plants (taxonomically and phylogenetically) than terrestrial invaders were to terrestrial native species.Additionally, aquatic plants of the Palearctic that are invasive in the Midwest were more closely related to Midwestern natives (phylogenetically, but not taxonomically) than were their non‐invasive counterparts, reinforcing the role of preadaptation.Synthesis and applications: Thin lines separating native from invasive aquatic plants pose challenges for response efforts. For resource managers, the prevalence of cryptic invasions requires dedicated, robust approaches to surveillance. For outreach, finer distinctions between native and invasive necessitate nuanced approaches to communication and education. And when control is needed, it should be implemented cautiously to minimize nontarget impacts to close native relatives, but thoroughly enough to prevent native relatives being displaced by competition and/or introgression. [ABSTRACT FROM AUTHOR]

Hybridisation and introgression are increasingly seen as important drivers of the evolution of organisms, particularly in Lepidoptera. One group that is gaining attention due to recently published cases of interspecific gene flow is the genus Melitaea Fabricius (Nymphalidae). In this study, we used genomics to investigate the role of hybridisation in the evolution of the western Palearctic species of the Melitaea phoebe group M. ornata Christoph, the recently described M. pseudornata Muñoz Sariot & Sánchez Mesa, M. phoebe (Denis & Schiffermüller), M. punica Oberthür, and M. telona (Fruhstorfer). We provide evidence of asymmetric gene flow from M. phoebe to both M. ornata and M. pseudornata. Gene flow from M. phoebe to M. pseudornata was very high (25.0%–31.9%), widespread throughout the distribution of the latter, and not equally distributed along the genome. The Z chromosome showed patterns compatible with the large‐Z effect, which were mimicked by two autosomes. Melitaea pseudornata endured massive introgression while remaining a separate entity from M. phoebe, although gene flow may have altered its phenotype, including its voltinism and the morphology of the adults and caterpillars. These findings suggest that hybridisation may be pervasive in this genus and highlight its key role in the evolution of butterflies, emphasising the need for further research on this topic. [ABSTRACT FROM AUTHOR]

Asplenium is one of the most species‐rich genera of ferns. While ubiquitous polyploidy and hybridization events, as well as vast distribution ranges, contribute to its remarkable diversity, these facts also lead to extreme classification difficulties. The A. exiguum complex is a natural morphological assemblage of taxa sharing part or all ancestral genomes due to polyploidy and hybridization. Consisting of 4 to 13 taxa mainly distributed in the Sino‐Himalayan region, taxonomic issues of this complex have been debatable for a long time. Here, we collected 49 samples representing the majority of the recognized taxa and reconstructed phylogenetic trees using two plastid loci (rbcL, rpl32‐trnP) and three nuclear loci (pgiC, SQD1, nrDNA). Evidence from ploidy, macro‐ and micromorphology, geographical pattern, and ecological niche was also integrated to illuminate the species boundaries and evolutionary history within the complex. According to our investigation, six taxa, including two diploid species (A. barkamense, A. lushanense), three tetraploid species (A. exiguum, A. glenniei, A. nesii), and one triploid nothospecies (A. ×mickelii), are accepted. Asplenium barkamense, which used to be treated as a synonym of A. nesii in Flora of China, is an independent species and the common diploid progenitor of autotetraploid A. nesii and allotetraploid A. glenniei. Moreover, A. glenniei (= A. yunnanense), widespread in the subtropical and temperate regions of East Asia and occasionally seen in the southwestern United States, Mexico, and northern Guatemala of North America, is an allotetraploid originated from A. barkamense and A. lushanense, whereas A. exiguum, known with a narrow distribution in tropical Asia, is a putative autotetraploid offspring of A. lushanense. Therefore, A. glenniei is restored as an independent species from A. exiguum. Asplenium ×mickelii is supported as a sterile hybrid of A. lushanense and A. glenniei. In addition, our study suggests that the majority of speciation events in the complex probably took place in the Hengduan Mountains, where complicated orogenic activities and climatic oscillations facilitate geographic isolation and polyploid establishment. The two tetraploids, A. nesii and A. glenniei, adapted to distinct climate conditions and colonized wider ranges compared to their parents. [ABSTRACT FROM AUTHOR]

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Hybridization is a common technique in the breeding of new varieties. In this study, we obtained F1 and F2 hybrids through interspecific hybridization between Siniperca chuatsi and Siniperca scherzeri and backcross offspring by backcrossing between F1 and Siniperca chuatsi. We analyzed the morphological traits and genetic diversity of the parents and their progeny. The results showed that although most morphological traits of the progeny were not significantly different from those of their parents, the F1 hybrids exhibited the most pronounced morphological variations. The F2 and backcross hybrids appeared morphological differentiation within their populations. The CPL/CPW ratio emerged as a reliable marker for identifying hybrids morphologically. The expected heterozygosity for F1 (0.6264), F2 (0.6677), and backcross offspring (0.5260) were intermediate between Siniperca chuatsi (0.7388) and Siniperca scherzeri (0.3910), indicating a relatively high level of genetic diversity in the offspring. Additionally, the private allele frequency of F1 and F2 was higher than backcross offspring. One SSR marker (G5220) was identified as a specific molecular marker to distinguish the hybrid F1 population from the parents, hybrid F2, and backcross F1 populations by analyzing specific alleles. The result of Ne, He, I, and PIC confirmed that F2 maintained the genetic diversity of F1. We speculated that both F1 and F2 have higher breeding potential. This study provides essential baseline data for genetic breeding of mandarin fish that will be instrumental in the future. [ABSTRACT FROM AUTHOR]

ABSTRACT Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation, dated to the Early‐Middle Eocene. Ancestral reconstructions including fossils suggest ancestors of Castanea + Castanopsis, Lithocarpus, and the Old World oak clade probably co‐occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co‐occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups. [ABSTRACT FROM AUTHOR]

Advances in cell fusion technology have propelled breeding into the realm of somatic hybridization, enabling the transfer of genetic material independent of sexual reproduction. This has facilitated genome recombination both within and between species. Despite its use in plant breeding for over fifty years, somatic hybridization has been limited by cumbersome procedures, such as protoplast isolation, hybridized-cell selection and cultivation, and regeneration, particularly in woody perennial species that are difficult to regenerate. This review summarizes the development of somatic hybridization, explores the challenges and solutions associated with cell fusion technology in woody perennials, and outlines the process of protoplast regeneration. Recent advancements in genome editing and plant cell regeneration present new opportunities for applying somatic hybridization in breeding. We offer a perspective on integrating these emerging technologies to enhance somatic hybridization in woody perennial plants. [ABSTRACT FROM AUTHOR]

Understanding how hybridization influences the morphology and fitness of hybrids is essential for studying adaptive evolution and ecological speciation. Secondary contact zones, where separately evolving populations meet and hybridize, offer valuable insights into the evolutionary processes driving speciation and provide an excellent system to address these questions. In this study, we investigate patterns of morphological and genetic variation of two congeneric viper species, Vipera aspis and V. latastei, across a contact zone in northern Spain (Oja‐Tirón), where vipers with mixed morphology are often detected, but genetic studies addressing hybridization and relating patterns of genetic and morphological admixture are lacking. Using nine morphological traits (scalation and colouration) and 18 microsatellite markers, we (1) estimated the extent of hybridization, (2) morphologically characterized parental species and hybrids, and (3) evaluated the correlation between patterns of genetic and morphological admixture. Analyses revealed a bimodal hybrid zone with high rate of hybridization (22%) and prevalence of late‐generation hybrids (F2 and backcrosses). Morphological analyses differentiated the two parental species, and a positive correlation (r = 0.95) was found between morphological and genetic patterns. The hybrid group displayed on average an intermediate morphology between the parentals, yet morphologically intermediate hybrids were rare in our dataset. Instead, most hybrids resembled the parental species with whom they share most of the genetic background. Notably, the hybrid group exhibited greater morphological variation than the parental groups. Traits with adaptative value, such as ventral scales and dorsal marks, showed significant differences between hybrids and the two parental species. Introgression of these traits may confer ecological advantages to hybrids, enhancing local adaptation. Overall, this study reveals a positive correlation between patterns of morphological and genetic variation across a hybrid zone and provides insights into the phenotypic consequences of hybridization on these viper species. [ABSTRACT FROM AUTHOR]

In this study, distant hybridisation was successfully conducted between Brassica rapa var. rosularis Tsen et Lee ‘Huangxinwu’ (2n = 20, AA) and B. oleracea var. alboglabra Bailey ‘Big Yellow Flower Kale’ (2n = 18, CC). A total of three hybrids were obtained through artificial hybridisation and ovary culture. Forty asexual seedlings were obtained by propagation, and thirty were doubled. The identifications of morphological analysis, cytological observation, and SSR molecular analysis showed that one strain was a true hybrid. Allotetraploid hybrids exhibited generally an intermediate phenotype between their parents. The wrinkled leaf surface and leaf colour were more inclined toward the maternal parent, while its leaf thickness and size were more inclined toward the paternal parent. Furthermore, the allotetraploid hybrids showed obvious over-parent heterosis in biomass and nutritional quality characteristics, including plant weight, soluble sugar, VC, and cellulose, with corresponding contents of 882.76 g, 2.84%, 107.91 mg/100 g and 1.27%. Moreover, the soluble solids and soluble protein contents of these hybrids were 5.62% and 2.56 g/100 g, respectively, which were similar to those of the high-value parent. In general, the newly synthesised allotetraploid is an innovative germplasm of Brassica vegetables that can be used for future heterosis utilisation and nutritional quality improvement. [ABSTRACT FROM AUTHOR]

Genetic relationships were examined for a total of 90 individuals of 90 species or species var. from 13 genera of Malawian cichlids based on the sequences of an amplified 991‐bp fragment of the mtDNA control region (mtDNA‐CR). In the network analysis, no exclusive clades were made by all the members of any genera in this study. However, congeneric clades were observed by genera Buccochromis, Copadichromis, Protomelas, and Sciaenochromis, whereas no congeneric clades were observed by genera Mylochromis, Nimbochromis, and Otopharynx. In non‐mbuna, an Aulonocara–Lethrinops group was divided into two groups, and the mean genetic distance of the larger group was much lower from mbuna than from other non‐mbuna. Overall mean genetic distance within a genus was generally low in mbuna, whereas it was relatively high in non‐mbuna. In the genetic tree of each genus, two or more large clades were observed, and some clades, such as those of Aulonocara hansbaenschi and Aulonocara nyassae in genus Aulonocara, Lethrinops micrentodon and Lethrinops sp. "gold harbor" in Lethrinops, and Otopharynx ovatus and Otopharynx brooksi in Otopharynx, were very deeply differentiated. Besides, a mbuna species, Pseudotropheus crabro, was extremely deeply differentiated from other members of this genus. These results suggest a widespread morphological convergence across the taxa in parallel with deep genetic differentiation in the long evolutionary story and some possibility of generation of the species of Aulonocara–Lethrinops group by hybridization of small non‐mbuna and mbuna species. Furthermore, taxonomical reexamination is necessary based on a strong support by genetic connection. [ABSTRACT FROM AUTHOR]

Classifying a yeast strain into a recognized species is not always straightforward. Currently, the taxonomic delineation of yeast strains involves multiple approaches covering phenotypic characteristics and molecular methodologies, including genome-based analysis. The aim of this study was to evaluate the suitability of the Average Nucleotide Identity (ANI) calculation through FastANI, a tool created for bacterial species identification, for the assignment of strains to some yeast species. FastANI, the alignment of in silico-extracted D1/D2 sequences of LSU rRNA, and multiple alignments of orthologous genes (MAOG) were employed to analyze 644 assemblies from 12 yeast genera, encompassing various species, and on a dataset of hybrid Saccharomyces species. Overall, the analysis showed high consistency between results obtained with FastANI and MAOG, although, FastANI proved to be more discriminating than the other two methods applied to genomic sequences. In particular, FastANI was effective in distinguishing between strains belonging to different species, defining clear boundaries between them (cutoff: 94–96%). Our results show that FastANI is a reliable method for attributing a known yeast species to a particular strain. Moreover, although hybridization events make species discrimination more complex, it was revealed to be useful in the identification of these cases. We suggest its inclusion as a key component in a comprehensive approach to species delineation. Using this approach with a larger number of yeasts would validate it as a rapid technique to identify yeasts based on whole genome sequences. [ABSTRACT FROM AUTHOR]

Simple Summary: The grey partridge (Perdix perdix Linnaeus, 1758), is a polytypic species with seven recognized subspecies, including one subspecies (P. p. italica Hartert, 1917) that is endemic to the Italian peninsula. Until World War II, the species was widespread across Europe, but then severely declined due to anthropogenic causes, including hybridization. The contraction of the endemic population distribution range and the introduction of allochthonous genotypes that started at the beginning of the past century led to the impoverishment of the endemic gene pool. This is still one of the main threats to this species and is only partially managed through ex situ conservation programs. To understand the native genetic composition of Italian grey partridge, we performed genetic characterization of museum specimens, proving that museum samples are a reliable source of DNA for investigating the genetic structure of species or populations from the recent past. The data obtained highlight, along with a contraction in the distribution, a high presence of specimens coming from other European populations, suggesting an uncertain situation of the species in Italy, despite the conservation efforts made. Extensive historical bibliographic research allowed us to define time baselines and periods with different restocking pressures. The grey partridge (Perdix perdix Linnaeus, 1758), is a polytypic species with seven recognized subspecies, including P. p. italica (Hartert, 1917), which is endemic to Italy. Until World War II, the species was widespread across Europe but severely declined due to anthropogenic causes, jeopardizing the Italian subspecies gene pool. Genetic characterization and haplotype identification were performed by analyzing the 5′-end of the mitochondrial control region (CR). A total of 15 haplotypes were detected, seven of which were present in the population before 1915. Among them, three haplotypes were never detected again in the individuals collected after 1915. Interestingly, eight of the 15 haplotypes detected in Italian museum samples belonged exclusively to individuals collected after 1915. The obtained data highlight a high presence of specimens originating from other European populations and, despite all the conservation efforts, suggest an uncertain situation of the subspecies in Italy. This research was strongly backed up by extensive bibliographic research on historical documents, allowing the identification of hundreds of restocking events all over Italy. This is an integral part of this research and has laid the foundations for identifying and circumscribing historical periods in which introductions from the rest of Europe had different pressures, aiming to define a baseline. [ABSTRACT FROM AUTHOR]

In certain tetraploid species resulting from interspecific hybridization, one parent's subgenome is known to selectively undergo DNA loss. The molecular mechanisms behind this remain unclear. In our study, we compared the genomes of a standard diploid species with two allotetraploid species from the Xenopus genus, both possessing L (longer) and S (shorter) homoeologous subgenomes. We observed substantial gene losses and intergenic DNA deletions in both the S and L subgenomes of the tetraploid species. Gene losses were around 1,000 to 3,000 for L and 4,000 to 6,000 for S, with especially prominent losses in the S subgenome. Many of these losses likely occurred shortly after interspecific hybridization in both L/S subgenomes. We also deduced frequent large inversions in the S subgenome. Upon reassessing transposon dynamics using updated genome databases, we reaffirmed heightened DNA transposon activity during the hybridization, as previously reported. We next investigated whether S subgenome-biased DNA loss could be correlated with the activation of DNA transposons following hybridization. Notably, distinct patterns were observed in the dynamics of DNA transposons between the L and S subgenomes. Several DNA transposon subfamilies correlated positively with DNA deletions in the S subgenome and negatively in the L subgenome. Based on these results, we propose a model that, upon and after hybridization between two related diploid Xenopus species, the mixture of their genomes resulted in the derepression of DNA transposons, especially in the S subgenome, leading to selective DNA loss in the S subgenome. [ABSTRACT FROM AUTHOR]

Hieracium is one of the largest flowering plant genera that has recently experienced a rapid evolutionary radiation. Due to the massive morphological variation among species, frequent hybridization, and polyploidization events, combined with apomictic reproduction in polyploids, the concept of species in Hieracium is widely debated, and species identification is incredibly challenging. Taxonomic investigation can lead to changes in conservation status or, in some cases, to de-extinctions of species. Taxa with doubtful classification are particularly sensitive to this kind of problem. Hieracium tolstoii was a narrow Italian endemic species that is nowadays considered extinct. Described as a morphological intermediate form between two other species, no further investigations were conducted after its first description. To clarify H. tolstoii's origin and ensure the validity of its current conservation status, we conducted a taxonomic investigation on herbaria specimens of the early XX century. Specimens were studied using a morphometric analysis that compared H. tolstoii with other closely related taxa. Moreover, we performed phylogenetic investigations using three plastid intergenic spacers to evaluate the relationship between species. Plastid markers revealed the presence of indels and SNPs in H. tolstoii sequences that differ from sequences of the supposed parental species. Morphometry revealed differences among species that led us to confirm the validity of H. tolstoii as an independent apomictic species and, therefore, unfortunately, its extinction. [ABSTRACT FROM AUTHOR]

Hybrid speciation plays an important role in species diversification. The establishment of reproductive isolation is crucial for hybrid speciation, and the identification of diverse types of hybrids, particularly homoploid hybrid species, contributes to a comprehensive understanding of this process. Reaumuria songarica is a constructive shrub widespread in arid Central Asia. Previous studies have inferred that the R. songarica populations in the Gurbantunggut Desert (GuD) originated from homoploid hybridizations between its eastern and western lineages and may have evolved into an incipient species. To further elucidate the genetic composition of different hybrid populations and to determine the species boundary of this hybrid lineage, we investigated the overall phylogeographic structure of R. songarica based on variation patterns of five cpDNA and one nrITS sequences across 32 populations. Phylogenetic analyses demonstrated that within the GuD lineage, the Wuerhe population evolved directly from ancestral lineages, whereas the others originated from hybridizations between the eastern and western lineages. PCoA and genetic barrier analysis supported the subdivision of the GuD lineage into the southern (GuD‐S) and northern (GuD‐N) groups. Populations in the GuD‐S group had a consistent genetic composition and the same ancestral female parent, indicating that they belonged to a homoploid hybrid lineage. However, the GuD‐N group experienced genetic admixture of the eastern and western lineages on nrITS and cpDNA, with some populations inferred to be allopolyploid based on ploidy data. Based on cpDNA haplotypes, BEAST analyses showed that the GuD‐S and GuD‐N groups originated after 0.5 Ma. Our results suggest that multiple expansions and contractions of GuD, driven by Quaternary climatic oscillations and the Kunlun‐Yellow River tectonic movement, are important causes of the complex origins of R. songarica populations in northern Xinjiang. This study highlights the complex origins of the Junggar Basin flora and the underappreciated role of hybridization in increasing its species diversity. [ABSTRACT FROM AUTHOR]

Earlier studies on Isothecium s.l. suggested potential interchange of genetic material between species that are nowadays known to belong to separate genera. In this study, we analyse the variation in three molecular markers (nuclear gpd ; mitochondrial nad 5; and plastid trn G) in a wide selection of Isothecium alopecuroides and Pseudisothecium myosuroides specimens to infer whether this potential exchange of genetic material is frequent. In addition, we explore the phylogeographic structure of these two species in Europe. Our results seem to show repeated genetic interchange for the nuclear and mitochondrial markers in both species, suggesting intergeneric hybridization, although horizontal gene transfer and/or incomplete lineage sorting could also explain the detected incongruences. The genetic lineages found indicate a complex biogeographical history for I. alopecuroides , including both post-glacial immigration from different glacial refugia and developing haplotypes potentially adapted to cold climates. As for P. myosuroides , genetic variants could either indicate a post-glacial immigration history or adaptation to oceanic conditions. Further studies including a larger set of more variable molecular markers could help to reach final conclusions on the results here presented. [ABSTRACT FROM AUTHOR]

Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi‐layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation‐by‐Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories. [ABSTRACT FROM AUTHOR]

Plastomes are used in phylogenetic reconstructions because of their relatively conserved nature. Nonetheless, some limitations arise, particularly at lower taxonomic levels due to reduced interspecific polymorphisms and frequent hybridization events that result in unsolved phylogenies including polytomies and reticulate evolutionary patterns. Next-generation sequencing technologies allow access to genomic data and strongly supported phylogenies, yet biased topologies may be obtained due to insufficient taxon sampling. We analyze the hypothesis that intraspecific plastome diversity reflects biogeographic history and hybridization cycles among taxa. We generated 12 new plastome sequences covering distinct latitudinal locations of all species of subgenus Nothofagus from North Patagonia. Chloroplast genomes were assembled, annotated, and searched for simple sequence repeats (SSRs). Phylogenetic reconstructions included species and sampled locations. The six Nothofagus species analyzed were of similar size and structure; only Nothofagus obliqua of subgenus Lophozonia , used as an outgroup, presented slight differences in size. We detected a variable number of SSRs in distinct species and locations. Phylogenetic analyses of plastomes confirmed that subgenus Nothofagus organizes into two monophyletic clades each consisting of individuals of different species. We detected a geographic structure within subgenus Nothofagus and found evidence of local chloroplast sharing due to past hybridization, followed by adaptive introgression and ecological divergence. These contributions enrich the comprehension of transversal evolutionary mechanisms such as chloroplast capture and its implications for phylogenetic and phylogenomic analyses. [ABSTRACT FROM AUTHOR]

This work demonstrates for the first time using molecular markers alongside chromosomes and the intermediate phenotype that a specimen of Dorcadion is an accidental first‐generation hybrid. The analyses were based on two mitochondrial and five nuclear molecular markers. While analysing the putative parental taxa of the hybrid, it was revealed that even Dorcadion lugubre lugubre Kraatz is likely a hybridogenic taxon. Coincidentally, a new lead was discovered concerning the parental taxa of Dorcadion aethiops (Scopoli), already known as a hybridogenic species. This new evidence of hybridisation adds to the recent publications to strengthen the hypothesis that, in Dorcadionini, this phenomenon is relatively frequent, and speciation is often reticulate: New taxa can appear through introgressive hybridisation, explaining in part the extreme species richness of the group. [ABSTRACT FROM AUTHOR]

Secondary contact between closely related taxa represents a "moment of truth" for speciation—an opportunity to test the efficacy of reproductive isolation that evolved in allopatry and to identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes that are transitioning from autosomal to sex-specific inheritance. Here we report that, in the Solomon Islands, two closely related bird species in the honeyeater family—Myzomela cardinalis and Myzomela tristrami—carry neo-sex chromosomes and have come into recent secondary contact after ~1.1 my of geographic isolation. Hybrids of the two species were first observed in sympatry ~100 years ago. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and in sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. For sympatric birds, autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. In other regions of the genome, however, the story is different. While introgression on the Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the invading M. cardinalis to the resident M. tristrami. The recent hybridization between these species has thus enabled gene flow in some genomic regions but the interaction of admixture, asymmetric mate choice, and/or natural selection has led to the variation in the amount and direction of gene flow at sex-linked regions of the genome. Author summary: When an invasive species colonizes an island and interacts with a closely related resident species, we are provided with a rare opportunity to study the consequences of interbreeding and the factors that keep species distinct. Regions of the genome that evolve rapidly and/or influence mate choice may be especially likely to act as incidental barriers to gene flow. The red Myzomela cardinalis, birds in the honeyeater family, have invaded Makira in the Solomon Islands, coming into contact with the endemic, all black Myzomela tristrami. We used population genomic analyses of individuals in geographic isolation, and those in geographic contact, to understand the history of these two species and the consequences of their recent range overlap. We found that sex-specific regions of the genome (i.e., sex chromosomes) were either limited in their ability to move between species, or only moved in one direction, from the invading M. cardinalis to the resident M. tristrami. This work highlights how certain regions of the genome may be especially important in defining species boundaries and the generation and maintenance of biodiversity. [ABSTRACT FROM AUTHOR]

Utilizing valuable genes and alleles from crop wild relatives (CWRs) and transferring them to elite varieties requires a thorough understanding of species cross compatibility and reproductive systems. In this review, we examine interspecific crossing among peanut CWRs, chromosome pairing during meiosis, and pollen viability of Filial 1 hybrids. We analyze each parameter in relation to phylogenetic distances and current taxonomic and genomic classification, aiming to develop a cross‐compatibility scheme for the crop's secondary gene pool. Analysis of passport information and species names from research groups worldwide over the past 60 years revealed diverse frequencies of genome combinations (17) and species (26) used in hybridization assays. However, only eight species accounted for nearly 50% of successful hybridizations. In intragenomic hybrids, bivalent frequency ranged from 9.1 to 10, with pollen viability typically between 30% and 60%. Intergenomic hybrids exhibited bivalent frequency between 4.8 and 8.5, with pollen viability below 10%. Outliers were observed in the various parameters and hybrids were analyzed. Phylogenetic distance presented an inverse relationship with all variables; the correlation was low with crossing success while moderate with bivalent frequency and pollen viability. These findings suggest that differences in DNA sequences are not the sole determinants of interspecific cross‐compatibility, indicating the presence of pre‐ or postzygotic hybridization barriers. This organized information is crucial for establishing a framework to facilitate the rational selection of parents with desired traits and appropriate genome combinations, ultimately aiding in the development of new amphidiploids compatible with peanut varieties. [ABSTRACT FROM AUTHOR]

The invasive tetraploid Cirsium vulgare hybridizes with both Cirsium and Lophiolepis. Its conflicted position in molecular phylogenies, and its peculiar combination of morphological, anatomical, and genomic features that are alternatively shared with representatives of Cirsium or Lophiolepis, strongly suggest its intergeneric hybrid origin.Genetic relationships of C. vulgare (8 samples) with genus Lophiolepis (11 species) and other representatives of genus Cirsium (12 species) were evaluated using restriction site‐associated DNA sequencing (RADseq) and examined using analytical and imaging approaches, such as NeighborNet, Heatmap, and STRUCTURE, to identify nuclear genomes admixture. Estimation of the intensity of spontaneous hybridization within and between Cirsium and Lophiolepis was based on herbarium revisions and published data for all reported hybrids pertinent to taxa currently included in Cirsium or Lophiolepis.The genome of any examined Cirsium species is more similar to C. vulgare than to any Lophiolepis species, and vice versa. The nuclear genome of the tetraploid C. vulgare is composed of two equivalent parts, each attributable either to Lophiolepis or to Cirsium; the organellar RADseq data clustered C. vulgare with the genus Cirsium. Spontaneous hybridization between Cirsium and Lophiolepis is significantly less intensive than within these genera.Our analyses provide compelling evidence that the invasive species C. vulgare has an allotetraploid intergeneric origin, with the maternal parent from Cirsium and the paternal from Lophiolepis. For the purpose of delimiting monophyletic genera, we propose keeping Lophiolepis separate from Cirsium and segregating C. vulgare into the hybridogenous genus Ascalea. [ABSTRACT FROM AUTHOR]

Species' ranges are shifting rapidly with climate change, altering the composition of biological communities and interactions within and among species. Hybridization is among the species interactions that may change markedly with climate change, yet it is understudied relative to others. We used non‐invasive genetic detections to build a maximum entropy species distribution model and investigate the factors that delimit the present and future ranges of American marten (Martes americana) and Pacific marten (Martes caurina) in a contact zone in the Northern Rockies. We found that climate change will decrease the suitable habitat predicted for both species, as well as the amount of overlap in predicted suitable habitat between the species. Interestingly, predicted suitable habitat for Pacific marten extended further north in the study region than our genetic detections for the species, suggesting that biotic factors, such as interactions with American marten, may affect the realized range of this species. Our results suggest that future work investigating the interactions among biotic and abiotic factors that influence hybrid zone dynamics is important for predicting the futures of these two species in this area under climate change. Climate change is altering the distributions of species worldwide, including those of hybridizing species. We use species distribution models, built from non‐invasive genetic detections of marten species, to show that the distributions of American marten and Pacific marten in the Northern Rockies of the United States will be differentially affected by climate change. [ABSTRACT FROM AUTHOR]

Simple Summary: This review aimed to provide an exhaustive overview of the advancements in avian SCZ research. In the review, we summarize the latest research on trait variations in avian SCZs, including vocalization, plumage, beak, and migratory traits. In addition, we discuss the mechanisms of different types of avian SCZ movements. Finally, we outline several significant questions for future studies. A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating the on-going evolutionary processes of speciation and the establishment of reproductive isolation. Interspecific hybridization is widely present in avian populations, making them an ideal system for SCZ studies. This review exhaustively summarizes the variations in unique traits within avian SCZs (vocalization, plumage, beak, and migratory traits) and the various movement patterns of SCZs observed in previous publications. It also highlights several potential future research directions in the genomic era, such as the relationship between phenotypic and genomic differentiation in SCZs, the genomic basis of trait differentiation, SCZs shared by multiple species, and accurate predictive models for forecasting future movements under climate change and human disturbances. This review aims to provide a more comprehensive understanding of speciation processes and offers a theoretical foundation for species conservation. [ABSTRACT FROM AUTHOR]

The wild rats in the genus Rattus represent a group of murids characterized by rapid lineage diversification but limited morphological variation. Within this genus, there are several commensal species with high invasive capacity, such as Rattus norvegicus and R. rattus, which pose a global threat. Investigating the mechanisms behind their adaptive evolution is of utmost importance. In this study, we conducted morphological study and whole‐genome sequencing on Rattus species distributed in China and adjacent regions to gain insights into morphological differentiation, as well as genomic divergence and gene flow using assembled mitochondrion genome and high‐quality single nucleotide polymorphisms. Despite their morphological similarity and large overlap in morphospace, our analyses revealed significant genetic differentiation at the genomic level among Rattus species in China and adjacent regions. Specifically, intraspecific differentiation was observed in R. nitidus, R. norvegicus, and R. tanezumi, which may be related to habitat heterogeneity and geographic isolation. We hypothesize that as invasive rats expand their habitat, the diversification of ecological environments might lead to more environmentally adapted evolution and accelerated genetic differentiation. Furthermore, Dsuite and TreeMix analyses detected substantial introgression among different Rattus species, particularly evident between R. norvegicus and R. tanezumi. Strong gene flow signals suggest frequent hybridization events among these species, which may facilitate the acquisition of new environmental adaptability during their expansion into new territories. This study provides a preliminary analysis that serves as a foundation for a more comprehensive investigation into the rapid lineage diversification and adaptive introgression among Rattus species. [ABSTRACT FROM AUTHOR]

ABSTRACT Chemical pollutants and/or climate change have the potential to break down reproductive barriers between species and facilitate hybridization. Hybrid zones may arise in response to environmental gradients and secondary contact between formerly allopatric populations, or due to the introduction of non‐native species. In freshwater ecosystems, field observations indicate that changes in water quality and chemistry, due to pollution and climate change, are correlated with an increased frequency of hybridization. Physical and chemical disturbances of water quality can alter the sensory environment, thereby affecting chemical and visual communication among fish. Moreover, multiple chemical compounds (e.g. pharmaceuticals, metals, pesticides, and industrial contaminants) may impair fish physiology, potentially affecting phenotypic traits relevant for mate selection (e.g. pheromone production, courtship, and coloration). Although warming waters have led to documented range shifts, and chemical pollution is ubiquitous in freshwater ecosystems, few studies have tested hypotheses about how these stressors may facilitate hybridization and what this means for biodiversity and species conservation. Through a systematic literature review across disciplines (i.e. ecotoxicology and evolutionary biology), we evaluate the biological interactions, toxic mechanisms, and roles of physical and chemical environmental stressors (i.e. chemical pollution and climate change) in disrupting mate preferences and inducing interspecific hybridization in freshwater fish. Our study indicates that climate change‐driven changes in water quality and chemical pollution may impact visual and chemical communication crucial for mate choice and thus could facilitate hybridization among fishes in freshwater ecosystems. To inform future studies and conservation management, we emphasize the importance of further research to identify the chemical and physical stressors affecting mate choice, understand the mechanisms behind these interactions, determine the concentrations at which they occur, and assess their impact on individuals, populations, species, and biological diversity in the Anthropocene. [ABSTRACT FROM AUTHOR]

Improving the understanding of the causes and effects of anthropogenic hybridization is fundamental to ensure species conservation, particularly in the case of hybridization between wild species and their domestic relatives. Knowledge is missing for many species also because of a lack of appropriate tools for hybrid identification. Here, coupling genotype and phenotype analysis, we carried out an extensive investigation of ongoing hybridization in Alpine ibex Capra ibex, a mountain ungulate of conservation concern from a genetic perspective. By genotyping 63 diagnostic and 465 neutral SNPs, 20 suspected hybrids and 126 Alpine ibex without suspicious phenotype, representing 8 populations across a major part of the species distribution, we found evidence for ongoing hybridization between Alpine ibex and domestic goat. We identified different levels of hybridization including backcrosses into both Alpine ibex and domestic goat. Our results suggest a lack of reproductive barriers between the two species and good survival and reproductive success of the hybrids. Hybridization was locally intense, like a hybrid swarm, but not spread across the rest of the species distribution. Most of the hybrids were discovered in two locations in the north‐west of Italy, while random sampling of individuals from different areas did not provide evidence of recent hybridization. Our method, based on amplicon sequencing of 63 diagnostic SNPs specifically developed for this purpose, allowed us to identify hybrids and backcrosses up to the fourth to fifth generations and was suitable for genetic samples of different quality, although with varying levels of certainty regarding the exact number of generations passed since hybridization. Based on the paired analysis of genotype and phenotype, we provide guidelines for the first identification of hybrids in the field and suggest a procedure for the reliable identification of hybrids. [ABSTRACT FROM AUTHOR]

The role of hybridization as a formative process in evolution has received much attention in the past few decades. A particularly fascinating outcome of hybrid speciation is the formation of asexual hybrid species. The Amazon molly (Poecilia formosa) is such a hybrid and originated from a P. mexicana mother and a P. latipinna father. Consequently, a heterospecific mating must have occurred leading to the Amazon molly, indicating a breakdown of any potential prezygotic isolation between parental species. Here we studied the female mate preferences of extant P. mexicana and P. latipinna from several populations using standard binary choice tests with males of both sexual species that were matched for size. Poecilia mexicana and P. latipinna can be crossed in the lab, however, the offspring are not asexual, but sexual F1s. In our study, we generated F1s and tested their mating preferences with sexual males of both P. mexicana and P. latipinna against F1 males. Overall, our results show that in extant P. mexicana and P. latipinna no female preference for conspecific males was detectable. Consequently, heterospecific matings are possible and not hindered by any apparent behavioral prezygotic isolation. If female preferences in these species were comparable around the time the Amazon molly originated as a hybrid species ca. 100,000 years ago, matings leading to hybrids would be very likely. F1 females also have no discernable mating preferences for either sexual males or F1 males. Such lack of prezygotic behavioral isolation could potentially lead to F2 individuals, backcrosses, and introgression. [ABSTRACT FROM AUTHOR]

Hibisceae subtribe Trionum is the largest clade within Hibiscus s.l. and contains genera with a wide range of growth forms: herbaceous (Abelmoschus), shrubs (Malvaviscus), trees (Wercklea), and exceptionally lianas. The rare and localized Thepparatia species are unique in that they combine a lianescent habit and trioecy. Several problems have delayed the study of Hibisceae classification including low genetic variability, lack of synapomorphic morphological characters, transoceanic dispersal events, and allopolyploidy. Here, we present a comprehensive phylogenomic hypothesis of Thepparatia based on analyses of the maternally inherited chloroplast and biparentally inherited nuclear ribosomal cistron sequences, and compare these results with its speciation, karyology, and breeding system. Chloroplast genomes in subtribe Trionum were highly conserved except in Abelmoschus where four additional genes were duplicated. Recent diploid interspecific hybridization is suggested in Thepparatia sipsongpannaensis between T. fragrans and T. scandens during the Pleistocene, around 640 000 years ago. Our observations also indicate Thepparatia have a trioecious breeding system that combined with a unique habit, and a highly localized distribution pattern, have created cross-pollination barriers and ecological specialization. This suggests hybridization events are rare but evolutionary significant in subtribe Trionum. Finally, our study supports important nomenclature changes: the synonymization of Hibiscus austroyunnanensis with Thepparatia fragrans and the publication of a new species, Thepparatia sipsongpannaensis. [ABSTRACT FROM AUTHOR]

Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger "instantaneous" speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage, but how often this scenario occurs is unclear. Here, we investigate the evolutionary history of the wild allotetraploid Mimulus sookensis , which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin. One M. sookensis subgenome is clearly derived from the selfer Mimulus nasutus , which organellar variation suggests is the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both Mimulus decorus and M. guttatus , two outcrossing diploids with geographic ranges that overlap broadly with M. sookensis. This study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploid's predisposition to self-fertilize. [ABSTRACT FROM AUTHOR]

SUMMARY: Aegilops longissima and Ae. sharonensis, being classified into the Sitopsis section of genus Aegilops, are distinct species both taxonomically and ecologically. Nevertheless, earlier observations indicate that the two species are not reproductively isolated to full extent and can inter‐bred upon secondary contact. However, the genomic underpinnings of the morpho‐ecological differentiation between the two foci species remained unexplored. Here, we resequenced 31 representative accessions of the two species and conducted in‐depth comparative genomic analyses. We demonstrate recurrent and ongoing natural hybridizations between Ae. longissima and Ae. sharonensis, and depict features of genome composition of the resultant hybrids at both individual and population levels. We also delineate genomic regions and candidate genes potentially underpinning the differential morphological and edaphic adaptations of the two species. Intriguingly, a binary morphology was observed in the hybrids, suggesting existence of highly diverged genomic regions that remain uneroded by the admixtures. Together, our results provide new insights into the molding effects of interspecific hybridization on genome composition and mechanisms preventing merge of the two species. Significance Statement: We demonstrate recurrent and ongoing natural hybridizations between Aegilops longissima and Ae. sharonensis, and depict features of genome composition of the resultant hybrids at both individual and population levels. [ABSTRACT FROM AUTHOR]

Summary: Bursaphelenchus xylophilus is the causative agent of pine wilt disease and is indigenous to North America. It has been introduced into Japan where the non-pathogenic close relative, B. mucronatus , is widely distributed. Both nematode species have similar life cycles with vectors of cerambycid beetles of the genus Monochamus. When interspecific hybrids are backcrossed with B. xylophilus nematodes repeatedly, a small proportion of B. mucronatus genes is infused into the B. xylophilus genome (introgression) and may lead to adaptation to locally harsh environments. Though cool temperatures had inhibited the development of pine wilt disease, B. xylophilus started expanding the range to cool-summer areas after suspending its range expansion for 10 years in Japan. To consider if the range expansion is related to the introgression hybridisation between the two Bursaphelenchus species, some traits of newly and already formed hybrid-derived populations were compared between three temperature conditions of 16, 20 and 25°C. Formation of F1 hybrids was not affected by temperature. There was no difference in the time required for hybrid formation and for population establishment at 16°C between an interspecific crossing and two intraspecific crossings of B. xylophilus. Using three hybrid-derived populations reared over multiple generations at 25°C, there was no difference in the early rate of population growth between each of two hybrid-derived populations and its parental-lineage population of B. xylophilus at 16°C. Thus, the results did not reject a hypothesis that introgression hybridisation may have enhanced the fitness components such as pathogenicity of B. xylophilus populations at cool temperatures. [ABSTRACT FROM AUTHOR]

Fluorescence in situ hybridization (FISH) with two different probes, the canonical insect telomeric sequence (TTAGG)n and the sequence (TTAGGGATGG)n, was performed on meiotic chromosomes of two members of the true bug family Cimicidae (Cimicomorpha), the common bed bug Cimex lectularius Linnaeus, 1758 and the tropical bed bug C. hemipterus (Fabricius, 1803), whose telomeric motifs were not known. In both species, there were no hybridization signals with the first probe, but strong signals at chromosomal ends were observed with the second probe, indicating the presence of a telomeric motif (TTAGGGATGG)n. This study represents the first FISH confirmation of the presence of a non-canonical telomeric motif not only for the infraorder Cimicomorpha but also for the suborder Heteroptera (Hemiptera) as a whole. The present finding is of key significance for unraveling the evolutionary shifts in the telomeric sequences in this suborder. [ABSTRACT FROM AUTHOR]

Premise: Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra‐ and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape. Methods: By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework. Results: We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other. Conclusions: The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages. [ABSTRACT FROM AUTHOR]

Objective: Hybridization between native and nonnative fishes represents a global threat to biodiversity. Understanding how hybridization changes in response to management actions is critical to evaluating the efficacy of conservation efforts. Methods: We quantified changes in levels of hybridization between Yellowstone Cutthroat Trout Oncorhynchus virginalis bouvieri and Rainbow Trout Oncorhynchus mykiss in the South Fork Snake River watershed, where a multipronged approach has been implemented to protect the evolutionary distinctiveness of one of the last remaining large‐river populations of Yellowstone Cutthroat Trout. Result: Over a 20‐year period, we observed an increase in the number of sample reaches without hybrids in the South Fork Snake River watershed; however, contrasting patterns were noted in main‐stem and tributary reaches. Through time, hybrid abundance increased at main‐stem reaches of the South Fork Snake River below Palisades Dam but decreased in tributaries. Efforts to reduce hybridization in spawning tributaries, including both suppression and selective passage weirs, were effective at preventing the expansion of hybridization in resident and migratory populations. Multimodel inference was used to understand factors affecting levels of hybridization, and year, sampling reach, and the interaction thereof was identified as the best‐fit model but explained only a small percentage of the overall variation, suggesting that other factors not captured in our model were driving patterns in hybridization. Conclusion: Changes in hybridization in the South Fork Snake River watershed are likely the result of multiple processes, namely management actions to reduce Rainbow Trout and hybrids in tributaries, as well as demographic changes in Rainbow Trout in the main‐stem river below Palisades Dam. Our results suggest that Yellowstone Cutthroat Trout populations in the South Fork Snake River watershed have not experienced widespread interspecific hybridization with Rainbow Trout but that proactive management will be necessary to ensure long‐term conservation. Impact statementOver the past 20 years, hybridization between introduced Rainbow Trout and native Yellowstone Cutthroat Trout in the South Fork Snake River watershed has declined in spawning tributaries because of management actions but increased in select main‐stem river reaches because of Rainbow Trout population growth. [ABSTRACT FROM AUTHOR]

Most wild rose species in the Netherlands belong to Rosa section Caninae (dogroses), with Rosa arvensis (section Synstylae) and Rosa spinosissima (section Pimpinellifoliae) as other indigenous species. All species are rare, often found in small populations or as scattered individuals, except for Rosa canina and Rosa corymbifera. Conservation strategies have been developed for these roses, with a focus on ex situ methods, including clonal archives and seed orchards, using vegetative propagation from the original shrubs. Efficient collection management aims at preservation of maximum genetic diversity with a minimum of duplicated genotypes. However, dogrose taxonomy is complex because of species hybridization, different ploidy levels, and their matroclinal inheritance due to Canina meiosis. They can also reproduce vegetatively through root suckers. In order to assess the genetic structure and the levels of genetic diversity and clonality within and among the wild rose populations in the Netherlands, we genotyped individuals in wild populations and accessions in the ex situ gene bank with 10 highly polymorphic microsatellite markers. The analysis revealed 337 distinct multilocus genotypes (MLGs) from 511 sampled individuals, with some MLGs shared across different species and sites. The genetic structure analysis showed distinct clusters separating non-dogrose species from the Caninae section. Geographic distribution of MLGs indicated both local and widespread occurrences. Redundancy analysis identified 152 distinct MLGs from 244 gene bank accessions, suggesting a 38% redundancy rate. Core collections were optimized to retain genetic diversity with minimal redundancy, selecting subsets of 20–40 individuals from different species groups. The study highlights the value of genetic characterization in guiding sampling strategies for dogroses. We propose a two-step approach that may be used to reveal clonality and redundancy and to optimize core collections of species that combine sexual and vegetative reproduction, to maximize genetic capture in ex situ gene banks. [ABSTRACT FROM AUTHOR]

Fertilization barriers often hinder the introgression of desired traits of interest in interspecific hybridization. In present study, the fertilization barriers in interspecific crosses of Cucurbita moschata (Punjab Nawab and Punjab Sardar) and Cucurbita pepo (PMK-1) were investigated. The results revealed that pollen grains were viable and stigmas were receptive at the time of pollination in all the genotypes. The maximum pollen germination (%) was observed in Punjab Nawab, while maximum pollen size, pollen tube length and style length were recorded in Punjab Sardar. Additionally, fluorescence microscopic images showed that the shorter pollen tubes of PMK-1 did not grow enough in the longer style of Punjab Sardar, hence the interspecific cross of Punjab Sardar × PMK-1 was incompatible. While in the reciprocal cross (PMK-1 × Punjab Sardar), formation of callose plugs in the pollen tubes of Punjab Sardar and its slow growth might had contributed to the failure of fertilization. However, in the interspecific cross of Punjab Nawab × PMK-1 and vice-versa, the pollen grains successfully germinated on stigma and pollen tubes reached the style but embryo was not able to attain a particular shape, therefore, the cross was partially incompatible. The fruit setting (%), fruit diameter, fruit weight, seed number, seed weight and seed germination (%) was lesser in interspecific crosses as compared to self-pollinated genotypes. Furthermore, cluster analysis revealed that partially compatible and incompatible crosses are present in different clusters and partially compatible cross showed strong positive correlation with fruit characters. Collectively, pre-and post-fertilization barriers hampered the interspecific hybridization between C. pepo and C. moschata genotypes. These findings would help the breeders to overcome such barriers and introgress the hull-less seed trait of C. pepo and disease resistant trait of C. moschata. [ABSTRACT FROM AUTHOR]

The Brassicaceae family is distinguished by its inclusion of high-value crops such as cabbage, broccoli, mustard, and wasabi, all noted for their glucosinolates. In this family, many polyploidy species are distributed and shaped by numerous whole-genome duplications, independent genome doublings, and hybridization events. The evolutionary trajectory of the family is marked by enhanced diversification and lineage splitting after paleo- and meso-polyploidization, with discernible remnants of whole-genome duplications within their genomes. The recent neopolyploidization events notably increased the proportion of polyploid species within the family. Although sequencing efforts for the Brassicaceae genome have been robust, accurately distinguishing sub-genomes remains a significant challenge, frequently complicating the assembly process. Assembly strategies include comparative analyses with ancestral species and examining k-mers, long terminal repeat retrotransposons, and pollen sequencing. This review comprehensively explores the unique genomic characteristics of the Brassicaceae family, with a particular emphasis on polyploidization events and the latest strategies for sequencing and assembly. This review will significantly improve our understanding of polyploidy in the Brassicaceae family and assist in future genome assembly methods. [ABSTRACT FROM AUTHOR]

Plant-pollinator relationships drive floral diversity. Among many floral signals, floral scent attracts and ensures efficient pollination, like benzyl acetone and its derivatives are important for hawkmoth species to detect flowers. Nicotiana is a diverse genus in terms of floral phenotypes. Its evolution was driven by the close relationship with pollinators through floral specialization and hybridization, causing the emergence of new species. Nicotiana has a wide variety of floral shapes and colors. Hybridization is prevalent in the group, resulting in transgressive phenotypes impacting pollination-related visual traits. This study investigated the diversity of floral Volatile Organic Compounds (VOCs) of Nicotiana species and discussed the data according to pollinator functional groups and the known phylogenetic relationships of the species. A bibliographic review was carried out, including 30 years of floral volatile emissions studies. The results of 18 studies investigating floral volatiles in 19 species of Nicotiana were revised and organized by temporal emissions, day and night emissions. We retrieved information concerning methodology, volatile compounds, day/night emissions, and pollinator functional groups for each study and species. In total, 179 compounds were found, including mono- and sesquiterpenoids, nitrogenous compounds, and benzenoids. Most allopolyploid species lack floral emissions data, and total temporal emissions in Nicotiana are still underrepresented. The results suggest that night-pollinated species of Nicotiana have high emission blends' similarity to each other, compound-wise and class-wise. However, phylogeny still plays an important role in scent emission for species with different pollinators functional groups, considering the known phylogenetic relationship in the genus. Species known to be closely related by current phylogeny, like N. forgetiana and N. alata, share similar blends even though their pollinator functional groups are entirely different and opposite, suggesting a phylogenetic relationship in this phenotype and/or other processes, such as hybridization. [ABSTRACT FROM AUTHOR]

Climatic variation along the elevation gradient promotes the natural parapatric occurrence of the European hare (Lepus europaeus) and Alpine mountain hare (Lepus timidus varronis) in the Alps. Recent data indicate a displacement of mountain hares caused by competition with the European hare. Competitive exclusion might take place at a fine spatial scale and hybrids may sharpen competition. Genetic non-invasive sampling (gNIS) demonstrates to be effective to retrieve information from wild animals. However, based on the accuracy of the differing genetic analysis methods, the selection of the method might decisively influence results. To examine habitat preferences of Alpine mountain hares, European hares and their hybrids with particular interest in the influence of the accuracy of the genetic analysis method on the results, we performed gNIS in Grisons (Switzerland) for four years and compared habitat associations of the genotyped samples. We recorded 137 individuals (i.e., 35 hybrids, 49 European hares, 53 Alpine mountain hares). Combined nuclear and mitochondrial DNA analysis including individual identification revealed to be the most accurate indirect method for the study of habitat preferences of hares. Alpine mountain hares had a narrow habitat breadth and used little habitat diversity. Hybrids showed great similarities in their habitat preferences to European hares. Hybrids might increase the competition in favour of European hares and the displacement of Alpine mountain hares, since they show similar patterns of habitat use to European hares. Ongoing climate change potentiate the niche overlap between species, increasing the risk of Alpine hare decline due to hybridisation and displacement. [ABSTRACT FROM AUTHOR]

The classification and identification of species in Populus has remained a formidable challenge due to widespread interspecies hybridization. The complete chloroplast genome of Populus maximowiczii was obtained by Illumina high-throughput sequencing technology, with a typical quadripartite structure and 37.0% GC content. The chloroplast genome of P. maximowiczii was 156,892 in length, including a large single-copy region (LSC: 84,988 bp), a small single-copy region (SSC: 16,630 bp), and a pair of inverted repeats (IRs: each 27,637 bp in length). A total of 131 genes were annotated, including 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The phylogenetic analysis indicated that 43 species belonging to Populus were classified into monophyly, with P. cathayana being the closest relatives to P. maximowiczii. In conclusion, this study provides valuable insights into understanding the phylogeny of Populus. [ABSTRACT FROM AUTHOR]

Introduction: Natural hybridization is common and plays a crucial role in driving biodiversity in nature. Despite its significance, the understanding of hybridization in ferns remains inadequate. Therefore, it is imperative to study fern hybridization to gain a more comprehensive understanding of fern biodiversity. Our study delves into the role of hybridization in shaping fern species, employing Microlepia matthewii as a case study to investigate its origins of hybridization. Methods: We performed double digest Genotyping-by-sequencing (dd-GBS) on M. matthewii and its potential parent species, identifying nuclear and chloroplast SNPs. Initially, nuclear SNPs were employed to construct the three cluster analysis: phylogenetic tree, principal component analysis, and population structure analysis. Subsequently, to confirm whether the observed genetic mixture pattern resulted from hybridization, we utilized two methods: ABBABABA statistical values in the D-suite program and gene frequency covariance in the Treemix software to detect gene flow. Finally, we employed chloroplast SNPs to construct a phylogenetic tree, tracing the maternal origin. Results and discussion: The analysis of the nuclear SNP cluster revealed that M. matthewii possesses a genetic composition that is a combination of M. hancei and M. calvescens. Furthermore, the analysis provided strong evidence of significant gene flow signatures from the parental species to the hybrid, as indicated by the two gene flow analyses. The samples of M. matthewii cluster separately with M. hancei or M. calvescens on the chloroplast systematic tree. However, the parentage ratio significantly differs from 1:1, suggesting that M. matthewii is a bidirectional and asymmetrical hybrid offspring of M. hancei and M. calvescens. [ABSTRACT FROM AUTHOR]