Hybridization and speciation

Fluctuating selection in a monkeyflower hybrid zone

While hybridization was viewed as a hindrance to adaptation and speciation by early evolutionary biologists, recent studies have demonstrated the importance of hybridization in facilitating evolutionary processes. However, it is still not well-known what role spatial and temporal variation in natural selection play in the maintenance of naturally occurring hybrid zones. To identify whether hybridization is adaptive between two closely related monkeyflower species, Mimulus guttatus and Mimulus laciniatus, we performed repeated reciprocal transplants between natural hybrid and pure species' populations. We planted parental genotypes along with multiple experimental hybrid generations in a dry (2021) and extremely wet (2023) year in the Sierra Nevada, CA. By taking fine-scale environmental measurements, we found that the environment of the hybrid zone is more similar to M. laciniatus's seasonally dry rocky outcrop habitat than M. guttatus's moist meadows. In our transplants hybridization does not appear to be maintained by a consistent fitness advantage of hybrids over parental species in hybrid zones, but rather a lack of strong selection against hybrids. We also found higher fitness of the drought-adapted species, M. laciniatus, than M. guttatus in both species' habitats, as well as phenotypic selection for M. laciniatus-like traits in the hybrid habitat in the dry year of our experiment. These findings suggest that in this system, hybridization might function to introduce drought-adapted traits and genes from M. laciniatus into M. guttatus, specifically in years with limited soil moisture. However, we also find evidence of genetic incompatibilities in second generation hybrids in the wetter year, which may balance a selective advantage of M. laciniatus introgression. Therefore, we find that hybridization in this system is both potentially adaptive and costly, and that the interaction of positive and negative selection likely determines patterns of gene flow between these Mimulus species.

Postmating prezygotic isolation occurs at two levels of divergence in Drosophila recens and D. subquinaria

Identifying the presence and strength of reproductive isolating barriers is necessary to understand how species form and then remain distinct in the face of ongoing gene flow. Here, we study reproductive isolation at two stages of the speciation process in the closely related mushroom-feeding species Drosophila recens and Drosophila subquinaria. We assess 3 isolating barriers that occur after mating, including the number of eggs laid, the proportion of eggs laid that hatched, and the number of adult offspring from a single mating. First, all 3 reproductive barriers are present between D. recens females and D. subquinaria males, which are at the late stages of speciation but still produce fertile daughters through which gene flow can occur. There is no evidence for geographic variation in any of these traits, concurrent with patterns of behavioural isolation. Second, all 3 of these reproductive barriers are strong between geographically distant conspecific populations of D. subquinaria, which are in the early stages of speciation and show genetic differentiation and asymmetric behavioural discrimination. The reduction in the number of eggs laid is asymmetric, consistent with patterns in behavioural isolation, and suggests the evolution of postmating prezygotic isolation due to cascade reinforcement against mating with D. recens. In summary, not only may postmating prezygotic reproductive barriers help maintain isolation between D. recens and D. subquinaria, but they may also drive the earliest stages of isolation within D. subquinaria.

In situ diversification and adaptive introgression in Taiwanese Scutellaria

Island habitats provide unique opportunities to study speciation. Recent work indicates that both ex situ origination and in situ speciation contribute to island species diversity. However, clear evidence of local adaptation of endemic plant species on islands requires in-depth studies, which are scarce. This study underscores the importance of local adaptation in maintaining species boundaries by examining how adaptive introgression, hybridization, and local adaptation contribute to genetic variation in island species. Multilocus genome scanning of 51 nuclear genes was used to investigate the evolutionary relationships of the Scutellaria species complex on Taiwan Island and assess the role of in situ diversification in generating high endemism and genetic diversity. Interspecies introgressions were detected by phylogenetic networks and ABBA-BABA-based analysis, suggesting ongoing or recent speciation processes. Coalescent-based simulation identified hybrid speciation in Scutellaria taiwanensis and Scutellaria hsiehii, with evidence of hybridization between more than two parental species. Genotype-environment association studies revealed that the influence of climate, particularly precipitation- and temperature-related factors, contributed to adaptive genetic divergence between species. Additionally, adaptive introgression related to environmental pressures that may have facilitated the colonization of new island habitats were identified. This research illustrates how hybridization, introgression, and adaptation shaped the evolutionary histories and divergence of this island-endemic plant species complex and sheds light on the multifaceted mechanisms of speciation on semi-isolated islands.

De novo transcriptome assembly of the Mediterranean sea-rock pool mosquitoes Aedes mariae and Aedes zammitii

Understanding the genomic consequences of hybridization is an essential research focus in global change biology. Species adapted to rapidly changing environments can offer valuable, yet largely underexplored insights in this context. Here, we present the first de novo transcriptomes of the sea-rock pools mosquitoes Aedes mariae and Aedes zammitii, two species adapted to highly variable habitats. Using RNA-seq data obtained from larval stages, we assembled and annotated 95,059,578 reads for Ae. mariae and 101,050,236 reads for Ae. zammitii, detecting 49,352 transcripts with N50 of 2,615 for the former and 43,461 transcripts with N50 of 2,570 for the latter. Validation by BUSCO confirmed the high quality of our resources. Homology alignments of predicted ORFs showed that 21,842 sequences from Ae. mariae and 21,944 sequences from Ae. zammitii mapped to the Nr, SwissProt, and TrEMBL databases, while 19,208 and 19,393 predicted ORFs, respectively, were functionally annotated using the COG and KEGG databases. These high-quality transcriptomes will provide valuable resources to investigate the role of hybridization in species adaptation to changing environments.

Genomic Rewilding of Domestic Animals: The Role of Hybridization and Selection in Wolfdog Breeds

Background/Objectives: The domestication of the grey wolf (Canis lupus) and subsequent creation of modern dog breeds have significantly shaped the genetic landscape of domestic canines. This study investigates the genomic effects of hybridization and breeding management practices in two hybrid wolfdog breeds: the Czechoslovakian Wolfdog (CSW) and the Saarloos Wolfdog (SAW). Methods: We analyzed the genomes of 46 CSWs and 20 SAWs, comparing them to 12 German Shepherds (GSHs) and 20 wolves (WLFs), which served as their ancestral populations approximately 70-90 years ago. Results: Our findings highlight that hybridization can increase genetic variability and mitigate the effects of inbreeding, as evidenced by the observed heterozygosity levels in both wolfdog breeds. However, the SAW genome revealed a higher coefficient of inbreeding and longer runs of homozygosity compared to the CSW, reflecting significant inbreeding during its development. Discriminant Analysis of Principal Components and fixation index analyses demonstrate that the CSW exhibits closer genetic proximity to the GSH than the SAW, likely due to differences in the numbers of GSHs used during their creation. Maximum likelihood clustering further confirmed clear genetic differentiation between these hybrid breeds and their respective ancestors, while shared ancestral polymorphism was detectable in all populations. Conclusions: These results highlight the role of controlled hybridization with captive-bred wolves and peculiar breeding strategies in shaping the genetic structure of wolfdog breeds. To ensure the long-term genetic health of these breeds, it is recommended to promote adequate and sustainable breeding practices to maintain genetic diversity, minimize inbreeding, and incorporate the careful selection of unrelated individuals from diverse lineages, while avoiding additional, uncontrolled crossings with wild wolves.

Emergence of fungal hybrids - Potential threat to humans

Fungal hybrids arise through the interbreeding of distinct species. This hybridization process fosters increased genetic diversity and the emergence of new traits. Mechanisms driving hybridization include the loss of heterozygosity, copy number variations, and horizontal gene transfer. Genetic mating barriers, changes in ploidy, chromosomal instability, and genomic diversity influence hybridization. These factors directly impact the fitness and adaptation of hybrid offspring. Epigenetic factors, including DNA methylation, histone modifications, non-coding RNAs, and chromatin remodelling, play a role in post-mating isolation in hybrids. In addition to all these mechanisms, successful hybridization in fungi is ensured by cellular mechanisms like mitochondrial inheritance, transposable elements, and other genome conversion mechanisms. These mechanisms support hybrid life and enhance the virulence and pathogenicity of fungal hybrids, which provoke diseases in host organisms. Recent advancements in sequencing have uncovered fungal hybrids in pathogens like Aspergillus, Candida, and Cryptococcus. Examples of these hybrids, such as Aspergillus latus, Candida metapsilosis, and Cryptococcus neoformans, induce severe human infections. Identifying fungal hybrids is challenging due to their altered genome traits. ITS sequencing has emerged as a promising method for diagnosing these hybrids. To prevent the emergence of novel hybrid fungal pathogens, it is crucial to develop effective diagnostic techniques and closely monitor pathogenic fungal populations for signs of hybridization. This comprehensive review delves into various facts about fungal hybridization, including its causes, genetic outcomes, barriers, diagnostic strategies, and examples of emerging fungal hybrids. The review emphasises the potential threat that fungal hybrids pose to human health and highlights their clinical significance.

Phenotypic homogenization and potential fitness constraints following non-native introgression in an endemic sportfish

Introgressive hybridization may lead to contrasting evolutionary outcomes that are difficult to predict since they depend on the fitness effects of endogenous genomic interactions and environmental factors. Conservation of endemic biodiversity may be more effective with require direct measurement of introgressed ancestry and fitness in wild populations, especially for keystone taxa at risk of hybridization following species introductions. We assessed the relationship of non-native ancestry with growth and body condition in the basin-restricted Neosho Bass (Micropterus velox; NB), focussing on two streams in the NB native range that are admixed extensively with non-native Smallmouth Bass (M. dolomieu; SMB). We quantified the genetic composition of 116 fish from Big Sugar Creek (N = 46) and Elk River (N = 70) at 14 microsatellite loci. Using back-calculated total length-at-age estimated from sagittal otoliths, we assessed whether genetic ancestry explained variation in von Bertalanffy growth model parameters, accounting for sex and stream effects. We then assessed the relationship between ancestry and body condition. We found no differences in growth parameters by sex, stream, or ancestry, suggesting phenotypic homogenization which could be mediated by selection on body size. We found a negative correlation between SMB ancestry and condition, including lower condition in Big Sugar Creek, possibly reflecting a trade-off between maximum length and condition with respect to overall fitness. We show that ongoing non-native introgression, which may be augmented by anthropogenic SMB introductions, may attenuate evolutionary differentiation between species and directly influence fitness, possibly having critical implications for long-term persistence and management of adaptive potential in a popular and ecologically important endemic sportfish.

The phenotype, sex ratio and gonadal development in triploid hybrids of rainbow trout (Oncorhynchus mykiss) ♀ and brook trout (Salvelinus fontinalis) ♂

The phenotype, genetic sex ratio and gonadal development characteristics were evaluated in randomly selected juvenile (15 months old), sub-adult (22 months old) and adult (30 months old) triploid hybrids of rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis). The examined fish originated from the family produced by application High Hydrostatic Pressure (HHP) shock (9500 psi for 5 minutes, applied 35 minutes post-fertilization at 10°C) to eggs stripped from five rainbow trout females and fertilized with sperm of two brook trout males. After hatching, all fish were reared under the same conditions for three years. The ploidy level and hybrid status of the fish were confirmed through cytogenetic analysis and DNA genotyping. Three distinct phenotypes; trout-like (Tr-l) phenotype, salmon-like (Sa-l) phenotype and intermediate (Tr/Sa-l) phenotype, with the following frequencies: f= 50.8 %, f= 31.7 % and f= 17.5 %, respectively, were observed among the sampled specimens. Genetic males exclusively detected among individuals with Tr-l phenotype developed macroscopically visible and histologically functional testes in their second year of life, representing the lowest value for the aquaculture production. A comparable proportion of males and females was recorded among individuals with Sa-l and Tr/Sa-l phenotypes. Males with these phenotypes developed macroscopically distinguishable and histologically functional testes in their third year of life. In the genetic males, underdeveloped intersex or completely reduced gonads were recorded. This study revealed that individuals with Sa-l phenotype represent the greatest value for commercial production because of their unique appearance and complete sterility (females) or delayed maturation observed only after reaching the market size (males).

Genomic data support reticulate evolution in whiptail lizards from the Brazilian Caatinga

Species relationships have traditionally been represented by phylogenetic trees, but not all evolutionary histories fit into bifurcating divergence models. Introgressive hybridization challenges this assumption by sometimes [or maybe often] leading to mitochondrial introgression, wherein one species' mitochondrial genome is entirely replaced by another's (mitochondrial capture). Such processes result in mitonuclear discrepancies, complicating species delimitation and phylogenetic inference. In our study, we used ultraconserved elements (UCE) and mitogenomic data to investigate the evolutionary history of the Ameivula ocellifera complex, a group of South American whiptail lizards widely distributed in semiarid environments of the Caatinga Domain in Brazil. We examine mitonuclear discordances, assessing reticulate evolution, evaluating species limits, and testing for adaptive mitochondrial capture that could explain higher introgression in the mitochondrial genome compared to nuclear DNA. Our findings support the occurrence of an ancient reticulation event during the diversification of these lizards, driven by introgressive hybridization, leading to mitochondrial capture, and explaining mitonuclear discrepancies. Overall, we did not find clear evidence of positive selection across mitochondrial protein-coding genes suggesting adaptive mitochondrial capture of individuals with introgressed mtDNA. Thus, the genetic diversification and mitogenome evolution could be neutral, with selection against hybridization in the autosomal loci only, or even mediated by mitonuclear incompatibilities. Analyses of mtDNA genomes alongside network and species delimitation methods were crucial for identifying and validating individuals with introgressed mtDNA as a distinct species, demonstrating the potential of genome sampling, and using innovative analytical techniques for elucidating speciation processes in the presence of introgressive hybridization.

Introgression of the Gamete Recognition Molecule, Bindin, in the Sea Urchin Diadema

Hybridization is important in evolution, because it is a necessary (though not sufficient) step in the introgression of potentially adaptive variation between species. Bindin is a gamete recognition protein in echinoids and asteroids, capable of blocking cross-fertilization between species to varying degrees. Four species of the sea urchin genus Diadema are broadly sympatric in the Indo-Pacific: D. paucispinum, D. savignyi, D. clarki, and D. setosum. Data from three published studies, one of identification of hybrids through allozymes, one of the phylogeography of mitochondrial DNA, and one of the phylogeny of bindin, were combined to assess the degree of bindin introgression between these four species. I analyzed sequences of the ATPase 8 and ATPase 6 mitochondrial genes and of bindin, sampled throughout the species ranges, with an isolation-migration algorithm, IMa3. IMa3 uses a coalescent approach to produce Bayesian estimates of effective population sizes and gene flow between populations. The results showed that bindin alleles coalesce completely within the species bounds of D. clarki and of D. setosum. The sister species D. paucispinum and D. savignyi, however, were estimated as having exchanged a bindin allele at an average of every one to two-and-a-half generations since they speciated from each other. As the allozyme study detected nine hybrids between three of these species in Okinawa (most of them between D. setosum and D. savignyi) in a single sample, hybrids between these species are produced, but bindin does not introgress. Therefore, bindin must not be efficient in blocking heterospecific fertilizations. Complete, or almost complete, reproductive isolation between species of Diadema must result from low hybrid fitness.

The Role of Hybridization in Species Formation and Persistence

Hybridization, or interbreeding between different taxa, was traditionally considered to be rare and to have a largely detrimental impact on biodiversity, sometimes leading to the breakdown of reproductive isolation and even to the reversal of speciation. However, modern genomic and analytical methods have shown that hybridization is common in some of the most diverse clades across the tree of life, sometimes leading to rapid increase of phenotypic variability, to introgression of adaptive alleles, to the formation of hybrid species, and even to entire species radiations. In this review, we identify consensus among diverse research programs to show how the field has progressed. Hybridization is a multifaceted evolutionary process that can strongly influence species formation and facilitate adaptation and persistence of species in a rapidly changing world. Progress on testing this hypothesis will require cooperation among different subdisciplines.

Behavioural underpinning of mito-nuclear discordances: insights from fire salamanders

Mito-nuclear discordances across secondary contact zones have been described in a wide range of organisms. They consist of a spatial mismatch between nuclear and mitochondrial genomes in terms of location and extension of the contact zone between distinct evolutionary lineages. Despite the evolutionary and biogeographic causes of mito-nuclear discordances having been extensively investigated, we still lack a clear understanding of their phenotypic underpinnings. Here, we test the hypothesis that mtDNA variation could be associated with behavioural variation and that such association could contribute to asymmetric mitochondrial introgression across a secondary contact zone. We analysed behavioural variation across the mtDNA secondary contact zone of the fire salamander Salamandra salamandra in central Italy, which is displaced 600 km from the nuclear contact zone. We found distinct behavioural profiles in the two mitotypes co-occurring in the contact zone. The introgressed mitotype was associated with a 'slow-thorough' dispersal profile, characterized by a less active but more cautious and accurate exploration strategy. This pattern was consistent across life stages and contexts: aquatic larvae and terrestrial juveniles, spontaneous activity and response to novelty. These results support the intriguing hypothesis that personality traits associated with distinct mitotypes could contribute to differential mitochondrial introgression and the formation of biogeographic patterns of mito-nuclear discordance.

Jumping through hoops: Structural rearrangements and accelerated mutation rates on Dendrodorididae (Mollusca: Nudibranchia) mitogenomes rumble their evolution

The systematics of the family Dendrodorididae, with only three valid genera, is a challenge for integrative taxonomists. Its members lack hard structures for morphological comparisons and their mitochondrial and nuclear markers provide contradictory phylogenetic signals, making phylogenetic reconstructions difficult. This molecular discordance has been hypothesized to be the result of nuclear pseudogenes or exogenous contamination. However, these hypotheses have not been tested. Here, we assembled the first genome drafts of seven Dendrodorididae species to investigate the evolutionary processes of this family. Two of the mitogenomes displayed an identical structural rearrangement involving the translocation of three coding genes and five tRNAs, described for the first time in nudibranchs. In addition, we found particularly high dN and dN/dS values and multiple insertions and deletions on the mitochondrial genes of smooth Dendrodoris. In contrast, nuclear single-copy ortholog genes showed no such mutational differences. Models of protein structures from mitochondrial genes are conserved, suggesting conserved functionality. Phylogenies using mitogenomic and nuclear data showed that species with rearranged mitogenomes form a clade, although Dendrodorididae relationships remained unresolved. The present study provides novel evidence for accelerated mutation rates in the mitogenomes of Dendrodorididae, which presumably have implications on respiratory adaptation, and highlights the importance of using genomic data to unveil rare evolutionary processes, crucial for correctly inferring phylogenies.

Reticulate evolution: Detection and utility in the phylogenomics era

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.

Eco-evolutionary dynamics of host-microbiome interactions in a natural population of closely related mouse subspecies and their hybrids

Closely related host species share similar symbionts, but the effects of host genetic admixture and environmental conditions on these communities remain largely unknown. We investigated the influence of host genetic admixture and environmental factors on the intestinal prokaryotic and eukaryotic communities (fungi, parasites) of two house mouse subspecies (Mus musculus domesticus and M. m. musculus) and their hybrids in two settings: (i) wild-caught mice from the European hybrid zone and (ii) wild-derived inbred mice in a controlled laboratory environment before and during a community perturbation (infection). In wild-caught mice, environmental factors strongly predicted the overall microbiome composition. Subspecies' genetic distance significantly influenced the overall microbiome composition, and each component (bacteria, parasites and fungi). While hybridization had a weak effect, it significantly impacted fungal composition. We observed similar patterns in wild-derived mice, where genetic distances and hybridization influenced microbiome composition, with fungi being more stable to infection-induced perturbations than other microbiome components. Subspecies' genetic distance has a stronger and consistent effect across microbiome components than differences in expected heterozygosity among hybrids, suggesting that host divergence and host filtering play a key role in microbiome divergence, influenced by environmental factors. Our findings offer new insights into the eco-evolutionary processes shaping host-microbiome interactions.

Biased Gene Introgression and Adaptation in the Face of Chloroplast Capture in Aquilegia amurensis

-Chloroplast capture, a phenomenon that can occur through interspecific hybridization and introgression, is frequently invoked to explain cytonuclear discordance in plants. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential for driving species differentiation and possible functional differences in the context of chloroplast capture. To address this crucial question, we chose the Aquilegia genus, which is known for having minimal sterility among species, and inferred that A. amurensis captured the plastome of A. parviflora based on cytonuclear discordance and gene flow between the 2 species. We focused on the introgression region and its differentiation from corresponding regions in closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes (CECs; i.e., organelle-targeted genes) of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast-receiving species due to cytonuclear interactions during introgression. Notably, the intrinsic correlation of CEC introgression was a greater degree of evolutionary distance for these CECs between A. amurensis and A. parviflora. Terpene synthase activity genes (GO: 0010333) were overrepresented among the introgressed genes, and more than 30% of these genes were CEC genes. These findings support our observations that floral terpene release pattern is similar between A. amurensis and A. parviflora compared with A. japonica. Our study clarifies the mechanisms of cytonuclear coevolution, species differentiation, and functional differences in the context of chloroplast capture and highlights the potential role of chloroplast capture in adaptation.

Y chromosome introgression between deeply divergent primate species

Hybridization and introgression are widespread in nature, with important implications for adaptation and speciation. Since heterogametic hybrids often have lower fitness than homogametic individuals, a phenomenon known as Haldane's rule, loci inherited strictly through the heterogametic sex rarely introgress. We focus on the Y-chromosomal history of guenons, African primates that hybridized extensively in the past. Although our inferences suggest that Haldane's rule generally applies, we uncover a Y chromosome introgression event between two species ca. six million years after their initial divergence. Using simulations, we show that selection likely drove the introgressing Y chromosome to fixation from a low initial frequency. We identify non-synonymous substitutions on the novel Y chromosome as candidate targets of selection, and explore meiotic drive as an alternative mechanism. Our results provide a rare example of Y chromosome introgression, showing that the ability to produce fertile heterogametic hybrids likely persisted for six million years in guenons.

Unravelling intermediate migration patterns in gull hybrids: insights from ring re-encounters

Hybridization is a common phenomenon in birds, particularly between closely related species, when reproductive isolation mechanisms are insufficiently developed. Hybrids differ from the parental species in genetic, morphological, and behavioural traits. However, the migration patterns of hybrids have been scarcely studied. Examining hybrid migration behaviour is essential as it may reveal their role as a "gene bridge" between species and enhance our understanding of speciation mechanisms and the genetics of migration. Most research focuses on tracking the migration of long-distance migrants, but the effect of hybridization on migration is poorly understood also in short-distance migrants. The study aimed to verify whether the migratory movements of interspecific hybrids between the Herring (Larus argentatus) and the Caspian Gull (L. cachinnans) are intermediate, as predicted by the genetic basis of migration. Migration patterns, based on distance and direction, were determined from re-encounter data of individuals ringed in Poland, for over 20 years (2002-2023). These included both allopatric (parental species) and sympatric (both parental species and hybrids) populations. The results indicated that large gull hybrids exhibit an intermediate migration patterns, similarly to other hybridizing species. Unlike many cases where intermediacy may select against hybrids, the absence of significant environmental barriers along gulls' migration routes and their wide wintering range likely mitigates selective pressures. This finding underscores the need for further investigation into the ecological implications of hybrid migration patterns. By using bird re-encounter data, we demonstrated that it provides a sufficient basis for analysing migration patterns and detecting intermediacy, even in within-continental and short-distance migrants.

How Important Is Variation in Extrinsic Reproductive Isolation to the Process of Speciation?

The strength of reproductive isolation (RI) between two or more lineages during the process of speciation can vary by the ecological conditions. However, most speciation research has been limited to studying how ecologically dependent RI varies among a handful of broadly categorized environments. Very few studies consider the variability of RI and its effects on speciation at finer scales-that is, within each environment due to spatial or temporal environmental heterogeneity. Such variation in RI across time and/or space may inhibit speciation through leaky reproductive barriers or promote speciation by facilitating reinforcement. To investigate this overlooked aspect of speciation research, we conducted a literature review of existing studies of variation in RI in the field and then conducted individual-based simulations to examine how variation in hybrid fitness across time and space affects the degree of gene flow. Our simulations indicate that the presence of variation in hybrid fitness across space and time often leads to an increase in gene flow compared to scenarios where hybrid fitness remains static. This observation can be attributed to the convex relationship between the degree of gene flow and the strength of selection on hybrids. Our simulations also show that the effect of variation in RI on facilitating gene flow is most pronounced when RI, on average, is relatively low. This finding suggests that it could serve as an important mechanism to explain why the completion of speciation is often challenging. While direct empirical evidence documenting variation in extrinsic RI is limited, we contend that it is a prevalent yet underexplored phenomenon. We support this argument by proposing common scenarios in which RI is likely to exhibit variability and thus influence the process of speciation.

Peering through the hedge: Multiple datasets yield insights into the phylogenetic relationships and incongruences in the tribe Lilieae (Liliaceae)

The increasing use of genome-scale data has significantly facilitated phylogenetic analyses, contributing to the dissection of the underlying evolutionary mechanisms that shape phylogenetic incongruences, such as incomplete lineage sorting (ILS) and hybridization. Lilieae, a prominent member of the Liliaceae family, comprises four genera and approximately 260 species, representing 43% of all species within Liliaceae. They possess high ornamental, medicinal and edible values. Yet, no study has explored the validity of various genome-scale data in phylogenetic analyses within this tribe, nor have potential evolutionary mechanisms underlying its phylogenetic incongruences been investigated. Here, transcriptome, Angiosperms353, plastid and mitochondrial data, were collected from 50 to 93 samples of Lilieae, covering all four recognized genera. Multiple datasets were created and used for phylogenetic analyses based on concatenated and coalescent-based methods. Evolutionary rates of different datasets were calculated, and divergence times were estimated. Various approaches, including coalescence simulation, Quartet Sampling (QS), calculation of concordance factors (gCF and sCF), as well as MSCquartets and reticulate network inference, were carried out to infer the phylogenetic discordances and analyze their underlying mechanisms using a reduced 33-taxon dataset. Despite extensive phylogenetic discordances among gene trees, robust phylogenies were inferred from nuclear and plastid data compared to mitochondrial data, with lower synonymous substitution detected in mitochondrial genes than in nuclear and plastid genes. Significant ILS was detected across the phylogeny of Lilieae, with clear evidence of reticulate evolution identified. Divergence time estimation indicated that most of lineages in Lilieae diverged during a narrow time frame (ranging from 5.0 Ma to 10.0 Ma), consistent with the notion of rapid radiation evolution. Our results suggest that integrating transcriptomic and plastid data can serve as cost-effective and efficient tools for phylogenetic inference and evolutionary analysis within Lilieae, and Angiosperms353 data is also a favorable choice. Mitochondrial data are more suitable for phylogenetic analyses at higher taxonomic levels due to their stronger conservation and lower synonymous substitution rates. Significant phylogenetic incongruences detected in Lilieae were caused by both incomplete lineage sorting (ILS) and reticulate evolution, with hybridization and "ghost introgression" likely prevalent in the evolution of Lilieae species. Our findings provide new insights into the phylogeny of Lilieae, enhancing our understanding of the evolution of species in this tribe.

Detection and quantification of introgression using Bayesian inference based on conjugate priors

SUMMARY

Introgression (the flow of genes between species) is a major force structuring the evolution of genomes, potentially providing raw material for adaptation. Here, we present a versatile Bayesian model selection approach for detecting and quantifying introgression, df-BF, that builds upon the recently published distance-based df statistic. Unlike df, df-BF accounts for the number of variant sites within a genomic region. The underlying model parameter of our df-BF method, here denoted as dfθ, accurately quantifies introgression, and the corresponding Bayes Factors (df-BF) enables weighing the strength of evidence for introgression. To ensure fast computation, we use conjugate priors with no need for computationally demanding MCMC iterations. We compare our method with other approaches including df, fd, Dp, and Patterson's D using a wide range of coalescent simulations. Furthermore, we showcase the applicability of df-BF and dfθ using whole-genome mosquito data. Finally, we integrate the new method into the powerful genomics R-package PopGenome.

AVAILABILITY AND IMPLEMENTATION

The presented methods are implemented within the R-package PopGenome (https://github.com/pievos101/PopGenome) and the simulation as the application results can be reproduced from the source code available from a dedicated GitHub repository (https://github.com/pievos101/Introgression-Simulation).

Reconciling Santa Rosalia: Both Reproductive Isolation and Coexistence Constrain Diversification

AbstractUnderstanding patterns of diversification necessarily requires accounting for both the generation and the persistence of species. Formal models of speciation genetics, however, focus on the generation of new species without explicitly considering the maintenance of biodiversity (e.g., coexistence, the focus of ecological studies of diversity). Consequently, it remains unclear whether and how new species will coexist following a speciation event, a gap limiting our ability to understand the rate-limiting controls of diversification over macroevolutionary timescales. To connect coexistence and speciation theory and assess the relative importance of ecological versus genetic constraints in diversification events, we develop a deterministic, three-locus, population-genetic model that includes a skewed distribution of available resources (to generate variation in fitness differences), frequency-dependent competition, and assortative mating. Both ecology and genetics play vital and interacting roles in shaping initial speciation events and long-term eco-evolutionary outcomes. Ecological constraints are especially important when fitness differences are large and competition remains strong among dissimilar phenotypes. Ephemeral species can occur in our model and are typically lost because of competitive exclusion, a result demonstrating that species persistence may serve as the rate-limiting control of long-term diversification rates. More broadly, our model adds evidence that the unification of ecological and evolutionary (including genetic) perspectives on biodiversity is needed to predict large-scale patterns.

Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings

Homo sapiens and Neanderthals underwent hybridization during the Middle/Upper Paleolithic age, culminating in retention of small amounts of Neanderthal-derived DNA in the modern human genome. In the current study, we address the potential roles Neanderthal single nucleotide polymorphisms (SNP) may be playing in autism susceptibility in samples of black non-Hispanic, white Hispanic, and white non-Hispanic people using data from the Simons Foundation Powering Autism Research (SPARK), Genotype-Tissue Expression (GTEx), and 1000 Genomes (1000G) databases. We have discovered that rare variants are significantly enriched in autistic probands compared to race-matched controls. In addition, we have identified 25 rare and common SNPs that are significantly enriched in autism on different ethnic backgrounds, some of which show significant clinical associations. We have also identified other SNPs that share more specific genotype-phenotype correlations but which are not necessarily enriched in autism and yet may nevertheless play roles in comorbid phenotype expression (e.g., intellectual disability, epilepsy, and language regression). These results strongly suggest Neanderthal-derived DNA is playing a significant role in autism susceptibility across major populations in the United States.

Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation

The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression-the exchange of genetic material through hybridization and backcrossing-are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report "ancient introgression"- referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome and implemented this test in the program Dsuite.

Asymmetric mate preference and reproductive interference mediate climate-induced changes in mate availability in a small mammal hybrid zone

Range expansion and contraction are among the most common biotic responses to changing environmental conditions, yet much is to be learned about the mechanisms that underlie range-edge population dynamics, especially when those areas are points of secondary contact between closely related species. Here, we present field-measured parentage data that document the reproductive outcomes of changes in mate availability at a secondary contact zone between two species of woodrat in the genus Neotoma. Changes in mate availability resulted from drought-driven differential survival between the species and their hybrids. As the availability of conspecific mates declined, rates of hybridization increased, leading to the accumulation of admixed individuals in the zone of contact. Patterns of reproductive success in the wild appear to be the result of a combination of both pre-mating isolation and post-zygotic selection resulting from genomic incompatibilities between the parental lineages. Evidence of asymmetric mate preference between the parental lineages came from both skewed reproductive output in the field and laboratory preference trials. Moreover, partial genomic incompatibility was evident from the near-zero reproductive success of F1 males and because nearly all surviving hybrids had one pure parent. Nonetheless, the high reproductive success of F1 females and backcrossing in both parental directions allow for introgression between the parental species. These findings reveal how climate change may alter evolutionary outcomes for species at the edge of their ranges through an interplay of behavioral, demographic, and genetic mechanisms.

Hybridization has localized effect on genetic variation in closely related pine species

BACKGROUND

Hybridization is a known phenomenon in nature but its genetic impact on populations of parental species remains less understood. We investigated the evolutionary consequences of the interspecific gene flow in several contact zones of closely related pine species. Using a set of genetic markers from both nuclear and organellar genomes, we analyzed four hybrid zones (384 individuals) and a large panel of reference allopatric populations of parental taxa (2104 individuals from 96 stands).

RESULTS

We observed reduced genetic diversity in maternally transmitted mitochondrial genomes of pure pine species and hybrids from contact zones compared to reference allopatric populations. The distribution of mtDNA haplotypes followed geographic rather than species boundaries. Additionally, no new haplotypes emerged in the contact zones, instead these zones contained the most common local variants. However, species diverged significantly at nuclear genomes and populations in contact zones exhibited similar or higher genetic diversity compared to the reference stands. There were no signs of admixture in any allopatric population, while clear admixture was evident in the contact zones, indicating that hybridization has a geographically localized effect on the genetic variation of the analyzed pine species.

CONCLUSIONS

Our results suggest that hybrid zones act as sinks rather than melting pots of genetic diversity. Hybridization influences sympatric populations but is confined to contact zones. The spectrum of parental species ancestry in hybrids reflects the old evolutionary history of the sympatric populations. These findings also imply that introgression may play a crucial role in the adaptation of hybrids to specific environments.

Whole Genome Analysis Reveals Evolutionary History and Introgression Events in Bale Monkeys

Background/Objective: The Bale monkey (Chlorocebus djamdjamensis) is a threatened primate species endemic to Ethiopia and, in contrast to other members of the genus Chlorocebus, lives at high altitudes and feeds mainly on bamboo. Two populations of the species are present, one in continuous bamboo forest (CF) in the eastern part of the species' range, and the other in fragmented forest (FF) in the western part. Based on mitochondrial DNA and phenotypic characteristics, previous studies have suggested introgression by parapatric congeners into the FF population but not into the CF population. The objective of this study was to gain insights into the evolutionary history of Bale monkeys and their potential genetic adaptations to high altitudes and for bamboo consumption. Methods: We sequenced the whole genomes of individuals from both populations and compared their genomes with those of the other five Chlorocebus species. We applied phylogenetic methods and conducted population demographic simulations to elucidate their evolutionary history. A genome-wide analysis was conducted to assess gene flow and identify mutations potentially associated with adaptations to high altitudes and for bamboo metabolism. Results: Our analyses revealed Bale monkeys as the sister clade to Chlorocebus aethiops and showed that gene flow occurred between C. aethiops and FF but not between C. aethiops and CF. In addition, we detected non-synonymous mutations in genes potentially associated with the adaptation to high altitudes (EPAS1) in both populations and with the adaptation for bamboo metabolism (TAS2R16, MPST, and TST) mainly in the CF population. Conclusions: Our study provides insights into the evolutionary history of a threatened primate species and reveals the genetic basis for its adaptions to unique environments and for diet specialization.

Two sides of the same coin? Transient hybridization in refugia and rapid postglacial ecological divergence ensure the evolutionary persistence of sister Nothofagus

Glacial periods have been considered as inhospitable environments that consist of treeless vegetation at higher latitudes. The fossil record suggests many species survived the Last Glacial Maximum within refugia, usually at lower latitudes. However, phylogeographic studies have given support to the existence of previously unknown high-latitude refugia that were not detected in the fossil record. Here, we test the hypothesis that cold-tolerant trees of Patagonia survived cold periods in microclimatically favourable locales where hybridization occurred between sister taxa. To study local presence through glacial periods in multiple refugia, we used pollen records and genetic information (isozymes, microsatellites, and combined nuclear and chloroplast DNA sequences) of population pairs of Nothofagus antarctica and N. pumilio that belong to the ancient subgenus Nothofagus which can potentially hybridize in nature, along their entire latitudinal range in Patagonia. Studied species share the N. dombeyi type pollen, which was abundant at >20% in the northernmost latitudinal bands (35-43°S), even during the Last Glacial Maximum. Mid- and southern latitudinal records (44-55°S) yielded lower abundances of ~10% that increased after c. 15.0 cal. ka BP. Therefore, fossil pollen evidence suggests a long-lasting local presence of Nothofagus throughout glacial-interglacial cycles but mostly as small populations between 44°S and 51°S. We found species-specific and shared genetic variants, the latter of which attained relatively high frequencies, thus providing evidence of ancestral polymorphisms. Populations of each species were similarly diverse, suggesting survival throughout the latitudinal range. Estimates of coalescent divergence times were broadly synchronous across latitudes, suggesting that regional climates similarly affected populations and species that hybridized through climate cycles, fostering local persistence.

Genomic changes and stabilization following homoploid hybrid speciation of the Oxford ragwort Senecio squalidus

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.

Biparental graph strategy to represent and analyze hybrid plant genomes

Hybrid plants are found extensively in the wild, and they often demonstrate superior performance of complex traits over their parents and other selfing plants. This phenomenon, known as heterosis, has been extensively applied in plant breeding for decades. However, the process of decoding hybrid plant genomes has seriously lagged due to the challenges associated with genome assembly and the lack of appropriate methodologies for their subsequent representation and analysis. Here, we present the assembly and analysis of 2 hybrids, an intraspecific hybrid between 2 maize (Zea mays ssp. mays) inbred lines and an interspecific hybrid between maize and its wild relative teosinte (Z. mays ssp. parviglumis), utilizing a combination of PacBio High Fidelity sequencing and chromatin conformation capture sequencing data. The haplotypic assemblies are well phased at chromosomal scale, successfully resolving the complex loci with extensive parental structural variations (SVs). By integrating into a biparental genome graph, the haplotypic assemblies can facilitate downstream short-read-based SV calling and allele-specific gene expression analysis, demonstrating outstanding advantages over a single linear genome. Our work offers a comprehensive workflow that aims to facilitate the decoding of numerous hybrid plant genomes, particularly those with unknown or inaccessible parentage, thereby enhancing our understanding of genome evolution and heterosis.

Towards the conservation of the crucian carp in Europe: Prolific hybridization but no evidence for introgression between native and non-native taxa

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.

Secondary contact zone and genetic introgression in closely related haplodiploid social spider mites

How frequently hybridisation and gene flow occur in the contact zones of diverging taxa is important for understanding the speciation process. Stigmaeopsis sabelisi and Stigmaeopsis miscanthi high-aggression form (hereafter, S. miscanthi HG) are haplodiploid, social spider mites that infest the Chinese silver grass, Miscanthus sinensis. These two species are closely related and parapatrically distributed in Japan. In mountainous areas, S. sabelisi and S. miscanthi HG are often found in the highlands and lowlands, respectively, suggesting that they are in contact at intermediate altitudes. It is estimated that they diverged from their common ancestors distributed in subtropical regions (south of Japan) during the last glacial period, expanded their distribution into the Japanese Archipelago, and came to have such a parapatric distribution (secondary contact). As their reproductive isolation is strong but incomplete, hybridisation and genetic introgression are expected at their distributional boundaries. In this study, we investigated their spatial distribution patterns along the elevation on Mt. Amagi using male morphological differences, and investigated their hybridisation status using single-nucleotide polymorphisms by MIG-seq. We found their contact zone at altitudes of 150-430 m, suggesting that their contact zone is prevalent in the parapatric area, which is in line with a previous study. Interspecific mating was predicted based on the sex ratio in the contact zone. No obvious hybrids were found, but genetic introgression was detected although it was extremely low.

Evolutionary origin and population diversity of a cryptic hybrid pathogen

Cryptic fungal pathogens pose disease management challenges due to their morphological resemblance to known pathogens. Here, we investigated the genomes and phenotypes of 53 globally distributed isolates of Aspergillus section Nidulantes fungi and found 30 clinical isolates-including four isolated from COVID-19 patients-were A. latus, a cryptic pathogen that originated via allodiploid hybridization. Notably, all A. latus isolates were misidentified. A. latus hybrids likely originated via a single hybridization event during the Miocene and harbor substantial genetic diversity. Transcriptome profiling of a clinical isolate revealed that both parental subgenomes are actively expressed and respond to environmental stimuli. Characterizing infection-relevant traits-such as drug resistance and growth under oxidative stress-revealed distinct phenotypic profiles among A. latus hybrids compared to parental and closely related species. Moreover, we identified four features that could aid A. latus taxonomic identification. Together, these findings deepen our understanding of the origin of cryptic pathogens.

Integrated cytological and transcriptomic analyses provide new insights into restoration of pollen viability in synthetic allotetraploid Brassica carinata

KEY MESSAGE

Upregulation of genes involved in DNA damage repair and sperm cell differentiation leads to restoration of pollen viability in synthetic allotetraploid B. carinata after chromosome doubling. Apart from the well-known contribution of polyploidy to crop improvement, polyploids can also be induced for other purposes, such as to restore the viability of sterile hybrids. The mechanism related to viability transition between the sterile allodiploid and the fertile allotetraploid after chromosome doubling are not well understood. Here, we synthesised allodiploid B. carinata (2n = 2x = 17) and allotetraploid B. carinata (2n = 4x = 34) as models to investigate the cytological and transcriptomic differences during pollen development. The results showed that after chromosome doubling, the recovery of pollen viability in allotetraploid was mainly reflected in the stabilisation of microtubule spindle morphology, normal meiotic chromosome behaviour, and normal microspore development. Interestingly, the deposition and degradation of synthetic anther tapetum were not affected by polyploidy. Transcription analysis showed that the expression of genes related to DNA repair (DMC1, RAD51, RAD17, SPO11-2), cell cycle differentiation (CYCA1;2, CYCA2;3) and ubiquitination proteasome pathway (UBC4, PIRH2, CDC53) were positively up-regulated during pollen development of synthetic allotetraploid B. carinata. In summary, these results provide some refreshing updates about the ploidy-related restoration of pollen viability in newly synthesised allotetraploid B. carinata.

Museum Genomics Reveals the Hybrid Origin of an Extinct Crater Lake Endemic

Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are, therefore, critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook a comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between 2 proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.

The Ecology of Hybrid Incompatibilities

Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from selection caused by epistatic Dobzhansky-Muller hybrid incompatibilities. Here, we show how selection against transgressive phenotypes in hybrids manifests as incompatibility. After outlining our logic, we summarize current approaches for studying ecology-based selection on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are typically polygenic. Next, we describe how verbal models of selection on hybrids translate to phenotypic and genetic fitness landscapes, highlighting emerging approaches for detecting polygenic incompatibilities. Finally, in a synthesis of published data, we report that trait transgression-and thus possibly extrinsic hybrid incompatibility in hybrids-escalates with the phenotypic divergence between parents. We discuss conceptual implications and conclude that studying the ecological basis of hybrid incompatibility will facilitate new discoveries about mechanisms of speciation.

Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone

Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed ~50 km asymmetrically across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989-1994) and contemporary (2017-2020) transect samples to survey both morphological and genetic variation. Genome-wide single nucleotide polymorphism data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.

Comparative genomics of dusky kob (Argyrosomus japonicus, Sciaenidae) conspecifics: Evidence for speciation and the genetic mechanisms underlying traits

Dusky kob (Argyrosomus japonicus) is a commercially important finfish, indigenous to South Africa, Australia, and China. Previous studies highlighted differences in genetic composition, life history, and morphology of the species across geographic regions. A draft genome sequence of 0.742 Gb (N50 = 5.49 Mb; BUSCO completeness = 97.8%) and 22,438 predicted protein-coding genes was generated for the South African (SA) conspecific. A comparison with the Chinese (CN) conspecific revealed a core set of 32,068 orthologous protein clusters across both genomes. The SA genome exhibited 440 unique clusters compared to 1928 unique clusters in the CN genome. Transportation and immune response processes were overrepresented among the SA accessory genome, whereas the CN accessory genome was enriched for immune response, DNA transposition, and sensory detection (FDR-adjusted p < 0.01). These unique clusters may represent an adaptive component of the species' pangenome that could explain population divergence due to differential environmental specialisation. Furthermore, 700 single-copy orthologues (SCOs) displayed evidence of positive selection between the SA and CN genomes, and globally these genomes shared only 92% similarity, suggesting they might be distinct species. These genes primarily play roles in metabolism and digestion, illustrating the evolutionary pathways that differentiate the species. Understanding these genomic mechanisms underlying adaptation and evolution within and between species provides valuable insights into growth and maturation of kob, traits that are particularly relevant to commercial aquaculture.

Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae)

Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.

Lineage diversification and rampant hybridization among subspecies explain taxonomic confusion in the endemic Hawaiian fern Polypodium pellucidum

PREMISE

Polypodium pellucidum, a fern endemic to the Hawaiian Islands, encompasses five ecologically and morphologically variable subspecies, suggesting a complex history involving both rapid divergence and rampant hybridization.

METHODS

We employed a large target-capture data set to investigate the evolution of genetic, morphological, and ecological variation in P. pellucidum. With a broad sampling across five Hawaiian Islands, we deciphered the evolutionary history of P. pellucidum, identified nonhybrid lineages and intraspecific hybrids, and inferred the relative influence of geography and ecology on their distributions.

RESULTS

Polypodium pellucidum is monophyletic, dispersing to the Hawaiian archipelago 11.53-7.77 Ma and diversifying into extant clades between 5.66 and 4.73 Ma. We identified four nonhybrid clades with unique morphologies, ecological niches, and distributions. Additionally, we elucidated several intraspecific hybrid combinations and evidence for undiscovered or extinct "ghost" lineages contributing to extant hybrid populations.

CONCLUSIONS

We provide a foundation for revising the taxonomy of P. pellucidum to account for cryptic lineages and intraspecific hybrids. Geologic succession of the Hawaiian Islands through cycles of volcanism, vegetative succession, and erosion has determined the available habitats and distribution of ecologically specific, divergent clades within P. pellucidum. Intraspecific hybrids have likely arisen due to ecological and or geological transitions, often persisting after the local extinction of their progenitors. This research contributes to our understanding of the evolution of Hawai'i's diverse fern flora and illuminated cryptic taxa to allow better-informed conservation efforts.

Phylogeographic analysis reveals multiple origins of the desert shrub Reaumuria songarica in northern Xinjiang, involving homoploid and tetraploid hybrids

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.

Complex patterns of gene flow and convergence in the evolutionary history of the spiral-horned antelopes (Tragelaphini)

The Tragelaphini, also known as spiral-horned antelope, is a phenotypically diverse mammalian tribe comprising a single genus, Tragelaphus. The evolutionary history of this tribe has attracted the attention of taxonomists and molecular geneticists for decades because its diversity is characterised by conflicts between morphological and molecular data as well as between mitochondrial, nuclear and chromosomal DNA. These inconsistencies point to a complex history of ecological diversification, coupled by either phenotypic convergence or introgression. Therefore, to unravel the phylogenetic relationships among spiral-horned antelopes, and to further investigate the role of divergence and gene flow in trait evolution, we sequenced genomes for all nine accepted species of the genus Tragelaphus, including a genome each for the highly divergent bushbuck lineages (T. s. scriptus and T. s. sylvaticus). We successfully reconstructed the Tragelaphus species tree, providing genome-level support for the early Pliocene divergence and monophyly of the nyala (T. angasii) and lesser kudu (T. imberbis), the monophyly of the two eland species (T. oryx and T. derbianus) and, importantly, the monophyly of kéwel (T. s. scriptus) and imbabala (T. s. sylvaticus) bushbuck. We found strong evidence for gene flow in at least four of eight nodes on the species tree. Among the six phenotypic traits assessed here, only habitat type mapped onto the species tree without homoplasy, showing that trait evolution was the result of complex patterns of divergence, introgression and convergent evolution.

The importance of reproductive isolation in driving diversification and speciation within Peruvian mimetic poison frogs (Dendrobatidae)

To explain how populations with distinct warning signals coexist in close parapatry, we experimentally assessed intrinsic mechanisms acting as reproductive barriers within three poison-frog species from the Peruvian Amazon belonging to a Müllerian mimetic ring (Ranitomeya variabilis, Ranitomeya imitator and Ranitomeya fantastica). We tested the role of prezygotic and postzygotic isolation barriers between phenotypically different ecotypes of each species, using no-choice mating experiments and offspring survival analysis. Our results show that prezygotic mating preference did not occur except for one specific ecotype of R. imitator, and that all three species were able to produce viable inter-population F1 hybrids. However, while R. variabilis and R. imitator hybrids were able to produce viable F2 generations, we found that for R. fantastica, every F1 hybrid males were sterile while females remained fertile. This unexpected result, echoing with Haldane's rule of speciation, validated phylogenetic studies which tentatively diagnose these populations of R. fantastica as two different species. Our work suggests that postzygotic genetic barriers likely participate in the extraordinary phenotypic diversity observed within Müllerian mimetic Ranitomeya populations, by maintaining species boundaries.

Meiotic deviations and endoreplication lead to diploid oocytes in female hybrids between bighead catfish (Clarias macrocephalus) and North African catfish (Clarias gariepinus)

Introduction

Reproductive isolation and hybrid sterility are mechanisms that maintain the genetic integrity of species and prevent the introgression of heterospecific genes. However, crosses of closely related species can lead to complex evolution, such as the formation of all-female lineages that reproduce clonally. Bighead catfish (Clarias macrocephalus) and North African catfish (C. gariepinus) diverged 40 million years ago. They are cultivated and hybridized in Thailand for human consumption. Male hybrids are sterile due to genome-wide chromosome asynapsis during meiosis. Although female hybrids are sometimes fertile, their chromosome configuration during meiosis has not yet been studied.

Methods

We analyzed meiosis in the hybrid female catfish at pachytene (synaptonemal complexes) and diplotene (lampbrush chromosomes), using immunostaining to detect chromosome pairing and double-stranded break formation, and FISH with species-specific satellite DNAs to distinguish the parental chromosomes.

Results

More than 95% of oocytes exhibited chromosome asynapsis in female hybrid catfish; however, they were able to progress to the diplotene stage and form mature eggs. The remaining oocytes underwent premeiotic endoreplication, followed by synapsis and crossing over between sister chromosomes, similar to known clonal lineages in fish and reptiles.

Discussion

The occurrence of clonal reproduction in female hybrid catfish suggests a unique model for studying gametogenic alterations caused by hybridization and their potential for asexual reproduction. Our results further support the view that clonal reproduction in certain hybrid animals relies on intrinsic mechanisms of sexually reproducing parental species, given their multiple independent origins with the same mechanism.

Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones

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.

Genomic architecture and population structure of Boreogadus saida from Canadian waters

The polar cod, Boreogadus saida, is an abundant and ubiquitous forage fish and a crucial link in Arctic marine trophic dynamics. Our objective was to unravel layers of genomic structure in B. saida from Canadian waters, specifically screening for potential hybridization with the Arctic cod, Arctogadus glacialis, large chromosomal inversions, and sex-linked regions, prior to interpreting population structure. Our analysis of 53,384 SNPs in 522 individuals revealed hybridization and introgression between A. glacialis and B. saida. Subsequent population level analyses of B. saida using 12,305 SNPs in 511 individuals revealed three large (ca. 7.4-16.1 Mbp) chromosomal inversions, and a 2 Mbp region featuring sex-linked loci. We showcase population structuring across the Western and Eastern North American Arctic, and subarctic regions ranging from the Hudson Bay to the Canadian Atlantic maritime provinces. Genomic signal for the inferred population structure was highly aggregated into a handful of SNPs (13.8%), pointing to potentially important adaptive evolution across the Canadian range. Our study provides a high-resolution perspective on the genomic structure of B. saida, providing a foundation for work that could be expanded to the entire circumpolar range for the species.

Species delimitation 4.0: integrative taxonomy meets artificial intelligence

Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.

The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae

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.

Do school Water, Sanitation, and Hygiene facilities affect students' health status, attendance, and educational achievements? A qualitative study in Nepal

Background and Aims

Access to safe and sufficient drinking Water, Sanitation, and good Hygiene (WASH) facilities in schools play a crucial role in preventing students from numerous Neglected Tropical Diseases, improving the learning environment in schools, and creating resilient communities living in a healthy environment. This study aims to explore the impact of combining WASH facilities on students' health status, school attendance, and educational achievements.

Methods

Four schools, two with improved and two without improved WASH facilities, were selected purposively from Dhanusha and Chitwan districts of Nepal. A total of 24 participants, 16 students, and eight teachers were also purposively selected based on the Theory of Data Saturation. The participants were interviewed face-to-face using study guidelines; Key Informants Interview for teachers and In-depth Interview for students. The data were audio recorded and analyzed thematically using Dedoose 9.0.17 qualitative data management and analysis software.

Results

School WASH facilities have a significant impact on students' health and well-being. Poor school-WASH facilities hindered students' school attendance, particularly for menstruating girls. School without separate toilets for girls, including menstruation hygiene facilities, lack of water and soap, sanitary pad, and secure toilet's door often have higher rates of absenteeism among girls. Poor teacher and students' relationships, students' low interest in education, household chores, and participation in social customs also contribute to students' absence from school and low educational performance. It is important to note that inadequate WASH facilities affect not only students, but also teachers in the same school.

Conclusion

The lack of safe and sufficient drinking water, unimproved sanitation, and poor hygiene facilities were seen by students and teachers as reducing their health and well-being, school attendance, and academic performance. Thus, schools need prioritize and promote the provision of improved WASH facilities for the betterment of students' health, attendance, and educational proficiency.

The role of Pleistocene dispersal in shaping species richness of sky island wintergreens from the Himalaya-Hengduan Mountains

In addition to topography and climate, biogeographic dispersal has been considered to influence plant diversity in the Himalaya-Hengduan Mountains (HHM), yet, the mode and tempo of sky island dispersal and its influence on species richness has been little explored. Through phylogenetic analysis of Gaultheria ser. Trichophyllae, a sky island alpine clade within the HHM, we test the hypothesis that dispersal has affected current local species richness. We inferred the dynamics of biogeographic dispersal with correlation tests on direction, distance, occurrence time, and regional species richness. We found that G. ser. Trichophyllae originated at the end of the Miocene and mostly dispersed toward higher longitudes (eastward). In particular, shorter intra-regional eastward dispersals and longer inter-regional westward dispersals were most frequently observed. We detected a prevalence of eastward intra-region dispersals in both glacial periods and interglacials. These dispersals may have been facilitated by the reorganization of paleo-drainages and monsoon intensification through time. We suggest that the timing of dispersal corresponding to glacial periods and the prevalence of intra-region dispersal, rather than dispersal frequency, most influenced the pattern of species richness of G. ser. Trichophyllae. This study facilitates a more comprehensive understanding of biodiversity in the sky islands within the HHM.