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The European endemic barbels represent important bioindicators of river quality and are nowadays threatened by changing environmental conditions and hybridization with the invasive alien Barbus barbus. It is therefore fundamental to investigate interactions among species and adaptability to climate changes in protected areas of Northern Apennines. An investigation was carried out considering 248 barbel samples that were analysed for Cytb mitochondrial DNA and 192 at 10 microsatellite loci, to delineate the distribution and population structure of the two native species as well as the impact of invasive B. barbus inside 15 sites of the Natura 2000 network. The complex distribution of the native barbel species was highlighted, together with a significant genetic structure emerging in different populations. Only one site revealed a "pure" population of B. caninus while the other ones showed a high level of hybridization between the different barbel species. For the B. plebejus two "genetically pure" populations were found in the hill‐mountain sector, while the hybridization level resulted in increasing in the lowest altitudinal stretch of watercourses with a consistent contribution driven by B. barbus. We herein present the first evidence of B. barbus introgression along an altitudinal gradient, carried from the lowland water course to mountain stretches driven by B. plebejus migration. B. plebejus is the species that can act as vicariant organism able to transfer the B. barbus genome from the plain habitats into B. caninus genome of the higher altitude waterstreams, as a consequence of habitat shifts due to climate changes and anthropogenic acitivities. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions The impact of Pleistocene climate fluctuations on the biogeographical history of aquatic species has been a topic of enduring debate. This issue poses particular challenges for parapatric closely related species, especially those situated in transition zones where species assemblages occur between distinct zoogeographic boundaries.Eastern China.Five closely related Sinopotamon species and subspecies, S. shensiense, S. honanense, S. y. yangtsekiense, S. y. shanxianense, and S. y. tongbaiense.These parapatric Sinopotamon species and subspecies, distributed along the boundary between the Palaearctic and Oriental realms in eastern China, offer an ideal model for addressing these challenges. We explored the biogeographic history of these species by conducting a comparative phylogeographic analysis using nine microsatellite loci and two mitochondrial DNA sequences, combined with morphological variation and fine‐tuned ecological niche modelling.Our phylogeographic analyses consistently revealed two well‐supported clades: clade A, for S. y. yangtsekiense, and clade B, which includes other species showing polyphyletic patterning and significant gene introgression. The Nanyang Basin and surrounding mountains regions (NBSM) was identified as a critical shared refuge and hybrid zone, facilitating interspecific introgression through at least two putative hybridisation events. During the Late Pleistocene glacial cycles, introgressive hybridisation of these species occurred in the NBSM, followed by rapid expansion and colonisation of heterogenous habitats during interglacial cycles, with dispersal corridors largely aligning with the local river system. In particular, the diffusion corridor of S. honanense significantly disrupted the continuous distribution of S. y. shanxianense and S. y. tongbaiense, indicating that S. honanense has replaced S. y. shanxianense and S. y. tongbaiense in the NYSM and caused a disruption in its distribution.The biogeographic histories of the species in clade B are consistent with a mixing–isolation–mixing model, which suggests that populations experienced repeated introgressive hybridisation during glacial periods and regional habitat isolation during interglacial periods. Our findings represent a classic case of fine tracking biogeographical scenarios in parapatric species and provide unprecedented insights into the evolutionary radiation of the freshwater fauna that occupies zoogeographic boundaries. [ABSTRACT FROM AUTHOR]

Carotenoid pigments produce the yellow and red colors of birds and other vertebrates. Despite their importance in social signaling and sexual selection, our understanding of how carotenoid ornamentation evolves in nature remains limited. Here, we examine the long-tailed finch Poephila acuticauda , an Australian songbird with a yellow-billed western subspecies acuticauda and a red-billed eastern subspecies hecki , which hybridize where their ranges overlap. We found that yellow bills can be explained by the loss of C(4)-oxidation, thus preventing yellow dietary carotenoids from being converted to red. Combining linked-read genomic sequencing and reflectance spectrophotometry measurements of bill color collected from wild-sampled finches and laboratory crosses, we identify four loci that together explain 53% of variance in this trait. The two loci of largest effect contain the genes CYP2J19 , an essential enzyme for producing red carotenoids, and TTC39B , an enhancer of carotenoid metabolism. A paucity of protein-coding changes and an enrichment of associated upstream variants suggest that the loss of C(4)-oxidation results from cis -regulatory evolution. Evolutionary genealogy reconstruction indicates that the red-billed phenotype is ancestral and that yellow alleles at CYP2J19 and TTC39B first arose and fixed in acuticauda approximately 100 kya. Yellow alleles subsequently introgressed into hecki less than 5 kya. Across all color loci, acuticauda -derived variants show evidence of selective sweeps, implying that yellow bill coloration has been favored by natural selection. Our study illustrates how evolutionary transitions between yellow and red coloration can be achieved by successive selective events acting on regulatory changes at a few interacting genes. [Display omitted] • Long-tailed finch bill color varies due to change in regulation of C(4)-oxidation • Yellow bill color is a derived, recessive trait associated with CYP2J19 and TTC39B • Selection on yellow alleles has driven their introgression between subspecies • Divergence of a carotenoid color ornament results from cis -regulatory changes Carotenoid color ornaments play important roles in social signaling and species recognition. Hooper et al. show that bill-color variation in long-tailed finches is associated with genes controlling the metabolism of red pigments from yellow dietary precursors. Selection favoring yellow alleles is causing the trait to introgress between subspecies. [ABSTRACT FROM AUTHOR]

Hybridization between exotic and native species can lead to negative ecological and economic consequences. The invasive winter moth (WM), Operophtera brumata, uses the same sex-attractant pheromone and mates and produces fertile offspring with a native congener the Bruce spanworm (BSW), O. bruceata, and a stable hybrid zone has formed where their ranges overlap in the northeastern United States. However, the fact that the two species have not merged, despite seasonal overlap of flight, suggests that one or more pre- or post-mating barriers to hybridization might therefore exist. Here, we evaluate the hypothesis that interspecies differences in diel timing of flight might provide pre-mating isolation and explore whether these two species change their diel timing of flight differently in response to changes in temperature. Our results indicate that the flight timing of WM and BSW broadly overlap during the nighttime hours, although WM males fly almost exclusively at dawn, dusk, and night whereas BSW males fly during both daytime and nighttime hours. Flight activity also differed between the two species in response to nighttime temperatures < 0 °C, wherein WM flight largely stopped while BSW flight continued and the proportion of males flying during the daytime increased. This partial partitioning may help explain why the native BSW has not been completely outcompeted by the invasive WM. [ABSTRACT FROM AUTHOR]

Hybrid zones, where genetically distinct groups of organisms meet and interbreed, offer valuable insights into the nature of species and speciation. Here, we present a new R package, bgchm, for population genomic analyses of hybrid zones. This R package extends and updates the existing bgc software and combines Bayesian analyses of hierarchical genomic clines with Bayesian methods for estimating hybrid indexes, interpopulation ancestry proportions, and geographic clines. Compared to existing software, bgchm offers enhanced efficiency through Hamiltonian Monte Carlo sampling and the ability to work with genotype likelihoods combined with a hierarchical Bayesian approach, enabling inference for diverse types of genetic data sets. The package also facilitates the quantification of introgression patterns across genomes, which is crucial for understanding reproductive isolation and speciation genetics. We first describe the models underlying bgchm and then provide an overview of the R package and illustrate its use through the analysis of simulated and empirical data sets. We show that bgchm generates accurate estimates of model parameters under a variety of conditions, especially when the genetic loci analyzed are highly ancestry informative. This includes relatively robust estimates of genome‐wide variability in clines, which has not been the focus of previous models and methods. We also illustrate how both selection and genetic drift contribute to variability in introgression among loci and how additional information can be used to help distinguish these contributions. We conclude by describing the promises and limitations of bgchm, comparing bgchm to other software for genomic cline analyses, and identifying areas for fruitful future development. [ABSTRACT FROM AUTHOR]

Populations in extreme environments at the margins of a species' range are often the most vulnerable to climate change, but they may also experience novel evolutionary processes, such as secondary contact and hybridization with their relatives. The range overlap resulting from secondary contact with related species that have adapted to different climatic zones may act as corridors for adaptive introgression. To test this hypothesis, we examined the hybrid zones along the altitude of two closely related Rubus species, one temperate and the other subtropical species, at their southern and northern limits on Yakushima Island, Japan. Genomic cline analysis revealed non‐neutral introgression throughout the genome in both directions in the two species. Some of these genomic regions involve gene ontology terms related to the regulation of several biological processes. Our niche modeling suggests that, assuming niche conservatism, the temperate species are likely to lose their suitable habitat, and the backcrossed hybrids with the subtropical species are already expanding upslope on the island. Adaptive introgression through the hybrid zone may contribute to the persistence and expansion of the species in the southernmost and northernmost populations. [ABSTRACT FROM AUTHOR]

The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress across broad environmental gradients with limited phenotypic disparity. In the ambiguous gray zone of speciation, where lineages are genetically delimitable but still interacting ecologically, it is expected that these lineages represent species in the context of ontology and the evolutionary species concept when they are maintained over time with geographically well‐defined hybrid zones, particularly at the intersection of distinct environments. As a result, genetic structure is correlated with environmental differences and not space alone, and a subset of genes fail to introgress across these zones as underlying genomic differences accumulate. We present a set of tests that synthesize species delimitation with the speciation process. We can thereby assess historical demographics and diversification processes while understanding how lineages are maintained through space and time by exploring spatial and genome clines, genotype‐environment interactions, and genome scans for selected loci. Employing these tests in eight lineage‐pairs of snakes in North America, we show that six pairs represent 12 "good" species and that two pairs represent local adaptation and regional population structure. The distinct species pairs all have the signature of divergence before or near the mid‐Pleistocene, often with low migration, stable hybrid zones of varying size, and a subset of loci showing selection on alleles at the hybrid zone corresponding to transitions between distinct ecoregions. Locally adapted populations are younger, exhibit higher migration, and less ecological differentiation. Our results demonstrate that interacting lineages can be delimited using phylogeographic and population genetic methods that properly integrate spatial, temporal, and environmental data. [ABSTRACT FROM AUTHOR]

Syngameons represent networks of otherwise distinct species connected by limited gene exchange. Although most studies have focused on how species maintain their cohesiveness despite gene flow, there are additional relevant questions regarding the evolutionary dynamics of syngameons and their drivers, as well as the success of their members and the network as a whole. Using a ddRADseq approach, we analysed the genetic structure, genomic clines and demographic history of a coastal hybrid zone involving two species of the Armeria (Plumbaginaceae) syngameon in southern Spain. We inferred that a peripheral population of the sand dune‐adapted A. pungens diverged from the rest of the conspecific populations and subsequently hybridized with a locally more abundant pinewood congener, A. macrophylla. Both species display extensive plastid DNA haplotype sharing. Genomic cline analysis identified bidirectional introgression, but more outlier loci with excess A. pungens than A. macrophylla ancestry, suggesting the possibility of selection for A. pungens alleles. This is consistent with the finding that the A. pungens phenotype is selected for in open habitats, and with the strong correlation found between ancestry and phenotype. Taken together, our analyses suggest an intriguing scenario in which bidirectional introgression may, on the one hand, help to avoid reduced levels of genetic diversity due to the small size and isolated location of the A. pungens range‐edge population, thereby minimizing demographic risks of stochastic extinction. On the other hand, the data also suggest that introgression into A. macrophylla may allow individuals to grow in open, highly irradiated, deep sandy, salt‐exposed habitats. [ABSTRACT FROM AUTHOR]

Telomere lengths and telomere dynamics can correlate with lifespan, behaviour and individual quality. Such relationships have spurred interest in understanding variation in telomere lengths and their dynamics within and between populations. Many studies have identified how environmental processes can influence telomere dynamics, but the role of genetic variation is much less well characterized. To provide a novel perspective on how telomeric variation relates to genetic variability, we longitudinally sampled individuals across a narrow hybrid zone (n = 127 samples), wherein two Manacus species characterized by contrasting genome‐wide heterozygosity interbreed. We measured individual (n = 66) and population (n = 3) differences in genome‐wide heterozygosity and, among hybrids, amount of genetic admixture using RADseq‐generated SNPs. We tested for population differences in telomere lengths and telomere dynamics. We then examined how telomere lengths and telomere dynamics covaried with genome‐wide heterozygosity within populations. Hybrid individuals exhibited longer telomeres, on average, than individuals sampled in the adjacent parental populations. No population differences in telomere dynamics were observed. Within the parental population characterized by relatively low heterozygosity, higher genome‐wide heterozygosity was associated with shorter telomeres and higher rates of telomere shortening—a pattern that was less apparent in the other populations. All of these relationships were independent of sex, despite the contrasting life histories of male and female manakins. Our study highlights how population comparisons can reveal interrelationships between genetic variation and telomeres, and how naturally occurring hybridization and genome‐wide heterozygosity can relate to telomere lengths and telomere dynamics. [ABSTRACT FROM AUTHOR]

Conservation and management of medicinally important plants are among the necessary tasks all over the world. The genus Dracocephalum (Lamiaceae) contains about 186 perennials, or annual herb species that have been used for their medicinal values in different parts of the world as an antihyperlipidemic, analgesic, antimicrobial, antioxidant, as well as anticancer medicine. Producing detailed data on the genetic structure of these species and their response against climate change and human landscape manipulation can be very important for conservation purposes. Therefore, the present study was performed on six geographical populations of two species in the Dracocephalum genus, namely, Dracocephalum kotschyi, and Dracocephalum oligadenium, as well as their inter-specific hybrid population. We carried out, population genetic study, landscape genetics, species modeling, and genetic cline analyses on these plants. We present here, new findings on the genetic structure of these populations, and provide data on both geographical and genetic clines, as well as morphological clines. We also identified genetic loci that are potentially adaptive to the geographical spatial features and genocide conditions. Different species distribution modeling (SDM) methods, used in this work revealed that bioclimatic variables related to the temperature and moisture, play an important role in Dracocephalum population's geographical distribution within IRAN and that due to the presence of some potentially adaptive genetic loci in the studied plants, they can survive well enough by the year 2050 and under climate change. The findings can be used for the protection of these medicinally important plant. [ABSTRACT FROM AUTHOR]

The rich genetic and phenotypic diversity of species complexes is best recognized through formal taxonomic naming, but one must first assess the evolutionary history of phylogeographic lineages to identify and delimit candidate taxa. Using genomic markers, mitochondrial DNA barcoding, and morphometric analyses, we examined lineage diversity and distribution in the Iberian endemic frog Rana parvipalmata. We confirmed two deep phylogeographic lineages, one relatively homogenous genetically, found in Asturias and adjacent areas (T2), and one more fragmented and locally genetically impoverished, restricted to Galicia (T1). Analyses of their hybrid zone suggested a shallow transition characterized by far-ranging admixture, which was modelled by a wide geographic cline (~60 km for the genome average) and no obvious barrier loci (i.e. loci showing disproportionally restricted introgression). The relatively young T1 and T2 have thus remained reproductively compatible, which argues against their distinction as biological species, and we accordingly describe T2 as a new subspecies, Rana parvipalmata asturiensis ssp. nov. Remarkably, we highlight striking discordances between mitochondrial and nuclear distributions across their hybrid zones, as well as between their genetic and morphological differentiation. Our study illustrates how genomic-based phylogeographic frameworks can help decipher the high genetic and phenotypic variation of species complexes and substantiate the taxonomic assessment of candidate lineages. [ABSTRACT FROM AUTHOR]

Interbreeding and introgression between recently diverged species is common. However, the processes that prevent these species from merging where they co‐occur are not well understood. We studied the mechanisms that allowed an isolated group of populations of the snail Helix thessalica to persist within the range of the related Helix pomatia despite high gene flow. Using genomic cline analysis, we found that the nuclear gene flow between the two taxa across the mosaic hybrid zone was not different from that expected under neutral admixture, but that the exchange of mtDNA was asymmetric. Tests showed that there is relaxed selection in the mitochondrial genome of H. thessalica and that the substitution rate is elevated compared to that of H. pomatia. A lack of hybrids that combine the mtDNA of H. thessalica with a mainly (>46%) H. pomatia genomic background indicates that the nuclear‐encoded mitochondrial proteins of H. pomatia are not well adapted to the more rapidly evolving proteins and RNAs encoded by the mitochondrion of H. thessalica. The presumed reduction of fitness of hybrids with the fast‐evolving mtDNA of H. thessalica and a high H. pomatia ancestry, similar to 'Darwin's Corollary to Haldane's rule', resulted in a relative loss of H. pomatia nuclear ancestry compared to H. thessalica ancestry in the hybrid zone. This probably prevents the H. thessalica populations from merging quickly with the surrounding H. pomatia populations and supports the hypothesis that incompatibilities between rapidly evolving mitochondrial genes and nuclear genes contribute to speciation. [ABSTRACT FROM AUTHOR]

Hybrid zones occur in nature when populations with limited reproductive barriers overlap in space. Many hybrid zones persist over time, and different models have been proposed to explain how selection can maintain hybrid zone stability. More empirical studies are needed to elucidate the role of ecological adaptation in maintaining stable hybrid zones. Here, we investigated the role of exogenous factors in maintaining a hybrid zone between western gulls (Larus occidentalis) and glaucous‐winged gulls (L. glaucescens). We used ecological niche models (ENMs) and niche similarity tests to quantify and examine the ecological niches of western gulls, glaucous‐winged gulls, and their hybrids. We found evidence of niche divergence between all three groups. Our results support the bounded superiority model, providing further evidence that exogenous selection favoring hybrids may be an important factor in maintaining this stable hybrid zone. [ABSTRACT FROM AUTHOR]

Differences in migratory behavior have been suggested to drive speciation, but the genetics underlying this process remain unknown. Identification and study of migratory divides can help us understand how differential migration can lead to reproductive isolation. Here, we genotyped Willow Warblers Phylloscopus trochilus, from the Åland islands, located in between the ranges of the differentially migrating subspecies P. t. trochilus and P. t. acredula. We found that Willow Warblers on the Åland islands were genetically intermediate to allopatric populations of both parental subspecies, providing evidence that the islands constitute a previously unknown hybrid swarm, likely to be a migratory divide. [ABSTRACT FROM AUTHOR]

This article explores the presence of putative hybrids between the Mountain Caracara and White-throated Caracara in northern Patagonia. The authors use eBird records and other sources to map the distribution and overlap of the two species. They identify potential hybrids based on plumage characteristics and discuss the ecological importance of northern Patagonia for the evolutionary processes within this group of caracaras. The study suggests that further research and genetic studies are needed to confirm these hybrids and understand their evolutionary history, with potential implications for the impact of climate change on Andean ecosystems and the conservation of national parks in the region. [Extracted from the article]

Seasonal migration is a widespread behavior relevant for adaptation and speciation, yet knowledge of its genetic basis is limited. We leveraged advances in tracking and sequencing technologies to bridge this gap in a well- characterized hybrid zone between songbirds that differ in migratory behavior. Migration requires the coordinated action of many traits, including orientation, timing, and wing morphology. We used genetic mapping to show these traits are highly heritable and genetically correlated, explaining how migration has evolved so rapidly in the past and suggesting future responses to climate change may be possible. Many of these traits mapped to the same genomic regions and small structural variants indicating the same, or tightly linked, genes underlie them. Analyses integrating transcriptomic data indicate cholinergic receptors could control multiple traits. Furthermore, analyses integrating genomic differentiation further suggested genes underlying migratory traits help maintain reproductive isolation in this hybrid zone. [ABSTRACT FROM AUTHOR]

Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest in natural hybridisation fuelled by developments in genomics has led to an improved understanding of the genetic factors that promote or prevent species cross‐mating. Despite this body of work overturning many widely held assumptions about the genetic barriers to hybridisation, it is still widely thought that ploidy differences between species will be an absolute barrier to hybridisation and introgression. Here, we revisit this assumption, reviewing findings from surveys of polyploidy and hybridisation in the wild. In a case study in the British flora, 203 hybrids representing 35% of hybrids with suitable data have formed via cross‐ploidy matings, while a wider literature search revealed 59 studies (56 in plants and 3 in animals) in which cross‐ploidy hybridisation has been confirmed with genetic data. These results show cross‐ploidy hybridisation is readily overlooked, and potentially common in some groups. General findings from these studies include strong directionality of hybridisation, with introgression usually towards the higher ploidy parent, and cross‐ploidy hybridisation being more likely to involve allopolyploids than autopolyploids. Evidence for adaptive introgression across a ploidy barrier and cases of cross‐ploidy hybrid speciation shows the potential for important evolutionary outcomes. [ABSTRACT FROM AUTHOR]

Iberian populations of large-bodied newts, with Triturus marmoratus in the north and T. pygmaeus in the south of the peninsula, were studied for external morphology, mitochondrial dna and for a panel of single nucleotide polymorphisms. This confirmed the species' low level of interspecific hybridization and their parapatric, mosaic-like mutual range border across the peninsula. The genetic data also revealed substantial variation within T. pygmaeus, with narrow (0.43-35.2 km) clinal transitions in the very centre of Portugal. Similar clines were observed for body size and colouration pattern. Pygmy newts in the west of Portugal are larger, with a more striped (less reticulated) green dorso-lateral colouration pattern than those in the east and south of the country. The western group of populations is described as a new species, Triturus rudolfi sp. nov., on account of a long, ca. 2.5 Ma, independent evolutionary history and limited hybridization with its sister-species T. pygmaeus, suggesting selection against hybrid offspring. The range of the newly described species may be restricted to the wider Lisbon Peninsula, stretching northwards along the Atlantic coast to the river Vouga estuary. Inland, the range border may be set by the lower Tejo River, or by the currently wide area of agricultural land at either side of that river, that may accommodate a residual hybrid zone. The close contact between both pygmy newt species is effectively limited to a ca. 20 × 40 km area directly north of the town Entroncamento, where T. rudolfi sp. nov. is sandwiched in between T. marmoratus and the river Tejo. [ABSTRACT FROM AUTHOR]

Hybrid systems represent 'new ecological opportunities', as the changes in their vegetative and reproductive traits may facilitate colonization of new niches. The Cactaceae species Xiquexique gounellei and Xiquexique tuberculatus present different habitat preferences in the Brazilian Caatinga, however, across their distributions, some populations occur sympatrically and some individuals showed vegetative characteristics intermediate between these two species, suggesting a hybrid zone. These individuals also clearly did not belong to either of the two species, leading us to suppose that they could be hybrids, named as X. × heptagonus. Taking into account this assumption, we used a series of protocols to compare the floral attributes and signals, and floral biology displayed by the putative hybrid with those of its parents. The results showed that the flowers of the hybrid are morphologically intermediate to those of their parents. The colour of the external elements of the perianth is transgressive, and the white colour of the internal perianth-segments is shared between the three taxa. Scent analyses showed that X. × heptagonus has a scent profile that is intermediate to those of its parents, with only a few compounds indicating a transgressive phenotype. Both taxa of Xiquexique received visits from nectarivorous bats (Glossophaginae and Lonchophyllinae) and from the hawkmoths Agrius cingulata and Erinnyis ello. Our results reinforce the existence of this hybrid in the genus Xiquexique being derived from the possible parent species present. We also revealed how the floral morphology and the visual and olfactory cues of X. × heptagonus were shaped by the hybridization. [ABSTRACT FROM AUTHOR]

Hybridization among related species is now recognized as common but it remains unclear how hybrid zones persist for prolonged periods. Here, we test the hypothesis that selection in different components of the life cycle may stabilize a hybrid zone. A hybrid zone occurs in southwest England between the marine mussels Mytilus edulis and M. galloprovincialis. Previous studies have found strong directional selection against alleles from M. edulis occurs among hybrids in the adult stage. Traditional hybrid zone models argue that alleles that are selected within the hybrid zone are replaced by migration from neighboring parental population into the hybrid zone. In this system, however, migration occurs out of this hybrid zone into neighboring parental populations. This hybrid zone should therefore be unstable and dissipate, yet this zone has persisted for more than 30 years. We tested and rejected the hypothesis that differences in fecundity may select for M. edulis alleles within this hybrid zone and thus counter the selection observed against these alleles among adults. We also tested the hypothesis that selection during the larval stage may counter selection against M. edulis alleles in the adult stage. We found that selection favors M. edulis alleles during the veliger stage of larval development. The direction and strength of selection during the larval stage are sufficient to counter strong selection during the adult portion of the life cycle. This hybrid zone is stabilized by opposing forms of directional selection operating in different portions of the life cycle. [ABSTRACT FROM AUTHOR]

Admixture, the interbreeding of individuals from differentiated source populations, is now known to be a widespread phenomenon. Genomic studies of natural hybridisation can help to answer many questions on the impacts of admixture on adaptive evolution, reproductive isolation, and speciation. When a large variety of admixture proportions between two source populations exist, both geographic and genomic cline analysis are suitable methods for inferring biased, restricted or excessive gene flow at individual loci into the foreign genomic background, providing evidence for reproductive isolation, selection across an environmental transition, balancing selection, and adaptive introgression. Genomic cline analysis replaces geographic location with genome‐wide hybrid index and is therefore useable in circumstances that violate geographic cline assumptions. Here, I introduce gghybrid, an R package for simple and flexible Bayesian estimation of Buerkle's hybrid index and Fitzpatrick's logit‐logistic genomic clines using bi‐allelic data, suitable for both small and large datasets. gghybrid allows any ploidy and uses Structure input file format. It has separate functions for hybrid index and cline estimation, treating each individual and locus respectively as an independent analysis, making it highly parallelisable. Admixture proportions from other software can alternatively be used in cline analysis, alongside parental allele frequencies. Parameters can be fixed and samples pooled for statistical model comparison with AIC or waic. Here, I describe the functions, pipeline, and statistical properties of gghybrid. Simulations reveal that model comparison with waic is preferred, and use of Bayesian posterior distributions and p values to select candidate non‐null loci is problematic and should be avoided. [ABSTRACT FROM AUTHOR]

Hybridisation is commonly observed in geographical zones of contact between distinct lineages. These contact zones have long been of interest for biogeographers because they provide insight into the evolutionary and ecological processes that influence the distribution of species as well as the process of speciation. Here we review research on hybrid zones and zones of past introgression, both terrestrial and marine, in Aotearoa New Zealand. Many of New Zealand's hybrid zones occur between lineages or species that diverged prior to the Last Glacial Maximum (LGM), with numerous divergences dating to the early Pleistocene or Pliocene. Few secondary contact zones have been detected in terrestrial plants and in marine taxa. This may reflect a lack of the intensive sampling required to detect hybrid zones in these groups but for plants may also indicate widespread Pleistocene survival across the country. Lastly, we suggest avenues for research into New Zealand hybrid zones that are likely to be fruitful. [ABSTRACT FROM AUTHOR]

Hybrid inviability is an important post-zygotic reproductive barrier between species, but emerging signs of reduced viability can be difficult to study across the lifespan of natural hybrids. We use a combination of long-term monitoring, extra-pair paternity, and mitochondrial DNA identification in a natural hybrid zone of Ficedula flycatchers to detect emerging signs of intrinsic hybrid inviability across their entire lifespan. We evaluate possible evidence of Darwin’s corollary to Haldane’s rule, predicting asymmetries in inviability between hybrids resulting from reciprocal crosses, due to incompatible genetic factors with sex-specific inheritance patterns. We found higher hatching failure among mixed-species pairs, possibly indicating early developmental impairments associated with specific parental genetic combinations. Adult hybrids had a higher basal mortality rate than both parental species and different age-specific mortality trajectories. There were signs of differences in age-independent mortality rates between the reciprocal hybrid crosses: hybrids with a pied flycatcher mother experienced slightly increased mortality later in life. Using an exceptional dataset with many natural hybrids tracked across life stages, we provide evidence for several emerging signs of reduced hybrid viability. Incompatibilities between alleles located on autosomes and uniparentally inherited factors such as Z-linked and/or mitochondrial genes are strong candidates underlying intrinsic hybrid dysfunction in this system. [ABSTRACT FROM AUTHOR]

Uncertainties on species taxonomy and distribution are major factors hampering efficient conservation planning in the current context of biodiversity erosion, even concerning widespread and abundant species in relatively well‐studied regions. Species delimitation have long been based on phylogenetic analyses of a small number of standard markers, but accurate lineage identification through this approach can be hampered by incomplete lineage sorting, introgression or isolation by distance. In that context, analyses of introgression patterns at secondary contact zones offer an interesting alternative by allowing a direct estimation of reproductive isolation, especially when using genome‐wide markers. Here, we investigated a contact zone between two genetic groups of the Spiny‐footed Lizard Acanthodactylus erythrurus (Schinz, 1833) in Morocco, whose status as separate lineages remained disputed in previous multilocus studies. Based on thousands of genome‐wide markers obtained through a RADseq approach, we confirmed that they represent distinct evolutionary lineages. Furthermore, the transition at their contact zone was very steep, with spatially restricted gene flow, highlighting levels of reproductive isolation consistent with species‐level lineages. Our study further illustrates the power of RADseq‐based studies of contact zones to understand cryptic diversity in non‐model organisms. [ABSTRACT FROM AUTHOR]

The question of how interactions between the gut microbiome and vertebrate hosts contribute to host adaptation and speciation is one of the major problems in current evolutionary research. Using bacteriome and mycobiome metabarcoding, we examined how these two components of the gut microbiota vary with the degree of host admixture in secondary contact between two house mouse subspecies (Musmusculus musculus and M. m. domesticus). We used a large data set collected at two replicates of the hybrid zone and model‐based statistical analyses to ensure the robustness of our results. Assuming that the microbiota of wild hosts suffers from spatial autocorrelation, we directly compared the results of statistical models that were spatially naive with those that accounted for spatial autocorrelation. We showed that neglecting spatial autocorrelation can strongly affect the results and lead to misleading conclusions. The spatial analyses showed little difference between subspecies, both in microbiome composition and in individual bacterial lineages. Similarly, the degree of admixture had minimal effects on the gut bacteriome and mycobiome and was caused by changes in a few microbial lineages that correspond to the common symbionts of free‐living house mice. In contrast to previous studies, these data do not support the hypothesis that the microbiota plays an important role in host reproductive isolation in this particular model system. [ABSTRACT FROM AUTHOR]

Introgressive hybridization caused by invasive species may lead to the extinction of pure native species, but a theoretical model of the invasion process with hybridization (the neutral demographic model) suggests that introgression occurs mainly from native to invasive species. Clarifying the direction of introgression is important to evaluate the impact of hybridization on native species. In southern Japan, a widely disseminated gecko, Gekko hokouensis , and a local gecko, Gekko yakuensis , have formed mosaic hybrid zones. Given the presumed invasiveness of Gekko hokouensis , the neutral demographic model predicts that introgression would mainly occur in the direction to Gekko hokouensis , whereas possible asymmetric assortative mating suggested by a previous study predicts the opposite direction of introgression. Our investigations using microsatellite markers and mitochondrial DNA for the gecko assemblages in 12 localities and comparisons with allozyme data collected 18 years ago indicated that Gekko hokouensis expanded its range and tended to have replaced hybrids and Gekko yakuensis. Introgression was skewed towards Gekko hokouensis , but interspecific mating between the parental species was reciprocal. These results suggest that their hybridization progress follows the neutral demographic model and that the higher population growth rate of Gekko hokouensis is the major cause of species replacement, although we cannot rule out the possibility that asymmetric assortative mating also influences the later stages of species replacement. [ABSTRACT FROM AUTHOR]

The research into the structure, population and genetic patterns of formation and long-term existence of natural hybrid zones is of paramount importance for modern biology and the theory of evolution. The article presents the research results on the 22-year monitoring (2002–2023) of a hybrid zone and hybrid colonies of russet (Spermophilus major Pallas, 1778) and yellow (Spermophilus fulvus Lichtenstein, 1823) ground squirrels. This hybrid zone arose as a result of active dispersal of S. major to the south in the Saratov Trans-Volga region in the early 2000s. Twelve rodent colonies attributed to different research periods were studied. A total of 405 individuals (including 103 individuals of S. major, 52 individuals of S. fulvus, and 250 genetically confirmed interspecific hybrids) were trapped and sampled. Based on evidence, the article examines the structure and factors for formation of the hybrid zone between russet and yellow ground squirrels. Hybrid colony features and the evolution of hybrid population are considered. Introgressive hybridization between russet and yellow ground squirrels clearly manifests itself towards actively dispersing S. major. The revealed structural and genetic features of the hybrid zone between S. major and S. fulvus have enabled it to be termed as a bimodal hybrid zone of an ecological type with introgressive hybridization and stable hybrid colonies. [ABSTRACT FROM AUTHOR]

Premise of research. Narrow hybrid zones are maintained by the counteracting forces of selection and gene flow. Understanding the mechanisms of formation and maintenance of narrow hybrid zones helps elucidate the evolutionary forces shaping reproductive biology, distribution, and diversification. We studied the ecology of the hybrid zone of two Impatiens species, Impatiens rosea and Impatiens balsamina , and the causes of the hybrid zone's restriction in space. Methodology. We characterized floral morphometry for the identification of hybrids and parents. To understand the selection on floral traits, we modeled and compared geographic clines of floral traits. We assessed the effect of environmental niche, local adaptation, reproductive niche, and hybrid fitness on maintaining the structure of the hybrid zone. We studied two hybridization sites, one with an altitudinal gradient (Mulshi) and one without (Dapoli), to test the importance of environmental gradients. Pivotal results. We found that pollination-related floral traits, the length of the nectar spur and the size and shape of the wing petal, differ strongly between the parental populations; that these traits are intermediate in hybrids; and that they form the steepest coincident clines across the hybrid zone. Abiotic environmental niche and hybrid fitness do not regulate the hybrid zone structure. Parental species and hybrids show overlapping pollinators but differ in visitation frequencies. Local adaptation for reproductive success influences hybridization only in the site with an altitudinal gradient. Conclusions. The hybrid zone structure and its influencing factors differ across hybridization sites with and without altitudinal gradient. Neither the tension zone model nor the environment-dependent selection model completely explain this hybrid zone. Pollinator-mediated selection on floral traits is important in maintaining the narrow hybrid zone structure. Ecological factors primarily responsible for lineage divergence are also most likely to govern the dynamics of hybridization of the lineages. [ABSTRACT FROM AUTHOR]

Background and Aims In eastern Neotropical South America, the Cerrado, a large savanna vegetation, and the Atlantic Forest harbour high biodiversity levels, and their habitats are rather different from each other. The biomes have intrinsic evolutionary relationships, with high lineage exchange that can be attributed, in part, to a large contact zone between them. The genomic study of ecotypes, i.e. populations adapted to divergent habitats, can be a model to study the genomic signatures of ecological divergence. Here, we investigated two ecotypes of the tree Plathymenia reticulata , one from the Cerrado and the other from the Atlantic Forest, which have a hybrid zone in the ecotonal zone of Atlantic Forest–Cerrado. Methods The ecotypes were sampled in the two biomes and their ecotone. The evolutionary history of the divergence of the species was analysed with double‐digest restriction site‐associated DNA sequencing. The genetic structure and the genotypic composition of the hybrid zone were determined. Genotype-association analyses were performed, and the loci under putative selection and their functions were investigated. Key Results High divergence between the two ecotypes was found, and only early-generation hybrids were found in the hybrid zone, suggesting a partial reproductive barrier. Ancient introgression between the Cerrado and Atlantic Forest was not detected. The soil and climate were associated with genetic divergence in Plathymenia ecotypes and outlier loci were found to be associated with the stress response, with stomatal and root development and with reproduction. Conclusions The high genomic, ecological and morphophysiological divergence between ecotypes, coupled with partial reproductive isolation, indicate that the ecotypes represent two species and should be managed as different evolutionary lineages. We advise that the forest species should be re-evaluated and restated as vulnerable. Our results provide insights into the genomic mechanisms underlying the diversification of species across savanna and forest habitats and the evolutionary forces acting in the species diversification in the Neotropics. [ABSTRACT FROM AUTHOR]

Speciation is often accompanied by frequent gene exchanges, which have been gradually recognized as a common phenomenon in nature. Although gene flow may influence different reproductive isolations, the specific mechanism of the process still requires more experimental evidence, especially in hybrid populations that have no significant differentiation and isolation. To address this challenge, this study aims to elucidate the underlying mechanisms of sympatry and parapatry in related species. Three sclerophyllous oaks (Quercus spinosa, Quercus aquifolioides and Quercus rehderiana), which are mainly distributed in the sympatry/parapatry of the East Himalaya–Hengduan Mountains and adjacent regions, were used to explore the population dynamics and evolutionary history. Based on 12,420 genome‐wide single nucleotide polymorphism datasets, gene flow detection showed that the three species did not present any obvious genetic barriers. Evolutionary analysis indicated that the three species diverged during the Tertiary Period, and no migration events occurred in the early stages of species divergence. Combined with the data of 19 ecological factors, geological movements and climatic turbulence caused the rapid radiated differentiation of the three species during the Neocene, and similar selective pressures resulted in the same evolutionary pattern based on demographic history analysis. In addition, the predicted niche occupancy profiles and Generalized Dissimilarity Modelling revealed that the three species occupied distinct niches and had significant differences in ecological adaptation, which may explain the specific morphological characteristics of the different species. Therefore, we believe that the populations of the three related species underwent adaptive evolution in different habitats during the early stages of divergence. This study provides new experimental evidence of the formation patterns of parallel speciation. [ABSTRACT FROM AUTHOR]

A major goal of evolutionary biology is to understand how sexual traits arise and diversify among populations. One way to address this objective is by studying sexual traits in closely related species and their hybrids. Here, we used this approach to study the evolution of elaborate behavioural display characteristics used during courtship. We focus on bearded manakins (genus: Manacus), where males of this avian clade perform an acrobatic jump-snap display to court females. Hybridization is common among Manacus taxa, and thus, we studied courtship dance behaviour in a hybrid population between golden-collared manakins, Manacus vitellinus , and white-collared manakins, Manacus candei. We found that, despite being genetically more similar to white-collared manakins, hybrid males performed key dance manoeuvres like golden-collared manakins. Hybrids performed other dance manoeuvres intermediate to the two species, or more like their white-collared parents. Select components of the birds' dance routines may have therefore introgressed from the golden-collared population into the white-collared populations. We hypothesize that such modular evolution occurs in response to sexual selection, whereby specific components of the bird's dance routine shift to yield a broader change in its functional appearance. • We studied courtship display in a hybrid population of manakin birds. • Hybrids performed many display traits intermediately to their parental lineages. • Some hybrid traits, however, resembled their high-performing parental line. • Asymmetrical introgression may account for display evolution in hybrids. [ABSTRACT FROM AUTHOR]

The mechanisms of hybridization can be elucidated by analyzing genotypes as well as phenotypes that could act as premating barriers, as the reproductive interactions among heterospecifics can alter the evolutionary history of species. In frogs, hybrids typically occur among species that reproduce explosively (in dense aggregations) with few opportunities for mate selection but are rare in species with elaborate courtship behaviors that may prevent erroneous mating. Using 21 microsatellite markers, we examined hybridization in the prolonged‐breeding tree frogs Bokermannohyla ibitiguara and B. sazimai sampled within a contact zone in the Brazilian savanna (72 tadpoles; 74 adults). We also compared acoustic and morphological data. We confirmed both parental species genetically; STRUCTURE results confirmed 14 hybrids, 11 of which were second‐generation according to NEWHYBRIDS, all with intermediate values of genetic dissimilarities compared to the parentals. Morphological and acoustic analyses revealed that hybrids showed variable but not necessarily intermediate phenotypes. Moreover, 2 hybrids exhibited call types different from parentals. The reproduction of B. ibitiguara involves territorial and aggressive males, elaborate courtships with acoustic and tactile stimuli, choosy females, and opportunistic strategies. Our study uncovers a rare case of viable hybridization among closely related frogs with such a combination of complex courtship behaviors and mate choice. We discuss the likely directionality and mechanisms behind this phenomenon, and highlight the importance of investigating hybridization even in species that show elaborate reproduction and female choice to advance our understanding of animal diversification. [ABSTRACT FROM AUTHOR]

Simple Summary: The chukar partridge (Alectoris chukar) is an important bird species with significant economic and ecological value. Every year, thousands of partridges raised in Ministry of Agriculture and Forestry breeding farms are released into nature for hunting purposes. Our investigation of the gene pools of different A. chukar populations using mitochondrial and microsatellite markers from across Türkiye revealed that the Eastern, Western, and Thracian genetic structures have been shaped by Türkiye's geography and topography, past climatic fluctuations, and human-mediated artificial hybridizations. There were no signs of congeneric genetic contamination in native chukar populations, but there were contaminations with the China clade-B, which were detected as reported in the previous studies. Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population. [ABSTRACT FROM AUTHOR]

Understanding how reproductive isolation arises and accumulates between incipient species is an important goal of evolutionary biology. Patterns of interspecific hybridization in naturally occurring hybrid zones can provide an important insight into this process since they reflect the strength, symmetry and nature of reproductive barriers separating the species. Here we studied patterns of hybridization in two closely related passerine species, the common nightingale Luscinia megarhynchos and the thrush nightingale L. luscinia, that diverged ~1.8 Mya and co‐occur in a secondary contact zone spanning across Europe. Genome‐wide genotyping of more than three hundred individuals from the sympatric population and adjacent allopatric populations revealed that the vast majority of sympatric individuals were pure parental species. Only 6.5% of sympatric individuals were hybrids, from which 3.4% were F1 hybrids and 3.1% backcross hybrids from the first to the fifth backcross generation. Most F1 hybrids arose from the cross of a thrush nightingale female and a common nightingale male. F1 hybrids showed intermediate morphology and could be distinguished with high confidence from the parental species based on several diagnostic traits. However, backcrosses were morphologically difficult to distinguish from the parental species from which they inherited most of the genome. Our results suggest strong, yet incomplete, reproductive isolation between the two nightingale species both at a prezygotic and postzygotic level. Nightingales thus represent a useful model system for exploring the late stages of speciation with ongoing gene flow after secondary contact. [ABSTRACT FROM AUTHOR]

The narrow-headed vole species complex is represented by Lasiopodomys gregalis and L. raddei, which probably diverged at the beginning of the Middle Pleistocene and came into secondary contact in the Transbaikal region. The current study analyzed mitochondrial gene cytochrome b, nuclear gene BRCA1, and microsatellite data and was aimed at clarifying geographic ranges of these species and searching for hybrid zones between them. It turned out that the geographic range of L. raddei is almost surrounded by that of L. gregalis; these species are strictly parapatric without a single detected sympatry zone. Although in none of the tested populations did the BRCA1 genotyping contradict the pattern revealed by mitochondrial cytb, microsatellite loci showed traces of hybridization in several populations. Results of species distribution modeling indicated that these species are characterized by quite similar (caused by the same environmental factors), but nevertheless significantly different, ecological preferences. [ABSTRACT FROM AUTHOR]

Natural hybridization between closely related species in sympatry is an evolutionary process that is common in orchids. Once seen as a threat to parent species, interspecific genetic change is increasingly viewed as a source of novel variation in some ecological contexts. Terrestrial fringed orchids in the genus Platanthera contain several clades with high genetic compatibility among species and many putative hybrids. We used biallelic SNPs generated with 3RAD sequencing to study the hybrid complex formed from the parent species P. blephariglottis, P. ciliaris, and P. cristata with high resolution. The genetic structure and phylogenetic relationship of the hybrid complex revealed site-dependent gene flow between species. We documented extensive hybridization and cryptic hybrids in sympatric sites. Interspecific genetic exchange is particularly common between P. blephariglottis and P. ciliaris, with cryptic hybrids among putative P. ciliaris samples being more common than parental assignments in sympatric sites. Hybridization across the triad species complex can reticulate lineages and introduce adaptive alleles. Conversely, it can reduce diversification rates and introduce maladaptive alleles. Investigation into whether anthropogenic forces are eroding species boundaries, particularly the permeable P. blephariglottis and P. ciliaris boundary, is appropriate for conservation efforts. [ABSTRACT FROM AUTHOR]

Recent advances in next generation sequencing (NGS) have greatly increased our understanding of non-coding tandem repeat (TR) DNA. Here we show how TR DNA can be useful for the study of hybrid zones (HZ), as it serves as a marker to identify introgression in areas where two biological entities come in contact. We used Illumina libraries to analyse two subspecies of the grasshopper Chorthippus parallelus, which currently form a HZ in the Pyrenees. We retrieved a total of 152 TR sequences, and used fluorescent in situ hybridization (FISH) to map 77 families in purebred individuals from both subspecies. Our analysis revealed 50 TR families that could serve as markers for analysis of this HZ, using FISH. Differential TR bands were unevenly distributed between chromosomes and subspecies. Some of these TR families yielded FISH bands in only one of the subspecies, suggesting the amplification of these TR families after the geographic separation of the subspecies in the Pleistocene. Our cytological analysis of two TR markers along a transect of the Pyrenean hybrid zone showed asymmetrical introgression of one subspecies into the other, consistent with previous findings using other markers. These results demonstrate the reliability of TR-band markers for hybrid zone studies. [ABSTRACT FROM AUTHOR]

Mating behavior can play a key role in speciation by inhibiting or facilitating gene flow between closely related taxa. Hybrid zones facilitate a direct examination of mating behavior and the traits involved in establishing species barriers. The long‐tailed finch (Poephila acuticauda) has two hybridizing subspecies that differ in bill color (red and yellow), and the yellow bill phenotype appears to have introgressed ~350 km eastward following secondary contact. To examine the role of mate choice on bill color introgression, we performed behavioral assays using natural and manipulated bill colors. We found an assortative female mating preference for males of their own subspecies when bill color was not manipulated. However, we did not find this assortative preference in trials based on artificially manipulated bill color. This could suggest that assortative preference is not fixed entirely on bill color and instead may be based on a different trait (e.g., song) or a combination of traits, or alternatively may be due to lower statistical power alongside the bill manipulations being unconvincing to the female choosers. Intriguingly, we find a bias in the inheritance of bill color in captive bred F1 hybrid females. Previous modeling suggests that assortative mate preference and this kind of partial dominance in the underlying genes may together contribute to introgression, making the genetic architecture of bill color in this system a priority for future research. [ABSTRACT FROM AUTHOR]

Coloration is an important target of both natural and sexual selection. Discovering the genetic basis of colour differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with both clear colour differences and shallow genomic divergences are unusually tractable for associating coloration phenotypes with their causal genotypes. Here, we leverage the extensive admixture between two common North American woodpeckers—yellow-shafted and red-shafted flickers—to identify the genomic bases of six distinct plumage patches involving both melanin and carotenoid pigments. Comparisons between flickers across approximately 7.25 million genome-wide SNPs show that these two forms differ at only a small proportion of the genome (mean FST = 0.008). Within the few highly differentiated genomic regions, we identify 368 SNPs significantly associated with four of the six plumage patches. These SNPs are linked to multiple genes known to be involved in melanin and carotenoid pigmentation. For example, a gene (CYP2J19) known to cause yellow to red colour transitions in other birds is strongly associated with the yellow versus red differences in the wing and tail feathers of these flickers. Additionally, our analyses suggest novel links between known melanin genes and carotenoid coloration. Our finding of patch-specific control of plumage coloration adds to the growing body of literature suggesting colour diversity in animals could be created through selection acting on novel combinations of coloration genes. [ABSTRACT FROM AUTHOR]

The microbiome is critical to an organism's phenotype, and its composition is shaped by, and a driver of, eco‐evolutionary interactions. We investigated how host ancestry, habitat and diet shape gut microbial composition in a mammalian hybrid zone between Neotoma lepida and N. bryanti that occurs across an ecotone between distinct vegetation communities. We found that habitat is the primary determinant of diet, while host genotype is the primary determinant of the gut microbiome—a finding further supported by intermediate microbiome composition in first‐generation hybrids. Despite these distinct primary drivers, microbial richness was correlated with diet richness, and individuals that maintained higher dietary richness had greater gut microbial community stability. Both relationships were stronger in the relative dietary generalist of the two parental species. Our findings show that host ancestry interacts with dietary habits to shape the microbiome, ultimately resulting in the phenotypic plasticity that host–microbial interactions allow. [ABSTRACT FROM AUTHOR]

The relationships between the yellowhammer (Еmberiza citrinella) and the pine bunting (Еmberiza leucocephalos) represent quite a rare case of mass hybridization in a broad sympatry zone. The hybrid population was monitored from 2008 to 2019 in a model area in the Altai Mountains, Russia, with the purpose to identify the potential pre- and postcopulatory isolation mechanisms in these species. The area selected as the model one is the only place in the vast secondary contact zone of the two species distinguished by the maximum hybridization level and a high proportion of birds with phenotypes of both parental species in approximately equal proportions. During the observation period, the proportion of phenotypic hybrids increased from 32 to 58%. Nevertheless, the population retains some precopulatory isolation mechanisms that are manifested in the positive mating assortativity and partial biotopic segregation between the species. On par with individuals featuring parental phenotypes, hybrids participate in breeding and successfully bring out nestlings: the phenotypic composition of feeding birds does not differ from the phenotypic composition of the population as a whole. However, the life span of hybrids is shorter; this applies even to birds featuring parental species phenotypes with slightly expressed characters indicating their hybrid origin. [ABSTRACT FROM AUTHOR]

Aim: Our main aim was to identify the distribution of, and potential mechanisms underpinning, hybrid‐rich zones – regions with a disproportionate number of unique interspecific hybrids. We investigated whether coral reef fish hybrids coincided with factors such as phylogenetic relatedness, biogeographic barriers, species richness, geographic isolation, endemism, and oceanic currents. Location: Global. Time period: Contemporary. Major taxa studied: Coral reef fishes. Methods: We conducted a literature review and mapping to assess the taxonomic and global prevalence of hybridisation in coral reef fishes. We then fit Generalised additive models using a full‐subsets and Bayesian framework to assess which variables are associated with hybrid‐rich zones. Results: We found 143 unique interspecific coral reef fish hybrids involving 204 species – which accounts for approximately 7% of coral reef fish species, indicating that hybridisation is as common in the sea as it is on land. Characteristic coral reef fish families were not homogeneously represented in our dataset, with particularly colourful groups standing out. Mapping our dataset revealed that coral reef fish hybrids are found worldwide, though some ecoregions (e.g., the Christmas and Cocos (Keeling) Islands, South Kuroshio, Hawaii, and Eastern Philippines) are more hybrid‐rich than others. Our analysis revealed that mean surface current velocity, phylogenetic relatedness, and geographic isolation were the best predictors of hybrid richness in a given location. Main conclusions: Phylogenetic distance between coral reef fish species may serve as a pre‐condition for hybridisation to occur, lying between introgression and reproductive incompatibility. We also propose a novel mechanism, with oceanic currents driving long‐distance larval dispersal events, transporting stray species to geographically remote sinks to maintain hybrid‐rich zones. [ABSTRACT FROM AUTHOR]

Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex‐determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex‐determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex‐determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment‐dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well‐studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female‐heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion‐sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex‐determining region between ecotypes. Such sex chromosome‐environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex‐specific selection and divergent natural selection is required to explain these highly unusual patterns. [ABSTRACT FROM AUTHOR]

Parapatrically distributed taxa pose a challenge for species delimitation due to the presence of gene flow and inherent arbitrariness of exactly defining the species boundaries in such systems. We tackled the problem of species delimitation in a parapatric species pair of Melitaea butterflies using two popular genomic methods—double digest restriction‐site associated DNA sequencing (ddRAD) and target enrichment. We compared newly generated target enrichment dataset with 1733 loci to the already available ddRAD data from a previous study on the same set of specimens using a suite of phylogenetic, population genetic, and species delimitation methods. We recovered consistent phylogenetic relationships across the datasets, both demonstrating the presence of a genetically distinct Balkan lineage and paraphyly of Melitaea athalia with respect to Melitaea celadussa. Population genetic STRUCTURE analyses supported the presence of two species when using ddRAD data, but three species when using target enrichment, while a Bayes factor delimitation analysis found both two and three species scenarios equally decisive in both datasets. As the results obtained from both methods were largely congruent, we discuss some practical considerations and benefits of target enrichment over RAD sequencing. We conclude that the choice of method of genomic data collection does not influence the results of phylogenetic analyses at alpha taxonomic level, given a sufficient number of loci. Finally, we recommend a solution for delineating species in parapatric scenarios by proposing that parapatric taxa be consistently classified as subspecies or complete species, but not both, to promote taxonomic stability. [ABSTRACT FROM AUTHOR]

The African Queen butterfly (Danaus chrysippus) is noted for its colour pattern polymorphism despite its aposematic and chemically defended lifestyle and for its infection with a male‐killing endosymbiont (Spiroplasma). The polymorphism is largely restricted to east and central Africa where three different colour forms meet and interbreed in a large contact or hybrid zone. The primary objective of this study is to present recent data on the polymorphism, sex ratio and the incidence of male killing in D. chrysippus populations in Rwanda. We also report previously unpublished data from a random sample collected in 1914 in Bujumbura in Burundi and on the differential effects of weather on males and females in Ghana from 1972 to 1974. We sampled butterflies using butterfly nets and either marked, recorded and released them or kept specimens for subsequent examination. We used PCR/microscopy on the preserved specimens to detect Spiroplasma and the presence of a protozoan parasite (Ophryocystis). Our findings suggest that Rwanda lies close to the western edge of the joint distribution of both Spiroplasma and the polymorphism. Further biogeographical studies are recommended to test the hypothesis that male killing is restricted to the contact zone in which polymorphism is commonly observed. [ABSTRACT FROM AUTHOR]

Unmanned aerial vehicles (UAVs), or drones, are being utilized by wildlife biologists to monitor populations of birds and mammals. However, the reaction of wildlife to drones varies by species, so a preliminary evaluation must be conducted to determine if the target species can be detected via drone footage and to determine how the target species will react to drone presence. Lek‐mating prairie‐chickens (Tympanuchus spp.) seem amenable to drone‐based surveys because they are relatively large and display in groups on elevated sites with sparse vegetation. The goal of our study was to determine what flight characteristics maximize prairie‐chicken detection on drone video footage, to document the birds' reactions to the drones, and to compare how the noise produced by the drones compares to ambient sounds. We tested 3 sizes of rotary‐winged drones, flown at 3 heights, with 3 different camera angles by flying over known prairie‐chicken leks. We determined that >65% of prairie‐chickens present were detected using video footage at a height of 100 m with a 10° camera angle. Drones of different sizes had similar detectability. However, observers in blinds adjacent to leks routinely detected more birds than were detected on drone footage (detection on drone footage was 39.7 ± 9.6% of birds present). Prairie‐chickens flushed in 96% of trials when a drone was flown over display locations. Time to return to the lek following drone disturbance was similar to prairie‐chickens' reactions to natural predators. Prairie‐chickens flushed when drone sound levels were comparable to ambient noise. Developing guidelines for the ethical use of drones in wildlife research will require quantifying the amount of taxa‐specific disturbance caused by drones. Our study begins to close this knowledge gap by documenting disturbance to upland, lek‐mating grouse of conservation concern, and suggests that the focal species' reaction to aerial predators may provide clues as to how that species may react to drones. [ABSTRACT FROM AUTHOR]

Identifying mechanisms limiting hybridization is a central goal of speciation research. Here, we studied premating and postmating barriers to hybridization between two ant species, Formica selysi and Formica cinerea. These species hybridize in the Rhône valley in Switzerland, where they form a mosaic hybrid zone, with limited introgression from F. selysi into F. cinerea. There was no sign of temporal isolation between the two species in the production of queens and males. With choice experiments, we showed that queens and males strongly prefer to mate with conspecifics. Yet, we did not detect postmating barriers caused by genetic incompatibilities. Specifically, hybrids of all sexes and castes were found in the field and F1 hybrid workers did not show reduced viability compared to nonhybrid workers. To gain insights into the cues involved in species recognition, we analyzed the cuticular hydrocarbons (CHCs) of queens, males, and workers and staged dyadic encounters between workers. CHC profiles differed markedly between species, but were similar in F. cinerea and hybrids. Accordingly, workers also discriminated species, but they did not discriminate F. cinerea and hybrids. We discuss how the CHC‐based recognition system of ants may facilitate the establishment of premating barriers to hybridization, independent of hybridization costs. [ABSTRACT FROM AUTHOR]

Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide‐ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype–environment associations in the hermit thrush (Catharus guttatus), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype–environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature‐associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature‐related barriers to gene flow and/or temperature‐driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype–environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population‐level sensitivity to climate change and other stressors. [ABSTRACT FROM AUTHOR]

It is thought that two species can coexist if they use different resources present in the environment, yet this assumes that species are completely reproductively isolated. We simulate coexistence outcomes for two sympatric species that are ecologically differentiated but have incomplete reproductive isolation. The consequences of interbreeding crucially depend on hybrid fitness. When hybrid fitness is high, just a small rate of hybridization can lead to collapse of two species into one. Low hybrid fitness can cause population declines, making extinction of one or both species likely. High intrinsic growth rates result in higher reproductive rates when populations are below carrying capacity, reducing the probability of extinction and increasing the probability of stable coexistence at moderate levels of assortative mating and hybrid fitness. Very strong but incomplete assortative mating can induce low hybrid fitness via a mating disadvantage to rare genotypes, and this can stabilize coexistence of two species at high but incomplete levels of assortative mating. Given these results and evidence that it may take many millions of years of divergence before related species become sympatric, we postulate that coexistence of closely related species is more often limited by insufficient assortative mating than by insufficient ecological differentiation. [ABSTRACT FROM AUTHOR]

• Molecular data suggest that there are still populations of purebred Senecio hercynicus in the Bavarian and Bohemian Forest. • While western populations are strongly introgressed by S. ovatus genotypes, introgressive hybridisation is less pronounced towards the (north)east of the study area. • Regression analyses show that bio-climatological conditions do not shape hybridisation intensity patterns in the species pair. • The fate of Senecio hercynicus in a climate-change scenario is discussed. Genetic swamping by introgressive hybridisation threatens diversity, caused by climate warming particularly in mountainous regions worldwide. Recent studies resulted in a threatening perspective for Senecio hercynicus in the Bavarian Forest due to genetic swamping by introgressive hybridisation with its cogener S. ovatus. To examine the situation more closely, the distribution and hybridization of S. hercynicus and S. ovatus in high elevation regions of the Bavarian and Bohemian Forest was analyzed by restriction enzyme digestion of nrDNA ITS1 (PCR-RFLP; PCR restriction fragment length polymorphism). For a total of 706 samples from 94 different sample localities a hybrid index was inferred from the fragment band intensities after PCR-RFLP digestion. Boxplot diagrams of the hybrid indices show a tendency of western populations towards S. ovatus genotypes and for populations to the east towards S. hercynicus genotypes. When the hybrid index data was subjected to a regression analysis with nine factors (five habitat patterns inferred during sampling and four bioclimatic variables), only geographical longitude and latitude seemed to describe the observed distribution of S. hercynicus and S. ovatus significantly, arguing for the distribution and hybridisation patterns being shaped rather due to historical than to eco-climatological determinants. While a broad zone of hybridisation between the two species in the Bavarian and Bohemian Forest region was inferred, our study demonstrates that purebred S. hercynicus still exists and remnant stands of this species should be the target of species conservation measures. [ABSTRACT FROM AUTHOR]