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Freshwater zooplankter Brachionus plicatilis is able to inhabit different habitats and locally adapt to their environmental conditions. It also shows a high degree of population structuring in small geographical regions. Here we try to shed light on the evolution of reproductive isolation in populations of B. plicatilis with presumptive gene flow among locally adapted populations. We have conducted laboratory experiments on admixed pairwise populations that differ in predictability of the water regime. We have assessed the potential for within-population reproductive preferences as a deviation of genotypes from Hardy–Weinberg equilibrium in diapausing eggs, a product of sexual reproduction. We expected heterozygote deficit to increase with environmental distance. We have found signs for incipient reproductive isolation in one third of our admixed populations, however no correlation with environmental distance was found, nor with genetic or geographic predictor variables. The overall inbreeding coefficient showed a tendency for within-population crosses preferences to decrease over time. [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]

Studying hybrid zones that form between morphologically cryptic taxa offers valuable insights into the mechanisms of cryptic speciation and the evolution of reproductive barriers. Although hybrid zones have long been the focus of evolutionary studies, the awareness of cryptic hybrid zones increased recently due to rapidly growing evidence of biological diversity lacking obvious phenotypic differentiation. The characterization of cryptic hybrid zones with genome‐wide analysis is in its early stages and offers new perspectives for studying population admixture and thus the impact of gene flow. In this study, we investigate the population genomics of the Myotis nattereri complex in one of its secondary contact zones, where a putative hybrid zone is formed between two of its cryptic lineages. By utilizing a whole‐genome shotgun sequencing approach, we aim to characterize this cryptic hybrid zone in detail. Demographic analysis suggests that the cryptic lineages diverged during the Pliocene, c. 3.6 million years ago. Despite this ancient separation, the populations in the contact zone exhibit mitochondrial introgression and a considerable amount of mixing in nuclear genomes. The genomic structure of the populations corresponds to geographic locations and the genomic admixture changes along a geographic gradient. These findings suggest that there is no effective hybridization barrier between both lineages, nevertheless, their population structure is shaped by dispersal barriers. Our findings highlight how such deeply diverged cryptic lineages can still readily hybridize in secondary contact. [ABSTRACT FROM AUTHOR]

Summary: Hybrid zones provide natural experimental settings to test hypotheses about species divergence. We concentrated on a hybrid swarm in which oil‐collecting bees and flower‐pecking birds act as pollinators of two Calceolaria species. We asked whether both pollinators contributed to flower divergence by differentially promoting prezygotic fitness at the phenotypic extremes that represent parentals.We studied pollinator‐mediated selection on phenotypic traits critical in plant–pollinator mechanical interaction, namely plant height, reward‐to‐stigma distance, and flower shape. We utilised the quantity and quality of pollen deposited as fitness measures and distinguished between the contribution of the two pollinator types.Results showed uni‐ and bivariate disruptive selection for most traits through pollen grains deposited by both pollinators. Bird‐mediated fitness favoured low plants with a long reward‐to‐stigma distance and a straight corolla, while bee‐mediated fitness favoured tall plants with a short reward‐to‐stigma distance and curved corolla. In addition, stabilising selection at one end of the phenotypic range showed a bird‐mediated reproductive asymmetry within the swarm. The disruptive pattern was countered, albeit weakly, by hybrids receiving higher‐quality pollen on the stigmas.Results suggest that pollinator‐mediated selection promotes divergence of integrated flower phenotypes mechanically adjusted either to bees or birds underscoring the importance of pollinator specialisation in diversification. [ABSTRACT FROM AUTHOR]

Idealized ring species, with approximately continuous gene flow around a geographic barrier but singular reproductive isolation at a ring terminus, are rare in nature. A broken ring species model preserves the geographic setting and fundamental features of an idealized model but accommodates varying degrees of gene flow restriction over complex landscapes through evolutionary time. Here we examine broken ring species dynamics in Calisoga spiders, which, like the classic ring species Ensatina salamanders, are distributed around the Central Valley of California. Using nuclear and mitogenomic data, we test key predictions of common ancestry, ringlike biogeography, biogeographic timing, population connectivity, and terminal overlap. We show that a ring complex of populations shares a single common ancestor, and from an ancestral area in the Sierra Nevada mountains, two distributional and phylogenomic arms encircle the Central Valley. Isolation by distance occurs along these distributional arms, although gene flow restriction is also evident. Where divergent lineages meet in the South Coast Ranges, we find rare lineage sympatry, without evidence for nuclear gene flow and with clear evidence for morphological and ecological divergence. We discuss general insights provided by broken ring species and how such a model could be explored and extended in other systems and future studies. [ABSTRACT FROM AUTHOR]

Aim: The British Isles have been worked for millennia to extract metal ores to feed industrial development, leaving a legacy of mine water pollution that continues to impact freshwater communities in many regions. Brown trout (Salmo trutta L.) have long been observed to persist in these metal‐impacted systems as apex predators, with previous studies showing a small number of impacted populations to be highly genetically divergent. We sought to understand the scale of genetic diversity across regions and the repeatability of genetic divergence in trout populations affected by metal pollution. Location: We examined four mine water‐impacted regions across the British Isles: west Wales, northeast England, southwest England and southeast Ireland. Methods: We employed a panel of 95 SNP loci to screen 1236 individuals from 71 sites representing paired metal‐impacted and clean sites from across the four regions. From these, we obtained diversity statistics, assessed genetic structuring of populations and modelled historical demographic scenarios to understand which factors most credibly explain genetic variation in divergent populations. Results: We evidenced hierarchical population structure in the regions studied, in line with expectations from phylogeographic history. However, in a hierarchical analysis of genetic structuring the first level of differentiation was driven by the divergence of the metal‐impacted trout of Cornwall in southwest England. Within regions we observed reduced genetic diversity and repeated patterns of local genetic sub‐structuring between paired samples from metal‐impacted and relatively clean sites. Demographic history analyses suggested the timing of these splits to be relatively recent and to be associated with periods of peak mining activity. Main conclusions: Our findings demonstrate distinct patterns of genetic isolation and reduced diversity arising from legacy pollution in freshwater ecosystems, with impacts being most apparent where both chemical pollution and physical barriers are present. Management should focus on the amelioration of mine water wash‐out and the removal of barriers to fish movement to safeguard genetic diversity in impacted populations. [ABSTRACT FROM AUTHOR]

The linguistic, historical, and subsistent uniqueness of Hmong–Mien (HM) speakers offers a wonderful opportunity to investigate how these factors impact the genetic structure. The genetic differentiation among HM speakers and their population history are not well characterized. Here, we generate genome‐wide data from 65 Yao ethnicity samples and analyze them with published data, particularly by leveraging haplotype‐based methods. We determined that the fine‐scale genetic substructure of HM speakers corresponds better with linguistic classification than with geography. Particularly, parallels between serial founder events and language differentiations can be observed in West Hmongic speakers. Multiple lines of evidence indicate that ~500‐year‐old GaoHuaHua individuals are most closely related to West Hmongic‐speaking Bunu. The strong genetic bottleneck of some HM‐speaking groups, especially Bunu, could potentially be associated with their long‐term practice of swidden agriculture to some degree. The inferred admixture dates for most of the HM speakers overlap with the reign of the Ming dynasty (1368–1644 CE). Besides a common genetic origin for HM speakers, their genetic ancestry is shared primarily with neighboring Han Chinese and Tai‐Kadai speakers in south China. In conclusion, our analyses reveal that recent isolation and admixture events have contributed to the genetic population history of present‐day HM speakers. [ABSTRACT FROM AUTHOR]

Knowledge of the reproductive isolation mechanisms that prevent gene flow between species is essential for understanding the process of speciation. In this study, we investigate the spawning periods in Fissurella cumingi and F. latimarginata, two closely related sympatric species of keyhole limpets with external fertilization, as a potential prezygotic barrier between them. The reproductive cycle was assessed in two distinct locations in northern Chile using the gonadosomatic index (GSI) and gonadal histology. Species, locality, and sex were designated as predictive variables, while average GSI values, as well as those of partial and total spawning, were considered dependent variables. Both species exhibit a continuous gametogenic cycle throughout the year, characterized by multiple spawning events. A generalized linear model (GLM) factorial ANOVA design revealed that neither species, locality nor sex were significant factors with respect to the GSI and partial spawning scores. However, sex was found to be the only significant factor related to total spawning. No significant interactions were observed among predictive factors. These findings suggest that reproductive periods may not serve as effective barriers to gamete encounters between species. Our study prompts questions about how closely-related externally-fertilizing species maintain reproductive isolation. [ABSTRACT FROM AUTHOR]

Summary: Nicotiana attenuata styles preferentially select pollen from among accessions with corresponding expression patterns of NaS‐like‐RNases (SLRs), and the postpollination ethylene burst (PPEB) is an accurate predictor of seed siring success. However, the ecological consequences of mate selection, its effect on the progeny, and the role of SLRs in the control of ethylene signaling remain unknown.We explored the link between the magnitude of the ethylene burst and expression of the SLRs in a set of recombinant inbred lines (RILs), dissected the genetic underpinnings of mate selection through genome‐wide association study (GWAS), and examined its outcome for phenotypes in the next generation.We found that high levels of PPEB are associated with the absence of SLR2 in most of the tested RILs. We identified candidate genes potentially involved in the control of mate selection and showed that pollination of maternal genotypes with their favored pollen donors produces offspring with longer roots. When the maternal genotypes are only able to select against nonfavored pollen donors, the selection for such positive traits is abolished.We conclude that plants' ability of mate choice contributes to measurable changes in progeny phenotypes and is thus likely a target of selection. [ABSTRACT FROM AUTHOR]

Acoustic differentiation in bird vocalisations is a key process for speciation. Calls have received little attention compared to songs, but their simplicity facilitates analysis using mathematical, non-biased, tools, as they can be described by means of very basic variables. Here, we combined PERMANOVA and machine learning techniques to analyse the differentiation in the contact calls of the closely related Dartford (Curruca undata), Marmora's (C. sarda) and Balearic (C. balearica) warblers (formerly in the genus Sylvia). The calls of the three species differed clearly, consistent with phylogenetic reconstructions based on DNA sequences. In C. sarda, significant call differences were observed between the population wintering in Tunisia (migratory) and those of Sardinia and Corsica (mainly sedentary). Such divergence could be favoured by assortative mating of migrant and resident individuals, working as a matching mechanism for reproductive isolation in sympatry. In contrast, there was no clear separation between the accepted subspecies of C. undata. We found, however, significant differences between the Atlantic and Mediterranean biogeographical regions in this species. The divergences detected within C. undata and C. sarda deserve further investigation, using additional traits to elucidate the phylogenetic status of these groups, as well as the factors driving their diversification. [ABSTRACT FROM AUTHOR]

Hybrid zones have been viewed as an opportunity to see speciation in action. When hybrid zones are replicated, it is assumed that if the same genetic incompatibilities are maintaining reproductive isolation across all instances of secondary contact, those incompatibilities should be identifiable by consistent patterns in the genome. In contrast, changes in allele frequencies due to genetic drift should be idiosyncratic for each hybrid zone. To test this assumption, we simulated 20 replicates of each of 12 hybrid zone scenarios with varied genetic incompatibilities, rates of migration, selection and different starting population size ratios of parental species. We found remarkable variability in the outcomes of hybridisation in replicate hybrid zones, particularly with Bateson–Dobzhansky–Muller incompatibilities and strong selection. We found substantial differences among replicates in the overall genomic composition of individuals, including admixture proportions, inter‐specific ancestry complement and number of ancestry junctions. Additionally, we found substantial variation in genomic clines among replicates at focal loci, regardless of locus‐specific selection. We conclude that processes other than selection are responsible for some consistent outcomes of hybridisation, whereas selection on incompatibilities can lead to genomically widespread and highly variable outcomes. We highlight the challenge of mapping between pattern and process in hybrid zones and call attention to how selection against incompatibilities will commonly lead to variable outcomes. We hope that this study informs future research on replicate hybrid zones and encourages further development of statistical techniques, theoretical models and exploration of additional axes of variation to understand reproductive isolation. [ABSTRACT FROM AUTHOR]

The continuously expanding field of Alzheimer's disease (AD) research is now beginning to defocus the brain to take a more systemic approach to the disease, as alterations in the peripheral organs could be related to disease progression. One emerging hypothesis is organ involvement in the process of Aβ clearance. In the present work, we aimed to examine the status and involvement of the kidney as a key organ for waste elimination and the spleen, which is in charge of filtering the blood and producing lymphocytes, and their influence on AD. The results showed morphological and structural changes due to acute amyloidosis in the kidney (glomeruli area) and spleen (red pulp area and red/white pulp ratio) together with reduced antioxidant defense activity (GPx) in 16-month-old male and female 3xTg-AD mice when compared to their age- and sex-matched non-transgenic (NTg) counterparts. All these alterations correlated with the anxious-like behavioral phenotype of this mouse model. In addition, forced isolation, a cause of psychological stress, had a negative effect by intensifying genotype differences and causing differences to appear in NTg animals. This study further supports the relevance of a more integrative view of the complex interplay between systems in aging, especially at advanced stages of Alzheimer's disease. [ABSTRACT FROM AUTHOR]

The evolution of behavioral isolation is often the first step toward speciation. While past studies show that behavioral isolation will sometimes evolve as a by-product of divergent ecological selection, we lack a more nuanced understanding of factors that may promote or hamper its evolution. The environment in which mating occurs may be important in mediating whether behavioral isolation evolves for two reasons. Ecological speciation could occur as a direct outcome of different sexual interactions being favored in different mating environments. Alternatively, mating environments may vary in the constraint they impose on traits underlying mating interactions, such that populations evolving in a "constraining" mating environment would be less likely to evolve behavioral isolation than populations evolving in a less constraining mating environment. In the latter, mating environment is not the direct cause of behavioral isolation but rather permits its evolution only if other drivers are present. We test these ideas with a set of 28 experimental fly populations, each of which evolved under one of two mating environments and one of two larval environments. Counter to the prediction of ecological speciation by mating environment, behavioral isolation was not maximal between populations evolved in different mating environments. Nonetheless, mating environment was an important factor as behavioral isolation evolved among populations from one mating environment but not among populations from the other. Though one mating environment was conducive to the evolution of behavioral isolation, it was not sufficient: assortative mating only evolved between populations adapting to different-larval environments within that mating environment, indicating a role for ecological speciation. Intriguingly, the mating environment that promoted behavioral isolation is characterized by less sexual conflict compared to the other mating environment. Our results suggest that mating environments play a key role in mediating ecological speciation via other axes of divergent selection. [ABSTRACT FROM AUTHOR]

Studies of reproductive behavior can help reveal patterns of sexual isolation and clarify species boundaries. In northern Georgia, Blue Ridge Two-lined Salamanders (Eurycea cf. wilderae) and Brown-backed Salamanders (Eurycea aquatica) are syntopic but do not hybridize. Within this region, Eurycea cf. wilderae males exhibit a reproductive polymorphism, with "searching" males that appear adapted for terrestrial courtship and "guarding" males that appear adapted for aquatic mate-guarding. To understand better how inter- and intraspecific reproductive variation might contribute to sexual isolation between E. aquatica and E. cf. wilderae, we staged T-maze trials and courtship trials, and we conducted preliminary analyses of sex hormones from noninvasive fecal samples. We found that males of both species preferred conspecific female scents to heterospecific female scents, but that searching male E. cf. wilderae were not better than guarding males at locating a conspecific female scent. We also found evidence for strong propensity asymmetry, with male and female E. cf. wilderae much more likely than E. aquatica to engage in courtship behaviors in the lab. Still, we observed some instances of heterospecific courtship through spermatophore transfer. Finally, we found evidence for higher fecal testosterone concentrations in males than females and higher concentrations in guarding male than in searching male E. cf. wilderae. Together, our data provide further insight into the reproductive ecologies of and the nature of reproductive isolation between Eurycea aquatica and Eurycea cf. wilderae. [ABSTRACT FROM AUTHOR]

The reproductive biology of the branching octocoral Antillogorgia americana was studied at a site on the Caribbean coast of Panama in 1990–1991 by examining the reproductive status of 11 colonies across 14 months. Colonies were gonochoric. The presence of large and mature eggs or spermaries was allochronic across colonies and months, with peak gonad volumes occurring in months ranging from October through May. Reproductive effort varied between branches on a colony, with variation between branches and branchlets accounting for 25% of the random variation between polyps. Branchlets at the tip of the colony had fewer mature eggs than those lower on the branch, and polyps at the tips of the branchlets had fewer still. Although the simultaneous release of eggs and sperm is critical to reproductive success, the lack of synchrony among colonies on the scale of months may reflect less need for all colonies to spawn in a single event among abundant species that release large numbers of gametes. Such a strategy also spreads the risk of reproductive failure due to environmental conditions during any single month. The presence of multiple spawning episodes can also drive the reproductive isolation of populations and may reflect the presence of cryptic species within the taxon. Studies of reproductive timing can be an important adjunct in identifying variation in life history strategies as well as assessing the validity of species boundaries. [ABSTRACT FROM AUTHOR]

We investigated the evolutionary patterns of two forest-dwelling endemic terrestrial snails (Gittenedouardia spadicea and Maizania wahlbergi) in the Maputaland–Pondoland–Albany biodiversity hotspot in South Africa to examine the degree of phylogeographical congruence between the two species. Phylogenetic relationships and divergence time estimations within each species were inferred using the combined mitochondrial DNA (mtDNA) sequence dataset for the cytochrome c oxidase subunit I (COI) and large subunit ribosomal RNA (16S rRNA). In addition, the rapidly evolving COI datasets were used to infer intraspecific genetic structure and population differentiation within both species. Phylogeographical concordance factor (PCF) analysis was used to statistically estimate the degree of congruence between the two species at localities where both species were sampled. Phylogenetically, G. spadicea exhibited two clades that diverged during the Plio/Pleistocene, while M. wahlbergi formed a single shallow clade that showed Pleistocene divergence. The haplotype networks for the COI locus demonstrated evidence of geographical and genetic isolation within both species. PCF analysis demonstrated partial phylogeographical concordance, suggesting that the two species may have been affected by similar ancient climatic events. Traits other than poor dispersal capabilities and limited gene flow may also influence how a species responds to fluctuating climate change. [ABSTRACT FROM AUTHOR]

Aim: We assessed the population genetic structure of the kleptoparasitic spider Argyrodes bonadea across the Southwestern Pacific islands. Our aim is to evaluate the impact of overseas distances and, in particular, the Kerama gap, as potential drivers of genetic differentiation. If no relationship exists, then we assume dispersal following adaptive change as alternative non‐vicariant mechanism that generates divergence. Location: Southwestern Pacific Islands. Taxon: Argyrodes bonadea. Methods: We used mitochondrial Cytochrome Oxidase 1 (CO1) gene sequences and Restriction Site‐associated DNA Sequencing (RAD‐seq) for our analyses. Results: Two strongly supported lineages, an Amami‐Okinawa Lineage (AOL) and an Austral‐Asia Lineage (AAL), correspond to two separate clades, roughly divided by the Kerama Gap, in phylogenetic trees estimated here. However, species delimitation led to the interpretation of only a single species present. The AOL exhibits complex, geographically structured host web spider species specificity, wherein the Amami population utilizes Cyrtophora, but AOL samples in Okinawa associate exclusively with Nephila—and yet all broadly distributed AAL populations show no evidence of host web spider species specificity. Main Conclusion: The population boundary between AOL and AAL likely results from local adaptation to novel hosts—instead of isolation by the Kerama Gap—following long‐distance dispersal and range expansion. Our results suggest kleptoparasitic spiders have the capacity to overcome permanent deep‐sea barriers and colonize distant landmasses. Whereas peripheral populations (AOL) demonstrate the capacity for specialization to a single host, which may have contributed to genetic differentiation and isolation, the broadly distributed AAL persists and has successfully expanded its geographical range as a host generalist, which may contribute to ongoing gene flow inferred in this study. [ABSTRACT FROM AUTHOR]

Animals have a deep evolutionary relationship with microbial symbionts, such that individual microbes or an entire microbial community can diverge alongside the host. Here, we explore these host-microbe relationships in Echinometra, a sea urchin genus that speciated with the Isthmus of Panama and throughout the Indo-West Pacific. We find that the eggs from five Echinometra species generally associate with a species-specific bacterial community and that the relatedness of these communities is largely congruent with host phylogeny. Microbiome divergence per million years was higher in more recent speciation events than in older ones. We, however, did not find any bacterial groups that displayed co-phylogeny with Echinometra. Together, these findings suggest that the evolutionary relationship between Echinometra and their microbiota operates at the community level. We find no evidence suggesting that the associated microbiota is the evolutionary driver of Echinometra speciation. Instead, divergence between Echinometra and their microbiota is likely the byproduct of ecological, geographic, and reproductive isolations. [ABSTRACT FROM AUTHOR]

Incomplete speciation can be leveraged to associate phenotypes with genotypes, thus providing insights into the traits relevant to the reproductive isolation of diverging taxa. We investigate the genetic underpinnings of the phenotypic differences between Sporophila plumbea and Sporophila beltoni. Sporophila beltoni has only recently been described based, most notably, based on differences in bill coloration (yellow vs. black in S. plumbea). Both species are indistinguishable through mtDNA or reduced-representation genomic data, and even whole-genome sequencing revealed low genetic differentiation. Demographic reconstructions attribute this genetic homogeneity to gene flow, despite divergence in the order of millions of generations. We found a narrow hybrid zone in southern Brazil where genetically, yet not phenotypically, admixed individuals appear to be prevalent. Despite the overall low genetic differentiation, we identified 3 narrow peaks along the genome with highly differentiated SNPs. These regions harbor 6 genes, one of which is involved in pigmentation (EDN3) and is a candidate for controlling bill color. Within the outlier peaks, we found signatures of resistance to gene flow, as expected for islands of speciation. Our study shows how genes related to coloration traits are likely involved in generating prezygotic isolation and establishing species boundaries early in speciation. [ABSTRACT FROM AUTHOR]

The genetic dissection of reproductive barriers between diverging lineages provides enticing clues into the origin of species. One strategy uses linkage analysis in experimental crosses to identify genomic locations involved in phenotypes that mediate reproductive isolation. A second framework searches for genomic regions that show reduced rates of exchange across natural hybrid zones. It is often assumed that these approaches will point to the same loci, but this assumption is rarely tested. In this perspective, we discuss the factors that determine whether loci connected to postzygotic reproductive barriers in the laboratory are inferred to reduce gene flow in nature. We synthesize data on the genetics of postzygotic isolation in house mice, one of the most intensively studied systems in speciation genetics. In a rare empirical comparison, we measure the correspondence of loci tied to postzygotic barriers via genetic mapping in the laboratory and loci at which gene flow is inhibited across a natural hybrid zone. We find no evidence that the two sets of loci overlap beyond what is expected by chance. In light of these results, we recommend avenues for empirical and theoretical research to resolve the potential incongruence between the two predominant strategies for understanding the genetics of speciation. [ABSTRACT FROM AUTHOR]

Aim: Darwin posited that invaders similar to native species are less likely to be successful due to competitive exclusion. A key axis across which such competition occurs across angiosperms is the timing of flowering, or reproductive phenology. It has been hypothesized that temporal isolation facilitates the establishment of introduced species. However, our knowledge of how the timing of flowering may influence invasion success is lacking at broader geographic and larger taxonomic scales. To address this impasse, we investigated: (i) how flowering phenology differs between native and non‐native species; (ii) whether the flowering phenology of successful invaders is distinct from native taxa; and (iii) whether invasive species tend to be more closely related to natives than other less successful, non‐invasive introduced species are. Location: California, USA. Time Period: Present. Major Taxa Studied: Angiosperms. Methods: We compiled phenological data for over 6000 angiosperm species across California, a highly invaded biodiversity hotspot, from published flora. Using these data, we assessed the degree of phenological and phylogenetic similarity among native, non‐invasive introduced, and invasive species. We also examined how this similarity varies with climate. Results: Both non‐invasive introduced and invasive species were more phenologically and phylogenetically distant from natives than natives were from each other. However, invasive plants tend to be more similar to native species in terms of flowering phenology and phylogenetic relationships than non‐invasive introduced species. Further, the degree of similarity between native and non‐native species was mediated by climate, where phenological and phylogenetic similarities were greater in cooler regions. Main Conclusions: Together, our results demonstrate that both similarity and distinctiveness can facilitate plant invasions and that invaders just similar enough to the native flora are more likely to be successful. [ABSTRACT FROM AUTHOR]

SUMMARY: Understanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non‐model tree species are not yet fully understood. To address this issue, we generated whole‐genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long‐term refugial isolation and recent differential introgression in low‐recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values. Significance Statement: We assembled a chromosome‐scale genome of Liquidambar formosana and resequenced 160 individuals of L. formosana and its high‐altitude sister species L. acalycina. Benefiting from advanced analytical methods and robust evidence, we found that multiple "genomic islands" mainly evolved as a result of divergence hitchhiking and recombination rate variation, as likely fostered by long‐term refugial isolation and recent differential introgression in low‐recombination genomic regions; and identified some candidate genes associated with climatic adaptation and reproductive isolation. [ABSTRACT FROM AUTHOR]

Trophic polymorphism and temporal reproductive isolation are the drivers of sympatric differentiation in many fish taxa. We present a new case of ecologically based diversification of Arctic charr in a Transbaikalian mountain lake inhabited by reproductively isolated dwarf and normal forms. These forms differ in size, diets and morphology and breed, respectively, in April–May and in September–October representing a rare example of sympatric spring- and autumn-spawning charr pair. Microsatellite analysis reveals clear-cut genetic differences and low-level hybridization between them. Dwarf form charr are planktivorous and manifest uniform slow growth. Normal form charr, though genetically homogeneous, are highly heterogeneous in size-at-age. They are subdivided into omnivorous small-size and piscivorous large-size groups, which can be considered as incipient forms at an early divergence stage. As evidenced by back-calculated growth data, their size-at-age heterogeneity results from highly variable individual growth patterns, which include different combinations of slow and fast growth periods presumably associated with spawning and non-spawning years. Growth acceleration in late ontogeny may result in the transformation of some normal charr from the smaller into the larger group during their lifetime. [ABSTRACT FROM AUTHOR]

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally ("residents") were often more resilient to fragmentation than long-ranging "migrants." This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world. [ABSTRACT FROM AUTHOR]

Premise of research. Reinforcement is the process through which prezygotic reproductive barriers evolve in sympatry owing to selection against hybridization between co-occurring, closely related species. The role of self-fertilization in reinforcement and reproductive isolation is uncertain, in part because its efficiency as a barrier against heterospecific mating can depend on the timing of autonomous selfing. Methodology. To investigate whether increased autonomous selfing has evolved as a mechanism for reinforcement, we compared Phlox cuspidata populations across their native Texas range using both estimates of genetic diversity and experimental manipulation with morphological measurements. Specifically, we investigated patterns of variation in floral traits and timing of selfing between individuals from allopatric populations of P. cuspidata and from populations sympatric with the closely related species Phlox drummondii. Pivotal results. We infer intermediate rates of selfing across field-collected individuals with no significant difference between allopatric and sympatric populations. Among greenhouse-grown plants, we find no differences in timing of selfing or other floral traits, including anther dehiscence timing, anther-stigma distance, autonomous selfing rate, and self-seed count, between allopatric and sympatric populations. However, our statistical analyses indicate that P. cuspidata individuals sympatric with P. drummondii seem to have generally larger flowers compared with allopatric individuals. Conclusions. Despite strong evidence of costly hybridization with P. drummondii , we find no evidence of trait divergence due to reinforcement in P. cuspidata. Although we document nearly complete autonomous self-seed set in the greenhouse, estimates of selfing rates from genetic data imply that realized selfing is much lower in nature, suggesting an opportunity for reinforcing selection to act on this trait. [ABSTRACT FROM AUTHOR]

Background and Aim: Short beak and dwarfism syndrome (SBDS), a highly contagious disease, has been reported in duck farms in Vietnam since 2019. In this study, we evaluated the virulence and characterized the virus obtained from SBDS cases in North Vietnam. Materials and Methods: Polymerase chain reaction was used to detect waterfowl parvovirus in ducks, and the virus from positive samples was inoculated into 10-day-old duck-embryonated eggs to reproduce the disease in young ducklings to determine the virulence and subjected to phylogenetic analysis of non-structural (NS) and VP1 gene sequences. Results and Discussion: Goose parvovirus (GPV) was isolated from ducks associated with SDBS in Vietnam. The virus Han-GPV2001 is highly virulent when inoculated into 10-day-old duck embryos and 3-day-old ducklings. The mortality rate of duck embryos was 94.35% within 6 days of virus inoculation. Inoculating 3-day-old ducks with the virus stock with 104.03 EID50 through intramuscular and neck intravenous administration resulted in 80% and 66.67% of clinical signs of SDBS, respectively, were shown. Phylogenetic analysis based on the partial NS and VP1 gene sequences revealed that the viral isolate obtained in this study belonged to novel GPV (NGPV) and was closely related to previous Vietnamese and Chinese strains. Conclusion: A GPV strain, Han-GPV2001, has been successfully isolated and has virulence in duck-embryonated eggs as well as caused clinical signs of SBDS in ducks. Phylogenetic analyses of partial genes encoding NS and capsid proteins indicated that the obtained GPV isolate belongs to the NGPV group. [ABSTRACT FROM AUTHOR]

Background and Aims Is the increase in species diversity patterns towards lower latitudes linked to reproductive traits? Plant reproductive organs influence reproductive isolation and hence species divergence. Abiotic differences between temperate and tropical regions can also directly impact on plant reproductive traits. Here we provide a novel overview of southern hemisphere, Afromontane forest tree taxonomical patterns and ask whether reproductive traits relate to latitude, while accounting for environmental (tree height) and evolutionary (biogeographical affinity) selective forces. Methods We compiled a novel dataset with (1) flower colour, size and pollination syndrome and (2) fruit colour, size and dispersal syndrome for 331 tree species found in six Afromontane forest regions. We categorized each species into latitudinal distribution using these six regions, spanning the southern Cape (34º S) to Mount Kenya (0º S). Additionally, we gathered maximum tree height (m) for each species and determined the global distribution of all 196 tree genera (Afrotropical, Palaeotropical or Pantropical). Key Results Species, genera and families showed a general decrease in richness away from tropical and subtropical forests towards warm temperate forests. Southern Afrotemperate forests (the furthest south) had the highest tree endemism. There was no relationship between latitude and the reproductive traits tested here. Biogeographical affinity related to fruit colour and dispersal syndrome, with palaeotropical genera showing relative increases in black-purple fruit colour compared with pantropical genera, and palaeotropical genera showing relative increases in biotic seed dispersal compared with Afrotropical genera, which showed higher relative abiotic seed dispersal. Taller trees had a higher chance to be wind or insect pollinated (compared with bird pollinated) and had larger fruits. Conclusions Latitude explained patterns in Afromontane tree taxonomic diversity; however, tree reproductive traits did not relate to latitude. We suggest that phylogenetic conservatism or convergence, or both, explain the reported patterns. [ABSTRACT FROM AUTHOR]

Interspecific trait divergence may reflect adaptation and reproductive isolation, particularly after the rapid differentiation that may follow the colonization of new environments. Although new lineages are generally expected to be morphologically and ecologically similar to their ancestors, environmental forces can also drive adaptive differentiation along specific phenotypic axes. We used climate niche models and comparative analyses based on a previously inferred phylogeny to examine the history of ecological and morphological divergence of Neotropical firs (Abies Mill., Pinaceae), a group of conifers that have recently colonized and diversified in the mountains of Mexico and northern Central America. We inferred past secondary contact zones by comparing current and past climate niche projections and looked for evidence of recent interspecific gene flow using genomic data. Neotropical firs have similar niches to each other and show a strong phylogenetic signal for most evaluated morphological traits. Analyses based on individual variables suggested a random walk model of differentiation. However, early adaptation to tropical conditions is inferred in the ancestor of the southernmost firs, as all modern southern taxa are differentiated climatically from Abies concolor, the northernmost species. In addition, observed autapomorphic traits for soil properties and the number of resin ducts in needles are consistent with possible species‐specific adaptations. Thus, a combination of nonadaptive and adaptive processes along different phenotypic axes, some related to the environment, likely operated after the southward migration of this plant lineage from North America and its subsequent radiation in the Neotropics. [ABSTRACT FROM AUTHOR]

Quantifying the relative strength of isolating barriers is a major focus of research on plant speciation. Contrasting life histories and mating systems have the potential to limit gene exchange between closely related populations growing in sympatry. However, few studies have quantified reproductive isolating barriers between conspecific annual and perennial populations and their contributions to total reproductive isolation (RI). Incarvillea sinensis Lam. (Bignoniaceae) is an insect‐pollinated herb with largely allopatric annual and perennial populations that differ in mating systems. The perennial populations are primarily outcrossing whereas annual populations are predominantly selfing. At a rare sympatric site in northern China we estimated prezygotic and postzygotic barriers to gene exchange between annual and perennial plants and found complete RI between the two life histories. Annuals exhibited significantly higher ecogeographic isolation than perennials whereas perennials experienced more isolation through pollen–pistil interactions than annuals. Crosses between annuals and perennials demonstrated that postzygotic barriers influencing fruit and seed formation, F1 germination and survival were negligible for annuals but played a small role for perennials. However, F1 hybrids of crosses between annuals and perennials produced no pollen and their ovules were largely sterile. Our study provides insight into the relative importance of prezygotic and postzygotic isolating barriers between closely related annual and perennial populations of I. sinensis and some of these barriers could have been involved with speciation. Annuals and perennials of I. sinensis represent two biological species and thus deserve to be recognized as distinct taxonomic species. [ABSTRACT FROM AUTHOR]

This article discusses the important role that microbes play in plant ecology and evolution. Microbes, which include diverse soil and foliar microbial communities, have a significant impact on various aspects of plant biology. They can influence maternal effects, phenotypic plasticity, and natural selection in plants. Ignoring the presence and effects of microbes can lead to a misunderstanding of plant processes and outcomes. Therefore, it is crucial for plant ecologists and evolutionary biologists to consider the influence of microbial communities in their research to gain a more accurate understanding of plant biology in the natural world. [Extracted from the article]

The paradox between the ubiquity of polyploid lineages in plants and the early obstacles to the establishment of polyploids is a long‐studied yet unresolved question in evolutionary biology. It is assumed that to successfully persist after emergence, newly formed polyploids need to display certain fitness advantages and show a certain extent of reproductive isolation with their diploid progenitors. In this study, we tested whether immediate floral changes following polyploidization can improve pollinator visitation and enable pollinator preference leading to assortative mating, i.e. build a premating reproductive barrier between diploids and polyploids. For this purpose, we generated synthetic tetraploids of Arabidopsis arenosa and measured insect visitor behavior on diploids and synthetic tetraploids. We found that the increased floral size that accompanied polyploidization did not lead to a measurable increase in visitor preference, with insects visiting diploid and tetraploid plants at equal frequency. Despite this observation, tetraploids set more fruits than diploids, suggesting a positive impact of polyploidization on pollen transfer via other means. In addition, polyploidization did not lead to assortative mating but instead promoted interploidy pollen exchange, since visitors preferentially switched between cytotypes rather than preferring one. Consistent with this switching behavior, most of the progeny from tetraploid plants were triploid. Our data suggest that polyploidization has an immediate impact on mating in plants, but in a more complex way than has been assumed previously. [ABSTRACT FROM AUTHOR]

The β′-component, a major allergen found in fish roe, is synthesized in the liver of female fish as part of the precursor of the egg yolk protein vitellogenin (Vg). Vg is distributed through the bloodstream and contributes to ovary development. In the present study, β′-component, present in Vg fragments, was detected in the muscles and internal organs of mature female salmon, with concentrations exceeding the recommended labeling level under Japan's food allergy labeling system. Additionally, total protein extracted from tissues of female salmon reacted with immunoglobulin E antibody against the salmon roe β′-component. No β′-component was detected in the tissues of mature male fish in the absence of sex hormone stimulation from females nor in immature salmon without sexual differentiation, but excess stimulation of the female sex hormone induced Vg synthesis containing the β′-component in the male fish. These findings suggest that taking into account fish sex, maturity, and sexual isolation of mature male fish could improve the safety of salmon meat for individuals with salmon roe allergy. [ABSTRACT FROM AUTHOR]

Characterizing the processes underlying reproductive isolation between diverging lineages is central to understanding speciation. Here, we present RIDGE—Reproductive Isolation Detection using Genomic polymorphisms—a tool tailored for quantifying gene flow barrier proportion and identifying the relevant genomic regions. RIDGE relies on an Approximate Bayesian Computation with a model‐averaging approach to accommodate diverse scenarios of lineage divergence. It captures heterogeneity in effective migration rate along the genome while accounting for variation in linked selection and recombination. The barrier detection test relies on numerous summary statistics to compute a Bayes factor, offering a robust statistical framework that facilitates cross‐species comparisons. Simulations revealed RIDGE's efficiency in capturing signals of ongoing migration. Model averaging proved particularly valuable in scenarios of high model uncertainty where no migration or migration homogeneity can be wrongly assumed, typically for recent divergence times <0.1 2Ne generations. Applying RIDGE to four published crow data sets, we first validated our tool by identifying a well‐known large genomic region associated with mate choice patterns. Second, while we identified a significant overlap of outlier loci using RIDGE and traditional genomic scans, our results suggest that a substantial portion of previously identified outliers are likely false positives. Outlier detection relies on allele differentiation, relative measures of divergence and the count of shared polymorphisms and fixed differences. Our analyses also highlight the value of incorporating multiple summary statistics including our newly developed outlier ones that can be useful in challenging detection conditions. [ABSTRACT FROM AUTHOR]

Floral and life history traits play important roles in plant speciation. The genus Mimulus is a model system for studying speciation. It includes examples of species in which floral colour facilitates isolation through pollinator shifts, as well as life history changes that result in temporal or ecogeographic isolation. We investigate the possibility that both floral colour and life history have shifted together in a recently described, genetically distinct group within the species Mimulus ringens. Using a large, range-wide citizen science dataset, we test for geographic trends in flower colour and flowering time. We combine this with greenhouse studies in populations of known life history to test for differences in flower colour with life history. We show that darker-flowered plants are more common at higher latitudes, that annual-like populations have darker flowers, and that flowering time varies with latitude only in the subset of populations that have lighter flowers. This suggests that annual-like populations (with the earlier flowering time typical of this life history) are restricted to the northern part of the species range and may have distinct trends in flowering date. [ABSTRACT FROM AUTHOR]

Seminal fluid protein (Sfp) genes show, in general, a higher rate of sequence divergence than genes from other categories, which is often attributed to forms of postcopulatory sexual selection or sexual conflict. Recently, the relaxation of selective constraints has been proposed as an alternative explanation for the rapid sequence evolution of Sfps and other genes with sex-limited expression. The expression of Sfp genes is a likely target of selection, but the evolution of differences in their expression levels is less understood. Here, we explore both polymorphism and divergence in Sfp gene expression between Drosophila melanogaster and Drosophila simulans , how selection might have influenced their expression, and whether changes in expression might trigger the evolution of reproductive isolating barriers. In our analysis, Sfp genes showed higher divergence, but not higher polymorphism, in expression than the average male reproductive glands gene. Sfp genes with reproductive-tissue-specific expression were enriched for both directional and stabilizing selection, while relaxed selection was the predominant mode of evolution among Sfp genes with any other nonreproductive tissue-specific or nontissue-specific expression. The knockdown of single genes known to affect intraspecific sperm competition, and with patterns of expression divergence and polymorphism suggestive of directional selection, was not enough to break down postmating reproductive isolation barriers between species. Our results identify the expression of male-specific Sfp genes as an enriched target of selection and suggest a complex molecular relationship between postcopulatory sexual selection on a single gene's expression and its effect on the onset of speciation. [ABSTRACT FROM AUTHOR]

Climate change is altering species ranges and reproductive interactions in existing ranges, offering species new scope to mate and hybridize. The outcomes will depend on how environmental factors shape reproductive barriers across life stages, yet this is rarely assessed across the environments that species encounter in nature. We assess prezygotic and postzygotic barriers, and their dependence on temperature and parental sex, in species of a reef-building tubeworm (Galeolaria) from a fast-warming biodiversity hotspot in southern Australia. By replicating pure and reciprocal hybrid crosses across 5 temperatures spanning species' thermal ranges, we estimate thermal tolerance curves (defining niches) for crosses and reproductive isolation at each temperature. By also replicating crosses at 3 life stages, we partition the contributions of prezygotic barriers at fertilization, postzygotic barriers at embryogenesis, and postzygotic barriers at larval development to reproductive isolation. We show that barriers are weaker at fertilization and embryogenesis, but stronger and more temperature sensitive at larval development, as species diverge in thermal niche. Asymmetry of barriers between parental sexes, moreover, suggests a complex interplay between niche differentiation and maternal inheritance. Our findings point to a key role for temperature in reproductive isolation, but also challenges for predicting the fate of isolation in future climates. [ABSTRACT FROM AUTHOR]

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]

Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome‐wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island‐like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated. [ABSTRACT FROM AUTHOR]

Large‐bodied mammals living in fragmented habitats are at higher risk of extinction, and such risk can be influenced by ecological factors such as predator–prey system dynamics. These dynamics can be particularly complex for conservation management when one endangered species preys on another endangered species in an isolated or poor‐quality habitat. Here we describe predation events observed over 19 months that involved two threatened species: the largest carnivore in Madagascar, the fosa (Cryptoprocta ferox), and three groups of diademed sifaka (Propithecus diadema) in the Betampona Strict Nature Reserve. This site is a 22 km2 low‐altitude rainforest that is surrounded by agricultural land and isolated from larger forest corridors. We aim to (1) assess the behavioral changes of P. diadema in response to fosa attacks and identify any antipredator strategies that they adopted, and (2) quantify the frequency of fosa attacks and the predation impact on the sifaka population. We report five direct observations of fosa predation attempts (one successful), the discovery of a dead sifaka with evidence of fosa predation, and the disappearance of three individuals. We describe the observed attacks and compare the sifaka activity budgets and movement patterns before and after the events. To escape the predator, sifakas fled short distances, hid, and remained vigilant. The impact of predation, combined with low reproductive rates and potentially high inbreeding of this isolated diademed sifaka population, could affect the survival of this species in Betampona. Given the compounding effects of habitat isolation and high hunting pressure, community‐specific conservation strategies should incorporate predator–prey dynamics via longitudinal monitoring of predator and prey population densities and quantifying the predation pressure between them. [ABSTRACT FROM AUTHOR]

Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis. A large comparative genomics study reveals that Serratia marcescens is composed of five main phylogenetic clusters, isolated by genetic barriers but not clearly separated by ecological specialisations. This results provides insights into the bacterial diversification process. [ABSTRACT FROM AUTHOR]

Studies of adaptive radiations have played a central role in our understanding of reproductive isolation. Yet the focus has been on human-biased visual and auditory signals, leaving gaps in our knowledge of other modalities. To date, studies on chemical signals in adaptive radiations have focused on systems with multimodal signalling, making it difficult to isolate the role chemicals play in reproductive isolation. In this study we examine the use of chemical signals in the species recognition and adaptive radiation of Hawaiian Tetragnatha spiders by focusing on entire communities of co-occurring species, and conducting behavioural assays in conjunction with chemical analysis of their silks using gas chromatography-mass spectrometry. Male spiders significantly preferred the silk extracts of conspecific mates over those of sympatric heterospecifics. The compounds found in the silk extracts, long chain alkyl methyl ethers, were remarkably species-specific in the combination and quantity. The differences in the profile were greatest between co-occurring species and between closely related sibling species. Lastly, there were significant differences in the chemical profile between two populations of a particular species. These findings provide key insights into the role chemical signals play in the attainment and maintenance of reproductive barriers between closely related co-occurring species. [ABSTRACT FROM AUTHOR]

Background: Avian influenza viruses (AIVs) constitute significant zoonotic pathogens encompassing a broad spectrum of subtypes. Notably, the H4 subtype of AIVs has a pronounced ability to shift hosts. The escalating prevalence of the H4 subtype heightens the concern for its zoonotic potential, signaling an urgent need for vigilance. Methods: During the period from December 2021 to November 2023, we collected AIV-related environmental samples and assessed them using a comprehensive protocol that included nucleic acid testing, gene sequencing, isolation culture, and resequencing. Results: In this study, a total of 934 environmental samples were assessed, revealing a remarkably high detection rate (43.66%, 289/662) of AIV in the live poultry market. Notably, the H4N1 subtype AIV (cs2301) was isolated from the live poultry market and its complete genome sequence was successfully determined. Subsequent analysis revealed that cs2301, resulting from a reassortment event between wild and domesticated waterfowl, exhibits multiple mutations and demonstrates potential for host transfer. Conclusions: Our research once again demonstrates the significant role of wild and domesticated waterfowl in the reassortment process of avian influenza virus, enriching the research on the H4 subtype of AIV, and emphasizing the importance of proactive monitoring the environment related to avian influenza virus. [ABSTRACT FROM AUTHOR]

Many university scholars, including the authors of this article, acknowledge that they feel like they are riding an emotional roller coaster with academic success, as well as many project failures. Except for our PhD thesis, many of us complete our research tasks in relatively established research groups. However, little research has examined the potential these groups might have to mitigate feelings of academic isolation. To fill in this gap, we designed two methodological steps. First, we adopted the Woolfian metaphor of a room of our own, where we composed individual vignettes regarding our feelings of isolation. We read each other's texts and then, in a second step, moved to a "living room" to negotiate our emerging ideas, echoing a Collaborative Autoethnography. Two full professors and two early-career researchers reflected on and talked about their feelings of academic isolation, from their personal and professional standpoints. Despite the differences in job stability, the four participants acknowledged having felt isolated and abandoned. We argue that viewing research groups not as a community of practice, but a community of care is a more humane and desirable framework to model university research groups in these current times of exacerbating neoliberalism. [ABSTRACT FROM AUTHOR]

Marine snails (genus Littorina) have recently emerged as a model for speciation research, with repeated formation of different types of barriers to gene flow in contact zones between ecotypes and taxa. Inversion polymorphisms are found in an increasing number of species, including Littorina snails, and have been suggested to promote both local adaptation, ecotype formation and speciation, but their roles can vary. In Littorina , their role in later stages of speciation remains particularly unclear. A one-dimensional speciation continuum is frequently used to frame our understanding of the speciation process. However, a number of recent studies have argued that no single measure adequately summarises reproductive isolation and, therefore, the speciation process is best viewed in multiple dimensions. The many Littorina contact zones provide empirical data to illustrate how this principle can be applied. Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems. [ABSTRACT FROM AUTHOR]

Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and present environments on diversification. Here, we use genomic‐scale data (1310 exons and whole mitogenomes from 111 samples) to investigate Pleistocene diversification, cryptic diversity, and secondary contact in the Australian delicate mice (Hydromyini: Pseudomys), a recent radiation spanning almost all Australian environments. Across northern Australia, we find no evidence for introgression between cryptic lineages within Pseudomys delicatulus sensu lato, with palaeoclimate models supporting contraction and expansion of suitable habitat since the last glacial maximum. Despite multiple contact zones, we also find little evidence of introgression at a continental scale, with the exception of a potential hybrid zone in the mesic biome. In the arid zone, combined insights from genetic data and palaeomodels support a recent expansion in the arid specialist P. hermannsburgensis and contraction in the semi‐arid P. bolami. In the face of repeated secondary contact, differences in sperm morphology and chromosomal rearrangements are potential mechanisms that maintain species boundaries in these recently diverged species. Additionally, we describe the western delicate mouse as a new species and recommend taxonomic reinstatement of the eastern delicate mouse. Overall, we show that speciation in an evolutionarily young and widespread clade has been driven by environmental change, and potentially maintained by divergence in reproductive morphology and chromosome rearrangements. [ABSTRACT FROM AUTHOR]

The harbour seal Phoca vitulina is a ubiquitous pinniped species found throughout coastal waters of the Northern Hemisphere. Harbour seal impacts on ecosystem dynamics may be significant due to their high abundance and food web position. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean and P. v. vitulina in the Atlantic. Strong natal philopatry of harbour seals can result in fine‐scale genetic structure and isolation by distance. Management of harbour seals is expected to benefit from improved resolution of seal population structure and dynamics. Here, we use genotyping‐by‐sequencing to genotype 146 harbour seals from the eastern Pacific Ocean (i.e. British Columbia (BC), Oregon and California) and the western Atlantic Ocean (i.e. Québec, Newfoundland and Labrador). Using 12,742 identified variants, we confirm the recently identified elevated genetic diversity in the eastern Pacific relative to the western Atlantic and greatest differentiation between the subspecies. Further, we demonstrate that this is independent of reference genome bias or other potential technical artefacts. Coast‐specific analyses with 8933 and 3828 variants in Pacific and Atlantic subspecies, respectively, identify divergence between BC and Oregon–California, and between Québec and Newfoundland–Labrador. Unexpected PCA outlier clusters were observed in two populations due to cryptic relatedness of individuals; subsequently, closely related samples were removed. Admixture analysis indicates an isolation‐by‐distance signature where Oregon seals contained some of the BC signature, whereas California did not. Additional sampling is needed in the central and north coast of BC to determine whether a discrete separation of populations exists within the region. [ABSTRACT FROM AUTHOR]

Premise: Barriers at different reproductive stages contribute to reproductive isolation. Self‐incompatibility (SI) systems that prevent self‐pollination could also act to control interspecific pollination and contribute to reproductive isolation, preventing hybridization. Here we evaluated whether SI contributes to reproductive isolation among four co‐occurring Opuntia species that flower at similar times and may hybridize with each other. Methods: We assessed whether Opuntia cantabrigiensis, O. robusta, O. streptacantha, and O. tomentosa, were self‐compatible and formed hybrid seeds in five manipulation treatments to achieve self‐pollination, intraspecific cross‐pollination, open pollination (control), interspecific crosses or apomixis, then recorded flowering phenology and synchrony. Results: All species flowered in the spring with a degree of synchrony, so that two pairs of species were predisposed to interspecific pollination (O. cantabrigiensis with O. robusta, O. streptacantha with O. tomentosa). All species had distinct reproductive systems: Opuntia cantabrigiensis is self‐incompatible and did not produce hybrid seeds as an interspecific pollen recipient; O. robusta is a dioecious species, which formed a low proportion of hybrid seeds; O. streptacantha and O. tomentosa are self‐compatible and produced hybrid seeds. Conclusions: Opuntia cantabrigiensis had a strong pollen–pistil barrier, likely due to its self‐incompatibility. Opuntia robusta, the dioecious species, is an obligate outcrosser and probably partially lost its ability to prevent interspecific pollen germination. Given that the self‐compatible species can set hybrid seeds, we conclude that pollen–pistil interaction and high flowering synchrony represent weak barriers; whether reproductive isolation occurs later in their life cycle (e.g., germination or seedling survival) needs to be determined. [ABSTRACT FROM AUTHOR]

Newcastle disease virus (NDV) is among the most important viruses of poultry; however, variants also cause clinical diseases in birds of the family Columbidae. From 2014 onwards, notable mortality rates have been observed in racing and rock pigeons, with a correlation to subgenotypes XXI.1.1 and XXI.1.2 of genotype XXI in Pakistan. In this study, we performed isolation and genetic characterization of 29 pigeon-derived NDV isolates of sub-genotypes XXI.1.1, XXI.1.2 and VII.2. Phylogenetic analysis based on complete fusion gene sequences classified seven (n = 7) isolates into sub-genotype XXI.1.1 and they were genetically closely related to isolates previously characterized in Pakistan (0.05–0.43% nucleotide divergence), and in Iran, Russia, Egypt, Nigeria, Kazakhstan and Ukraine (3.75% to 6.67% nucleotide divergence) in the period from 2005–2018. In addition, nineteen (n = 19) isolates were clustered with viruses previously isolated in Pakistan (2014–2018) in sub-genotype XXI.1.2. In addition, three (n = 3) F-gene sequences assigned to subgenotype VII.2 were identified along with viruses repeatedly isolated (2011–2020) from several poultry and non-poultry avian species in Pakistan. The analysis showed that all isolates of sub-genotypes XXI.1.1 and XXI.1.2 were mesogenic (1.42–1.49) and the isolates belonging to sub-genotype VII.2 were velogenic (1.63–1.71) in nature according to the intracerebral pathogenicity index (ICPI). This study delivers a comprehensive description of the prevalence of sub-genotypes XXI.1.1 and XXI.1.2 in Pakistan since 2014. Additionally, it underscores the role of free-range pigeons as effective carriers of virulent sub-genotype VII.2 viruses, impacting both poultry and non-poultry avian species reared in open environments. Virulent NDV genotypes were repeatedly isolated from pigeons. Evidence of epidemiological links among viruses isolated from various locations. Distinct phylogenetic branches suggest separate, simultaneous evolution of NDVs. Study information could be helpful in the development of an effective vaccine. [ABSTRACT FROM AUTHOR]

Large‐bodied mammals living in fragmented habitats are at higher risk of extinction, and such risk can be influenced by ecological factors such as predator–prey system dynamics. These dynamics can be particularly complex for conservation management when one endangered species preys on another endangered species in an isolated or poor‐quality habitat. Here we describe predation events observed over 19 months that involved two threatened species: the largest carnivore in Madagascar, the fosa (Cryptoprocta ferox), and three groups of diademed sifaka (Propithecus diadema) in the Betampona Strict Nature Reserve. This site is a 22 km2 low‐altitude rainforest that is surrounded by agricultural land and isolated from larger forest corridors. We aim to (1) assess the behavioral changes of P. diadema in response to fosa attacks and identify any antipredator strategies that they adopted, and (2) quantify the frequency of fosa attacks and the predation impact on the sifaka population. We report five direct observations of fosa predation attempts (one successful), the discovery of a dead sifaka with evidence of fosa predation, and the disappearance of three individuals. We describe the observed attacks and compare the sifaka activity budgets and movement patterns before and after the events. To escape the predator, sifakas fled short distances, hid, and remained vigilant. The impact of predation, combined with low reproductive rates and potentially high inbreeding of this isolated diademed sifaka population, could affect the survival of this species in Betampona. Given the compounding effects of habitat isolation and high hunting pressure, community‐specific conservation strategies should incorporate predator–prey dynamics via longitudinal monitoring of predator and prey population densities and quantifying the predation pressure between them. [ABSTRACT FROM AUTHOR]

The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non‐lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting. see also the Perspective by Kristen M. Martinet and Luke J. Harmon [ABSTRACT FROM AUTHOR]