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Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforests dynamism on wild primates genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.

A few iconic examples have proven the value of facilitated gene flow for counteracting inbreeding depression and staving off extinction; yet, the practice is often not implemented for fear of causing outbreeding depression. Using genomic sequencing, climatic niche modeling, and demographic reconstruction, we sought to assess the risks and benefits of using translocations as a tool for recovery of endangered montane red fox (Vulpes vulpes) populations in the western United States. We demonstrated elevated inbreeding and homozygosity of deleterious alleles across all populations, but especially those isolated in the Cascade and Sierra Nevada ranges. Consequently, translocations would be expected to increase population growth by masking deleterious recessive alleles. Demographic reconstructions further indicated shallow divergences of less than a few thousand years among montane populations, suggesting low risk of outbreeding depression. These genomic-guided findings set the stage for future management, the documentation of which will provide a roadmap for recovery of other data-deficient taxa.

Recent work has revealed the importance of contemporary evolution in shaping ecological outcomes. In particular, rapid evolutionary divergence between populations has been shown to impact the ecology of populations, communities, and ecosystems. While studies have focused largely on the role of adaptive divergence in generating ecologically important variation among populations, much less is known about the role of gene flow in shaping ecological outcomes. After divergence, populations may continue to interact through gene flow, which may influence evolutionary and ecological processes. Here, we investigate the role of gene flow in shaping the contemporary evolution and ecology of recently diverged populations of anadromous steelhead and resident rainbow trout (Oncorhynchus mykiss). Results show that resident rainbow trout introduced above waterfalls have diverged evolutionarily from downstream anadromous steelhead, which were the source of introductions. However, the movement of fish from above to below the waterfalls has facilitated gene flow, which has reshaped genetic and phenotypic variation in the anadromous source population. In particular, gene flow has led to an increased frequency of residency, which in turn has altered population density, size structure, and sex ratio. This result establishes gene flow as a contemporary evolutionary process that can have important ecological outcomes. From a management perspective, anadromous steelhead are generally regarded as a higher conservation priority than resident rainbow trout, even when found within the same watershed. Our results show that anadromous and resident O. mykiss populations may be connected via gene flow, with important ecological consequences. Such eco-evolutionary processes should be considered when managing recently diverged populations connected by gene flow.

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.

The recognition and delineation of cryptic species remains a perplexing problem in systematics, evolution, and species delimitation. Once recognized as such, cryptic species complexes provide fertile ground for studying genetic divergence within the context of phenotypic and ecological divergence (or lack thereof). Herein we document the discovery of a new cryptic species of trapdoor spider, Promyrmekiaphila korematsui sp. nov. Using subgenomic data obtained via target enrichment, we document the phylogeography of the California endemic genus Promyrmekiaphila and its constituent species, which also includes P. clathrata and P. winnemem. Based on these data we show a pattern of strong geographic structuring among populations but cannot entirely discount recent gene flow among populations that are parapatric, particularly for deeply diverged lineages within P. clathrata. The genetic data, in addition to revealing a new undescribed species, also allude to a pattern of potential phenotypic differentiation where species likely come into close contact. Alternatively, phenotypic cohesion among genetically divergent P. clathrata lineages suggests that some level of gene flow is ongoing or occurred in the recent past. Despite considerable field collection efforts over many years, additional sampling in potential zones of contact for both species and lineages is needed to completely resolve the dynamics of divergence in Promyrmekiaphila at the population-species interface.

Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.

Predator-prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defences in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defence exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature more than 3000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that over short geographical distances, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.

Background: Outbreaks of the coral predator Crown-of-Thorns Starfish (CoTS) pose a severe threat to coral reefs in the Indo-Pacific Ocean. In 2018, the South China Sea (SCS) experienced significant CoTS outbreaks, leading to extensive coral mortality across the Xisha, Zhongsha, Dongsha, and Nansha Islands, severely impacting the coral reef ecosystem. Results: To explore the origins of these outbreaks, we conducted a comprehensive genomic analysis using data from genomic single nucleotide polymorphism sites (SNPs) and mitochondrial haplotypes. Our analysis reveals that CoTS populations in the SCS, which exhibit moderate genetic diversity and may have undergone positive selection or population expansion. There was limited genetic differentiation among CoTS populations from XS, ZS, and NS groups. Especially between the XS and ZS groups, there was almost no genetic differentiation. The populations from XS, ZS, and NS groups have strong genetic connections with populations in Vietnam and the Philippines. There was high gene flow from Vietnam to the Xisha Islands and from the Philippines to the Nansha Islands, suggesting that the CoTS populations in these regions primarily originate from these neighboring countries. Conclusion: The comprehensive analyses of SNP and mitochondrial genomes have provided valuable insights into the population genetics of CoTS. This research has generated significant genomic resources and facilitated important studies on the genetics of the CoTS species. By identifying potential source populations and understanding the genetic basis of their spread, managers can develop more effective conservation strategies to protect vulnerable coral reef ecosystems in the SCS. [ABSTRACT FROM AUTHOR]

Panax (Araliaceae) is a small genus containing several well known medicinally important species. It has a disjunct distribution between Eastern Asia and Eastern North America, with most species from eastern Asia, especially the Himalayan‐Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was probably widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of Southwest China and tropical Indochina, where some taxa migrated northwestward to the HHM, eastward to central and eastern China, and then onward toward Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax. We hypothesize that the common ancestors of the medicinally important P. ginseng + P. japonicus + P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax. Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax. [ABSTRACT FROM AUTHOR]

Captive breeding can be a useful tool for the management of threatened species, but such programs often begin with a bottleneck which may lower reproductive fitness by increasing inbreeding and allowing deleterious alleles to increase in frequency by reducing effective population size. Dryococelus australis, the Lord Howe Island stick insect, is a critically endangered insect that has been bred at the Melbourne Zoo in Melbourne, Australia, since shortly after the species was rediscovered in 2001. We analysed a long‐term dataset of phenotypic measurements from this captive breeding program to determine whether reproductive fitness has declined in captivity. We found a clear signal of decline in direct (egg hatching success) and indirect (egg and nymph size) fitness indicators over time. We compared a captive line descended from the original program founders to a new hybrid line that has recent wild ancestry. The hybrid line showed an immediate improvement in egg hatch rate, suggesting the potential for genetic rescue. Egg and nymph size did not show as dramatic a change, although this line had only existed for just over a single generation at the time of data collection. These results argue strongly for the regular sourcing of new genetic material from the wild D. australis population to counteract fitness declines in captivity. Aside from benefiting the captive population, this would also improve the prospects of establishing new wild populations in the future, using individuals sourced from captivity. [ABSTRACT FROM AUTHOR]

ABSTRACT The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (Sceloporus) occurring mostly in northeastern Mexico, which show striking variation in morphology and habitat among closely related species and populations. We developed a new time‐calibrated phylogeny for the group using RADseq data from 152 individuals. This phylogeny identified 12 putative species‐level clades, including at least two undescribed species. We then estimated levels of gene flow among 21 geographically adjacent pairs of species and populations. We also estimated divergence in morphological and climatic niche variables among these same pairs, along with divergence times and geographic distances. Using Bayesian generalised linear models, we found that gene flow between pairs of lineages is negatively related to divergence time and morphological divergence among them (which are uncorrelated), and not to geographic distance or climatic divergence. The framework used here can be applied to study speciation in many other organisms having genomic data but lacking direct data on reproductive isolation. We also found several other intriguing patterns in this system, including the parallel evolution of a strikingly similar montane blue–red morph from more dull‐coloured desert ancestors within two different, nonsister species. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Method Results Main Conclusion As climate change increasingly threatens the world's coral reefs, enhancing their resilience by improving population connectivity for key reef species is crucial for ensuring their persistence. Here, we evaluate the population genomic structure of two common coral species, Pocillopora acuta and Porites sp., chosen due to their divergent life histories. Thousands of single‐nucleotide polymorphisms (SNPs) were sequenced and analysed to infer regional connectivity patterns in Southeast Asia, a region that harbours a tremendous diversity of marine life.Coasts of the Malay Peninsula and northern Borneo, covering ~1 million km2.NextRAD genotyping‐by‐sequencing of 185 Porites sp. and 221 Pocillopora acuta colonies. Libraries were prepared and sequenced on Illumina NovaSeq 6000. Genotyping involved initial quality controls, allele frequency filtering and checks for contamination. Genetic structure was assessed with Bayesian clustering, and relationships between genetic variation and environmental factors were studied through redundancy analysis. Contemporary gene flow was estimated using BayesAss.We observed panmixia among the broadcasting Porites sp. populations, while for the brooding Pocillopora acuta, the Malay Peninsula acts a strong barrier to dispersal between the Malacca Strait and the southern South China Sea. Moreover, its genomic structure seems to follow current marine ecoregion delineation. By analysing contemporary migrant movement, we can prioritise reef localities for conservation. In particular, localities at the Andaman Coral Coast are contemporarily isolated from the other localities, and Tioman is identified as a major larval source for both species.Our analyses highlight contrasting population differentiation patterns between the two species that can be explained by the disparity in their reproductive strategies. These findings are important for biodiversity managers in Southeast Asia; incorporation of regional connectivity considerations into conservation planning can help safeguard ecosystem resilience and persistence. [ABSTRACT FROM AUTHOR]

ABSTRACT Habitat association has been proposed to affect evolutionary dynamics through its control on dispersal propensity, which is considered a key trait for lineage survival in habitats of low durational stability. The Habitat Constraint hypothesis predicts different micro‐ and macroevolutionary patterns for stable versus dynamic habitat specialists, but the empirical evidence remains controversial and in insects mostly derives from winged lineages. We here use genome‐wide SNP data to assess the effect of habitat association on the population dynamics of two closely related flightless lineages of the genus Eutagenia (Coleoptera: Tenebrionidae), which are co‐distributed across the Cyclades islands in the Eastern Mediterranean but are associated with habitat types of different presumed stability: the psammophilous lineage is associated with dynamic sandy coastal habitats, while the geophilous lineage is associated with comparatively stable compact soil habitats. Our comparative population genomic and demographic analyses support higher inter‐island gene flow in the psammophilous lineage, presumably due to the physical properties of dynamic sand‐dune habitats that promote passive dispersal. We also find consistent bottlenecks in the psammophilous demes, suggesting that lineage evolution in the dynamic habitat is punctuated by local extinction and recolonisation events. The inferred demographic processes are surprisingly uniform among psammophilous demes, but vary considerably among geophilous demes depending on historical island connectivity, indicating more stringent constraints on the dynamic habitat lineage. This study extends the Habitat Constraint hypothesis by demonstrating that selection on dispersal traits is not the only mechanism that can drive consistent differences in evolutionary dynamics between stable versus dynamic habitat specialists. [ABSTRACT FROM AUTHOR]

ABSTRACT Genomic vulnerability is a measure of how much evolutionary change is required for a population to maintain optimal genotype‐environment associations under projected climates. Aquatic species, and in particular migratory ectotherms, are largely underrepresented in studies of genomic vulnerability. Such species might be well equipped for tracking suitable habitat and spreading diversity that could promote adaptation to future climates. We characterised range‐wide genomic diversity and genomic vulnerability in the migratory and fisheries‐important golden perch (Macquaria ambigua) from Australia's expansive Murray–Darling Basin (MDB). The MDB has a steep hydroclimatic gradient and is one of the world's most variable regions in terms of climate and streamflow. Golden perch are threatened by fragmentation and obstruction of waterways, alteration of flow regimes, and a progressively hotter and drying climate. We gathered a genomic dataset of 1049 individuals from 186 MDB localities. Despite high range‐wide gene flow, golden perch in the warmer, northern catchments had higher predicted vulnerability than those in the cooler, southern catchments. A new cross‐validation approach showed that these predictions were insensitive to the exclusion of individual catchments. The results raise concern for populations at warm range edges, which may already be close to their thermal limits. However, a population with functional variants beneficial for climate adaptation found in the most arid and hydrologically variable catchment was predicted to be less vulnerable. Native fish management plans, such as captive breeding and stocking, should consider spatial variation in genomic vulnerability to improve conservation outcomes under climate change, even for dispersive species with high connectivity. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxa Methods Results Main Conclusions The combined influences of demographic dynamics and gene flow on local adaptation in plants is still poorly understood. Here, we used a genome scan approach on three closely related Neotropical palms, Acrocomia aculeata, A. intumescens and A. totai, to identify the evolutionary processes generating shared and lineage‐specific patterns of differentiation and selection across the genomic landscape.Amazonia, Atlantic Forest, Cerrado and Caatinga ecoregions of Brazil.Arecaceae.We used target sequence capture and analysis of climatic correlation, detection of selective sweeps, balancing selection, and spatial and non‐spatial models to identify signatures of natural selection and admixture. We also determined temporal dynamics in spatial distribution and demographic changes.We found a higher number of lineage‐specific than shared adaptive sites (SNPs) and no evidence of selective sweeps in shared genes, suggesting lineage specific natural selection across species. Further, evidence of balancing selection in several genes was also identified in the three species. Niche‐based and coalescent models suggest that shifts in spatial range during the Quaternary caused overlapping distributions between species, leading to hybridisation between parapatric localities.Interspecific hybridisation may have spread both neutral and adaptive SNPs, which may explain the shared adaptive genes between species. Taken together, we show how genomic adaptation can occur despite introgression, through evolutionary processes that likely drive similar patterns of adaptation in other organisms. [ABSTRACT FROM AUTHOR]

The East Asian finless porpoise, Neophocaena asiaeorientalis sunameri, is an endangered species that inhabits the coastal marine environments of East Asia. In the present study, we investigated the overall infection status of anisakid nematodes in East Asian finless porpoises from three sea sectors off the Korean Peninsula. The genetic diversity and population genetic structure of the identified nematode species were evaluated. The prevalence of all stages of anisakid nematodes collected from the stomach was 57.55% (61 among the 106 porpoises examined), and 16 of the hosts were found to have adult worms. The mean number of infected adults was 211 (± 419.54, 5–1455 per host). Only one species of anisakids, Anisakis pegreffii, was identified from randomly selected worms by molecular approaches. Analysis of the mitochondrial (mt) cox2 partial gene in 50 newly generated sequences of A. pegreffii revealed 24 haplotypes, including 14 new haplotypes. We observed below-average levels of nucleotide diversity and haplotype diversity compared to other seas around the world. The mtDNA cox2 haplotypes of the species in the three Korean sea areas showed no genetic structure, suggesting well-connected gene flow within these areas. This study represents the first record of a definitive host of A. pegreffii in Korean waters, providing important information regarding anisakids genetic diversity in the cetacean species inhabiting limited regions. [ABSTRACT FROM AUTHOR]

Hatchery production is common in salmonid management for harvest and conservation. Many hatcheries employ integrated broodstock programs, where wild-origin fish are included as broodstock and uni- or bi-directional gene flow between wild and hatchery components of the population is encouraged. Such approaches often assume that opportunistically obtained wild fish meet the genetic goals of minimizing hatchery–wild differentiation and maintaining genetic diversity. This may be incorrect if fine-scale spatial genetic structure exists. Here we investigate the population genetic consequences of such hatchery operations in coho salmon (Oncorhynchus kisutch) in a small river system featuring a large integrated broodstock program. We do so using 11 082 SNPs scored in wild-origin and hatchery-origin fish collected throughout the system. We found no evidence for genetic differentiation between hatchery-origin and wild-origin fish, no evidence of lowered genetic diversity in hatchery-origin fish, and no evidence for genetic differentiation among fish sampled throughout the river system. In addition, we did not detect inbreeding. Collectively, these results are consistent with current practices meeting integrated hatchery program goals of adequately sampling the genetic diversity present in wild-origin fish, although they may slightly reduce the effective population size of the combined population. [ABSTRACT FROM AUTHOR]

Large structural variants in the genome, such as inversions, may play an important role in producing population structure and local adaptation to the environment through suppression of recombination. However, relatively few studies have linked inversions to phenotypic traits that are sexually selected and may play a role in reproductive isolation. Here, we found that geographic differences in the sexually selected plumage of a warbler, the common yellowthroat (Geothlypis trichas), are largely due to differences in the Z (sex) chromosome (males are ZZ), which contains at least one putative inversion spanning 40% (31/77 Mb) of its length. The inversions on the Z chromosome vary dramatically east and west of the Appalachian Mountains, which provides evidence of cryptic population structure within the range of the most widespread eastern subspecies (G. t. trichas). In an eastern (New York) and western (Wisconsin) population of this subspecies, female prefer different male ornaments; larger black facial masks are preferred in Wisconsin and larger yellow breasts are preferred in New York. The putative inversion also contains genes related to vision, which could influence mating preferences. Thus, structural variants on the Z chromosome are associated with geographic differences in male ornaments and female choice, which may provide a mechanism for maintaining different patterns of sexual selection in spite of gene flow between populations of the same subspecies. [ABSTRACT FROM AUTHOR]

Aim: We reconstructed the genetic patterns and identified the main genetic breaks of several taxa across California and Baja California coast. Additionally, we evaluated the contribution of different variables to the level of structure. Location: California and Baja California coast. Taxon: Fish, invertebrates, algae, seagrass and mammals. Methods: We generated a map to reconstruct the genetic patterns using genetic information (Fst index and phylogenetic clades distribution) from a literature review of population genetics publications from 2000 to 2023. For the analysis of genetic connectivity drivers, we explored the effect of different variables representing life history traits, reproductive strategies and biogeographic variables and generated five working hypotheses which were evaluated with generalized linear models (GLMs). Results: We identified 42 genetic breaks from 63 species across our study area. The largest number of breaks occurs from 27° N to 29° N and from 31° N to 35° N. This range includes transition zones between ecoregions such as Punta Eugenia, Baja California, Mexico and Point Conception, California, USA. We also identified Ensenada, Baja California region as a barrier to gene flow. From a transboundary perspective, we found 40 species with connectivity between California and Baja California, including 14 commercial and or recreational species. We found none of the variables explored had a clear effect on the level of genetic differentiation of the species assessed in the region. Main Conclusion: Genetic breaks among different taxa do not distribute randomly across the latitudinal range from California and Baja California coastal area, rather they are mainly located in transition zones between marine ecoregions. The challenge to identify specific variables that explain general genetic patterns highlights the complexity that drives population connectivity processes in marine species. [ABSTRACT FROM AUTHOR]

Aim: Whether widespread gene flow among primates is emblematic of their initial radiation or resulted from secondary contactremains a long‐standing question. We address this question on 'sinica' group macaques, highlighting the origin of the white‐cheeked macaque (Macaca leucogenys). Location: Eastern Himalayan highlands of Arunachal Pradesh, India. Taxon: Macaca leucogenys Li, Zhao, Fan, 2015b (Cercopithecidae). Methods: Mitochondrial genomes and Y‐chromosomal TSPY gene sequences of WCM were obtained from two distant populations through low‐depth genome sequencing. Phylogenetic analyses were conducted along with sequences of other available species within the genus Macaca. Results: We observed the presence of a single maternal lineage but two parental lineages. Interestingly, one paternal lineage of the white‐cheeked macaque clustered with a common lineage of M. assamensis and M. munzala. The other paternal lineage clustered with the sequences of the white‐cheeked macaque from the type locality in Southeastern Tibet. Main Conclusions: The result indicates a possible historic male‐mediated introgression in the white‐cheeked macaque, which is also present in the two other species belonging to the 'sinica' group. Therefore, extensive gene flow in 'sinica' group macaques possibly came from one or more introgression events in the past that also played a role in the origin and evolution of these macaque species. [ABSTRACT FROM AUTHOR]

Two morphologically and genetically distinct salamander species (the crested newt, Triturus cristatus and the marbled newt, T. marmoratus) engage over a large area in the west of France where they hybridize at ca. 4%. The species interaction is characterized by ecological differentiation and limited gene flow beyond the F1 hybrid generation. Incompletely isolated species like these allow to investigate the genetic mechanisms and evolutionary forces that maintain their identity in the face of ongoing gene flow, to which a large mosaic hybrid zone provides excellent opportunities. A reanalysis of published morphological data supports the partial breakdown of the species barrier whereas extensive genetic data show that introgression is low yet asymmetric, in line with the dynamics of species replacement inferred earlier. The current work, with seven diagnostic nuclear markers studied for a large sample, revises the estimates of introgression in both T. cristatus (to 0.24%) and T. marmoratus (to 0.11%). Difficulties remain in the recognition of potential triploid hybrids versus backcross hybrids. Haldane's rule is partially supported, but deeper analyses require the use of a molecular marker for sex that is not yet available. [ABSTRACT FROM AUTHOR]

Pherosphaera fitzgeraldii , the Dwarf Mountain Pine, is a critically endangered conifer restricted to cliff ledges within waterfall spray zones in the Greater Blue Mountains Area of New South Wales, Australia. This species is under threat from pollution, invasive weeds, and limited recruitment, which are contributing to its declining population. Using a comprehensive conservation genomic approach, we assessed the population health of P. fitzgeraldii and developed strategic recommendations for its management. Genomic analysis of P. fitzgeraldii revealed the presence of two distinct genetic groups despite the limited distribution of the species. This genetic structure aligns with prevailing wind currents, indicating potential restrictions to pollen or seed exchange between subpopulations. Furthermore, limited gene flow was observed even among nearby subpopulations, emphasizing the risk of increased genetic differentiation due to ongoing isolation. Clonality is widespread in some subpopulations, and all subpopulations displayed signs of inbreeding and genetic depletion despite subdioecy, indicative of historical constraints on gene flow and small population sizes. We offer genomic-based recommendations for prioritizing conservation sites, enhancing genetic diversity in ex situ collections, and guiding future management. Further studies to uncover the sex determination mechanism of P. fitzgeraldii could help maintain balanced sex ratios in ex situ collections and support future genetic rescue efforts. This study underscores the value of genomics in informing protection and recovery of unique threatened species. [ABSTRACT FROM AUTHOR]

Understanding how ocean currents influence larval dispersal and measuring its magnitude is critical for conservation and sustainable exploitation, especially in the Tropical Eastern Pacific (TEP), where the larval transport of rocky reef fish remains untested. For this reason, a lagrangian simulation model was implemented to estimate larval transport pathways in Northwestern Mexico and TEP. Particle trajectories were simulated with data from the Hybrid Ocean Coordinate Model, focusing on three simulation scenarios: (1) using the occurrence records of Lutjanus peru and L. argentiventris as release sites; (2) considering a continuous distribution along the study area, and (3) taking the reproduction seasonality into account in both species. It was found that the continuous distribution scenario largely explained the genetic structure previously found in both species (genetic brakes between central and southern Mexico and Central America), confirming that the ocean currents play a significant role as predictors of genetic differentiation and gene flow in Northwestern Mexico and the TEP. Due to the oceanography of the area, the southern localities supply larvae from the northern localities; therefore, disturbances in any southern localities could affect the surrounding areas and have impacts that spread beyond their political boundaries. [ABSTRACT FROM AUTHOR]

A critical component of ecosystem restoration projects involves using genetic data to select source material that will enhance success under current and future climates. However, the complexity and expense of applying genetic data is a barrier to its use outside of specialised scientific contexts. To help overcome this barrier, we developed Reef Adapt (www.reefadapt.org), an innovative, globally applicable and expandable web platform that incorporates genetic, biophysical and environmental prediction data into marine restoration and assisted gene flow planning. The Reef Adapt tool provides maps that identify areas with populations suited to user-specified restoration/recipient sites under current and future climate scenarios. We demonstrate its versatility and practicality with four case studies of ecologically and evolutionarily diverse taxa: the habitat-forming corals Pocillopora damicornis and Acropora kenti, and macroalgae Phyllospora comosa and Ecklonia radiata. Reef Adapt is a management-ready tool to aid restoration and conservation efforts amidst ongoing habitat degradation and climate change. Aiming to accelerate research in the field of marine restoration, 'Reef Adapt' integrates genetic, environmental, and biophysical data to predict populations suited to 'local' and 'future' climates for marine restoration [ABSTRACT FROM AUTHOR]

Interspecific genomic introgression is an important evolutionary process with respect to the generation of novel phenotypic diversity and adaptation. A key question is how gene flow perturbs gene expression networks and regulatory interactions. Here, an introgression population of two species of allopolyploid cotton (Gossypium) to delineate the regulatory perturbations of gene expression regarding fiber development accompanying fiber quality change is utilized. De novo assembly of the recipient parent (G. hirsutum Emian22) genome allowed the identification of genomic variation and introgression segments (ISs) in 323 introgression lines (ILs) from the donor parent (G. barbadense 3–79). It documented gene expression dynamics by sequencing 1,284 transcriptomes of developing fibers and characterized genetic regulatory perturbations mediated by genomic introgression using a multi‐locus model. Introgression of individual homoeologous genes exhibiting extreme low or high expression bias can lead to a parallel expression bias in their non‐introgressed duplicates, implying a shared yet divergent regulatory fate of duplicated genes following allopolyploidy. Additionally, the IL N182 with improved fiber quality is characterized, and the candidate gene GhFLAP1 related to fiber length is validated. This study outlines a framework for understanding introgression‐mediated regulatory perturbations in polyploids, and provides insights for targeted breeding of superior upland cotton fiber. [ABSTRACT FROM AUTHOR]

Premise Methods Results Conclusions Obligate fire ephemerals are annual plants that have germination and reproduction cued by fire occurrence, persisting between fire events in a long‐lived soil seed bank. Within these species, gene flow is restricted not only geographically but also temporally because individuals are limited to reproducing with others affected by the same fire event. The patchwork‐like distribution of fires may therefore promote population isolation. In contrast to past fires, the Australian fires of 2019–2020 were of unprecedented extent, providing an opportunity to investigate the landscape genetics of a fire ephemeral, Actinotus forsythii, across multiple populations and to compare it to a common congener, Actinotus helianthi.For both species, we used single nucleotide polymorphisms to infer patterns of population structure and calculate measures of genetic diversity. We also estimated a phylogeny of Actinotus forsythii to understand the differentiation of a geographically isolated population.For A. forsythii, the within‐population diversity (allelic richness = 1.56) was greater, and the among‐population differentiation (FST = 0.30) was lower than that observed for A. helianthi (allelic richness = 1.33, FST = 0.57). Actinotus forsythii had distinct geographic groupings, and a geographically isolated population of this species was genetically highly differentiated.Despite the fire‐dependent, asynchronous gene flow, predicted between site disconnect, and possible within‐site homogeneity, our results suggest that burn mosaic could be influencing gene flow patterns and fire‐triggered mass flowering may promote genetic diversity within Actinotus forsythii. [ABSTRACT FROM AUTHOR]

ABSTRACT Across the tree of life, many organisms are able to reproduce clonally, via vegetative spread, budding or parthenogenesis. In population genetic analyses of clonally reproducing organisms, it is common practice to retain only a single representative per multilocus genotype. Though this practice of clone correction is widespread, the theoretical justification behind it has been very little studied. Here, I use individual‐based simulations to study the effect of clone correction on the estimation of the genetic summary statistics HO, HS, FIS, FST, F′′ST and Dest. The simulations follow the standard finite island model, consisting of a set of populations connected by gene flow, but with a variable rate of sexual versus asexual reproduction. The results of the simulations show that by itself, the inclusion of replicated genotypes does not lead to a deviation in the values of the summary statistics, except when the rate of sexual reproduction is less than about one in thousand. However, clone correction can introduce a strong deviation in the values of most of the statistics, when compared to a scenario of full sexual reproduction. For HS and FIS, this deviation can be informative about the process of asexual reproduction, but for FST, F′′ST and Dest, clone correction can lead to incorrect conclusions. I therefore argue that clone correction is not strictly necessary, but can in some cases be insightful. However, when clone correction is applied, it is imperative that results for both the corrected and uncorrected data are presented. [ABSTRACT FROM AUTHOR]

Ferula huber‐morathii is an endemic and medicinally important plant. This species is distributed in eight Turkish localities, including three newly identified ones. Its extent of occurrence and area of occupancy is determined to be 3963 km2 and 32 km2 respectively. All localities are characterized by East Mediterranean and sub‐Mediterranean precipitation regimes; however, temperatures increase excessively and precipitation decreases during the flowering period of the species. The population sizes are quite small, and the number of reproducing individuals in some populations is below ten. Analyses of ISSR markers showed the percentage of polymorphic loci to be 94% at the species level and 56% at the population level. The level of genetic differentiation (measured by GST) was 0.37 and the estimated level of gene flow among populations (NM) was 0.84. The percentage of variance occurring within and among populations, determined by AMOVA, was 75% and 25%, respectively. STRUCTURE analysis revealed two genetic clusters of individuals with a geographic structure, similar to that found in UPGMA and an ordination analysis. Some populations turned out to have both low numbers of individuals and low genetic diversity. Since many of the populations are subject to anthropogenic disturbance, the species should remain in the EN category. At the same time, it is suggested that a new in‐situ conservation area should be created around nearby dams, situated in the same climate area as the currently known populations. [ABSTRACT FROM AUTHOR]

Background: Hybridization is a known phenomenon in nature but its genetic impact on populations of parental species remains less understood. We investigated the evolutionary consequences of the interspecific gene flow in several contact zones of closely related pine species. Using a set of genetic markers from both nuclear and organellar genomes, we analyzed four hybrid zones (384 individuals) and a large panel of reference allopatric populations of parental taxa (2104 individuals from 96 stands). Results: We observed reduced genetic diversity in maternally transmitted mitochondrial genomes of pure pine species and hybrids from contact zones compared to reference allopatric populations. The distribution of mtDNA haplotypes followed geographic rather than species boundaries. Additionally, no new haplotypes emerged in the contact zones, instead these zones contained the most common local variants. However, species diverged significantly at nuclear genomes and populations in contact zones exhibited similar or higher genetic diversity compared to the reference stands. There were no signs of admixture in any allopatric population, while clear admixture was evident in the contact zones, indicating that hybridization has a geographically localized effect on the genetic variation of the analyzed pine species. Conclusions: Our results suggest that hybrid zones act as sinks rather than melting pots of genetic diversity. Hybridization influences sympatric populations but is confined to contact zones. The spectrum of parental species ancestry in hybrids reflects the old evolutionary history of the sympatric populations. These findings also imply that introgression may play a crucial role in the adaptation of hybrids to specific environments. [ABSTRACT FROM AUTHOR]

Background: Anemone shikokiana (Makino) Makino is a perennial herb of the genus Anemone in the family Ranunculaceae. Endemic to the Shandong Peninsula in China and Shikoku Island in Japan, it is a rare and endangered plant with a narrow, disjunct distribution. It is threatened with extinction and is in urgent need of conservation. Evaluating the genetic diversity of species, revealing the population genetic structure and gene flow, and inferring the population history are of great importance for species conservation, especially for rare and endangered plants. Results: In our study, 73 samples from eight wild populations in China were sequenced by Super-GBS, yielding a total of 40.59 G clean reads and 52,231 SNPs. Based on the obtained SNP data set, we evaluated the population genetic diversity, genetic structure, and gene flow of A. shikokiana. A low level of genetic diversity was found (He = 0.1925, Ho = 0.1422). The neighbor-joining (NJ) tree, principal component analysis and ADMIXTURE analysis suggested that these 73 A. shikokiana could be considered as two groups. Pairwise genetic differentiation coefficients (Fst) indicated that genetic differentiation was lower between adjacent populations and higher between geographically separated populations. The gene flow between Kunyu Mountain and Lao Mountain was very low. However, neither of the two regions showed evidence of Isolation by Distance. Conclusions: Here, we revealed the population genetic structure and gene flow of A. shikokiana from the Shandong Peninsula, China. This research provides valuable genetic resources for A. shikokiana and contributes to the scientific and effective conservation of the species. [ABSTRACT FROM AUTHOR]

Out‐planting corals onto coral reefs as a mechanism to increase coral cover on degraded reef systems is an increasing global activity. Current practices typically focus on asexual out‐planting of coral fragments (coral gardening). Newer sexual reproductive approaches are being developed to out‐plant younger corals produced in aquaculture facilities or sea‐based rearing pools to enable assisted evolution or assisted gene flow conservation genetics approaches. Designing out‐planting deployment operations requires decisions to be made on planting density and location in order to maximize future recruitment on both the out‐planted reefs, and on nearby reefs that are connected through oceanographic transport processes. The thinking presented here seeks to unpack how out‐planting density may be influenced, especially by local oceanographic conditions, in order to guide practitioners undertaking restoration projects. [ABSTRACT FROM AUTHOR]

The importance of genetic diversity has been recognised by the Convention on Biological Diversity but attempts at monitoring or improving the genetic diversity of populations have been minimal. Here, we investigate changes over time in the genetic diversity of a wild insect species, Maniola jurtina (Lepidoptera: Nymphalidae) and present a large‐scale investigation into contemporary spatial genetic diversity. Using microsatellite markers, we calculate multiple measures of genetic diversity and divergence for M. jurtina populations over 8 years in the UK and compare these findings with long‐term abundance trends. We also conduct a large‐scale spatial analysis into the genetic diversity and population structuring of M. jurtina across Europe. All UK populations sampled have high levels of gene flow and genetic diversity, with genetic diversity stable over time. Across Europe, we find some population structuring between populations in the UK and the European mainland, suggesting restricted geneflow between the two regions. The monitoring of a wild species' genetic diversity is an achievable aim, and one that could be carried out for many species, particularly Lepidoptera. Future approaches may aim to develop higher resolution genetic markers and cover a wider range of species. The use of abundance data offers additional insight, and we find that concurrent, dedicated genetic monitoring can provide effective tracking of biodiversity trends. [ABSTRACT FROM AUTHOR]

Modelling population connectivity is central to biodiversity conservation and often relies on resistance surfaces reflecting multi‐generational gene flow. ResistanceGA (RGA) is a common optimization framework for parameterizing these surfaces by maximizing the fit between genetic distances and cost distances using maximum likelihood population effect models. As the reliability of this framework has rarely been studied, we investigated the conditions maximizing its accuracy for both prediction and interpretation of landscape features' permeability. We ran demo‐genetic simulations in contrasted landscapes for species with distinct dispersal capacities and specialization levels, using corresponding reference cost scenarios. We then optimized resistance surfaces from the simulated genetic distances using RGA. First, we evaluated whether RGA identified the drivers of the genetic patterns, that is, distinguished Isolation‐by‐Resistance (IBR) patterns from either Isolation‐by‐Distance or patterns unrelated to ecological distances. We then assessed RGA predictive performance using a cross‐validation method, and its ability to recover the reference cost scenarios shaping genetic structure in simulations. IBR patterns were well detected and genetic distances were predicted with great accuracy. This performance depended on the strength of the genetic structuring, sampling design and landscape structure. Matching the scale of the genetic pattern by focusing on population pairs connected through gene flow and limiting overfitting through cross‐validation further enhanced inference reliability. Yet, the optimized cost values often departed from the reference values, making their interpretation and extrapolation potentially dubious. While demonstrating the value of RGA for predictive modelling, we call for caution and provide additional guidance for its optimal use. [ABSTRACT FROM AUTHOR]

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

The apparent lack of physical barriers in the marine realm has created the conception that many groups have a constant gene flow. However, changes in ocean circulation patterns, glacial cycles, temperature, and salinity gradients are responsible for vicariant events in many fish species, including sharks. The bonnethead shark, Sphyrna tiburo, is an endangered small coastal shark species. Although considerable efforts have recently been undertaken, little remains known about the possible biogeographic scenario that can explain its actual distribution within the western Atlantic (WA). Here, we used 599 mitochondrial sequences to assess the phylogeographic structure and implement Bayesian phylogenetic analyses to obtain divergence times and reconstruct the ancestral geographic range. This allowed us to infer processes responsible for the diversification of S. tiburo into major divergent lineages. Our results indicated that S. tiburo in the WA represents three independent lineages, with Brazilian samples differentiated into a distinct genetic cluster. The posterior probability of ancestral range analysis indicated that the species likely originated in the northern region (Carolina Province and the southern Gulf of Mexico), where it colonized southward through the uplifting of the Central American Isthmus (CAI). The Northern and Caribbean genetic clusters appear to have arisen from the intensification of the Loop Current, which currently flows northward passing the Yucatan Peninsula, Gulf of Mexico, and east Florida. Following initial colonization, the Northeastern Brazil group differentiated from the Caribbean region due to the sediment and freshwater discharge of the Amazon‐Orinoco Plume. Thus, the evolutionary history of the S. tiburo complex can be explained by a combination of dispersal and vicariance events that occurred over the last ~5 million years (MY). We established and confirmed the species and population limits, demonstrating that the Amazon‐Orinoco Plume constitutes a significant dispersal barrier for coastal sharks. Finally, we discuss some recommendations for the conservation of the bonnethead shark. [ABSTRACT FROM AUTHOR]

Genetic diversity is crucial for determining the evolutionary potential of a species and is essential for developing optimal conservation strategies. The impact of habitat fragmentation on the genetic diversity of food-deceptive orchids seems to be unpredictable because of their specialized seed and pollen dispersal mechanisms. The habitat of deceptive Cypripedium flavum was severely fragmented during the past half century. This study investigated the genetic diversity and structure of seven fragmented Cypripedium flavum populations in Shangrila County using AFLP markers. A total of 376 alleles were identified, with a range of 70 to 81 alleles per locus. The species exhibited considerable genetic diversity, as evidenced by an average Nei's gene diversity (H) of 0.339 and a Shannon's information index (I) of 0.505, with all loci being polymorphic. Based on Molecular Variance (AMOVA), 8.75% of the genetic differentiation was found among populations, while the remaining 91.25% of genetic variation occurred within populations. Population structure analysis revealed that the C. flavum germplasm can be categorized into 2 distinct groups, among which there was significant gene flow. Despite habitat fragmentation, C. flavum still retained a high level of genetic diversity, and the substantial gene flow (5.0826) is a key factor in maintaining the genetic diversity. These findings offer valuable insights for the conservation and potential use of C. flavum genetic resources. [ABSTRACT FROM AUTHOR]

Baobab (Adansonia digitata) is a long-lived tree endemic to Africa with economic, ecological, and cultural importance, yet its genomic features are underexplored. Here, we report a chromosome-level reference genome anchored to 42 chromosomes for A. digitata, alongside draft assemblies for a sibling tree, two trees from distinct locations in Africa, and A. za from Madagascar. The baobab genome is uniquely rich in DNA transposons, which make up 33%, while LTR retrotransposons account for 10%. A. digitata experienced whole genome multiplication (WGM) around 30 million years ago (MYA), followed by a second WGM event 3–11 MYA, likely linked to autotetraploidy. Resequencing of 25 trees identify three subpopulations, with gene flow across West Africa distinct from East Africa. Gene enrichment and fixation index (Fst) analyses show baobab retained multiple circadian, flowering, and light-responsive genes, which likely support longevity through the UV RESISTANCE LOCUS 8 (UVR8) pathway. In sum, we provide genomic resources and insights for baobab breeding and conservation. Baobab is a long-lived tree that holds great economic, ecological, and cultural value. Here, the authors report haploid chromosome-level reference genome of Adansonia digitata and draft assemblies for a sibling tree, two trees from distinct locations in Africa, and a related species from Madagascar. [ABSTRACT FROM AUTHOR]

AbstractSix substituted α-cyano-indolylchalcones have been prepared and their structures were verified by various spectral analysis tools. Compared with the standard drug 5-Fluorouracil) 5-FU(, the anticancer activity against prostate cancer (PC3) and breast cancer cell line (MCF7) was determined using the cytotoxic MTT assay. Also, the cytotoxic effect against normal melanocytes (HFB4) was studied to detect the selectivity of the compounds. Among the series, compound 3e was the most active and selective one toward MCF7 (IC50= 0.18 µmole/mL, SI= 7.6). In silico studies were performed to demonstrate the inhibitory effect of compound 3e on EGFRK, CDK2, and MDM2 domains. Different molecular techniques were performed to know the efficacy of the novel 3e on apoptotic death of breast carcinoma cells. [ABSTRACT FROM AUTHOR]

The distribution of species and the way that lineages are structured are the result of intrinsic historical processes of the species and their relationships with landscape features. Paleosuchus palpebrosus is one of the smallest crocodilians in the world and has a wide geographic distribution in South America, occurring in different habitats. Here, we analyzed mitochondrial cytochrome b sequences of 227 individuals, investigated how elements of landscape heterogeneity impact genetic differentiation, and evaluated the evolutionary and phylogeographic history of the species. Thus, we hypothesized that landscape structures, such as aridity and slope, should act as resistance surfaces to population connectivity, while rivers could mediate the dispersion of the species as a conductor of the gene flow. The analyses recovered three main lineages of P. palpebrosus. While most of the observed genetic variation was explained by geographic resistance distance, river connectivity had a smaller contribution for the observed variation. We also found a recent history with limited genetic divergence throughout the wide distribution of the species. Our findings highlight the main drivers for the evolutionary history of the species and how landscape features can shape the diversification, especially if we consider rivers as a facilitator of gene flow. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions The Amazon rainforest is one of the most biodiverse regions on earth, but our understanding of the processes that have shaped its patterns of diversity remains incomplete. One hypothesis for Amazonian speciation is the river‐refuge hypothesis, which suggests that retraction of forests away from the periphery of Amazonia, where rivers are narrow, facilitated divergence of populations separated by wide rivers. Later re‐expansion of forests would have allowed secondary contact between these populations, and co‐occurring hybrid zones may reveal the location where expanding forests first reconnected. Here, we test whether a widespread Amazonian songbird species shows evidence of population contact zones in the eastern headwaters of the Tapajós river, hypothesised to be an area of secondary contact under the river‐refuge hypothesis.Amazon and Atlantic forests of South America.Ceratopipra rubrocapilla (Pipridae, Passeriformes).We sampled 147 C. rubrocapilla (Red‐headed Manakin) across its vast range, with 70 samples sequenced using reduced‐representation genomic sequencing and 139 sequenced at the mitochondrial gene cytochrome b. We use population genetic and phylogenetic analyses to investigate patterns of gene flow and population structure across the range, with a particular focus on samples from the headwaters of the Tapajós River to evaluate the potential role of the river‐refuge hypothesis.We observe shallow population structure and evidence for widespread gene flow across the range of C. rubrocapilla. Patterns in the Tapajós headwaters match predictions of the river‐refuge hypothesis, with eastern headwater samples most similar to samples farther west on the opposite bank of the Tapajós River.The close co‐occurrence between population contact zones within C. rubrocapilla and other previously studied hybrid zones reinforces the hypothesis that the eastern Tapajós headwaters is where rainforest populations reconnected in the past, following predictions of the river‐refuge hypothesis of Amazonian speciation. [ABSTRACT FROM AUTHOR]

Aim: In order to provide a more comprehensive, community‐level understanding of marine gene flow and connectivity, we wished to first identify geographic regions of common spatial genetic divergence across multiple species along a southern temperate coastline, and then to determine which biological and ecological factors best explain the diversity in genetic patterns among species. Location: New Zealand (NZ) marine coastline. Taxon: Twenty‐one species of benthic invertebrate. Materials and Methods: A novel approach was used that involved: (1) use of genetic divergences (FST) from previously published studies to quantitatively describe patterns of population structure within each species as a fitted spline curve, (2) quantitatively clustering species by their similarity in geographic pattern using a dendrogram of curve similarities, and (3) then testing whether nine known life‐history and ecological traits are associated with the species sharing similar genetic patterns, using distance‐based regression. Results: Comparisons among species revealed not one, but four major common geographic patterns, within unexpected groups of species. The common locations of genetic divergence are similar to those previously identified, but differ substantially in their relative importance, compared to prior expectations. Two variables, Spawning Time and Taxon, explained significant proportions (26% and 16%) of the variation in the multivariate data. Main Conclusions: The genogeographic clustering of population genetic divergences provided considerable insight into the concordance of marine spatial structure across species, and some potential biological drivers of those patterns. The four common patterns of population structure identified revealed that different species responded to the same environmental drivers in very different and unexpected ways. Although larval dispersal is an important factor uniting groups of species, the timing of dispersal may be more important than pelagic larval duration in NZ. These results should contribute greatly to the integration of population genetics into both community ecology and conservation management. [ABSTRACT FROM AUTHOR]

Aim: Arctic plants survived the Pleistocene glaciations in unglaciated refugia. The number, ages, and locations of these refugia are often unclear. We use high‐resolution genomic data from present‐day and Little‐Ice‐Age populations of Arctic Bell‐Heather to re‐evaluate the biogeography of this species and determine whether it had multiple independent refugia or a single refugium in Beringia. Location: Circumpolar Arctic and Coastal British Columbia (BC) alpine. Taxon: Cassiope tetragona L., subspecies saximontana and tetragona, outgroup C. mertensiana (Ericaceae). Methods: We built genotyping‐by‐sequencing (GBS) libraries using Cassiope tetragona tissue from 36 Arctic locations, including two ~250‐ to 500‐year‐old populations collected under glacial ice on Ellesmere Island, Canada. We assembled a de novo GBS reference to call variants. Population structure, genetic diversity and demography were inferred from PCA, ADMIXTURE, fastsimcoal2, SplitsTree, and several population genomics statistics. Results: Population structure analyses identified 4–5 clusters that align with geographic locations. Nucleotide diversity was highest in Beringia and decreased eastwards across Canada. Demographic coalescent analyses dated the following splits with Alaska: BC subspecies saximontana (5 mya), Russia (~1.4 mya), Europe (>200–600 kya), and Greenland (~60 kya). Northern Canada populations appear to have formed during the current interglacial (7–9 kya). Admixture analyses show genetic variants from Alaska appear more frequently in present‐day than historic plants on Ellesmere Island. Conclusions: Population and demographic analyses support BC, Alaska, Russia, Europe and Greenland as all having had independent Pleistocene refugia. Northern Canadian populations appear to be founded during the current interglacial with genetic contributions from Alaska, Europe and Greenland. We found evidence, on Ellesmere Island, for continued recent gene flow in the last 250–500 years. These results suggest that a re‐analysis of other Arctic species with shallow population structure using higher resolution genomic markers and demographic analyses may help reveal deeper structure and other circumpolar glacial refugia. [ABSTRACT FROM AUTHOR]

Background Whole-genome duplication (polyploidization) is a dominant force in sympatric speciation, particularly in plants. Genome doubling instantly poses a barrier to gene flow owing to the strong crossing incompatibilities between individuals differing in ploidy. The strength of the barrier, however, varies from species to species and recent genetic investigations revealed cases of rampant interploidy introgression in multiple ploidy-variable species. Scope Here, we review novel insights into the frequency of interploidy gene flow in natural systems and summarize the underlying mechanisms promoting interploidy gene flow. Field surveys, occasionally complemented by crossing experiments, suggest frequent opportunities for interploidy gene flow, particularly in the direction from diploid to tetraploid, and between (higher) polyploids. However, a scarcity of accompanying population genetic evidence and a virtual lack of integration of these approaches leave the underlying mechanisms and levels of realized interploidy gene flow in nature largely unknown. Finally, we discuss potential consequences of interploidy genome permeability on polyploid speciation and adaptation and highlight novel avenues that have just recently been opened by the very first genomic studies of ploidy-variable species. Standing in stark contrast with rapidly accumulating evidence for evolutionary importance of homoploid introgression, similar cases in ploidy-variable systems are yet to be documented. Conclusions The genomics era provides novel opportunity to re-evaluate the role of interploidy introgression in speciation and adaptation. To achieve this goal, interdisciplinary studies bordering ecology and population genetics and genomics are needed. [ABSTRACT FROM AUTHOR]

Background and Aims Pleistocene climatic oscillations, characterized by arid (interglacial) and pluvial (glacial) phases, have profoundly impacted the floras of Mediterranean climates. Our study investigates the hypothesis that these climatic extremes have promoted phases of range expansion and contraction in the Eriosyce sect. Neoporteria , resulting in pronounced genetic structuring and restricted gene flow. Methods Using nuclear microsatellite markers, we genotyped 251 individuals across 18 populations, encompassing all 14 species and one subspecies within the Eriosyce sect. Neoporteria. Additionally, species distribution models were used to reconstruct past (Last Interglacial, Last Glacial Maximum and Mid-Holocene) and current potential distribution patterns, aiming to delineate the climatic influences on species range dynamics. Key Results The gene flow analysis disclosed disparate levels of genetic interchange among species, with marked restrictions observed between entities that are geographically or ecologically separated. Notably, Eriosyce subgibbosa from Hualpen emerged as genetically distinct, warranting its exclusion for clearer genetic clustering into north, central and south clusters. The species distribution models corroborated these findings, showing marked range expansions during warmer periods and contractions during colder times, indicating significant shifts in distribution patterns in response to climatic changes. Conclusions Our findings emphasize the critical role of Pleistocene climatic fluctuations in driving the dynamic patterns of range expansions and contractions that have led to geographical isolation and speciation within the Eriosyce sect. Neoporteria. Even in the face of ongoing gene flow, these climate-driven processes have played a pivotal role in sculpting the genetic architecture and diversity of species. This study elucidates the complex interplay between climatic variability and evolutionary dynamics among mediterranean cacti in central Chile, highlighting the necessity of considering historical climatic millennial oscillations in conservation and evolutionary biology studies. [ABSTRACT FROM AUTHOR]

Purpose: P300 is a lysine acetyltransferase that plays a significant role in regulating transcription and the nuclear acetylome. While P300 has been shown to be required for the transcription of certain early flow responsive genes, relatively little is known about its role in the endothelial response to hemodynamic fluid stress. Here we sought to define the role of P300 in mechanotransduction of fluid shear stress in the vascular endothelium. Methods: To characterize cellular mechanotransduction and physical properties after perturbation of P300, we performed bulk RNA sequencing, confocal and Brillouin microscopy, and functional assays on HUVEC. Results: Inhibition of P300 in HUVEC triggers a hyper-alignment phenotype, with cells aligning to flow sooner and more uniformly in the presence of the P300 inhibitor A-485 compared to load controls. Bulk transcriptomics revealed differential expression of genes related to the actin cytoskeleton and migration in cells exposed to A-485. Scratch wound and bead sprouting assays demonstrated that treatment with A-485 increased 2D and 3D migration of HUVEC. Closer examination of filamentous actin revealed the presence of a perinuclear actin cap in both P300 knockdown HUVEC and HUVEC treated with A-485. Interrogation of cell mechanical properties via Brillouin microscopy demonstrated that HUVEC treated with A-485 had lower Brillouin shifts in both the cell body and the nucleus, suggesting that P300 inhibition triggers an increase in cellular and nuclear compliance. Conclusions: Together, these results point to a novel role of P300 in modulating endothelial cell mechanics and mechanotransduction of hemodynamic shear stress. [ABSTRACT FROM AUTHOR]

The threatened springsnail subgenus Alzoniella (Navarriella) in the Iberian Peninsula has been suggested to be an old and relict lineage of the family Hydrobiidae. The subgenus is represented by two morphological species, both endemic to the Pyrenees and their southern foothills. We conducted phylogenetic analyses based on mitochondrial and nuclear gene fragments of topotypes and other populations, four molecular species delimitation methods, and morphological examinations to clarify the uncertain systematic position of the subgenus within the family, assess its species diversity, and understand the population genetic structure of the two geographically restricted species. Our phylogenetic results revealed that Alzoniella (Navarriella) is distantly related to all other species of Alzoniella , even belonging to an independent subfamily-level clade, for which we introduce the new genus Navarriella and the new subfamily Navarriellinae subfam. nov. Molecular methods and geometric morphometric analysis of shell shape identified a single species in the new genus. The significant phylogenetic distance from other hydrobiid taxa, narrow distribution, and limited gene flow among its populations (estimated from mitochondrial cytochrome c oxidase subunit I sequences) highlight Navarriella as an isolated lineage within the family that requires urgent conservation attention. Furthermore, our results cast a new light on the northern Iberian Mountains as a dispersal barrier for ancient spring lineages. [ABSTRACT FROM AUTHOR]

Dispersal is a ubiquitous ecological process that has been extensively studied in many plants and animals. Anadromous salmonids are an interesting system for examining dispersal, in part because of their well‐known philopatric behaviour, but also because of the conservation challenges related to the dispersal of hatchery‐origin fish. Building on earlier work, we provide an updated systematic review of dispersal and gene flow in anadromous salmonids. In particular, we compared studies on the dispersal of anadromous salmonids from wild and hatchery origins, including studies providing estimates of dispersal rates, observations of dispersal and results from modelling studies. We reviewed 228 studies and found these were unevenly distributed among species, with Atlantic salmon, Chinook salmon and sea trout being well‐represented. Our results showcase considerable variability in estimated dispersal rates within and across studies, which is likely related to the different methodologies, dispersal propensities across species and populations, and spatial extents considered. Overall, our results confirmed a higher tendency of hatchery fish to disperse relative to wild fish, but we also found some variation across species that warrants further study. Moreover, we found that dispersal propensity tended to decline exponentially with distance and that the drivers of dispersal varied considerably among studies. Additionally, we highlight various facets of dispersal captured across this suite of studies, including variation in terminology, methods and metrics for characterising dispersal, and the spatio‐temporal scales considered. Finally, our review revealed that few studies considered, and even fewer assessed, the implications of dispersal for the conservation and management of anadromous salmonids. [ABSTRACT FROM AUTHOR]

A species' demographic history gives important context to contemporary population genetics and a possible insight into past responses to climate change; with an individual's genome providing a window into the evolutionary history of contemporary populations. Pairwise sequentially Markovian coalescent (PSMC) analysis uses information from a single genome to derive fluctuations in effective population size change over the last ~5 million years. Here, we apply PSMC analysis to two European nightjar (Caprimulgus europaeus) genomes, sampled in Northwest and Southern Europe, with the aim of revealing the demographic history of nightjar in Europe. We successfully reconstructed effective population size over the last 5 million years. Our analysis shows that in response to global climate change, the effective population size of nightjar broadly increased under stable warm periods and decreased during cooler spans and prolonged glacial periods. PSMC analysis on the pseudo‐diploid combination of the two genomes revealed fluctuations in gene flow between ancestral populations over time, with gene flow ceasing by the last‐glacial period. Our results are tentatively suggestive of divergence in the European nightjar population, with timings consistent with differentiation being driven by restriction to different refugia during periods of glaciation. Finally, our results suggest that migratory behaviour in nightjar likely evolved prior to the last‐glacial period, with long‐distance migration seemingly persisting throughout the Pleistocene. However, further genetic structure analysis of individuals from known breeding sites across the species' contemporary range is needed to understand the extent and origins of range‐wide differentiation in nightjar. [ABSTRACT FROM AUTHOR]

Norway lobster Nephrops norvegicus, a prized decapod crustacean species, is found at different depths across the East Atlantic Ocean and Mediterranean Sea. Despite management efforts, the stocks are globally characterised as overexploited. In the present study, the impact of biogeographical boundaries on the phylogeographical and demographic population status was investigated within the Adriatic Sea, addressing important genetic indices for decapod functional conservation management. Central Mediterranean, Adriatic Sea A total of 482 individuals of Nephrops divided into the 12 samples were collected across biogeographical range of the Adriatic Sea. Using the mtDNA D‐loop and microsatellite markers, methods of phylogeography and seascape genetics were applied to infer offshore versus coastal population divergence, demography and structure. Significant findings include genetic differentiation between offshore and coastal samples, with higher diversity indices in open waters. The limited gene flow observed between these two areas emphasises the self‐sustained nature of coastal populations. Recent demographic changes in coastal populations reflect geographical constraints, fishing pressures and fluctuations in self‐recruitment success. Additionally, the study reveals historical biogeographic events shaping the Adriatic populations, with evidence suggesting lineage divergence during the upper Pleistocene and postglacial recolonisation from southern Adriatic refugia. The role of biogeographical conditions in shaping genetic structure and limited gene flow between inshore and offshore areas underscore the need for improved management strategies, emphasising the importance of marine protected areas in conserving coastal populations and maintaining overall genetic diversity of the Norway lobster in the Adriatic Sea. Genomic monitoring within current management practices is recommended. [ABSTRACT FROM AUTHOR]