Gene Flow Research Articles

Temporal Changes in Tasmanian Devil Genetic Diversity at Sites With and Without Supplementation.

Management interventions for threatened species are well documented with genetic data now playing a pivotal role in informing their outcomes. However, insitu actions like supplementations (releasing individuals into an existing population) are often restricted to a singular site. Considerable research and management effort have been dedicated to conserving the Tasmanian devil (Sarcophilus harrisii), offering a unique opportunity to investigate the temporal genetic consequences of supplementation at multiple sites, in comparison to outcomes observed in the absence of management interventions. Using 1,778 genome-wide SNPs across 1,546 individuals, we compared four wild-supplemented sites to four monitoring-only sites (not supplemented; control sites) over 9 years (2014-2022). At the study completion, genetic differentiation among supplemented sites had significantly decreased compared to among not-supplemented sites. We found statistically significant variation in genetic change over time between sites using linear mixed-effects modelling with random slopes. Investigating this among-site variation showed that three of the supplemented sites conformed to predictions that supplementations would have a positive impact on the genetic diversity of devils at these sites. We predicted no change over time at our fourth site due to the observed relatively high gene flow, however, this site did not align with predictions, instead showing decreased genetic diversity and increased relatedness. Amongst not supplemented sites, there was no consistent pattern of temporal genetic change, suggesting devil sites across Tasmania are highly heterogeneous, likely reflecting variation in site connectivity and genetic drift. Our study demonstrates that long-term concurrent monitoring of multiple sites, including controls, is necessary to contextualise the influence of management interventions on natural species fluctuations.

Comparative population genomics unveils congruent secondary suture zone in Southwest Pacific Hydrothermal Vents.

How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure across lineages. To shed light on the factors that shape community-level genetic variation and to improve our understanding of deep-sea biogeographic patterns, we conducted a comparative population genomics study on seven hydrothermal vent species co-distributed in the Back-Arc Basins (BABs) of the Southwest Pacific region. Using ddRAD-seq, we compared the range-wide distribution of genomic diversity across species and discovered a shared phylogeographic break. Demogenetic inference revealed shared histories of lineage divergence and a secondary contact. Low levels of asymmetric gene flow probably occurred in most species between the Woodlark and North Fiji basins, but the exact location of contact zones varied from species to species. For two species, we found individuals from the two lineages co-occurring in sympatry in Woodlark Basin. Although species exhibit congruent patterns of spatial structure (Eastern vs Western sites), they also show variation in the degree of divergence among lineages across the suture zone. Our results also show heterogeneous gene flow across the genome, indicating possible partial reproductive isolation between lineages and early speciation. Our comparative study highlights the pivotal role of historical and contemporary factors, underscoring the need for a comprehensive approach-especially in addressing knowledge gaps on the life history traits of deep-sea species.

Caerin 1.1/1.9-mediated antitumor immunity depends on IFNAR-Stat1 signalling of tumour infiltrating macrophage by autocrine IFNα and is enhanced by CD47 blockade

Previously, we demonstrated that natural host-defence peptide caerin 1.1/caerin 1.9 (F1/F3) increases the efficacy of anti-PD-1 and therapeutic vaccine, in a HPV16 + TC-1 tumour model, but the anti-tumor mechanism of F1/F3 is still unclear. In this study, we explored the impact of F1/F3 on the tumor microenvironment in a transplanted B16 melanoma model, and further investigated the mechanism of action of F1/F3 using monoclonal antibodies to deplete relevant cells, gene knockout mice and flow cytometry. We show that F1/F3 is able to inhibit the growth of melanoma B16 tumour cells both in vitro and in vivo. Depletion of macrophages, blockade of IFNα receptor, and Stat1 inhibition each abolishes F1/F3-mediated antitumor responses. Subsequent analysis reveals that F1/F3 increases the tumour infiltration of inflammatory macrophages, upregulates the level of IFNα receptor, and promotes the secretion of IFNα by macrophages. Interestingly, F1/F3 upregulates CD47 level on tumour cells; and blocking CD47 increases F1/F3-mediated antitumor responses. Furthermore, F1/F3 intratumor injection, CD47 blockade, and therapeutic vaccination significantly increases the survival time of B16 tumour-bearing mice. These results indicate that F1/F3 may be effective to improve the efficacy of ICB and therapeutic vaccine-based immunotherapy for human epithelial cancers and warrants consideration for clinical trials.

Climate-driven range expansion via long-distance larval dispersal

Climate-driven warming and changes in major ocean currents enable poleward larval transport and range expansions of many marine species. Here, we report the population genetic structure of the gastropod Kelletia kelletii, a commercial fisheries species and subtidal predator with top-down food web effects, whose populations have recently undergone climate-driven northward range expansion. We used reduced representation genomic sequencing (RAD-seq) to genotype 598 adults from 13 locations spanning approximately 800 km across the historical and expanded range of this species. Analyses of 40747 single nucleotide polymorphisms (SNPs) showed evidence for long-distance dispersal of K. kelletii larvae from a central historical range site (Point Loma, CA, USA) hundreds of km into the expanded northern range (Big Creek, CA), which seems most likely to result from transport during an El Niño-Southern Oscillation (ENSO) event rather than consistent on-going gene flow. Furthermore, the high genetic differentiation among some sampled expanded-range populations and their close genetic proximity with distinct populations from the historical range suggested multiple origins of the expanded-range populations. Given that the frequency and magnitude of ENSO events are predicted to increase with climate change, understanding the factors driving changes in population connectivity is crucial for establishing effective management strategies to ensure the persistence of this and other economically and ecologically important species.

Successive cycles of allopatric differentiation and secondary contact shape phylogeographical structure in an Indo-West Pacific reef fish

Abstract Geographical barriers and sea-level fluctuations have significantly influenced the population genetic structure and evolutionary history of Indo-West Pacific (IWP) reef species. This study examines these effects in Abudefduf septemfasciatus (banded sergeant), a widely distributed egg-brooding IWP damselfish. Using 4700 genome-wide single nucleotide polymorphisms obtained from double-digest restriction site-associated DNA sequencing and a 1638-bp mitochondrial gene fragment from 106 samples across six IWP locations, we identified two main genetic clusters: one in the Indian Ocean and another in the Pacific Ocean. Within the Pacific, two distinct subclusters were detected, with overlapping ranges in Taiwan. Demographic analysis of the dataset using two-population genetic models in ∂a∂I, based on diffusion approximation, revealed asymmetric gene flow, with stronger migration from the Indian Ocean to the Pacific. Recurrent episodes of isolation and secondary contact during Pleistocene glacial cycles further shaped these genetic patterns. Our findings provide new insights into the complex phylogeography and evolutionary dynamics of banded sergeants, contributing to a broader understanding of how historical environmental changes have driven the diversification of IWP reef fishes.

Responses of Littorina spp. Intertidal Snails to Thermal Extremes Indicate Countergradient Variation in Fitness.

Global change models predict not only a steady increase in temperatures but also an increase in the occurrence of hot and cold extremes. Organisms' responses to thermal extremes will depend on species-specific traits and the degree of within-species variation (among populations), with populations from warmer latitudes often predicted to have higher thermal tolerance than populations from colder latitudes. The evolution of population-specific responses, however, can be limited by gene flow that homogenises populations. Here, we investigate this relationship with a study of the survival of Littorina littorea, L. obtusata, and L. saxatilis-marine snails with varying dispersal potential-collected on either side of a known biogeographic break. Snails were laboratory-acclimated for several weeks before undergoing exposures to extreme heat, extreme cold, or ambient conditions, and individual mortality was recorded after each exposure. In line with common predictions, we observed that the degree of population divergence in survival under thermal extremes was negatively related to dispersal potential, and that populations from the colder latitude generally had higher survival of sub-freezing temperatures. Contrary to common predictions, however, we observed greater survival after extreme heat in populations from colder latitudes than in their warmer-latitude counterparts, a pattern known as countergradient variation. This experiment highlights counterintuitive responses to thermal extremes, emphasising that colder-latitude populations could experience population growth under more extreme climates due to higher survival at both hot and sub-freezing thermal extremes.

Reassessing Hybridisation in Australian Tetragonula Stingless Bees Using Multiple Genetic Markers.

We re-examined reports of hybridisation in three cryptic stingless bee species in the genus Tetragonula in South East Queensland, Australia (T. carbonaria, T. davenporti and T. hockingsi). Previous studies on this group using microsatellite markers proposed that hybridisation occasionally takes place. In contrast, we find that using 1745 SNPs we could reliably separate the three species, with no evidence of contemporary (or recent) hybridisation. We found identical amplicon sequences of the nuclear gene EF1alpha across most individuals of the three species, but low and moderate species-specific polymorphisms in the nuclear gene Opsin and the mitochondrial 16S rRNA gene, respectively, with no cases of mito-nuclear discordance at these genes. We confirm that nuclear divergence across these species is low, based on 10-26 kb of non-coding sequence flanking EF1alpha and Opsin (0.7%-1% pairwise difference between species). However, we find mitogenomes to be far more diverged than nuclear genomes (21.6%-23.6% pairwise difference between species). Based on these comprehensive analyses of multiple marker types, we conclude there is no ongoing gene flow among the Tetragonula species of South East Queensland, despite their morphological similarity to one another and the low nuclear divergence among them. The higher resolution provided by multiple SNP markers may lead to lower estimates of contemporary hybridisation more generally.

Long-term genetic and demographic surveys reveal the impact of population history, habitat change, and conservation efforts on the globally endangered Turdus helleri (Taita Thrush)

Abstract Predicting the fate of threatened populations remains a challenge in conservation biology. The study of genetic and demographic time series is crucial to unravel the role of population history, anthropogenic disturbance and conservation actions on current demographic and genetic patterns. However, such studies are still rare in threatened species. In this study, we integrate a quarter century of population demographic (capture–mark–recapture) and genetic (microsatellites) data for the globally endangered Turdus helleri (Taita Thrush), a songbird endemic to the fragmented cloud forest of the Taita Hills, southeast Kenya. We found that the two largest remaining populations are prone to high demographic and genetic stochasticity. Furthermore, despite relatively high genetic diversity, the increase in inbreeding in recent years suggests vulnerability to extinction. Moreover, while the smallest population was close to extinction, assisted gene flow midway through the study led to a demographic rescue. We conclude that habitat protection, continued monitoring and conservation efforts are required for long-term survival of the endangered T. helleri, as the species may be prone to an extinction debt.

Genetic characteristics of the bred group of deer and assessment of gene flow from it to natural populations

Here we present the results of genetic analysis of an artificial deer population, inhabiting an enclosed territory near Lida. The analysis was aimed at determining the precise origins and genetic characteristics of the population and disco vering presence of any gene flow between the artificial population and the wild deer of the region. We employed mitochondrial control region haplotypes analysis to identify origins and possible matrilineal hybrids, and hybrid classification of migration analysis based on microsatellite data to discover hybrid specimens and gene flow, respectively. We have determined that the artificial population in question belongs to the species Cervus canadensis sibiricus, or Altai wapiti, originates in the South Altai region, and possesses mediocre genetic diversity as can be expected from a population of this size. While singular results of hybrid analysis seem to indicate a possibility of rare interbreeding between escaped wapiti and wild deer, there are no indicators of any substantial gene flow from the artificial population into the wild, but we believe that it still warrants additional attention in order to prevent undesirable introgression.

Isolation by environment is more important than isolation by distance along a tropical gradient in direct developing frogs

Abstract Abiotic factors are important for defining population structure and limiting gene flow, especially in ectotherm species. In amphibians, abiotic factors like temperature and precipitation can facilitate or restrict gene flow. The challenge is identifying if these factors can lead to a pattern of isolation by environment. Our study aims to quantify the extent to which divergence is driven by abiotic factors such as temperature, precipitation and elevation. To do so, we used a direct-developing frog species, Craugastor loki that occurs along a steep elevation gradient. Using restriction-site associated DNA sequencing (RADseq) from individuals collected from 100 m to 2250 m of elevation across 13 localities at Sierra Madre de Chiapas in southern Mexico, we described population structure using a variety of model-based clustering and landscape genomics approaches. We found that populations sampled at higher elevation probably correspond to an undescribed new species of Craugastor, and that populations from Craugastor loki between 120 m and 1500 m are clustered in two different genetic groups: a Pacific slope group and a Central Depression slope group. We found signatures of isolation by environment more important than isolation by distance in contributing to genetic divergence in this group of frogs at a fine scale. The environmental variables such as: mean temperature of wettest and warmest quarter, annual mean temperature, and seasonality in temperature and precipitation play an important role on population differentiation. Our results underscore the importance of abiotic factors as drivers of genetic differentiation and highlight the use of different approaches to illuminate fine scale population divergence given the complexity of disentangling the contribution of both patterns of isolation.

Whole-Genome Evaluation of Genetic Rescue: The Case of a Curiously Isolated and Endangered Butterfly.

Genetic rescue, or the translocation of individuals among populations to augment gene flow, can help ameliorate inbreeding depression and loss of adaptive potential in small and isolated populations. Genetic rescue is currently under consideration for an endangered butterfly in Canada, the Half-moon Hairstreak (Satyrium semiluna). A small, unique population persists in Waterton Lakes National Park, Alberta, isolated from other populations by more than 400 km. However, whether genetic rescue would actually be helpful has not been evaluated. Here, we generate the first chromosome-level genome assembly and whole-genome resequence data for the species. We find that the Alberta population maintains extremely low genetic diversity andis genetically very divergent from the nearest populations in British Columbia and Montana. Runs of homozygosity suggest this is due to a long history of inbreeding, and coalescent analyses show that the population has been small and isolated, yet stable, for up to 40k years. When a population like this maintains its viability despite inbreeding and low genetic diversity, it has likely undergone purging of deleterious recessive alleles and could be threatened by the reintroduction of such alleles via genetic rescue. Ecological niche modelling indicates that the Alberta population also exhibits environmental associations that are atypical of the species. Together, these evolutionary and ecological divergences suggest that population crosses may result in outbreeding depression. We therefore infer that genetic rescue has a relatively unique potential to be harmful rather than helpful for this population at present. However, because of its reduced adaptive potential, the Alberta population may still benefit from future genetic rescue as climate and habitat conditions change. Proactive experimental population crosses should therefore be completed to assess reproductive compatibility and progeny fitness.

Intraspecific identification and genetic diversity analysis of Paeonia lactiflora based on chloroplast genes rpoB and psbK-psbI.

Paeonia lactiflora Pall., a member of Paeoniaceae family, is a medicinal herb widely used in traditional Chinese medicine. Chloroplasts are multifunctional organelles containing distinct genetic material. This study provides a foundation for identifying P. lactiflora, protecting and utilizing germplasm resources, and supporting molecular breeding efforts. In this study, five complete chloroplast genome sequences of P. lactiflora samples originating from different regions in China were sequenced using the Illumina NovaSeq 4000 platform. All five P. lactiflora chloroplasts had a typical cyclic tetrameric structure with 130 genes annotated. Comparative genomic analysis indicated that rpoB and psbK-psbI function as thepotential specific DNA barcodes for intraspecific identification of P. lactiflora. PCR amplification of rpoB and psbK-psbI was performed on 246 samples from 7 production areas, achieving 100% amplification efficiency. Sequence analysis revealed that 5 and 10 haplotypes were identified based on rpoB and psbK-psbI, respectively. The joint analysis of two sequences identified 15 haplotypes named Hap1 ~ Hap15. Hap5 emerged as the most prevalent and geographically widespread haplotype across China. Haplotypic diversity (Hd) was 0.786, and nucleotide diversity was 0.00281, suggesting that P. lactiflora had high genetic diversity at the species level. The Neighbor-Joining tree showed that the 15 haplotypes were clustered into two branches, indicating extensive genetic exchange between clusters. The introduction of new individuals or rare genes into different clusters through gene flow increased genetic variation within clusters, enriching P. lactiflora genetic diversity.

Comparative Population Genetics of Two Alvinocaridid Shrimp Species in Chemosynthetic Ecosystems of the Western Pacific.

Deep-sea shrimps from the family Alvinocarididae are prominent inhabitants of chemosynthesis-based habitats worldwide. However, their genetic diversity and population connectivity remain poorly understood due to limited sampling. To fill these knowledge gaps, we compared the population genetics of two vent- and seep-dwelling alvinocaridid species with overlapped geographic ranges between the South China Sea and the Manus Basin. Alvinocaris longirostris has a wider distribution, ranging from 35°N to 3°S and at depths of 930 to 1736 m, while Alvinocaris kexueae is more restricted, found between 16°N and 3°S at depths of 1300 to 1910 m. Our analysis, based on the mitochondrial cytochrome c oxidase subunit 1 gene, revealed that A. longirostris had lower genetic diversity and minimal genetic differentiation across eight disjoint vent and seep populations. In contrast, the narrower-distributed A. kexueae exhibited higher genetic diversity and significant genetic differentiation, with stronger gene flow observed from its Haima seep population to the Manus Basin vent population. In addition, both species appear to have experienced population expansion in their recent evolutionary history. These results suggest that A. longirostris and A. kexueae may possess distinct life-history traits that contribute to their differing distribution ranges in the Western Pacific.

A phylogenetic approach to delimitate species in a probabilistic way.

Different species concepts and their associated criteria have been used to delimit species boundaries, such as the absence of gene flow for the biological species concept and the presence of morphological distinction for the morphological species concept. The need for different delimitation criteria largely reflects the fact that species are generated under various speciation mechanisms. A key question is how to make species delimitation consistent in a species group, especially when we want to delimit the species boundaries over many newly discovered evolutionary lineages and add these new lineages into a comparative analysis. Instead of forcing a single definition of 'species', we can acknowledge different delimitation criteria by modelling how fast lineages in a species group evolve to meet these criteria along a phylogenetic tree. This study presents such a new model and a new delimitation approach that calculates the probability of each possible species identity of a lineage. We use simulations to show that our likelihood function gives accurate estimates of parameters in the model and our approach have high power to correctly identify species identities. We apply the approach to lineages in two real species groups that already have genomic and morphological evidence for their species identities. Our approach gives consistent inference of species identities with these existing pieces of evidence. We also demonstrate how to use our model to test a popular hypothesis about speciation process across all lineages in a species group and discuss further extension of the model to study speciation.

Variability in the impact of linear transportation infrastructures on gene flow in French wild ungulate populations

ContextLinear Transportation Infrastructures (LTIs) are among the largest factors responsible for landscape fragmentation, in turn increasing population isolation. In this context, studies have mainly focused on a single species’ response to barrier elements and mitigation thereof. Yet, the implementation of conservation strategies to restore landscape connectivity may be challenging when multi-specific responses are not measured and fully considered.ObjectivesWe aimed to assess the effect of two different types of LTIs, a fenced highway and a navigation canal on gene flow in three ungulate species in Northeastern France.MethodsWe genotyped 98 red deer (C. elaphus), 120 wild boars (S. scrofa) and 140 roe deer (C. capreolus) with species-specific microsatellite markers from 3 sampling sites located on either side of both LTIs considered in the study area. We assessed the continuity of gene flow using Bayesian clustering methods and a mapping approach to determine inter-individual genetic dissimilarity in relation to landscape characteristics.ResultsOur study showed different impacts of LTIs on the gene flow of species belonging a priori to the same functional group. Genetic differentiation among red deer and wild boar sampling units was observed on either side of the highway, but no such differentiation was identified for roe deer. However, no genetic structuring was associated with the presence of the canal in any species.ConclusionsThe impact of LTIs on gene flow in large species results from the structural characteristics of the infrastructure, and our study shows that mitigation measures should consider species-specific behaviors to facilitate the use of crossing structures and thus ensure gene flow across ILTs.

Monitoring genetic diversity of Torminalis glaberrima for resilient forests in the face of population fragmentation.

Torminalis glaberrima (Gand.) Sennikov & Kurtto is a European tree species currently underutilized in forestry, valued for its high-quality wood and contribution to ecosystem stability. Despite a projected range expansion as climate change progresses, current population fragmentation levels may inhibit the species' ability to migrate and stabilize fragile forest ecosystems. To investigate the relationship between structural and functional connectivity, we surveyed the genetic diversity, spatial genetic structure, and gene flow of T. glaberrima across Austria, to understand which populations should be given conservation priority. Our sampling encompasses 21 natural and planted populations and 910 individuals of T. glaberrima covering the species' distribution in Austria. We estimated genetic diversity indices, the extent of gene dispersal, and conducted SPAGeDi, STRUCTURE, and discriminant analyses of principal components analyses using one chloroplast minisatellite and eight nuclear microsatellite markers. Despite a highly fragmented distribution of T. glaberrima in the southern, western and central part of its range in Austria, we found high genetic diversity, low population differentiation and inbreeding, and estimated higher gene dispersal values than previous studies. Population structure analyses identified two main regions of genetic ancestry in the northwestern and southeastern part of the species' range in Austria and evidence for the usage of foreign genetic material in two planted populations. Only two of the established ex situ plantations and seed orchards appear to well represent the fine-scale population structure present in Austria, and existing in situ gene conservation units (GCUs) are insufficient to conserve the current natural genetic diversity. We suggest the establishment of further in situ GCUs to maximize the conservation of extant forest genetic diversity. Additionally, we encourage corridor plantings between isolated populations, bolstering the genetic connectivity and diversity of populations.

Genomic and transcriptomic insights into vitamin A-induced thermogenesis and gene reuse as a cold adaptation strategy in wild boars

Wild boars inhabit diverse climates, including frigid regions like Siberia, but their migration history and cold adaptation mechanisms into high latitudes remain poorly understood. We constructed the most comprehensive wild boar whole-genome variant dataset to date, comprising 124 samples from tropical to frigid zones, among which 47 Russian, 8 South Chinese and 3 Vietnamese wild boars were newly supplemented. We also gathered 75 high-quality RNA-seq datasets from 10 tissues of 6 wild boars from Russia and 6 from southern China. Demographic analysis revealed the appearance of Russian wild boars in Far East of Asia (RUA) and Europe (RUE) after the last glacial maximum till ~ 10 thousand years ago. Recent gene flow (<100 years) from RUA to RUE reflects human-mediated introductions. Cold-region wild boars exhibit strong selection signatures indicative of genetic adaptation to cold climates. Further pathway and transcriptomic analyses reveal a novel cold resistance mechanism centered on enhanced vitamin A metabolism and catalysis, involving the reuse of UGT2B31 and rhythm regulation by ANGPTL8, RLN3 and ZBTB20. This may compensate for the pig’s lack of brown fat/UCP1 thermogenesis. These findings provide new insights into the molecular basis of cold adaptation and improve our understanding of Eurasian wild boar migration history.

Population genetic structure of Phaedranassa cinerea Ravenna (Amaryllidaceae) and conservation implications

BackgroundAndean orography has shaped the endemism of plant species in montane forests, creating a mosaic of habitats in small and isolated areas. Understanding these endemic species' genetic diversity patterns is crucial for their conservation. Phaedranassa cinerea (Amaryllidaceae), a species restricted to the western Andes of Ecuador, is listed as “vulnerable” according to the IUCN criteria. This study seeks to determine whether there is genetic structure among and within Phaedranassa cinerea populations, estimate the timing of their genetic divergence, and recommend conservation strategies based on these genetic structure findings.ResultsUsing 13 microsatellites and a Bayesian approach, we analyzed the genetic differentiation of P. cinerea and possible diversification scenarios. Our results indicate that the genetic diversity of P. cinerea is lower than congeneric species. The Bayesian analysis identified two genetic groups, with no evidence of isolation by distance. Populations in the northwest of the Ecuadorean Andes have less allele richness compared to those in the southwest. Additionally, the species exhibits excess homozygosity and evidence of bottlenecks. Our Bayesian analysis suggests that the differentiation among populations was not older than 5,000 years and was as recent as 600 years ago for some of the populations. Based on the geographic distribution of the known populations, the species should be listed as endangered instead of vulnerable to extinction.ConclusionsPhaedranassa cinerea shows lower genetic diversity than related species, with the most variation within populations. We identified two to four genetic groups, suggesting recent divergence along the ridges of the western Andes. The findings suggest that conservation efforts should focus on securing genetic exchange between populations to preserve the genetic diversity of P. cinerea.

Understanding bacterial ecology to combat antibiotic resistance dissemination.

The dissemination of antibiotic resistance from environmental sources is a growing concern. Despite the widespread occurrence of antibiotic resistance transmission events, there are actually multiple obstacles in the ecosystem that restrict the flow of bacteria and genes, in particular nonnegligible biological barriers. How these ecological factors help combat the dissemination of antibiotic resistance and relevant antibiotic resistance-diminishing organisms (ARDOs) deserves further exploration. This review summarizes the factors that influence the growth, metabolism, and environmental adaptation of antibiotic-resistant bacteria (ARB) and restrict the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Additionally, this review discusses the achievements in the application of ARDOs to improve biotechnology for wastewater and solid waste remediation while highlighting current challenges limiting their broader implementation.

Genetic structure and divergence of marginal populations of black poplar (Populus nigra L.) in Poland

Genetic diversity is crucial to secure the survival and sustainability of ecosystems. Given anthropogenic pressure, as well as the projected alterations connected with the level and circulation of water, riparian forests are of particular concern. In this paper, we assessed the genetic variation of black poplar – one of the keystone tree species of riverine forests. The natural habitats of black poplar have been severely transformed leading to a significant decline of its population size. Using a set of 18 nuclear microsatellites and geographic location data, we studied 26 remnant populations (1,261 trees) located along the biggest river valleys in Poland. Our main goal was to assess the overall genetic variation and to verify if range fragmentation and habitat transformation have disrupted gene exchange among populations. Genotyping revealed that 261 trees were clones. The level of clonality was higher in more transformed river sections. All populations have probably gone through a drastic genetic bottleneck in the distant past, and most of them have low effective population sizes. Still, the overall level of genetic variation remains high, but certain populations require attention due to their lower genetic variation, higher clonality and strong spatial genetic structure. Genetic differentiation was low, yet Bayesian clustering supported the existence of 11 genetic clusters. According to the results, gene exchange is most prevalent between adjacent populations. Relatively free gene flow occurs only along the Vistula, particularly in its middle section which is characterized by the highest genetic variation. Noticeable genetic structuring was observed along the Oder. Populations located at the range margin showed signs of genetic divergence and reduction of variation. We conclude that human activities have impacted the gene pool of black poplar in Poland by disrupting landscape connectivity and preventing the species from generative reproduction. The study provides practical guidelines on how to develop and implement the conservation program for the gene pool of black poplar in Poland. It also presents a strong case favoring river renaturation and genetic monitoring, particularly concerning keystone species.