Gene Flow Research Articles

Whole genome re-sequencing in 437 tobacco germplasms identifies plant height candidate genes

Tobacco is one of the most important model plants. Plant height is one of the most important agronomic traits in tobacco. To better understand the population genetic structure and the genetic basis of plant height in tobacco, 437 tobacco germplasms were whole genome re-sequencing in this study. A total of 2,263,775 high-quality single nucleotide polymorphisms were identified. The analysis of the population genetic structure showed that tobacco germplasm could be divided into 8 clusters. In addition, gene flow was found between flue-cured tobacco and ustic tobacco, as well as between oriental tobacco and air-cured tobacco. Three genes associated with plant height were identified as candidate genes by genome-wide association study. This study provides valuable genetic resources for population structure analysis and elucidation of the genetic basis of various traits. It helps to improve the efficiency of molecular breeding.

Everchanging range: How the changing environment has influenced the genetic diversity and differentiation of an iconic North American palm species.

Understanding spatial patterns of neutral and adaptive genetic variation and linking them to future climate change have become crucial in assessing the genetic vulnerability of species and developing conservation strategies. Using a combination of genomic approaches, this study aimed to explain the demographic history, predict the adaptive potential in Washingtonia palm populations on the Baja California Peninsula (BCP) and southern California and determine the geographic areas where climate change will have the most drastic effects. We used over 5000 SNPs from 155 individuals across 18 populations spanning the entire distribution range of Washingtonia palms on the BCP and southern California. We examined past and current genetic diversity distribution patterns and identified outliers using genetic differentiation and genotype-environment association methods. Genetic vulnerability was predicted, and species distribution modeling was done to the geographic regions that will be at risk under future climate scenarios. Demographic modeling supported a bottleneck related to the Wisconsin glaciation, which was stronger and longer in northern Washingtonia populations. Genomic diversity presented a strong relationship to geography and provided evidence for range expansions from several refugia. Gradient Forest Analysis revealed that the genetic variation was primarily shaped by variables related to latitude and temperature during the coldest quarter, indicating adaptation to local thermal environments. We found limited adaptive potential and high levels of genetic vulnerability in lowland southern and central populations. Accordingly, species distribution modeling found that the southern distribution range will be affected by climate change, particularly under the high-emission scenario. Our findings include a history of population bottleneck related to postglacial range expansion, population divergence with limited gene flow, and probable future changes in distribution under changing conditions. Under long-term climate change, Washingtonia's southern and central lowland populations will experience harsher climate conditions and strong genomic offset.

Linking phenotypic variation to patterns of genetic isolation along a speciation continuum.

Investigating taxa at varying stages of divergence can shed light on the evolutionary forces that lead to reproductive isolation and eventual speciation. The forces promoting isolation vary in space and time, which makes it difficult to reconstruct the trajectory that resulted in the divergence observed among species today. The red macroalgal genus Plocamium is known worldwide for its cryptic genetic and chemical diversity. Previous work on the genus Plocamium in Antarctica observed two haplotypes along the western Antarctic Peninsula that have been treated as the same species. Using 10 microsatellite loci, we observed that these two haplotypes correspond to two highly divergent, co-occurring genetic entities in Antarctic Plocamium, which are located within close vicinity of each other at the same sites. The morphology of the reproductive structures, a feature commonly used to identify cryptic species in Plocamium, as well as the timing of reproduction, differed significantly between the two genetic entities. Altogether, this suggests that two Antarctic Plocamium species exist on the western Antarctic Peninsula. We observed evidence for high levels of selfing in both genetic entities, which likely exacerbated the lack of gene flow between them. In addition, we identified concomitant chemodiversity that generates compelling evidence of early evolutionary divergence within one of these entities. This chemodiversity has ecological consequences for its main grazer, which alludes to one putative evolutionary driver of divergence. Antarctic Plocamium spp. provide a promising model system for investigating the eco-evolutionary forces that initiate and maintain species boundaries.

Assessment of Genetic Variability and Population Structure of Betula utilis subsp. jacquemontii in the Western Himalayan Region of India.

Betula utilis subsp. jacquemontii (Spach) Ashburner & McAll. is a medicinally and ecologically important tree species in the Western Himalayan Region (WHR) of India. Estimation of genetic variability and population structure of 11 populations of B. utilis subsp. jacquemontii in the WHR were carried out using 15 ISSR and 10 DAMD markers. The cumulative analyses of the markers (ISSR + DAMD) revealed a moderate level (49.47%) of polymorphism at the species level. Khilanmarg, Gangotri, and Khaliya top populations showed the highest polymorphism, while the Bhyundar Valley and Chatru-Kaza road populations showed the lowest polymorphism across 11 populations. Mantel test revealed a positive correlation between pair-wise genetic and geographical distances in wild populations of B. utilis subsp. jacquemontii in theWHR. The AMOVA analysis showed that majority of variation of the species exists among populations (54%), followed by within populations (20%). The clustering pattern obtained from UPGMA, PCoA, and STRUCTURE analyses revealed that 11 natural populations of B. utilis subsp. jacquemontii separated into two distinct genetic clusters. The genetic differentiation is notably high (GST = 0.74) among populations with a low gene flow (Nm = 0.16), which could be attributed to geographic isolation, high mountain ranges, regional climatic conditions, and habitat destruction in theWHR. The genetically diverse populations recognized in this study could be a valuable genetic resource for conservation and management of this important timberline tree species.

Genetic differentiation and historical dynamics of the endemic species Rheum pumilum on the Qinghai-Tibetan Plateau inferred from phylogeography implications

BackgroundRheum pumilum, an endemic species on the Qinghai-Tibetan Plateau (QTP), serves as an ideal material for investigating the phylogeography of alpine plants. This study employs chloroplast DNA fragments (trnL-F, trnS-G, and matK) to delve into how Rh. pumilum adapted to the extreme environmental changes on the QTP, during its evolutionary process through phylogenetic geographical analysis, revealing its population differentiation and historical dynamics.ResultsThe examination of 39 haplotypes across 26 populations of Rh. pumilum reveals distinct regional distribution, reflecting a phylogeographic pattern resembling “alpine-island”. The total genetic diversity of Rh. pumilum is remarkably high (Ht = 0.910), with the majority of genetic variation primarily occurred among populations (84.5%) with limited gene flow, indicating geographic isolation influenced by diverse habitats of plateau. The geographic isolation model is further supported by various analytical methods, including AMOVA analysis, UPGMA dendrogram, PCoA, Structure analysis, and Mantel test. Micro-refugia for Rh. pumilum during the Quaternary ice ages are supported by haplotype network and genetic diversity analysis. The absence of a typical “star-shape” pattern in the overall haplotype network suggests that Rh. pumilum likely maintains a stable state without experiencing rapid expansion, which has been supported by mismatch distribution analysis. Ecological Niche Modeling (ENM) indicates sensitivity of Rh. pumilum to humidity, temperature and altitude, aligning with a historical distribution resembling a “displacement refugia” model during the Quaternary ice ages. The involvement of Rh. kialense and Rh. sublanceolatum in the origin and gene introgression of Rh. pumilum is suggested, possibly as maternal ancestors of closely related haplotypes. Haplotype divergence of Rh. pumilum approximately 11 million years ago, with notable divergence peaks observed during the late Miocene, as well as the Pliocene, Pleistocene and Holocene.ConclusionThese findings suggest a correlation between genetic diversity, haplotype lineage divergence and key geological and climatic events, notably the uplift of the QTP, monsoon climate changes, and the climatic oscillations during the Quaternary ice ages. This study might provide valuable insights into the formation mechanisms of plant diversity on the QTP, crucial for biodiversity conservation and sustainable species development in extreme environments.

Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA.

Mitonuclear discordance between species is readily documented in marine fishes. Such discordance may either be the result of past natural phenomena or the result of recent introgression from previously seperated species after shifts in their spatial distributions. Using ancient DNA spanning five millennia, we here investigate the long-term presence of Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) -like mitochondrial (MT) genomes in Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance and age structure. Comparing ancient (n = 130) and modern (n = 78) Atlantic bluefin MT genomes from most of its range, we detect no significant spatial or temporal population structure, which implies ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify discordant MT haplotypes in ancient specimens up to 5000 years old and find that the frequency of these haplotypes has remained similar through time. We therefore conclude that MT discordance in the Atlantic bluefin tuna is not driven by recent introgression. Our observations provide oldest example of directly observed MT discordance in the marine environment, highlighting the utility of ancient DNA to obtain insights in the long-term persistence of such phenomena.

The influence of elevation on genetic structure and variability in a wetland crucifer of the Rocky Mountains.

In mountain ecosystems, environmental conditions (e.g., temperature, ultraviolet radiation) covary with elevation, potentially limiting gene flow over steep gradients. We hypothesized that, (1) due to stark elevational differences in environmental factors, populations from dissimilar elevations (e.g., montane versus alpine) are more strongly differentiated than populations from similar elevations; (2) patterns of migration reflect downslope dispersal more than upslope dispersal; and (3) alpine populations at the cold edge show evidence of expansion, while montane populations at the warm edge have declined. DNA polymorphisms in whole-genome sequences were studied from 6-10 genotypes each in populations of Cardamine cordifolia found at three montane sites (ranging from 2200 to 2800 m a.s.l.) and three alpine sites (ranging from 3000 to 3500 m a.s.l.). Statistical analyses assessed patterns of population structure, genetic diversity, migration, and historical demography since the Pleistocene. Populations maintained very high levels of nucleotide diversity (π range: 0.062-0.071) and were weakly differentiated (pairwise FST = 0.027) on average. Migration among alpine populations was also inferred, with no directionality of migration across elevation bands. Demographic inference suggests that both montane and alpine populations have declined in size since the Pleistocene. Environmental differences across elevation represent diffuse barriers to gene flow. Recent polyploidy and clonal reproduction likely explain excess heterozygosity and high nucleotide diversity within populations. The genetic similarity of populations across elevation suggests highly connected refugia during the Pleistocene; such results may indicate that montane and alpine populations will respond similarly to changing environmental conditions associated with climate change.

Red deer resequencing reveals the importance of sex chromosomes for reconstructing Late Quaternary events.

Sex chromosomes differ in their inheritance properties from autosomes, and hence may encode complementary information about past demographic events. We compiled and analysed a range-wide resequencing dataset of the red deer (Cervus elaphus), one of the few Eurasian herbivores of the Late Pleistocene megafauna still found throughout much of its historic range. Our analyses of 144 whole genomes reveal striking discrepancies between the population clusters suggested by autosomal and X-chromosomal data. We postulate that the genetic legacy of Late Glacial population structure is better captured and preserved by the X chromosome than by autosomes, for two reasons. First, X chromosomes have a lower Ne and hence lose genetic variation faster during isolation in glacial refugia, causing increased population differentiation. Second, following postglacial recolonisation and secondary contact, immigrant males pass on their X chromosomes to female offspring only, which effectively halves the migration rate when gene flow is male-mediated. Our study illustrates how a comparison between autosomal and sex chromosomal phylogeographic signals unravels past demographic processes which otherwise would remain hidden.

Weak genetic divergence and signals of adaptation obscured by high gene flow in an economically important aquaculture species

BackgroundThe genetic diversity of a population defines its ability to adapt to episodic and fluctuating environmental changes. For species of agricultural value, available genetic diversity also determines their breeding potential and remains fundamental to the development of practices that maintain health and productivity. In this study, we used whole-genome resequencing to investigate genetic diversity within and between naturalized and captively reared populations of Pacific oysters from the US Pacific coast. The analyses included individuals from preserved samples dating to 1998 and 2004, two contemporary naturalized populations, and one domesticated population.ResultsDespite high overall heterozygosity, there was extremely low but significant genetic divergence between populations, indicative of high gene flow and/or little variability from founding events. The captive population, which was reared for over 25 years was the most genetically distinct population and exhibited reduced nucleotide diversity, attributable to inbreeding. Individuals from populations that were separated both geographically and temporally did not show detectable genetic differences, illustrating the consequences of human intervention in the form translocation of animals between farms, hatcheries and natural settings. Fifty-nine significant FST outlier sites were identified, the majority of which were present in high proportions of the captive population individuals, and which are possibly associated with domestication.ConclusionPacific oysters in the US Pacific coast harbor high genetic heterozygosity which obscures weak population structure. Differences between these Pacific oyster populations could be leveraged for breeding and might be a source of adaptation to new environments.

East Asian Gene flow bridged by northern coastal populations over past 6000 years

Coastal areas of northern East Asia in the ShanDong region, which show complex cultural transitions in the last 10,000 years, have helped to facilitate population interactions between more inland regions of mainland East Asia and islands such as those in the Japanese archipelago. To examine how ShanDong populations changed over time and interacted with island and inland East Asian populations, we sequenced 85 individuals from 11 ancient sites in the ShanDong region dating to ~6000-1500 BP. We found that ancestry related to ShanDong populations likely explains the mainland East Asian ancestry observed in post-Yayoi populations from the Japanese archipelago, particularly recent populations who lived in the Ryukyu Islands after ~2800 BP. In the ShanDong region, we observed gene flow from populations to the north and south of this region by at least ~7700 BP, and two waves of gene flow associated with the inland Yellow River populations into the ShanDong region during the DaWenKou cultural period (6000-4600 BP) and in the early dynastic period (3500-1500 BP). Reconstructing the genetic history of the Neolithic, Bronze, and Iron Age populations of coastal northern East Asia shows gene flow on both a north-south and an east-west (inland-coastal-island) scale.

A genetically confirmed hybrid between Natrix astreptophora and N. maura, two deeply divergent and ancient snake species

Using two mitochondrial DNA fragments and six nuclear genes, we confirmed that a morphologically intermediate snake, captured in Andalusia, southwestern Spain (municipality of Huelva), was an F1 hybrid between a female Natrix astreptophora and a male N. maura. The two parental species diverged 21.5 million years ago, which is why their capability to hybridize is remarkable. The interspecific mating could have been facilitated by the rarity of N. astreptophora and the abundance of N. maura in southwestern Spain, making it difficult for N. astreptophora females to find conspecific males. In the face of previously published genomic signatures for ancient gene flow between N. astreptophora and N. maura, our finding raises the question of whether occasional hybridization still contributes to a continued exchange of genetic information between these two deeply divergent and old taxa.

A Genome-Wide Analysis of Nuclear Mitochondrial DNA Sequences (NUMTs) in Chrysomelidae Species (Coleoptera)

Nuclear mitochondrial DNA sequences (NUMTs) are mitochondrial DNA fragments in the nuclear genome, and their unclear distribution in Chrysomelidae species hinders the selection of accurate molecular markers for species identification and phylogenetic analysis. Our study presents a genome-wide survey of NUMTs in 32 Chrysomelidae species. Filtering strategies based on sequence length and open reading frame (ORF) features were employed to identify mitochondrial protein-coding genes (PCGs) minimally affected by NUMTs. Phylogenetic relationships were inferred from both mitochondrial PCG datasets and a COX1 dataset containing NUMTs. Our results show that NUMTs are chromosomally specific, species-specific, and widely distributed. ATP8, COX1, ND1, and ND4 are identified as relatively reliable molecular markers. Phylogenetic analysis is influenced by NUMTs and other factors such as sequence type and saturation. A total of 66 independent COX1 gene nuclear integration events were estimated across 32 species, mostly from distinct mitochondrial lineages. These findings suggest that NUMTs reflect key evolutionary processes such as gene flow and mitochondrial lineage diversification. Their prevalence emphasizes the need for refined molecular markers in species identification and phylogenetic analysis, while also highlighting the importance of NUMTs in understanding mitochondrial DNA integration and their contribution to species’ evolutionary history.

Genomic insights into Enterococcus faecalis implicated in endodontic infections: resistance, virulence, and genetic variability.

Endodontic infections, often involving multispecies bacterial communities, present significant challenges in treatment due to their complex pathogenic mechanisms and resistance to conventional therapies. Enterococcus faecalis is a facultative anaerobic gram-positive bacterium that has been frequently recovered from secondary or persistent endodontic infections. This study investigates the population structure, resistome, mobilome, and virulome of E. faecalis isolated from oral cavity sources, focusing on 22 genomes sequenced from saliva and root canal samples. The genome sequence analysis revealed a diversity of 14 sequence types (STs), highlighting genetic variability within oral E. faecalis populations. Virulence profiling identified 39 genes involved in adherence, biofilm formation, toxin production, stress response, and immune evasion. Antimicrobial resistance (AMR) genes, including lsa(A), efrA, and tetM, were prevalent across all genomes, indicating potential multidrug resistance. Mobile genetic elements (MGEs), such as insertion sequences, transposons, prophages, and plasmids, were also identified, facilitating genetic exchange within and between species. Network analyses identified central virulence genes (e.g., asa1, gelE) and AMR genes (e.g., ANT (6)-Ia, dfrE) crucial for pathogenicity and resistance, highlighting their pivotal roles in E. faecalis infections. This study provides comprehensive insights into the genomic characteristics, AMR genes, virulence factors, and genetic mobile elements associated with E. faecalis isolates from the oral cavity, offering implications for dental health and potential strategies for infection control and treatment.

Ecological speciation with gene flow followed initial large-scale geographic speciation in the enigmatic afroalpine giant senecios (Dendrosenecio).

Mountains have highly heterogeneous environments that generate ample opportunities for lineage differentiation through ecological adaptation, geographic isolation and secondary contact. The geographic and ecological isolation of the afroalpine vegetation fragments on the East African mountain tops makes them an excellent system to study speciation. The initial diversification within the afroalpine endemic genus Dendrosenecio was shown to occur via allopatric divergence among four isolated mountain groups, but the potential role of ecological speciation within these groups and the role of gene flow in speciation remained uncertain. Here we extend the sampling of Dendrosenecio and use phylogenomics to assess the importance of gene flow in the diversification of the genus. Then, population genomics, demographic modelling and habitat differentiation analyses are used to study ecological speciation in two sister species occurring on Mount Kenya. We found that two sympatric sister species on Mt Kenya occupy distinct microhabitats, and our analyses support that they originated in situ via ecological speciation with gene flow. In addition, we obtained signals of admixture history between mountain groups. Taken together, these results suggest that geographic isolation shaped main lineages, while ecologically mediated speciation occurred within a single mountain.

Dynamic history of the Central Plain and Haidai region inferred from Late Neolithic to Iron Age ancient human genomes.

The peopling history of the Yellow River basin (YR) remains largely unexplored due to the limited number of ancient genomes. Our study sheds light on the dynamic demographic history of the YR by co-analyzing previously published genomes and 31 newly generated Late Neolithic to Iron Age genomes from Shandong in the lower YR and the Central Plain in the middle YR. Our analysis reveals the population structure in Shandong and the Central Plain in the Late Neolithic Longshan cultural period. We provide a genetic parallel to the observation of a significant increase in rice farming in the middle and lower YR in the Longshan period. However, the rice-farmer-related gene flow in the Longshan period did not arrive in groups from the Yuzhuang sites in the Central Plain or previously published groups in Shandong. The Bronze Age Erlitou culture genomes validate the genetic stability in the Central Plain and the relative genetic homogeneity between the Central Plain and Shandong.

Stages and causes of the evolution of language and consciousness: A theoretical reconstruction.

This article presents a refinement of theoretical explanations of the main stages of linguistic and cognitive evolution in anthropogenesis. The concepts of language, consciousness, self-consciousness, the self, the unconscious, the subconscious, and the relation between free will and determinism remain at the center of active and complex debates in philosophy and neuroscience. A basic theoretical apparatus comprising the central concepts of "concern" and "providing structure" (an extension of the biological concept of "adaptation") develops the paradigm of the extended evolutionary synthesis. Challenge-threats and challenge-opportunities are invariably associated with concerns pertaining to sustenance, safety, sexuality, parenthood, status, and emotional support. The consolidation of successful behavioral tries (tries), in response to these challenges occurs through the formation of a variety of providing structures including practices, abilities, and attitudes. These structures are formed through mechanisms of interactive rituals and internalization. These novel practices facilitate the transformation of both techno-natural environmental niches and group niches. The emergence of new structures gives rise to new challenges and concerns, which in turn necessitate undertaking of new tries. In the context of African multiregionalism, hominin groups and populations that experienced favorable periods of demographic growth, active migration, genetic, technological, and skill exchange also underwent significant demographic disasters. During the most unfavorable bottleneck periods only the most advanced groups, populations and species survived. The achieved potential for these abilities was consolidated as complexes of innate assignments in gene pools through the Baldwin effect and the multilevel selection. This logic provides an explanation for the main stages of language and speech complication (from holophrases and articulation to complex syntax), as well as the emergence of new abilities of consciousness (from the expansion of attention field to self-consciousness and the "I"-structure).

Genetic Differentiation of Abies alba Outside Its Main Range Under Warm Meso- and Sub-Mediterranean Conditions in Italy and Switzerland.

Abies alba is an important European tree species currently mostly found at cool and humid sites in the montane zone. In the past, it grew under markedly warmer and drier climates during the Eemian and mid-Holocene, and cryptic Mediterranean populations confirm the species' capacity to grow under warm, summer-dry conditions. However, it is unknown if warm-loving Mediterranean occurrences are related to specific genetic properties (e.g., subspecies or ecotypes). Investigating the genetics of cryptic warm-loving populations is crucial for a better understanding of past and future population dynamics of A. alba. We genotyped 478 A. alba samples at 174 single-nucleotide polymorphisms (SNP), covering a broad latitudinal range from Southern Italy to Switzerland while accounting for local altitudinal gradients, and combined these newly introduced genotypes with those of other European Abies populations from the literature. Population genetic structure analyses grouped the warm-loving meso- and sub-Mediterranean populations into the same genetic cluster as the mountain populations of each region. The occurrence of three genetic clusters from Northern to Southern Italy is in line with the glacial refugia history. The inferred evolutionary and demographic history suggests a northward expansion of A. alba after glaciation, as well as a trans-Adriatic gene flow between Balkan and Southern Italian populations. Collectively, the combined genotypic data from individuals across the species' range demonstrate that cryptic Mediterranean populations of A. alba align with the local and large-scale genetic structure of populations from its main range, suggesting that the species is able to thrive in a warmer and drier environmental range than hitherto anticipated. This finding implies that it is unneeded to postulate extinct subspecies or ecotypes to explain the occurrence of meso- and sub-Mediterranean Eemian or mid-Holocene silver fir forests, with important implications for future A. alba population dynamics.

Genome-Assisted Gene-Flow Rescued Genetic Diversity Without Hindering Growth Performance in an Inbred Coho Salmon (Oncorhynchus kisutch) Population Selected for High Growth Phenotype

Selective breeding is a powerful tool for improving aquaculture production. A well-managed breeding program is essential, as populations can otherwise lose genetic diversity, leading to reduced selection response and inbreeding excesses. In such cases, genetic diversity in broodstock must be restored by introducing individuals from external populations. However, this can reduce the accumulated genetic gains from selective breeding. However, the selective introduction of individuals with superior phenotypes will allow the restoration of genetic diversity without sacrificing these gains. In this study, we demonstrated this possibility using a selectively bred (SB) and a randomly bred (RB) population of coho salmon (Oncorhynchus kisutch). Forty males with superior growth were selected from the RB population using genomic selection and crossed with 127 randomly collected females from the SB population, producing a newly bred (NB) population. Genetic diversity, assessed from population statistics such as effective number of alleles, allele richness, and observed heterozygosity of 11 microsatellite markers, was higher in NB than in SB and RB. Additionally, fork length and body weight were compared among the three populations after 12 months of growth post-fertilization in common tanks. The least-squares means of fork length and body weight were similar between NB (164.9 mm and 57.9 g) and SB (161.1 mm and 53.7 g), while both were significantly greater than RB (150.4 mm and 43.0 g). Our results highlight the effectiveness of genome-assisted gene flow in restoring the genetic diversity of a population without compromising accumulated genetic gain in growth.

Why Didn't the Sifaka Cross the Road? Divergence of Propithecus edwardsi Gut Microbiomes Across Geographic Barriers in Ranomafana National Park, Madagascar.

This study uses a biogeographic framework to identify patterns of gut microbiome divergence in an endangered lemur species endemic to Madagascar's southeastern rainforests, the Milne-Edwards's sifaka (Propithecus edwardsi). Specifically, we tested the effects of (1) geographic barriers, (2) habitat disturbance, and (3) geographic distance on gut microbiome alpha and beta diversity. We selected 10 social groups from 4 sites in Ranomafana National Park with varied histories of selective logging. Sites were spaced between 4 and 17 km apart falling on either side of two parallel barriers to animal movement: the Namorona River and the RN25 highway. Using 16S rRNA metabarcoding, we found the greatest beta diversity differentiation to occur between social groups, with significant divisions on opposite sides of geographic barriers (road/river). Habitat disturbance had the most significant effect on alpha diversity, though, contrary to many other studies, disturbance was associated with higher microbial species richness. Without biomedical context, it is unclear whether microbiome differences observed herein are neutral, adaptive, or maladaptive. However, microbiome divergence associated with the road/river may be a symptom of reduced host gene flow, warranting further investigation and perhaps conservation action (e.g., construction of wildlife bridges). Finally, this work demonstrates that significant microbiome variation can accrue over small sampling areas, lending new insight into host-microbe-environmental interactions.

Assessment of Genetic Diversity and Construction of Core Germplasm in Populations of Acorus tatarinowii Based on SNP Markers

Acorus tatarinowii is a natural medicinal plant integral to traditional aromatic therapies. It is commonly employed in the treatment of depression, epilepsy, and Alzheimer's disease due to its significant medicinal and aromatic properties. However, the genetic diversity of wild A. tatarinowii resources has declined due to over-exploitation and habitat destruction. This study aims to assess the genetic diversity of the natural populations of A. tatarinowii, establish a core germplasm bank, explore its genetic richness and uniqueness, prevent genetic erosion, and identify beneficial genes. In this study, for the first time, 429A. tatarinowii samples from 40 populations were analyzed for genetic diversity and population structure using Hyper-Seq technology. A total of 4,772,850 high-quality Single Nucleotide Polymorphisms (SNPs) and 1,563,000 Insertions and Deletions (InDels) variant loci were identified, with C/T as the predominant variant type and a Ts/Tv ratio of 1.079. Annotation of these loci indicated that the majority of variants occurring in intergenic regions, accounting for 50.59% of the total. Moreover, the heterozygosity, nucleotide diversity, and FST of A. tatarinowii suggested low genetic diversity within this species within the populations. The analysis of molecular variance (AMOVA) revealed that the population variation of A. tatarinowii is mainly caused by the variation between populations (72.06%), while the variation within populations only contributes a small part (27.94%) Through NJ tree, PCA, and ADMIXTURE analyses, the 429A. tatarinowii samples were classified into five subgroups, with some genetic exchange observed. A total of 7,163 high-quality polymorphic SNPs were identified, and a core germplasm consisting of 85 samples was established, achieving genotype retention rates similar to those of the original germplasm. This indicates that a smaller number of germplasm resources can effectively represent the majority of the genetic diversity. Additionally, PCA analysis further confirmed the representativeness and validity of the constructed core germplasm resources. Furthermore, the DNA fingerprints of the 429 accessions were established using the most effective combinations of 26 SNP markers, which served as specific markers to effectively distinguish all samples. In conclusion, these findings offer valuable insights into the genetic structure of A. tatarinowii, facilitating the identification of high-quality genes and providing a scientific foundation for the development of breeding programs and conservation strategies for A. tatarinowii.