Population Structuring Research Articles

The past, the recent, and the ongoing evolutionary processes of the worldwide invasive ascidian Styela plicata.

Invasive species are one of the main threats to global biodiversity and, within marine ecosystems, tunicates feature some prominent examples. Styela plicata is an ascidian species inhabiting harbours in all temperate oceans and seas, thus being considered a thriving invasive species. However, this species' adaptive mechanisms, introduction history, and population structure have never been completely elucidated. Here, by genotyping 87 S. plicata individuals from 18 localities worldwide with 2b-RADseq, we confirm the global presence of four chromosome inversions, demonstrate population structuring on this species, detect local adaptation signals, and infer historical demographic events. We show that North Carolina individuals constitute an unrelated population, Atlanto-Mediterranean and Pacific localities form their own genetic clusters with substructuring, being the most evident the split between northern and southern Atlantic localities. The locality of South Carolina presents an intermediate genetic position between North Carolina and the other two groups pointing to a hybrid origin with recurrent gene flow. We generate and test demographic models, providing evidence of two independent introduction events to the Atlantic and Pacific, and an admixture that originated the population of South Carolina. Finally, we identify candidate loci for adaptation, with functions involved with cell processes, metabolism, development, and ion transport, among others. Overall, this study highlights the complex historical processes of S. plicata, which have led this species to its current distribution, population structure, and local adaptation footprint in oceans worldwide.

Genomic architecture and population structure of Boreogadus saida from Canadian waters

The polar cod, Boreogadus saida, is an abundant and ubiquitous forage fish and a crucial link in Arctic marine trophic dynamics. Our objective was to unravel layers of genomic structure in B. saida from Canadian waters, specifically screening for potential hybridization with the Arctic cod, Arctogadus glacialis, large chromosomal inversions, and sex-linked regions, prior to interpreting population structure. Our analysis of 53,384 SNPs in 522 individuals revealed hybridization and introgression between A. glacialis and B. saida. Subsequent population level analyses of B. saida using 12,305 SNPs in 511 individuals revealed three large (ca. 7.4–16.1 Mbp) chromosomal inversions, and a 2 Mbp region featuring sex-linked loci. We showcase population structuring across the Western and Eastern North American Arctic, and subarctic regions ranging from the Hudson Bay to the Canadian Atlantic maritime provinces. Genomic signal for the inferred population structure was highly aggregated into a handful of SNPs (13.8%), pointing to potentially important adaptive evolution across the Canadian range. Our study provides a high-resolution perspective on the genomic structure of B. saida, providing a foundation for work that could be expanded to the entire circumpolar range for the species.

Neutral genetic structuring of pathogen populations during rapid adaptation.

Pathogen species are experiencing strong joint demographic and selective events, especially when they adapt to a new host, for example through overcoming plant resistance. Stochasticity in the founding event and the associated demographic variations hinder our understanding of the expected evolutionary trajectories and the genetic structure emerging at both neutral and selected loci. What would be the typical genetic signatures of such a rapid adaptation event is not elucidated. Here, we build a demogenetic model to monitor pathogen population dynamics and genetic evolution on two host compartments (susceptible and resistant). We design our model to fit two plant pathogen life cycles, 'with' and 'without' host alternation. Our aim is to draw a typology of eco-evolutionary dynamics. Using time-series clustering, we identify three main scenarios: 1) small variations in the pathogen population size and small changes in genetic structure, 2) a strong founder event on the resistant host that in turn leads to the emergence of genetic structure on the susceptible host, and 3) evolutionary rescue that results in a strong founder event on the resistant host, preceded by a bot- tleneck on the susceptible host. We pinpoint differences between life cycles with notably more evolutionary rescue 'with' host alternation. Beyond the selective event itself, the demographic trajectory imposes specific changes in the genetic structure of the pathogen population. Most of these genetic changes are transient, with a signature of resistance overcoming that vanishes within a few years only. Considering time-series is therefore of utmost importance to accurately decipher pathogen evolution.

Mastication and oral myofunctional status in excess weight children and adolescents: A cross-sectional observational study.

Masticatory function seems to play a role in the aetiology of obesity. However, literature on the association between oral myofunctional status and overweight and obesity in children and adolescents is scarce and contrasting. To compare masticatory performance, orofacial myofunctional status and tongue strength and endurance between children and adolescents with overweight and obesity and those with normal weight. Thirty children and adolescents with overweight and obesity and 30 subjects with normal weight matched for age and sex were recruited. All subjects were evaluated with the Test of Masticating and Swallowing Solids in Children (TOMASS-C) for masticatory performance and with the Italian Orofacial Myofunctional Evaluation with Scores (I-OMES) for the orofacial myofunctional status. Anterior and posterior maximum tongue pressures and tongue endurance were measured. Parents-reported (PRO) duration of meals was recorded. Data were compared between the groups through the paired samples t-test or the Wilcoxon signed-rank test. Children and adolescents with overweight showed significantly lower number of bites (p = .033), lower I-OMES scores (p < .05), and shorter meal duration (p = .005) compared to their peers with normal weight. No significant differences were found between the two groups for the number of swallows, the number of masticatory cycles and the total time of the TOMASS-C, and none of the tongue pressure measurements. Eating in children and adolescents with overweight and obesity is characterised by a larger bolus sizes and shorter PRO meal duration. Additionally, overweight and obesity seem to be associated with poorer orofacial skills and structures in the paediatric population.

Integrative taxonomy reveals inflated biodiversity in the European Temnothorax unifasciatus complex (Hymenoptera: Formicidae)

AbstractTemnothorax unifasciatus (Latreille, 1798) is a widely distributed pan‐European species from the Iberian Peninsula to the Caucasus. This taxon's relatively high morphological variability prompts the taxonomists of earlier times and today to mention the morphologically different elements at specific or subspecific ranks. This paper aims to understand the population structure and genetic diversity within this lineage via integrative taxonomy, incorporating molecular phylogenetics, species delimitation analyses and multivariate analyses of continuous morphometric data from across the geographic range of the T. unifasciatus complex. Phylogenetic analyses yielded incongruent trees. The genealogical diversity index (gdi) and the confirmatory analyses on morphological data found only weak, ambiguous delimitations within the unifasciatus complex. The most highly supported scenario splits T. brackoi from the remaining unifasciatus complex with ambiguous support (gdi = 0.56). This scenario is supported by multivariate morphometry with 100% accuracy in classification success. Instead, our results suggest complex morphological and genetic population structuring within the broad range of T. unifasciatus. Therefore, we confirm the validity of two species, T. brackoi Salata &amp; Borowiec, 2019 and T. unifasciatus (Latreille, 1798), and propose five new junior synonymies, T. cordieri (Bondroit, 1918) syn. nov., T. tauricus (Ruzsky, 1902) syn. nov., T. berlandi (Bondroit, 1918) syn. nov., T. unifasciatus staegeri (Bondroit, 1918) syn. nov., T. tuberum ciscaucasicus (Arnol'di, 1977) syn. nov. with the latter. To achieve maximal taxonomic stability, we designated a lectotype for Temnothorax unifasciatus (Latreille, 1798).

A scoping review of cephalometric normative data in children.

Understanding the orofacial characteristics and growth patterns in children is essential for both orthodontics and research on children with orofacial abnormalities. However, a concise resource of normative data on the size and relative position of these structures in different populations is not available. Our objective was to aggregate normative data to assess the growth of the orofacial skeletal structures in children with a well-balanced face and normal occlusion. The MEDLINE, Embase, and Scopus databases were searched. Inclusion criteria included longitudinal and cross-sectional studies on cephalometric measurement of skeletal tissues and a study population ≤ 18 years with a well-balanced face and normal occlusion. Key study parameters were extracted, and knowledge was synthesized. A quality appraisal was performed using a 10-point scale. The final selection comprised of 12 longitudinal and 33 cross-sectional studies, the quality of which ranged from good to excellent. Our results showed that from childhood to adulthood, the length of the cranial base increased significantly while the cranial base angle remained constant; both the maxilla and mandible moved forward and downward. The profile becomes straighter with age. Growth patterns in children with a well-balanced face and normal occlusion follow accepted theories of growth.

Spatial invasion of cooperative parasites

In this paper we study invasion probabilities and invasion times of cooperative parasites spreading in spatially structured host populations. The spatial structure of the host population is given by a random geometric graph on [0,1]n, n∈N, with a Poisson(N)-distributed number of vertices and in which vertices are connected over an edge when they have a distance of at most rN with rN of order N(β−1)/n for some 0<β<1. At a host infection many parasites are generated and parasites move along edges to neighbouring hosts. We assume that parasites have to cooperate to infect hosts, in the sense that at least two parasites need to attack a host simultaneously. We find lower and upper bounds on the invasion probability of the parasites in terms of survival probabilities of branching processes with cooperation. Furthermore, we characterize the asymptotic invasion time.An important ingredient of the proofs is a comparison with infection dynamics of cooperative parasites in host populations structured according to a complete graph, i.e. in well-mixed host populations. For these infection processes we can show that invasion probabilities are asymptotically equal to survival probabilities of branching processes with cooperation. Furthermore, we build on proof techniques developed in Brouard and Pokalyuk (2022), where an analogous invasion process has been studied for host populations structured according to a configuration model.We substantiate our results with simulations.

Altered metapopulation dynamics in a headwater specialist in geomorphically dynamic catchments

Abstract Human activities have widely disrupted the spatial ecological processes critical for population and ecosystem integrity. Local effects of altered sediment regimes in rivers are well explored, but how they impact connectivity at a catchment scale is less explored. In this paper we document evidence for altered metapopulation dynamics for a headwater specialist, blackspotted topminnow (Fundulus olivaceus) in catchments with geomorphically dynamic river mainstems. We quantified decade‐scale patterns of fluvial geomorphic activity via planform analysis of historical and recent aerial imagery, and patterns of gene flow in F. olivaceus via analysis of single nucleotide polymorphisms, identified by genotype‐by‐sequencing. Mainstem streams narrowed and increased in sinuosity, probably in recovery from historic flood events. Substantial variability in response indicated underlying differences due to differential disturbance history and catchment sensitivity to change. Multiple analytical approaches all found geography to be a major factor in genetic structuring among catchments. Metrics of genetic differentiation and heterozygosity for F. olivaceus within catchments were related to the degree of geomorphic change inferred from a multivariate composite metric. Catchments with more geomorphic change tended to have more population structuring. Five populations assigned to adjacent catchments. Analysis of heterozygosity in presumed donor, recipient, and mis‐assigned catchments indicated founder effects in recipient catchments and probable subsequent allopatric recolonisation following local extirpations. Our results demonstrate complex nonlocal effects of channel evolution on metapopulation dynamics in a pool‐dwelling non‐lithophilous headwater specialist. Our integrative approach allows strong insight into deeper effects of geomorphic processes on aquatic ecosystems. F. olivaceus is ecologically dissimilar to taxa traditionally anticipated to respond to sediment‐related disturbances and demonstrates how broader channel morphological change can affect habitats beyond sedimentation of the stream bed.

Population genetics and phylogeography of Trachylepis sulcata (Peters, 1867) and T. ansorgii (Boulenger, 1907) in south-western Africa

ABSTRACT Ansorge’s Rock Skink Trachylepis ansorgii (Boulenger, 1907) is an Angolan taxon, the taxonomic distinctiveness and geographic distribution of which are poorly understood. It is closely related to the widespread Western Rock Skink T. sulcata (Peters, 1867) from Namibia and South Africa, but heretofore a lack of samples has prevented a comprehensive assessment of T. ansorgii in a molecular phylogenetic context. We combine new genetic sampling from south-western Angola, including topotypical material of T. ansorgii, with published sequences from South Africa and Namibia to identify population structure, phylogenetic relationships, and divergence dates within this species complex. A multi-locus dataset of three nuclear and two mitochondrial loci recovered significant population structuring with a centre of diversity in south-western Angola and northern Namibia. Mitochondrial data recovered seven clades representing distinct geographic populations, while the nuclear data supported either two or three deeper groupings. Mito-nuclear discordance was observed with respect to the geographic boundary between T. ansorgii and T. sulcata. The nuclear data support a break along the western Kunene River (the political boundary between Angola and Namibia), while the mitochondrial data support this break ∼250 km to the north in south-western Angola. A time-calibrated BEAST phylogeny found the deepest species-level divergence to have occurred in the late Miocene/early Pliocene (∼6 mya), potentially related to the formation of the Kunene River. Our results support the recognition of both taxa at the species level, and add further evidence that south-western Angola is a centre of reptile diversity.

Variation of the 3'RR1 HS1.2 Enhancer and Its Genomic Context.

In humans, the HS1.2 enhancer in the Ig heavy-chain locus is modular, with length polymorphism. Previous studies have shown the following features for this variation: (i) strong population structuring; (ii) association with autoimmune diseases; and (iii) association with developmental changes in Ig expression. The HS1.2 region could then be considered as a contributor to inter-individual diversity in humoral response in adaptive immunity. We experimentally determined the HS1.2-length class genotype in 72 of the 1000 Genomes CEU cell lines and assigned the HS1.2 alleles to haplotypes defined by 18 landmark SNPs. We also sequenced the variable portion and ~200 bp of the flanking DNA of 34 HS1.2 alleles. Furthermore, we computationally explored the ability of different allelic arrangements to bind transcription factors. Non-random association between HS1.2 and Gm allotypes in the European population clearly emerged. We show a wealth of variation in the modular composition of HS1.2, with five SNPs further contributing to diversity. Longer alleles offer more potential sites for binding but, for same-length alleles, SNP variation creates/destroys potential binding sites. Altogether, the arrangements of modules and SNP alleles both inside and outside HS1.2 denote an organization of diversity far from randomness. In the context of the strong divergence of human populations for this genomic region and the reported disease associations, our results suggest that selective forces shaped the pattern of its diversity.

Genetic analysis of yield and fiber quality traits in cotton (Gossypium hirsutum L.) under full and deficit irrigation conditions using full diallel method

The aim of the study was to assess the genetic structure and quantitative heritability of cotton yield, yield components and fiber quality parameters under well-watered (100%) and deficit (50%) irrigation conditions using a complete full diallel cross method with six cotton genotypes. The F1 and F2 generations were obtained to study the effect of irrigation conditions on genotypic variation and maternal effects on the traits studied. Parental, F1 and F2 generations were growed under full and deficit irrigation conditions and selected agronomic and fiber quality traits were measured. The data were analysed using various methods, including Griffing Method I, Model I analysis of variance, full diallel table analysis of variance, Jinks-Hayman diallel hybrid analysis. The Jinks-Hayman analysis of variance showed that dominant effects were more important in the inheritance of all traits, as indicated by the negative value of the difference between the additive variance and the dominance variance (D-H1). In addition, the average degree of dominance (H1/D)1/2 was greater than 1, indicating the predominance of dominant gene action in inheritance. The study concluded that starting selection in the F5–F6 generation is appropriate for drought resistant cotton breeding studies. It also emphasised the importance of conducting drought resistant cotton breeding under drought conditions due to the differences in gene movement between well-watered irrigation and drought stress conditions. The study highlighted the importance of population selection, environmental factors, data collection and analysis interpretation in breeding studies. It suggested that the Griffing diallel analysis method is suitable for hybrid breeding studies, while the Jinks-Hayman type analysis method is suitable for studying the genetic structures of populations.

Phenotypic switching mechanisms determine the structure of cell migration into extracellular matrix under the ‘go-or-grow’ hypothesis

A fundamental feature of collective cell migration is phenotypic heterogeneity which, for example, influences tumour progression and relapse. While current mathematical models often consider discrete phenotypic structuring of the cell population, in-line with the ‘go-or-grow’ hypothesis (Hatzikirou et al., 2012; Stepien et al., 2018), they regularly overlook the role that the environment may play in determining the cells’ phenotype during migration. Comparing a previously studied volume-filling model for a homogeneous population of generalist cells that can proliferate, move and degrade extracellular matrix (ECM) (Crossley et al., 2023) to a novel model for a heterogeneous population comprising two distinct sub-populations of specialist cells that can either move and degrade ECM or proliferate, this study explores how different hypothetical phenotypic switching mechanisms affect the speed and structure of the invading cell populations. Through a continuum model derived from its individual-based counterpart, insights into the influence of the ECM and the impact of phenotypic switching on migrating cell populations emerge. Notably, specialist cell populations that cannot switch phenotype show reduced invasiveness compared to generalist cell populations, while implementing different forms of switching significantly alters the structure of migrating cell fronts. This key result suggests that the structure of an invading cell population could be used to infer the underlying mechanisms governing phenotypic switching.

Morphological variation in blackthorn (&lt;i&gt;Prunus spinosa&lt;/i&gt; L.) populations in the Northwestern part of the Balkan Peninsula - Absence of geographical and environmental structure

Blackthorn (&lt;i&gt;Prunus spinosa&lt;/i&gt; L., Rosaceae) is a deciduous, insect-pollinated, and animal-dispersed shrub or a small tree that naturally occurs throughout Europe. The aims of this study were to describe fruit morphological variability of natural populations in the northwestern part of the Balkan Peninsula and to determine the impact of geographical and environmental conditions on shaping the species’ variability. In total, ten fruit and stone morphological traits were studied using data from twelve natural populations. e obtained data was analyzed using descriptive and multivariate statistical methods. High morphological variability was determined both among and within the studied populations. However, our study revealed no clear eco-geographical differentiation of the studied populations. High morphological variability of the populations, but also the absence of geographical and environmental structuring of populations, could be attributed to the animal-mediated dispersal of fruits over greater distances, combined with the vegetative regeneration and high levels of seed flow among populations, as well as the influence of founder effect. Based on the conducted research, valuable information on intra- and interpopulation variability of fruits’ morphological traits was obtained, which can be useful in creating the guidelines for conservation, breeding, and afforestation programs.

Grapevine (Vitis vinifera L.) Germplasm from Siena (Italy) Includes Rare Strains and Reveals Population Structuring

Molecular characterization was carried out on samples of historical grapevine populations that were gathered from within and around the medieval walls of Siena. Forty-nine grapevines were selected based on their age, historical site of growth, grapevines’ ampelography, and for being relict accessions, obsolete to cultivation. SSR profiling data were compared to 44 known grapevines, revealing six functional genetic groups with significant similarity to grapevine types generally grown in Tuscany. The Sienese germplasm is enriched with rare grapevines at risk of extinction, such as Zuccaccio, Gorgottesco, Tenerone, Prugnolo gentile, Occhio di Pernice, Procanico, Rossone, Mammolo, and Canina. Population genetics analysis revealed the existence of five subpopulations structure (-k5) in analogy with cluster analysis.

Unveiling the genetic diversity of bicolored-spined porcupines (Rodentia: Erethizontidae): a novel karyotype, population structuring, and evolutionary insights

Unveiling the genetic diversity of bicolored-spined porcupines (Rodentia: Erethizontidae): a novel karyotype, population structuring, and evolutionary insights

Disentangling genetic diversity of Myotis septentrionalis: population structure, demographic history, and effective population size

Abstract Myotis septentrionalis (Northern Long-eared Bat) has recently suffered a &amp;gt;90% decline in population size in North America due to white-nose syndrome (WNS). We assessed genetic diversity, population structure, current effective population size, and demographic history of M. septentrionalis distributed across the United States to determine baseline levels pre-WNS. We analyzed RADseq data from 81 individuals from Kentucky, Louisiana, Michigan, Minnesota, North Carolina, Oklahoma, and Wisconsin. Additionally, we examined population genetic structure using discriminant analysis of principal components, fastStructure, and STRUCTURE. We then estimated effective population size and demographic history using fastsimcoal2. Similar levels of genetic diversity were found across all samples. We found no population genetic structure in the varied analyses from these contemporary samples. The best model for demographic history estimated a rapid population expansion followed by a slower expansion approximately 340,000 years ago. The vagility of M. septentrionalis, along with male dispersal and random mating, may provide a buffer against serious bottleneck effects stemming from rapid population declines due to WNS. This research provides a baseline for tracking and monitoring the influence of WNS on genetic diversity such as potential reduced diversity or increased population structuring in the future.

Living in a post‐industrial landscape: repeated patterns of genetic divergence in brown trout (Salmo trutta L.) across the British Isles

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

Adaptive divergence, historical population dynamics, and simulation of suitable distributions for Picea Meyeri and P. Mongolica at the whole-genome level

The taxonomic classification of Picea meyeri and P. mongolica has long been controversial. To investigate the genetic relatedness, evolutionary history, and population history dynamics of these species, genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses at the genomic level indicated that although the ancestor of P. mongolica was a hybrid of P. meyeri and P. koraiensis, P. mongolica is an independent Picea species. Additionally, P. mongolica is more closely related to P. meyeri than to P. koraiensis, which is consistent with its geographic distribution. There were up to eight instances of interspecific and intraspecific gene flow between P. meyeri and P. mongolica. The P. meyeri and P. mongolica effective population sizes generally decreased, and Maxent modeling revealed that from the Last Glacial Maximum (LGM) to the present, their habitat areas decreased initially and then increased. However, under future climate scenarios, the habitat areas of both species were projected to decrease, especially under high-emission scenarios, which would place P. mongolica at risk of extinction and in urgent need of protection. Local adaptation has promoted differentiation between P. meyeri and P. mongolica. Genotype‒environment association analysis revealed 96,543 SNPs associated with environmental factors, mainly related to plant adaptations to moisture and temperature. Selective sweeps revealed that the selected genes among P. meyeri, P. mongolica and P. koraiensis are primarily associated in vascular plants with flowering, fruit development, and stress resistance. This research enhances our understanding of Picea species classification and provides a basis for future genetic improvement and species conservation efforts.

A deep learning model for brain segmentation across pediatric and adult populations.

Automated quantification of brain tissues on MR images has greatly contributed to the diagnosis and follow-up of neurological pathologies across various life stages. However, existing solutions are specifically designed for certain age ranges, limiting their applicability in monitoring brain development from infancy to late adulthood. This retrospective study aims to develop and validate a brain segmentation model across pediatric and adult populations. First, we trained a deep learning model to segment tissues and brain structures using T1-weighted MR images from 390 patients (age range: 2-81 years) across four different datasets. Subsequently, the model was validated on a cohort of 280 patients from six distinct test datasets (age range: 4-90 years). In the initial experiment, the proposed deep learning-based pipeline, icobrain-dl, demonstrated segmentation accuracy comparable to both pediatric and adult-specific models across diverse age groups. Subsequently, we evaluated intra- and inter-scanner variability in measurements of various tissues and structures in both pediatric and adult populations computed by icobrain-dl. Results demonstrated significantly higher reproducibility compared to similar brain quantification tools, including childmetrix, FastSurfer, and the medical device icobrain v5.9 (p-value< 0.01). Finally, we explored the potential clinical applications of icobrain-dl measurements in diagnosing pediatric patients with Cerebral Visual Impairment and adult patients with Alzheimer's Disease.

Characterization of rice (Oryza sativa L.) landraces from Majuli and surrounding riverine ecologies in Assam: Assessment of morphogenetic variability and submergence tolerance

AbstractRice landraces from the fragile riverine ecosystems surrounding Majuli islands in Assam are pivotal for local livelihoods, as well as for their potential in developing flood tolerant varieties. We characterized 87 landraces from Majuli, Dhemaji, and North Lakhimpur districts in Assam by assessing 36 agro‐morphological traits, submergence tolerance, and microsatellite diversity. Multivariate analyses revealed that grain and leaf characteristics, plant height, and tillering are important traits differentiating the cultivar types. Sixty‐six SSR markers generated 271 alleles with an average of 4.1 alleles per marker with population structuring in two clusters having an allele frequency divergence of 0.124. The Bao or deep‐water landraces displayed the highest phenotypic and genetic diversity, with potential genetic links to the aus and wild species. Sali (winter rice) and bora (sticky rice) landraces were predominantly indica type. Nearly 47% of the germplasm exhibited tolerance to two‐week submergence at seedling stage. Surveying SUB1A and SNORKEL genes revealed the presence of SUB1A‐1 and SNORKEL genes in 64% and 57% of the tolerant accessions, respectively. This study highlights the untapped potential of rice landraces in a fragile ecological region, providing insights into their agronomical traits, submergence tolerance, and genetic diversity. The findings lay the foundation for improved germplasm management and developing flood‐resilient rice varieties, crucial for sustainable agriculture in riverine ecosystems.