Estimates Of Population Structure Research Articles

Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine.

Annual medic (Medicago spp.) germplasm was collected from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the United States department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS) temperate-adapted forage legume collection. A total of 102 accessions across 10 Medicago species were collected. To assess genetic diversity, population structure, and to confirm taxonomic identities, the collections were phenotypically and genetically characterized. Phenotyping included the use of 24 descriptor traits while genetic characterization was accomplished using a 3K Diversity Array Technologies (DArTag) panel developed for alfalfa (Medicago sativa L.). For both field and molecular characterizations, a reference set of 92 geographically diverse and species-representative accessions were obtained from the NPGS collection. Phenotypic descriptors showed consistency among replicated plants within accessions, some variation across accessions within species, and evident distinctions between species. Because the DArTag panel was developed for cultivated alfalfa, the transferability of markers to the species being evaluated was limited, resulting in an average of ~1,500 marker loci detected per species. From these loci, 448 markers were present in 95% of the samples. Principal component and phylogenetic analysis based on a larger set of 2,396 selected markers clustered accessions by species and predicted evolutionary relationships among species. Additionally, the markers aided in the taxonomic identity of a few accessions that were likely mislabeled. The genotyping results also showed that sampling individual plants for these mostly self-pollinating species is sufficient due to high reproducibility between single (n=3) and pooled (n=7) biological replicate leaf samples. The phenotyping and the 2,396 Single Nucleotide Polymorphism (SNP) marker set were useful in estimating population structure in the Crimean and reference accessions, highlighting novel and unique genetic diversity captured in the Crimean accessions. This research not only demonstrated the utility of the DArTag marker panel in evaluating the Crimean germplasm but also highlighted its broader application in assessing genetic resources within the Medicago genus. Furthermore, we anticipate that our findings will underscore the importance of leveraging genetic resources and advanced genotyping tools for sustainable crop improvement and biodiversity conservation in annual medic species.

Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape.

Phrynosoma mcallii (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analysed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and the Salton Sea. We recommend additional lands in the United States and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy. We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change, and other long-term impacts.

Using genomic data to estimate population structure of Gopher Tortoise (Gopherus polyphemus) populations in Southern Alabama

Using genomic data to estimate population structure of Gopher Tortoise (Gopherus polyphemus) populations in Southern Alabama

Sequence-based population structure, relatedness, and inbreeding estimates for forensic autosomal STR markers

Population data have become available for sequence data to aid forensic investigations and prepare the forensic community in the move towards implementing NGS methods. This comes with a need for updated population genetic parameters estimates to allow DNA evidence evaluations using sequence data. Initial work has been done on a small sample and here we expand this work by providing estimates of population structure and relatedness for autosomal STR data generated by sequencing technologies. We also discuss the effect of inbreeding on forensic calculations and discuss why the use of genotypic-based estimates may be preferred over allelic-based estimates.

Establishing Age-Based Color Changes for the American Burying Beetle, Nicrophorus americanus Olivier, with Implications for Conservation Efforts.

The American burying beetle, Nicrophorus americanus Olivier, is a federally protected insect that once occupied most of eastern North America. Adult beetles feature distinct, recognizable markings on the pronotum and elytra, and color changes with age have been observed. Among the challenges faced by research scientists and conservation practitioners is the ability to determine beetle age in the field between and including teneral (young) and senescent (old) adult stages. Using 20 (10 male and 10 female) captive-bred beetles, we characterized the change in greyscale and red, green, and blue (RGB) color channels over the lifespan of each beetle for field-aging applications. Individual beetles were photographed at set intervals from eclosion to death, and color data were extracted using open-source ImageJ Version 1.54f software. A series of linear mixed-effects models determined that red color showed the steepest decrease among all color channels in the pronotum and elytral markings, with a more significant decrease in the pronotum. The change in greyscale between the pronotum and elytral markings was visibly different, with more rapid darkening in the pronotum. The resulting pronotum color chart was tested under field conditions in Oklahoma, aging 299 adult N. americanus, and six age categories (day range) were discernable by eye: teneral (0-15), late teneral (15-31), early mature (31-45), mature (45-59), early senescent (59-76), and senescent (76-90). The ability to more precisely estimate age will improve population structure estimates, laboratory breeding programs, and potential reintroduction efforts.

Genome wide association studies and candidate gene mining for understanding the genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions.

Rice is a high-silica (SiO2·nH2O) accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crops. However, the presence of high silica content is detrimental to rice straw management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in north-western India, and it is eventually burned in situ by farmers, contributing to air pollution. A practical solution could lie in reducing the silica content in rice while also attaining sound plant growth. A set of 258 Oryza nivara accessions along with 25 cultivated varieties of Oryza sativa was used to assess the variation in straw silica content using the molybdenum blue colorimetry method. A large continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08% to 16%, while it varied from 6.18% to 15.81% in the cultivated varieties. The O. nivara accessions containing 43%-54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphisms (SNPs) among 258 O. nivara accessions was used for estimating population structure and genome-wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker-trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported quantitative trait loci (QTL). Twelve out of 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses revealed the presence of promising candidate genes, including those encoding the ATP-binding cassette (ABC) transporter, Casparian thickening, multi-drug and toxin extrusion (MATE) protein, F-box, and MYB-transcription factors. Besides, ortho-QTLs among rice and maize genomes were identified, which could open ways for further genetic analysis of this trait. The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programs to develop rice varieties with lower silica content and higher yield potential.

PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data

BackgroundPopulation structure and cryptic relatedness between individuals (samples) are two major factors affecting false positives in genome-wide association studies (GWAS). In addition, population stratification and genetic relatedness in genomic selection in animal and plant breeding can affect prediction accuracy. The methods commonly used for solving these problems are principal component analysis (to adjust for population stratification) and marker-based kinship estimates (to correct for the confounding effects of genetic relatedness). Currently, many tools and software are available that analyze genetic variation among individuals to determine population structure and genetic relationships. However, none of these tools or pipelines perform such analyses in a single workflow and visualize all the various results in a single interactive web application.ResultsWe developed PSReliP, a standalone, freely available pipeline for the analysis and visualization of population structure and relatedness between individuals in a user-specified genetic variant dataset. The analysis stage of PSReliP is responsible for executing all steps of data filtering and analysis and contains an ordered sequence of commands from PLINK, a whole-genome association analysis toolset, along with in-house shell scripts and Perl programs that support data pipelining. The visualization stage is provided by Shiny apps, an R-based interactive web application. In this study, we describe the characteristics and features of PSReliP and demonstrate how it can be applied to real genome-wide genetic variant data.ConclusionsThe PSReliP pipeline allows users to quickly analyze genetic variants such as single nucleotide polymorphisms and small insertions or deletions at the genome level to estimate population structure and cryptic relatedness using PLINK software and to visualize the analysis results in interactive tables, plots, and charts using Shiny technology. The analysis and assessment of population stratification and genetic relatedness can aid in choosing an appropriate approach for the statistical analysis of GWAS data and predictions in genomic selection. The various outputs from PLINK can be used for further downstream analysis. The code and manual for PSReliP are available at https://github.com/solelena/PSReliP.

Estimation of population structure, growth and condition of Parastromateus niger in the Bay of Bengal

Black pomfret (Parastromateus niger) is one of the major commercial species of pomfret fishery in Bangladesh. This study illustrates the population structure (Length Frequency Distribution, LFD), relationship between length and weight (LWR), relationships between length and length (LLRs), Fulton’s condition factor (KF) and relative weight (WR) of P. niger in the Bay of Bengal (BoB). A total of 225 P. niger were collected from the four locations during January to December 2020. LFD analysis indicates three length classes 21-27 cm, 30-32 cm and 35-37 cm, respectively. This species showed isometric growth pattern (b = 2.981) that indicates that the size and weight increases proportionally and the surrounding habitat provides favourable environment for the growth. LWR between TL and BW were highly correlated (r² = 0.951). LLRs also showed significant correlation between TL and SL (r² = 0.845) and TL and FL (r² = 0.861). The mean value of KF was found as 1.60 which indicates that the BoB provides healthy environment for this species. The mean value of WR (101.09) indicates that the relationship between prey and predator was in balanced condition. This study suggests optimum catchable length for P. niger at 27 cm. Therefore, these findings could provide important information to design effective conservation and management planning for this species.

Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago.

The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semipermeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation, rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence capture to generate a dataset of 1154 nuclear genes (∼1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three pairs of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and nonstepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection.

Inferring population structure in biobank-scale genomic data

SummaryInferring the structure of human populations from genetic variation data is a key task in population and medical genomic studies. Although a number of methods for population structure inference have been proposed, current methods are impractical to run on biobank-scale genomic datasets containing millions of individuals and genetic variants. We introduce SCOPE, a method for population structure inference that is orders of magnitude faster than existing methods while achieving comparable accuracy. SCOPE infers population structure in about a day on a dataset containing one million individuals and variants as well as on the UK Biobank dataset containing 488,363 individuals and 569,346 variants. Furthermore, SCOPE can leverage allele frequencies from previous studies to improve the interpretability of population structure estimates.

Genetic and Morphological Approach for Western Corn Rootworm Resistance Management

The western corn rootworm (WCR), is one of the most serious pests of maize in the United States. In this study, we aimed to find a reliable pattern of difference related to resistance type using population genetic and geometric morphometric approaches. To perform a detailed population genetic analysis of the whole genome, we used single nucleotide polymorphisms (SNPs) markers. For the morphometric analyses, hindwings of the resistant and non-resistant WCR populations from the US were used. Genetic results showed that there were some differences among the resistant US populations. The low value of pairwise FST = 0.0181 estimated suggests a lack of genetic differentiation and structuring among the putative populations genotyped. However, STRUCTURE analysis revealed three genetic clusters. Heterozygosity estimates (HO and HE) over all loci and populations were very similar. There was no exact pattern, and resistance could be found throughout the whole genome. The geometric morphometric results confirmed the genetic results, with the different genetic populations showing similar wing shape. Our results also confirmed that the hindwings of WCR carry valuable genetic information. This study highlights the ability of geometric morphometrics to capture genetic patterns and provides a reliable and low-cost alternative for preliminary estimation of population structure. The combined use of SNPs and geometric morphometrics to detect resistant variants is a novel approach where morphological traits can provide additional information about underlying population genetics, and morphology can retain useful information about genetic structure. Additionally, it offers new insights into an important and ongoing area of pest management on how to prevent or delay pest evolution towards resistant populations, minimizing the negative impacts of resistance.

Landscape configuration of an Amazonian island-like ecosystem drives population structure and genetic diversity of a habitat-specialist bird

ContextAmazonian white-sand ecosystems (campinas) are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to a clear distinction from the surrounding matrix, the spatial characteristics of campina patches may affect the genetic diversity and composition of their specialized organisms, such as the small and endemic passerine Elaenia ruficeps.ObjectivesTo estimate the relative contribution of the current extension, configuration and geographical context of campina patches to the patterns of genetic diversity and population structure of E. ruficeps.MethodsWe sampled individuals of E. ruficeps from three landscapes in central Amazonia with contrasting campina spatial distribution, from landscapes with large and connected patches to landscapes with small and isolated patches. We estimated population structure, genetic diversity, and contemporary and historical migration within and among the three landscapes and used landscape metrics as predictor variables. Furthermore, we estimated genetic isolation by distance and resistance within landscapes.ResultsWe identified three genetically distinct populations with asymmetrical gene flow among landscapes and a decreasing migration rate with distance. Within each landscape, we found low differentiation without genetic isolation by distance nor by resistance. In contrast, we found differentiation and spatial correlation between landscapes.ConclusionsTogether with previous studies, the population dynamics of E. ruficeps suggests that both regional context and landscape structure shape the connectivity among populations of campina specialist birds. Also, the spatial distribution of Amazonian landscapes, together with their associated biota, has changed in response to climatic changes in the Late Pleistocene.

Population Genomics and Conservation of Erigenia bulbosa (Apiaceae), an Edge-of-Range Species in Pennsylvania

Premise of research. Erigenia bulbosa, or the harbinger of spring, is one of the earliest-blooming wildflowers in eastern North America. As a spring ephemeral of forests and woodlands, it is a common species throughout the Midwest. In Pennsylvania, E. bulbosa exhibits an east-west disjunct distribution, where widespread western populations are contiguous with the midwestern range and a handful of smaller populations in the eastern part of the state are restricted to the lower Susquehanna River Valley. The relative isolation of the eastern populations suggests a possible conservation concern; the smaller, less connected populations may be threatened by fluctuations in size and the potential for low genetic diversity. As a consequence, establishing regulatory measures in Pennsylvania has been problematic because of disagreement regarding how to treat E. bulbosa during the Pennsylvania Department of Conservation and Natural Resources (PA DCNR) environmental review process. Currently, populations in the east are subject to regulation, while populations in the west are not.Methodology. To better understand the population genetics of the species, we coupled field assessments of E. bulbosa with a population genomics approach. We sampled multiple individuals from eight populations and generated a genotyping-by-sequencing data set of single-nucleotide polymorphisms (SNPs) that we used to calculate population statistics (genetic variation [FST], inbreeding coefficient [FIS], and heterozygosity), estimate population structure (sparse nonnegative matrix factorization), identify clusters of genetically related individuals (discriminant analysis of principal components), estimate a NeighborNet, look at signatures of isolation by distance (IBD), and detect population differentiation (analysis of molecular variance) using the filtered SNP data set.Pivotal results. Our data reveal structure in all populations and suggest genetic isolation between the groups of populations in the eastern and western portions of the state. Genetic groups identified using multivariate methods correspond to populations. Within populations, we estimate low levels of heterozygosity, a significant signature of IBD, and that most of the genetic variation we find is due to differences between populations.Conclusions. Our results indicate that any conservation measures undertaken by the PA DCNR should be applied evenly throughout Pennsylvania. We expect that most populations will continue to be threatened by land use and other development activities. This work illustrates the strength of academic and nonacademic partnerships in fostering outcomes that inform conservation activities for local species of concern.

Expansion of the mangrove species Rhizophora mucronata in the Western Indian Ocean launched contrasting genetic patterns

Estimates of population structure and gene flow allow exploring the historical and contemporary processes that determine a species’ biogeographic pattern. In mangroves, large-scale genetic studies to estimate gene flow have been conducted predominantly in the Indo-Pacific and Atlantic region. Here we examine the genetic diversity and connectivity of Rhizophora mucronata across a > 3,000 km coastal stretch in the Western Indian Ocean (WIO) including WIO islands. Based on 359 trees from 13 populations and using 17 polymorphic microsatellite loci we detected genetic breaks between populations of the (1) East African coastline, (2) Mozambique Channel Area (3) granitic Seychelles, and (4) Aldabra and northern Madagascar. Genetic structure, diversity levels, and patterns of inferred connectivity, aligned with the directionality of major ocean currents, driven by bifurcation of the South Equatorial Current, northward into the East African Coastal Current and southward into the Mozambique Channel Area. A secondary genetic break between nearby populations in the Delagoa Bight coincided with high inbreeding levels and fixed loci. Results illustrate how oceanographic processes can connect and separate mangrove populations regardless of geographic distance.

Movement and Seasonal Energetics Mediate Vulnerability to Disturbance in Marine Mammal Populations.

AbstractIn marine environments, noise from human activities is increasing dramatically, causing animals to alter their behavior and forage less efficiently. These alterations incur energetic costs that can result in reproductive failure and death and may ultimately influence population viability, yet the link between population dynamics and individual energetics is poorly understood. We present an energy budget model for simulating effects of acoustic disturbance on populations. It accounts for environmental variability and individual state, while incorporating realistic animal movements. Using harbor porpoises (Phocoena phocoena) as a case study, we evaluated population consequences of disturbance from seismic surveys and investigated underlying drivers of vulnerability. The framework reproduced empirical estimates of population structure and seasonal variations in energetics. The largest effects predicted for seismic surveys were in late summer and fall and were unrelated to local abundance, but instead were related to lactation costs, water temperature, and body fat. Our results demonstrate that consideration of temporal variation in individual energetics and their link to costs associated with disturbances is imperative when predicting disturbance impacts. These mechanisms are general to animal species, and the framework presented here can be used for gaining new insights into the spatiotemporal variability of animal movements and energetics that control population dynamics.

Characterization of a pericentric inversion in plateau fence lizards (Sceloporus tristichus): evidence from chromosome-scale genomes.

Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n = 36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n = 22 to 46 chromosomes. We present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n = 22 with six pairs of macrochromosomes and five pairs of microchromosomes and a pericentric inversion polymorphism on chromosome 7 that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84–1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in ∼15K predicted gene models. Our assemblies confirmed the presence of a 4.62-Mb pericentric inversion on chromosome 7, which contains 62 annotated coding genes with known functions. In addition, we collected population genomics data using double digest RAD-sequencing for 44 S. tristichus to estimate population structure and phylogeny across the Colorado Plateau. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.

Otolith shape as a tool for representing different growth in young and adult yellowfin tuna (Thunnus albacares, Bonnaterre, 1788)

The stock status of yellowfin tuna (Thunnus albacares) (YFT) in the Indian Ocean is currently concluded overfished and is subject to overfishing. The information about the YFT population structure is fundamental for effective fisheries management and conservation. The otolith shape as a tool for estimating population structure is the cheapest technique compared to other methods, such as genetic, parasite, and otolith chemistry, especially for analyzing the large samples. This study investigates the use of otolith shapes to determine the yellowfin stock from two different locations. Data collection was carried out at two locations, namely Kedonganan and Benoa, throughout 2018. Total samples collected from the two study sites were 314 otoliths, but only 147 whole otoliths could be analyzed. Image analysis was performed using ANOVA-like permutation (n=1000 to determine whether the individual can be reclassified to their sample origin. The subsequent analysis is the variations in the shape of the otolith with multivariate statistical methods using cluster analysis with Canonical Analysis of Principal Coordinates. The result shows that the YFT otolith Benoa is significantly different from the YFT otolith Kedonganan with the P-value = 0.0015.

Distribution and Density of Haemaphysalis longicornis (Acari: Ixodidae) on Public Lands in Pennsylvania, United States.

Since the recent introduction of the Asian longhorned tick (Haemaphysalis longicornis Neumann) in the United States, quantitative surveillance information remains lacking, which hinders accurate estimates of population structure and entomological risk. We conducted statewide, active tick surveillance from May to August 2019 and report data on H. longicornis geographical distribution and population density in Pennsylvania. In total, 615 H. longicornis were collected from four counties. Across samples recovering H. longicornis, mean density of H. longicornis was 9.2/100 m2, comparably greater than Ixodes scapularis Say (8.5/100 m2). Density of H. longicornis was also significantly greater in August, largely driven by larvae, and greater in recreational habitat types (12.6/100 m2) and in Bucks County (11.7/100 m2), situated adjacent to the location of the first U.S. discovery of intense infestations. These data are among the first to document H. longicornis from statewide tick surveillance and provide initial measures of population density enabling more quantitative characterizations of distributional patterns.

Genome-wide genetic variation coupled with demographic and ecological niche modeling of the dusky-footed woodrat (Neotoma fuscipes) reveal patterns of deep divergence and widespread Holocene expansion across northern California.

Understanding how species have responded to past climate change may help refine projections of how species and biotic communities will respond to future change. Here, we integrate estimates of genome-wide genetic variation with demographic and niche modeling to investigate the historical biogeography of an important ecological engineer: the dusky-footed woodrat, Neotoma fuscipes. We use RADseq to generate a genome-wide dataset for 71 individuals from across the geographic distribution of the species in California. We estimate population structure using several model-based methods and infer the demographic history of regional populations using a site frequency spectrum-based approach. Additionally, we use ecological niche modeling to infer current and past (Last Glacial Maximum) environmental suitability across the species' distribution. Finally, we estimate the directionality and possible spatial origins of regional population expansions. Our analyses indicate this species is subdivided into three regionally distinct populations, with the deepest divergence occurring ~1.7 million years ago across the modern-day San Francisco-Bay Delta region; a common biogeographic barrier for the flora and fauna of California. Our models of environmental suitability through time coincide with our estimates of population expansion, with relative long-term stability in the southern portion of the range, and more recent expansion into the northern end of the range. Our study illustrates how the integration of genome-wide data with spatial and demographic modeling can reveal the timing and spatial extent of historic events that determine patterns of biotic diversity and may help predict biotic response to future change.

Detection of fish movement patterns across management unit boundaries using age-structured Bayesian hierarchical models with tag-recovery data.

Tagging studies have been widely conducted to investigate the movement pattern of wild fish populations. In this study, we present a set of length-based, age-structured Bayesian hierarchical models to explore variabilities and uncertainties in modeling tag-recovery data. These models fully incorporate uncertainties in age classifications of tagged fish based on length and uncertainties in estimated population structure. Results of a tagging experiment conducted by the Ontario Ministry of Natural Resources and Forestry (OMNRF) on yellow perch in Lake Erie was analyzed as a case study. A total of 13,694 yellow perch were tagged with PIT tags from 2009 to 2015; 322 of these were recaptured in the Ontario commercial gillnet fishery and recorded by OMNRF personnel. Different movement configurations modeling the tag-recovery data were compared, and all configurations revealed that yellow perch individuals in the western basin (MU1) exhibited relatively strong site fidelity, and individuals from the central basin (MU2 and MU3) moved within this basin, but their movements to the western basin (MU1) appeared small. Model with random effects of year and age on movement had the best performance, indicating variations in movement of yellow perch across the lake among years and age classes. This kind of model is applicable to other tagging studies to explore temporal and age-class variations while incorporating uncertainties in age classification.