Estimates Of Genetic Diversity Research Articles

Genetic diversity and population structure of Lupinus albus (L.) from the Amhara region of Ethiopia using seed storage protein markers

The genetic diversity in 48 lupin (Lupinus albus (L.) accessions collected from the Amhara region, Ethiopia, was assessed using seed storage protein markers (SDS-PAGE). A total of 30 different protein bands with sizes ranging from 11 to 100 kDa were detected. The average number of protein bands, the percentage of polymorphism, and gene diversity in the accessions were 16.96, 20.35, and 0.072, respectively. Genetic diversity estimates showed that West Gojam and Bahir Dar areas could be the most important sources for lupin genetic resources. The pair-wise comparison of genetic distances (GDs) among the accessions ranged from 0.011 to 0.378. The most distantly related accessions were accession 6, collected from the West Gojam zone, and accession 28 from the Bahir Dar area. Principal coordinate analysis (PCoA) showed the absence of a distinct group, and most of the accessions were intermixed. Population structure analysis revealed that the 48 lupin accessions could be assigned to three clusters. Similar to PCoA, no defined grouping based on geographic origin was observed. Accessions from different geographic origins being grouped together could be attributed to a common origin for the various accessions in the different zones, or it could be the result of seed-mediated gene flow among different lupin growing areas of the country.

Genetic diversity estimates for the Caenorhabditis Intervention Testing Program screening panel.

The Caenorhabditis Intervention Testing Program (CITP) was founded on the principle that compounds with positive effects across a genetically diverse test-set should have an increased probability of engaging conserved biochemical pathways with mammalian translational potential. To fulfill its mandate, the CITP uses a genetic diversity panel of Caenorhabditis strains for assaying longevity effects of candidate compounds. The panel comprises 22 strains from three different species, collected globally, to achieve inter-population genetic diversity. The three represented species, C. elegans, C. briggsae, and C. tropicalis, are all sequential hermaphrodites, which simplifies experimental procedures while maximizing intra-population homogeneity. Here, we present estimates of the genetic diversity encapsulated by the constituent strains in the panel based on their most recently published and publicly available whole-genome sequences, as well as two newly generated genomic data sets. We observed average genome-wide nucleotide diversity (π) within the C. elegans (1.2e-3), C. briggsae (7.5e-3), and C. tropicalis strains (2.6e-3) greater than estimates for human populations, and comparable to that found in mouse populations. Our analysis supports the assumption that the CITP screening panel encompasses broad genetic diversity, suggesting that lifespan-extending chemicals with efficacy across the panel should be enriched for interventions that function on conserved processes that are shared across genetic backgrounds. While the diversity panel was established by the CITP for studying longevity interventions, the panel may prove useful for the broader research community when seeking broadly efficacious interventions for any phenotype with potential genetic background effects.

GENETIC STRUCTURE AND DIVERSITY OF A PERUVIAN COLLECTION OF A HIGH-QUALITY WOOD TREE SPECIES, ULCUMANO (Retrophyllum rospigliosii, PODOCARPACEAE)

Ulcumano, which is native to South America, is an important conifer in Peru. Molecular studies are scarce, limiting modern breeding and appropriate conservation activities. Currently, molecular markers are widely employed to explore genetic structure and diversity parameters of plant species in a fast and precise manner. The objective of this study was to analyze the genetic diversity and population structure of ulcumano in Peru by using DNA-based molecular markers. Nine Randomly Amplified Polymorphic DNA (RAPD) markers were used, while 95 individuals of ulcumano were sampled from three departments of Peru. A total of 265 DNA fragments were manually scored, but 247 of them were kept after removing the non-polymorphic markers. Genetic distances were calculated using R software based on Provesti´s coefficient. A dendrogram was obtained using the UPGMA clustering algorithm, showing no clear clustering. The principal coordinate analysis agreed with two population structure analyses, demonstrating that ulcumano is contained within two clusters, (i) Junín + Pasco, and (ii) Cajamarca, while very few individuals are intermixed. Genetic diversity parameters were estimated considering the two groups (populations) identified by STRUCTURE software. Nei's genetic diversity estimate varied between 0.22 and 0.28, while Shannon index ranged from 3.43 to 4.16. Population divergence (Fst) between the two clusters revealed low genetic differentiation (0.064). AMOVA analysis revealed that 87.31 and 12.69% of the total genetic variation were found within populations and between individuals, respectively. To the best of our knowledge, this is the first molecular study in ulcumano in Peru, and provides valuable information for the genetic improvement and sustainable management of this conifer in the country.

White-footed dunnarts (

A population of white-footed dunnarts (Sminthopsis leucopus) occurs in the Wet Tropics bioregion of tropical north Queensland, Australia separated by about 1800 km from conspecifics in temperate New South Wales, Victoria and Tasmania. We conducted targeted surveys for S. leucopus in north-east Queensland and obtained new records, including the first reported capture of the species in Queensland in 18 years. We assessed the genetic and morphological divergence of the north Queensland population against New South Wales, Victorian and Tasmanian S. leucopus, in conjunction with distribution and habitat differences, to assess whether this isolate should be described as a distinct taxon. Sequencing of the mitochondrial Cytochrome b gene revealed genetic divergence estimates of 2.3–2.8% and 4.3–4.8% between the north Queensland population and S. l. ferruginifrons (Victoria) and S. l. leucopus (Tasmania) respectively. Based on genetic divergence, cranial morphology, differences in habitat, and geographical isolation, we describe the north Queensland population as a new subspecies of Sminthopsis leucopus. We suggest a conservation classification of Endangered given its small distribution, apparent low density, tropical upland location and potential threats, especially related to climate change.

Estimation of Genetic Variability, Heritability and Genetic Advance in Potato (Solanum tuberosum L.) Genotypes for Tuber Yield and Yield Related Traits

Potato is a high potential food security crop in Ethiopia. Genetic variability is the basis of all crop improvement programs. The study was conducted at Adet in 2018 with the objective of assessing the extent and pattern of genetic variability of potato genotypes for yield and yield related traits. A total of 36 potato genotypes were evaluated for 18 quantitative traits in simple lattice design. The analysis of variance revealed that highly significant difference among the tested potato genotypes for all quantitative traits except stem number per hill. The phenotypic coefficient of variation was ranged from 4.56 to 56.01% (for specific gravity and unmarketable tuber yield ha-1 respectively) and the genotypic coefficient of variation was ranged from 2.32 to 40.66% (specific gravity and late blight severity percentage respectively). Days to attain 50% emergence, leaf area index, number of marketable and total tubers per plant, marketable and total tuber yield ha-1, and late blight severity percentage showed high heritability and high genetic advance as percent of mean. Most of the traits had high phenotypic coefficient of variation and genotypic coefficient of variation; and coupled high heritability with high genetic advance as percent of mean. Traits having high heritability and high genetic advance as percent of means is effective for simple selection.

Exploration of Genetic Parameters of Pea Genotypes Using Different Environmental Conditions

The estimate of genetic variability was observed for fifteen traits on fifty two genotypes. The ANOVA indicated that the mean sum of squares due to genotypes were highly significant for all the traits, respectively in all the environmental conditions. High magnitude of phenotypic coefficient of variation was observed than the genotypic coefficient of variation for all the characters under study. High genotypic and phenotypic coefficient of variations were exhibited for number of secondary branches/plant, Pod bearing length, number of primary branches/plant, number of pods/plants, number of seeds/plant, seed yield/plant (gm), biological yield/plant (gm), First flowering node and harvest index (%) in all six and pooled over environments. The above finding revealed the presence of substantial amount of genetic variability for the traits, which exhibited high magnitudes as well as less influence of environment on the expression of concerned traits. Day to first flowering node, number of seed/pods , hundred seed weight (gm), harvest index and days to flower initiation exhibited moderate genotypic and phenotypic coefficient variation in all the environments. Low genotypic and phenotypic coefficient of variation was observed for pod bearing length in all the environments, this reveled high influence of environment.

The genetic diversity of wild grapes in Mexico

This is the first report evaluating the genetic diversity of Mexican grape species utilizing DNA-based markers to understand the distribution of grape species, and patterns of hybridization. The study utilized accessions maintained in three collections in Mexico, one in the USA and recently collected germplasm. Fifteen SSR markers were used to develop a fingerprint database to identify unique germplasm. Two different clustering analyses without prior population assignment, were used to identify groups that were verified by a Discriminant Analysis of Principal Components and a Principal Coordinate Analysis. Genetic diversity estimates were made across and within groups to validate the results obtained from the clustering analyses. Multiple clustering analyses and diversity parameters supported six genetic groups representing different geographic regions. The Northeastern group was the most diverse with a geographic range extending to Eastern and Central Mexico, while the Coahuila group was the least diverse. Vitis arizonica Engelm. and Vitis cinerea Engelm. ex Millardet were the most abundant species with many hybrid forms. We provide evidence that wild grape species in Mexico follow the physical barriers of mountain ranges like the Sierra Madre Oriental with an east–west divide and the Trans-Mexican Volcanic Belt as a corridor for gene flow among different grape species. Additional collections are required to fully understand the extent of hybridization and to clarify hybrid zones.

Batch effects in population genomic studies with low-coverage whole genome sequencing data: Causes, detection and mitigation.

Over the past few decades, there has been an explosion in the amount of publicly available sequencing data. This opens new opportunities for combining data sets to achieve unprecedented sample sizes, spatial coverage or temporal replication in population genomic studies. However, a common concern is that nonbiological differences between data sets may generate patterns of variation in the data that can confound real biological patterns, a problem known as batch effects. In this paper, we compare two batches of low-coverage whole genome sequencing (lcWGS) data generated from the same populations of Atlantic cod (Gadus morhua). First, we show that with a "batch-effect-naive" bioinformatic pipeline, batch effects systematically biased our genetic diversity estimates, population structure inference and selection scans. We then demonstrate that these batch effects resulted from multiple technical differences between our data sets, including the sequencing chemistry (four-channel vs. two-channel), sequencing run, read type (single-end vs. paired-end), read length (125 vs. 150bp), DNA degradation level (degraded vs. well preserved) and sequencing depth (0.8× vs. 0.3× on average). Lastly, we illustrate that a set of simple bioinformatic strategies (such as different read trimming and single nucleotide polymorphism filtering) can be used to detect batch effects in our data and substantially mitigate their impact. We conclude that combining data sets remains a powerful approach as long as batch effects are explicitly accounted for. We focus on lcWGS data in this paper, which may be particularly vulnerable to certain causes of batch effects, but many of our conclusions also apply to other sequencing strategies.

Genetic and species-level biodiversity patterns are linked by demography and ecological opportunity.

The processes that give rise to species richness gradients are not well understood, but may be linked to resource-based limits on the number of species a region can support. Ecological limits placed on regional species richness should also affect population demography, suggesting that these processes could also generate genetic diversity gradients. If true, we might better understand how broad-scale biodiversity patterns are formed by identifying the common causes of genetic diversity and species richness. We develop a hypothetical framework based on the consequences of regional variation in ecological limits set by resource availability and heterogeneity to simultaneously explain spatial patterns of species richness and neutral genetic diversity. Repurposing raw genotypic data spanning 38 mammal species sampled across 801 sites in North America, we show that estimates of genome-wide genetic diversity and species richness share spatial structure. Notably, species richness hotspots tend to harbor lower levels of within-species genetic variation. A structural equation model encompassing eco-evolutionary processes related to resource availability, habitat heterogeneity, and contemporary human disturbance supports the spatial patterns we detect. These results suggest broad-scale patterns of species richness and genetic diversity could both partly be caused by intraspecific demographic and evolutionary processes acting simultaneously across species.

Genome-wide association study and genomic heritabilities for blood protein levels in Lori-Bakhtiari sheep

Serum protein levels are related to physiological and pathological status of animals and could be affected by both genetic and environmental factors. This study aimed to evaluate genetic variation of serum protein profile in sheep. Blood samples were randomly collected from 96 Lori-Bakhtiari ewes, a heavy meat-type breed. Total protein, albumin, globulin, α1, α2, β and γ globulins and IgG levels were measured in blood serum. The samples were genotyped using the Illumina OvineSNP50 BeadChip. The studied traits adjusted for age, birth type, birth season and estimate of breeding value for body weight were considered as pseudo-phenotypes in genome-wide association analysis. In the GWAS model, the first five principal components were fitted as covariates to correct the biases due to possible population stratification. The Plink, R and GCTA software were used for genome-wide association analysis, construction of Q-Q and Manhattan plots and estimation of genetic variances, respectively. Noticeable genomic heritabilities ± SE were estimated for total and γ globulins (0.868 ± 0.262 and 0.831 ± 0.364, respectively), but other protein fractions had zero or close to zero estimates. Based on the Bonferroni adjusted p values, four QTLs located on 181.7 Mbp of OAR3, 107.7 Mbp of OAR4, 86.3 Mbp of OAR7 and 83.0 Mbp of OAR8 were significantly associated with α1, β, β and γ globulins, respectively. The results showed that the PKP2, IGF2R, SLC22A1 and SLC22A2 genes could be considered as candidate genes for blood serum proteins. The present study showed significant genetic variations of some blood protein fractions.

Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses

BackgroundThe possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance.ResultsThere was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP.ConclusionsSpecific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations.

Low genome-wide divergence between two lizard populations with high adaptive phenotypic differentiation.

Usually, adaptive phenotypic differentiation is paralleled by genetic divergence between locally adapted populations. However, adaptation can also happen in a scenario of nonsignificant genetic divergence due to intense gene flow and/or recent differentiation. While this phenomenon is rarely published, findings on incipient ecologically driven divergence or isolation by adaptation are relatively common, which could confound our understanding about the frequency at which they actually occur in nature. Here, we explore genome‐wide traces of divergence between two populations of the lacertid lizard Psammodromus algirus separated by a 600 m elevational gradient. These populations seem to be differentially adapted to their environments despite showing low levels of genetic differentiation (according to previously studies of mtDNA and microsatellite data). We performed a search for outliers (i.e., loci subject to selection) trying to identify specific loci with FST statistics significantly higher than those expected on the basis of overall, genome‐wide estimates of genetic divergence. We find that local phenotypic adaptation (in terms of a wide diversity of characters) was not accompanied by genome‐wide differentiation, even when we maximized the chances of unveiling such differentiation at particular loci with FST‐based outlier detection tests. Instead, our analyses confirmed the lack of genome‐wide differentiation on the basis of more than 70,000 SNPs, which is concordant with a scenario of local adaptation without isolation by environment. Our results add evidence to previous studies in which local adaptation does not lead to any kind of isolation (or early stages of ecological speciation), but maintains phenotypic divergence despite the lack of a differentiated genomic background.

Genetics of tolerance to heat stress in milk yield of dairy buffaloes assessed by a reaction norm model.

The objectives of this study were to assess the effects of heat stress on the milk yield and investigate the presence of genotype×environment interaction (G×E) in Brazilian Murrah buffaloes reared under tropical conditions. With this, 58,070 test-day (TD) records for milk yield from 3,459 first lactations of buffaloes collected between 1987 and 2018 were evaluated. A mixed model considering days in milk (DIM) and temperature-humidity index (THI) was applied to quantify milk yield losses due to heat stress. The most detrimental effect of THI on TD milk yield was observed in the mid-stages of lactation, after lactation peak, in DIM 105-154 and 155-204days (-0.020 and -0.015kg/day per THI, respectively). The least-squares means of TD milk yield were used to identify a heat stress threshold using a piecewise linear regression model. A substantial reduction in TD milk yield due to heat stress was observed for THI values above 77.8 (-0.251kg/day per increase of 1 THI unit). An analysis using a single-trait random regression animal model was carried out to estimate variance components and genetic parameters for TD milk yield over THI and DIM values. Increased additive genetic variance and heritability estimates were observed for extreme THI values (THI=60 and 80) combined with mid-lactation stages. The lowest genetic correlation (0.50) was observed between TD records at opposite extremes of the THI scale (THI=60 vs. THI=80). The genetic trends observed for the regression coefficients related to the general level of production (0.02) and specific ability to respond to heat stress (-0.002) indicated that selection to increase milk yield did not affect the specific ability to respond to heat stress until the present moment. These trends reflect the low genetic correlation between these components (0.05±0.14). In this sense, monitoring trends of genetic components related to response to heat stress is recommended.

Genetic Diversity of Peach Cultivars from the Collection of the Nikita Botanical Garden Based on SSR Markers.

The Nikita Botanical Garden (NBG) has a unique Prunus L. collection (peach, apricot, plum, cherry) comprising more than 3000 accessions. NBG is also a breeding center for stone fruits, including peach (Prunus persica (L.) Batsch). In the present study a set of 85 peach cultivars bred in NBG, Europe, and North America was analyzed using 12 SSR markers to assess their genetic diversity and relatedness. The detected polymorphism level was comparable to the previous estimates of genetic variability in peach cultivars. The average number of alleles per locus was 5.67, PIC value averaged 0.49, expected, and observed heterozygosity averaged 0.52 and 0.31, respectively. Among the detected alleles, 19 (27.94%) were rare and 12 (17.65%) were unique. All studied accessions except two could be identified with the used marker set. Cluster analysis revealed some groups according to the cultivars’ pedigrees. No clear differentiation of the studied sample according to geographic origin or fruit characteristics of peach cultivars was revealed. The results provide valuable information for identification and rational management of the material preserved in the NBG peach collection.

Estimation of genetic diversity and its exploitation in plant breeding

Estimation of genetic diversity and its exploitation in plant breeding

Broadscale Population Structure and Hatchery Introgression of Midwestern Brook Trout

AbstractBrook Trout Salvelinus fontinalis have faced significant declines throughout their native range and have been stocked in Midwestern waters since the late 1800s to offset such losses. Several studies have investigated the genetic effects of these stockings, but these efforts have been confined to relatively small spatial scales. In this study, we compiled 8,454 Brook Trout microsatellite genotypes from 188 wild Midwestern populations and 26 hatchery strains to provide novel insights of broadscale population structure, regional patterns of genetic diversity, and estimates of hatchery introgression for inland Wisconsin populations. Our results indicate high levels of differentiation among our study populations, a lack of hydrological population structuring, lower estimates of genetic diversity in the Driftless Area, and that hatchery introgression has been largely confined to regions of inland Wisconsin that have been heavily affected by anthropogenic disturbances (i.e., the Driftless Area). We also provide evidence that populations may be able to purge hatchery‐derived alleles, discuss possible mechanisms behind this phenomenon, and consider their relevance to accurate estimation of hatchery introgression. Collectively, these results summarize the genetic effects of over a century of anthropogenic disturbance on native Brook Trout populations and emphasize the importance of integrating historical data into contemporary genetic research of intensively managed species.

Assessment of Genetic Diversity and Population Structure in Pea (Pisum sativum L.) Germplasm based on Morphological Traits and SSR Markers

Background: The study was undertaken to assess the genetic diversity and genetic structure among fifty-five pea accessions using morphological traits and SSR markers. Methods: A total of 55 pea accessions were analyzed using eleven phenotypic traits and twenty SSR markers. The data obtained by morphological and molecular profiling was used for the analysis of genetic diversity and for the estimation of genetic diversity estimates, correlation, principal components analysis and population structure. Result: This study reveals that majority of genetic variation was due to variation within population and were clustered into two distinct groups, which reveals a high admixture within individuals. Accessions viz., VRP-82, VRP-320, VRP-194, VRP-375, EC-97280 and EC-8724, showed great diversity as compared to the other accessions based on both morphological and molecular markers. These accessions may assist in developing and planning breeding strategies aimed to produce new varieties in the future.

Assessment of Morphological and Molecular Genetic Diversity in Pigeonpea [Cajanus cajan (L.) Millspaugh

Background: The estimation of genetic diversity in pigeonpea is crucial for desiging breeding programmes and germplasm conservation. Morphological studies alone do not provide sufficient information to understand genetic diversity. Molecular analysis using SSRs can provide additional information on genetic diversity that can be used for selection of diverse parents. Methods: The experimental material for present study consisted of 50 diverse genotypes of pigeonpea. The fifty genotypes were planted in Randomized Complete Block Design consisted of three replications during the kharif 2020-21. The estimation of morphological genetic diversity was done by Mahalanobis D2 statistics. The molecular genetic diversity analysis was done by using 30 molecular markers in same genotypes. Result: The assessment of morphological diversity revealed that the fifty pigeonpea genotypes were grouped into four different clusters with cluster I as the largest cluster (33 genotypes). The molecular markers differentiated the 50 genotypes in five major clusters with cluster II as the largest cluster (24 genotypes). The results of present study suggested that morphological and molecular diversity in pigeonpea is different. On the basis of genetic distance, the genotypes RVSA 2014-1 and PA 406 were found most genetically distant and may be used in hybridization programme to create diverse progenies.

Genetic Variability, Heritability, and Genetic Advance Estimates in Garlic (Allium sativum) from the Gamo Highlands of Southern Ethiopia

Genetic variability is the fundamental requirement for any plant breeding program to develop a superior cultivar. This study aimed to estimate the genetic variability and determine the correlation between the various quantitative characteristics of garlic accessions. The experiment was carried out in the Ezo-Otte area of the Chencha district in the Gamo highlands of southern Ethiopia and 28 garlic accessions were evaluated in a Randomized Complete Block Design with three replicates. Various morphological descriptors were measured to evaluate the variability and correlation coefficients. The analysis of variance showed a highly significant variation for all characters, which indicates greater variability in the accession. High and moderate heritability in broad sense estimates were obtained for the majority of the traits examined. Days to maturity (28.09), bulb weight (22.33), and bulb diameter (equatorial) (21.33) showed higher genetic advance. The maximum value of the genetic progress as a percentage of the mean was observed in bulb yield, clove weight, bulb diameter (equatorial), and number of leaves. In addition, bulb diameter (equatorial), clove weight, bulb weight, and plant height were observed to be highly hereditary coupled with high genetic advance as a percentage of the mean, suggesting that they can be improved by direct selection. Coefficient analysis has shown that maximum attention should be paid to bulb diameter (equatorial), the number of cloves, bulb diameter (equatorial), bulb weight, plant height, and leaf length, as these traits also correlate positively and significantly with bulb yield.

Genomics reveals identity, phenology and population demographics of larval ciscoes (Coregonus artedi, C. hoyi, and C. kiyi) in the Apostle Islands, Lake Superior

We demonstrate, for the first time, the ability to reliably assign an assemblage of larval coregonines [Salmonidae Coregoninae] to shallow and multiple deepwater species. Larval coregonines from the Apostle Islands, Lake Superior, were genotyped using restriction site-associated DNA sequencing (RADseq) and were assigned to species using reference genotypes from adult corgonines from the same region. Of the 193 genotyped larvae, 101 were assigned as Coregonus artedi (average assignment probability = 97.6%), 57 were assigned as C. kiyi (average assignment probability = 95.5%), and 28 were assigned as C. hoyi (average assignment probability = 89.0%). Coregonus artedi were collected earliest in the season, followed by C. kiyi and then C. hoyi. Estimates of genetic diversity within each species provide a baseline for future monitoring in the Apostle Islands. Our success with species assignment indicates the promise of leveraging genomic data for larval coregonine identification, which could enable assessing and evaluating early life history dynamics and recruitment processes at the species level to the benefit of ongoing coregonine restoration and management efforts.