Mitochondrial cytochrome b DNA sequence variation of Atlantic cod from Iceland and Greenland

Sequence variation of a 250–bp (base pair) fragment of the mitochondrial cytochrome b gene has been studied using polymerase chain reaction and direct sequencing of 519 Atlantic cod Gadus morhua from Iceland and 78 cod from Greenland. Twenty-four variable nucleotide sites, mostly silent, define 34 haplotypes. The amount of variation is high ( ĥC =0·73, π=0·52 per 100 bp) with five haplotypes at polymorphic frequencies in Iceland and a number of widely dispersed rather rare haplotypes. A tree of genetic relationships among haplotypes has considerable homoplasy yet it is relatively shallow implying a high turnover of variants of the polymorphism. Net nucleotide genetic divergences among localities are nil. Geographic locality overall area, and inshore/offshore comparison explain none of the variation in an AMOVA, all the variation is among individuals and a null hypothesis of non-differentiation of haplotype frequencies among localities or overall areas cannot be rejected. A temporal year-class effect is found. The evolutionary difference between Greenland and Iceland cod is not significant and the percentage of variation accounted for by the Greenland/Iceland difference is half of what a temporal effect within Iceland explains. There is no evidence for considering the cod at Greenland and Iceland to consist of separate evolutionary units and the question of separate management units must address the lack of diagnostic genotypes and evidence for gene flow from clinal variation.     

Geographic variation in Pemphigus populicaulis (Insecta: Aphididae) in Eastern North America*,†

The geographic variation of 33 morphological characters of the gall-forming aphid Pemphigus populicaulis is studied for 118 localities east of 100^oW longitude. Variation can be partitioned into within-gall, among-gall and among-locality components. Among localities variation ranges from 26 to 54%, being significant for all characters. Variation among galls within localities ranges from 24 to. 56%, that within-galls from 8 to 4796. The design of the study permits computation of character correlation matrices within and among localities. Gall size is correlated with tnorphometric characters only on an interlocality but not on an intralocality basis. Interlocalily correlations are a function of intralocality correlations, confirming earlier predictions. There is little correlation between characters of stem mother and alate morphotypes within localities, whereas among localities such correlation is appreciable. This phenomenon may be caused by aspects ol the environment that vary among localities but remain reasonably constant through the earlv life cycle of the aphid. When subjected to factor analysis both correlation matrices yield four factors. Multiple discriminant analysis of the data set results in five interpretable significant axes. Maps are furnished for characters representing the independent dimensions of variation and for discriminant function scores. The patterns of variation can be shown to be significantly nonrandom by Mantel's test and by spatial autocorrelation analysis. All variables are significantly positively autocorrelated at 200 km, many at 400 km and a few at 600 km; few general statements can be made about significant autocorrelations at higher distances. The positive autocorrelation at relatively short distances may be related to the pool of clones from which the genotypes of any one locality sample are taken. There are three correlogram patterns that can be associated with four clusters of variation patterns of characters. The separate patterns presumably cannot be explained by a single microevolutionary process.     

Mitochondrial DNA Diversity of the Asian Moon Scallop, <Emphasis Type="Italic">Amusium pleuronectes</Emphasis> (Pectinidae), in Thailand

Sequence variation of the mitochondrial DNA 16S rRNA region of the Asian moon scallop, Amusium pleuronectes, was surveyed in seven populations along the coast of Thailand. A total of 16 unique haplotypes were detected among 174 individuals with a total 27 variable sites out of 534 bp sequenced. The mitochondrial haplotypes grouped into two distinct arrays (estimated to differ by about 2.62% to 2.99% nucleotide divergence) that characterized samples collected from the Gulf of Thailand versus the Andaman Sea. Low levels of intrapopulation variation were observed, while in contrast, significant divergence was observed between populations from the Gulf of Thailand and Andaman Sea. Results of AMOVA reveal a high F _ST value (0.765) and showed that the majority of the total genetic variance (76.03%) occurred among groups (i.e., Andaman Sea and the Gulf of Thailand) and little among populations within the group (0.52%) and within populations (23.45%). The genetic differentiation between the populations recorded in the present study is similar to that observed in a variety of marine species in the Indo-Pacific. The implications of the findings for management of A. pleuronectes genetic resources in Thailand are discussed.     

Geographic variation in Pemphigus populitransversus (Insecta: Aphididae)*†

The geographic variation of 33 morphological characters of two morphs of the gall-forming aphid Pemphigus populitransversus is studied in 214 locality samples. Among-locality variation ranges from 1 to 69% in the elongate morph and from 0 to 44% in the globular morph. The design of the study permits separation of interlocality correlations from intralocality correlations. The former are partly a function of the latter, confirming early observations on another Pemphigus species and on ticks. Factor analyses of both correlation matrices for both morphs yield four factors. Within localities these factors agree for the two morphs; among localities only one factor corresponds. Multiple discriminant analyses among localities of the two data sets do not correspond. There is little correlation between characters of stem mother and alate morphotypes within localities but such correlations are strong among localities. Maps are furnished for characters representing the independent dimensions of variation for each morph. Patterns of variation are shown to be significant by spatial autocorrelation analysis for both morphs but are much more marked in the elongate morph. Significant positive autocorrelation occurs up to 1000 km in the elongate morph – mostly only up to 200 km in the globular morph. There are two to three geographic variation patterns in the elongate morph, whereas in the globular morph the classes of patterns are less well defined and involve few characters. The environmental factors to which the globular and elongate morphs are adapting would appear to have different autocorrelation patterns. In each morph the patterns are clearly different and cannot be explained by a single microevolutionary process. The findings are compared with an earlier study in the related and largely sympatric P. populicaulis.     

Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

Background  

Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution.     

Cod, Gadus morhua L., populations identified by mitochondrial DNA

Isozyme and haemoglobin analysis has shown that the cod, Gadus morhua L., in the NE Atlantic can be regarded as two populations: Arctic and coastal cod. One hundred and one individual cod from nine different locations were sampled and restriction fragment analysis uncovered 14 different mtDNA clones. Calculation of sequence divergence between localities displayed large divergence between samples from coastal and Arctic areas (l.77–5.62%), as opposed to the low intrapopulation divergence (∼0.10%) and the divergence between localities along the coast (∼0.17%) and in the Barents Sea (∼ 1.00%).     

Variation of mitochondrial DNA in chinook salmon <Emphasis Type="Italic">Oncorhynchus tschawytscha</Emphasis> Walbaum populations from Kamchatka

The variation in mitochondrial DNA (mtDNA) structure among chinook salmon Oncorhynchus tschawytscha Walbaum populations from Kamchatka was inferred from restriction length polymorphism analysis using eight restriction endonucleases. The nucleotide sequence variation in three amplified mtDNA regions was examined at seven polymorphic restriction sites in 579 fish from 13 localities. Based on the frequencies of 11 combined haplotypes and the number of nucleotide substitutions, the among-and within-population variation was estimated. The heterogeneity test showed highly significant differences among all the populations. The estimated maximum time of independent divergence of the asian chinook salmon populations, whose differences was about 0.02% nucleotide substitutions, did not exceed 10 000–20 000 years. Apparently, the retreat of the late Pleistocene glacier triggered spreading, recolonization, and formation of the present-day pattern of the species subdivision into structural components.     

中国近海细鳞鯻线粒体控制区的遗传多样性

通过线粒体控制区序列的分析,研究采自中国南海及东海5个群体102尾细鳞鯻的遗传多样性。发现在962 bp序列中有205个变异位点,其中135个为简约信息位点,共定义102个单倍型。中国近海细鳞鯻总体呈现出较高的遗传多样性特征(Hd=1.000,Pi=0.022),其中博鳌最高(Hd=1.000,Pi=0.028),平潭最低(Hd=1.000,Pi=0.014)。不同地理群体间无明显分化,基因交流频繁(Fst=-0.014—0.041,P0.05);中性检验均为显著负值,推测在16.9万年—5.06万年前,即中-晚更新世出现种群扩张。系统邻接树和单倍型网络图均出现3个显著分化的谱系(谱系间Fst=0.508—0.698,P0.001;净遗传距离Da=0.024—0.031),且各谱系中均有不同地理来源的群体。3个谱系间分歧时间大约在1.07百万年—0.24百万年前,推测可能是更新世冰期边缘海的出现导致群体隔离而产生分化。谱系A(Lineage A)包含85.3%的个体,其总体遗传多样性较高(Hd=1.000,Pi=0.012),其中平潭最高(Hd=1.000,Pi=0.014),合浦最低(Hd=1.000,Pi=0.010);群体间Fst在-0.021—0.068之间,P0.005;AMOVA分析显示只有1.97%的变异来自于种群间,表明群体间也无明显分化;中性检验均为显著负值,推测在25.4万年—7.6万年前出现种群扩张。中国近海细鳞鯻主要受到中-晚更新世海侵和海退的影响而出现种群扩张使得谱系间发生二次接触,最终形成具有显著谱系结构但无地理分化的情况。     

Genetic variation in the mitochondrial 16S rRNA gene of the American dog tick,Dermacentor variabilis (Acari: Ixodidae)

Genetic variation in the mitochondrial (mt) 16S ribosomal RNA (rRNA) gene was examined for the American dog tick, Dermacentor variabilis (Say, 1821). Nine different haplotypes were detected among 369 adult D. variabilis collected from four localities in Canada. There were eight variable nucleotide positions in the 404 bp sequence alignment. Individuals of haplotype 1 occurred at frequency of >75% at all localities. Five haplotypes were detected at only one of the four localities. High haplotype diversity and low nucleotide diversity, combined with significantly negative F_s values for ticks at three localities, suggest a recent population expansion. Genetic differences were found between populations at different localities, but a Mantel regression analysis revealed no association between genetic differences and geographical distances. There was also no association between tick haplotype and the prevalence of the bacterium, Rickettsia montanensis Weiss and Moulder, 1984, in D. variabilis among localities or on opposite sides of Blackstrap Lake (Saskatchewan). The 16S rDNA haplotypes from Canadian populations of D. variabilis formed a clade with those from the eastern and central U.S.A., to the exclusion of D. variabilis from geographically isolated populations in the western U.S.A. Although sample sizes for D. variabilis in the eastern U.S.A. are small, there may be genetic divergence between populations in Canada and those in the eastern U.S.A., which may have implications for studies on the pathogenic agents transmitted by D. variabilis to its hosts.     

Streaked horned lark <Emphasis Type="Italic">Eremophila alpestris strigata</Emphasis> has distinct mitochondrial DNA

The Streaked Horned Lark (STHL; Eremophila alpestris strigata) is a federal candidate for listing under the Endangered Species Act. We evaluated the conservation status and level of genetic diversity of the STHL using the complete mitochondrial ND2 gene. We sampled 32 STHLs from the southern Puget Sound region, the Pacific coast, and Whites Island in the Columbia River of Washington, and additional 68 horned larks from Alaska, alpine and eastern Washington, Oregon, California, and Asia (outgroups). Our Maximum Likelihood analysis of 32 haplotypes identified three geographically concordant clades in Pacific coast states: Pacific Northwest (alpine and eastern Washington, Alaska), Pacific Coast (western Washington, California), and Great Basin (eastern Oregon). Each of the three clades was supported by bootstrap values ≥86%. The distance among them varied from 0.72 to 0.79% nucleotide divergence excluding intraclade variation. The relationship among the clades was not resolved. AMOVA also showed significant structuring of haplotypes among the three clades. Differences among clades accounted for 75.7% of sequence variation, differences among localities within clades accounted for 12.1%, and differences among individuals within localities accounted for the remaining 12.2%. Although STHL populations were closely related to the Californian sample, they appeared unique and isolated. All pairwise F _st values involving the STHL samples were significant (except between themselves). STHLs appear to have remarkably low genetic diversity; all 32 STHLs shared the same haplotype. Even with small sample sizes, all other localities had multiple haplotypes. Because the STHL appears to be unique and isolated, and to have little genetic diversity our data suggest it should be a conservation priority.     

Extent of mitochondrial DNA sequence variation in Atlantic cod from the Faroe Islands: a resolution of gene genealogy

Variation in a 250 base pair (bp) fragment of the mitochondrial cytochrome b (cyt b) has been used extensively for population studies in Atlantic cod Gadus morhua. To study the shape of the gene genealogy and the nature of the polymorphism, sequences of another region of the cyt b gene and the TP intergenic spacer were added, making a total of 566 bp from 74 cod from the Faroe Islands. A total of 44 segregating sites defined 41 haplotypes, many at frequencies greater than 5%. Haplotype diversity was 0.97 and nucleotide diversity 0.73% per base. A topology referred to as a constellation gene genealogy was observed with four major haplotypes at high frequencies, from each of which a number of rare variants were derived. A young relative age of the haplotypes was gauged from the structure of the genealogy. The variation was mostly at synonymous sites within the coding region and thus likely to be neutral or under weak purifying selection. By comparative analysis this also applies to the TP spacer. Applying the locus to study population variation in the Faroe Islands by AMOVA revealed that the overall areas and localities within areas accounted for none of the variation, and all the variation was due to differences among individuals.     

Rangewide phylogeography and landscape genetics of the Western U.S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers

Genetic data are increasingly being used in conservation planning for declining species. We sampled both the ecological and distributional limits of the foothill yellow-legged frog, Rana boylii to characterize mitochondrial DNA (mtDNA) variation in this declining, riverine amphibian. We evaluated 1525 base pairs (bp) of cytochrome b and ND2 fragments for 77 individuals from 34 localities using phylogenetic and population genetic analyses. We constructed gene trees using maximum likelihood and Bayesian inference, and quantified genetic variance (using AMOVA and partial Mantel tests) within and among hydrologic regions and river basins. Several moderately supported, geographically-cohesive mtDNA clades were recovered for R. boylii. While genetic variation was low among populations in the largest, most inclusive clade, samples from localities at the edges of the geographic range demonstrated substantial genetic divergence from each other and from more central populations. Hydrologic regions and river basins, which represent likely dispersal corridors for R. boylii, accounted for significant levels of genetic variation. These results suggest that both rivers and larger hydrologic and geographic regions should be used in conservation planning for R. boylii.     

THE ROLE OF INTROGRESSIVE HYBRIDIZATION IN THE EVOLUTION OF THE GILA ROBUSTA COMPLEX (TELEOSTEI: CYPRINIDAE)

Abstract The extent and impact of introgressive hybridization was examined in the Gila robusta complex of cyprinid fishes using mitochondrial DNA (mtDNA) sequence variation. Lower Colorado River basin populations of G. robusta, G. elegans, and G. cypha exhibited distinct mtDNAs, with only limited introgression of G. elegans into G. cypha. The impact of hybridization was significant in upper Colorado River basin populations; most upper basin fishes sampled exhibited only G. cypha mtDNA haplotypes, with some individuals exhibiting mtDNA from G. elegans. The complete absence of G. robusta mtDNA, even in populations of morphologically pure G. robusta, indicates extensive introgression that predates human influence. Analysis of the geographic distribution of variation identified two distinctive G. elegans lineages; however, the small number of individuals and localities sampled precluded a comprehensive analysis. Analysis of haplotype and population networks for G. cypha mtDNAs from 15 localities revealed low divergence among haplotypes; however, significant frequency differences among populations within and among drainages were found, largely attributable to samples in the Little Colorado River region. This structure was not associated with G. cypha and G. robusta, as morphotypes from the same location are more similar than conspecific forms in other locations. This indicates that morphological and mtDNA variation are affected by different evolutionary forces in Colorado River Gila and illustrates how both hybridization and local adaptation can play important roles in evolution.     

HISTORICAL DEMOGRAPHY AND PRESENT DAY POPULATION STRUCTURE OF THE GREENFINCH,CARDUEUS CHLORIS—AN ANALYSIS OF mtDNA CONTROL-REGION SEQUENCES

Genetic variability within and among 10 geographically distinct populations of Greenfinches (Carduelis chloris) was assayed by directly sequencing a 637 BP part of the mtDNA control region from 194 individuals. Thirteen variable positions defined 18 haplotypes with a maximum sequence divergence of 0.8%. Haplotype (h = 0.28–0.77) and nucleotide (π = 0.058–0.17%) diversities within populations were low, and decreased with increasing latitude (h:r_s = –0.81; π: r_s = –0.89). The distribution of pairwise nucleotide differences fit better with expectations of a “sudden expansion” than of an “equilibrium” model, and the estimates of long term effective population sizes were considerably lower than current census estimates, especially in northern European samples. Selection is an unlikely cause of observed patterns because the distribution of variability conformed to expectations of neutral infinite alleles model and haplotype diversity across populations was positively correlated with heterozygosity (H_E) in nuclear genes (r_s = 0.74, P < 0.05). Hence, a recent bottleneck, followed by serial bottlenecking during the process of post-Pleistocene recolonization of northern Europe, together with recent population expansion provide a plausible explanation for the low genetic diversity in the north. Genetic distances among populations showed a clear pattern of isolation-by-distance, and 14% of the haplotypic variation was among populations, the rest being distributed among individuals within populations. In accordance with allozyme and morphological data, a hierarchical analysis of nucleotide diversity recognized southern European populations as distinct from northern European ones. However, the magnitude of divergence in mtDNA, allozymes and morphology were highly dissimilar (morphology > mtDNA > allozymes).     

Heteroplasmy of Short Tandem Repeats in Mitochondrial DNA of Atlantic Cod, Gadus Morhua

The mitochondrial DNA of the Atlantic cod (Gadus morhua) contains a tandem array of 40-bp repeats in the D-loop region of the molecule. Variation among molecules in the copy number of these repeats results in mtDNA length variation and heteroplasmy (the presence of more than one form of mtDNA in an individual). In a sample of fish collected from different localities around Iceland and off George's Bank, each individual was heteroplasmic for two or more mtDNAs ranging in repeat copy number from two (common) to six (rare). An earlier report on mtDNA heteroplasmy in sturgeon (Acipenser transmontanus) presented a competitive displacement model for length mutations in mtDNAs containing tandem arrays and the cod data deviate from this model. Depending on the nature of putative secondary structures and the location of D-loop strand termination, additional mechanisms of length mutation may be needed to explain the range of mtDNA length variants maintained in these populations. The balance between genetic drift and mutation in maintaining this length polymorphism is estimated through a hierarchical analysis of diversity of mtDNA length variation in the Iceland samples. Eighty percent of the diversity lies within individuals, 8% among individuals and 12% among localities. An estimate of theta = 2N(eo) mu greater than 1 indicates that this system is characterized by a high mutation rate and is governed primarily by deterministic dynamics. The sequences of repeat arrays from fish collected in Norway, Iceland and George's Bank show no nucleotide variation suggesting that there is very little substructuring to the North Atlantic cod population.     

Genetic differentiation between populations of swimming crab <Emphasis Type="Italic">Portunus trituberculatus</Emphasis> along the coastal waters of the East China Sea

Portunus trituberculatus is a commercially important species widely spread in the East China Sea. Intraspecific variation of the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) gene was investigated in 213 individuals from six localities (Changjiang Estuary, Shengsi Islands, Zhoushan Islands, Dongtou Islands, Dinghai Bay, and Quanzhou Bay) ranging from north (31°21′N) to south (24°55′N) coastal waters of the East China Sea. Overall, a total of 27 mtDNA haplotypes and 21 variable sites were detected in the 787 bp segment of COI gene. Analysis of mtDNA COI sequence data revealed that crabs from the six localities were characterized by moderately high haplotypic diversity (h = 0.787 ± 0.026), while sequence divergence values between haplotypes were relatively low (π = 0.00241 ± 0.00098). Each population was characterized by a single most frequent haplotype, shared among all six localities, and a small number of rare ones, typically present in only one or two individuals and representative of a specific population. However, neither the neighbor-joining tree nor the minimum spanning network (MSN) based on the haplotype data exhibited geographical patterns of the six populations. Mismatch distribution analysis of P. trituberculatus individuals sampled from the six localities suggested that sudden population expansion might have occurred in CJ and SS population that might be consistent with over-exploitation of the swimming crab. Analysis of molecular variance (AMOVA) and F _ST statistics showed that significant genetic differentiation existed among the SS, ZS, DT, DH, and QZ populations, suggesting that gene flow might be reduced, even between the geographically close sites, despite the high potential of dispersal. The possible causes of the observed genetic heterogeneity among the P. trituberculatus populations and the potential applications of the mtDNA COI marker in the artificial breeding and fisheries management are discussed. Handling editor: C. Sturmbauer     

Low mtDNA variation and shallow population structure of the Chinese pomfret Pampus chinensis along the China coast

In the present study, population genetic structure and genetic diversity of the Chinese pomfret Pampus chinensis, along the China coast were investigated and compared with that from Indonesia using mitochondrial DNA cytochrome b gene sequences. A total of 28 variable sites (including 18 singleton sites and 10 parsimony information sites) were observed and 23 haplotypes were defined in 330 individuals from 11 localities. The haplotype diversity (H_D) of the populations ranged from 0·540 to 0·828, the nucleotide diversity (π) ranged from 0·081 to 0·295%. Pairwise F_ST statistics showed that significant genetic divergence occurred among populations from different geographical regions. The high dispersal capabilities, geographic segregation and ocean currents may be responsible for the present population genetic structure in this species. In addition, a population expansion event during the late Pleistocene period was inferred. The time of population expansion was estimated to occur about 117 000–169 000 years ago.     

A River Metapopulation Structure of a Japanese Freshwater Goby, Odontobutis Obscura, Deduced from Allozyme Genetic Indices

Gene products of 18 allozyme loci from 1268 individuals of a Japanese freshwater goby called donko, Odontobutis obscura (Odontobutidae; Gobioidei), from 33 localities in the Koya River, Yamaguchi Prefecture, Japan, were investigated to determine the extent of genetic divergence and gene flow within a river metapopulation. Genetic indices including GST(mean FST 0.182), FIT(mean 0.192) and D(mean 0.015) indicated a considerable divergence of local populations in the river. The genetic distance (D) and channel distance between pairs of populations did not show a good correlation, and geographical neighbors were not always genetic neighbors. Therefore, the genetic divergence of populations is attributable to independent genetic drift with restricted gene flow among populations. The agricultural dams and weirs constructed across the river must be responsible for the restricted gene flow. The metapopulation structure of O. obscura in the Koya River may be barely sustained by one-way gene flow only from the upper to the lower populations. An occasional artificial transplantation of some individuals from the lower to the upper populations may be one alternative to maintain a river metapopulation structure safely.     

Genetic and morphological assessment of a vulnerable large catfish,Silonia silondia (Hamilton, 1822), in natural populations from India

Silonia silondia is a commercially important fish distributed in Asian countries, which is under threat due to overexploitation. This study focuses on the morphological analysis and genetic variation of S. silondia individuals, through truss network and sequencing of two mitochondrial regions, respectively, from six wild populations of the Ganga and Mahanadi river systems in India. A total of 38 haplotypes was observed by analysing combined mitochondrial genes (cytochrome b + ATPase 6/8) in 247 individuals of S. silondia collected from six populations. Average haplotype and nucleotide diversities were 0.8508 and 0.00231, respectively. Genetic structure analysis showed the predominant cause of genetic variation to be within populations. The two clades were observed among the haplotypes and time of divergence from their most probable ancestor was estimated to be around 0.3949 mya. Analysis of combined mitochondrial genes in six populations of S. silondia resulted into three management units or genetic stocks. The truss network analysis was carried out by interconnecting 12 landmarks from digital images of specimens to identify phenotypic stocks. Sixty-five truss morphometric variables were analysed for geometric shape variation which revealed morphological divergence in River Son specimens. The present study presents molecular markers and genetic diversity data which can be critical input for conservation and management of differentiated populations and future monitoring of the genetic bottleneck. The morphological shape analysis clearly shows that variation in the insertion of adipose fin is an important parameter influencing the morphological discrimination.     

Genomic signatures of the plateless phenotype in the threespine stickleback

Understanding the genetic basis of traits involved in adaptive divergence and speciation is one of the most fundamental objectives in evolutionary biology. Toward that end, we look for signatures of extreme plate loss in the genome of freshwater threespine sticklebacks (Gasterosteus aculeatus). Plateless stickleback have been found in only a few lakes and streams across the world; they represent the far extreme of a phenotypic continuum (plate number) that has been studied for years, although plateless individuals have not yet been the subject of much investigation. We use a dense single nucleotide polymorphism dataset made using RADseq to study fish from three freshwater populations containing plateless and low plated individuals, as well as fish from full plated marine populations. Analyses were performed using FastStructure, sliding windows F_ST, Bayescan and latent factor mixed models to search for genomic differences between the low plated and plateless phenotypes both within and among the three lakes. At least 18 genomic regions which may contribute to within‐morph plate number variation were detected in our low plated stickleback populations. We see no evidence of a selective sweep between low and plateless fish; rather reduction of plate number within the low plated morph seems to be polygenic.