Genetic variation in the longear sunfish (Lepomis megalotis)

1992 ◽  
Vol 70 (9) ◽  
pp. 1673-1680 ◽  
Author(s):  
Martin J. Jennings ◽  
David P. Philipp
Keyword(s):  
Genetic Variation ◽  
Principal Component ◽  
Distinct Group ◽  
Protein Electrophoresis ◽  
Distinct Form ◽  
Separate Species ◽  
Ozark Highlands ◽  
Lepomis Megalotis ◽  
Longear Sunfish ◽  
Distribution Limits

The systematics and zoogeography of the longear sunfish (Lepomis megalotis) are poorly understood. Relationships among geographic variants throughout the range of the species are unclear, and it is uncertain whether the northern longear sunfish, L. m. peltastes, should be classified as a separate species. We used protein electrophoresis to examine genetic variation among 22 longear sunfish populations and one dollar sunfish (Lepomis marginatus) population. Principal component analysis of allele frequency data could not separate the most morphologically distinct form, the northern longear sunfish, from the central long-ear sunfish, L. m. megalotis. Populations distributed from the Missouri River basin to the Colorado River in Texas, for which the subspecific names L. m. breviceps and L. m. aquilensis are available, clustered as a distinct group. No evidence was found to suggest that a distinct form exists in the Ozark Highlands. Lepomis marginatus was genetically distinct from all L. megalotis populations, but most distinct from L. m. megalotis and L. m. peltastes. Protein electrophoresis should allow diagnosis of distribution limits and intergrade zones of southwestern forms, but a more sensitive technique is required to separate L. m. megalotis and L. m. peltastes.

Genetic Analysis of Chinese Cucumber Collections in the U.S. National Germplasm Collection

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 534e-534 ◽  
Author(s):  
J. Staub ◽  
Felix Sequen ◽  
Tom Horejsi ◽  
Jin Feng Chen
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Allelic Variation ◽  
Germplasm Collection ◽  
Principal Component ◽  
Isozyme Loci ◽  
National Plant Germplasm System ◽  
The U.S

Genetic variation in cucumber accessions from China was assessed by examining variation at 21 polymorphic isozyme loci. Principal component analysis of allelic variation allowed for the depiction of two distinct groupings of Chinese accessions collected in 1994 and 1996 (67 accessions). Six isozyme loci (Gpi, Gr, Mdh-2, Mpi-2, Pep-gl, and Pep-la) were important in elucidating these major groups. These groupings were different from a single grouping of Chinese 146 accessions acquired before 1994. Allelic variation in Chinese accessions allowed for comparisons with other accessions in the U.S. National Plant Germplasm System (U.S. NPGS) collection grouped by continent and sub-continent. When Chinese accessions taken collectively were compared with an array of 853 C. sativus U.S. NPGS accessions examined previously, relationships differed between accessions grouped by country or subcontinent. Data indicate that acquisition of additional Chinese and Indian cucumber accessions would be strategically important for increasing genetic diversity in the U.S. NPGS cucumber collection.

scholarly journals River Otter, Lontra canadensis, Food Habits in the Missouri Ozarks

2008 ◽  
Vol 122 (4) ◽  
pp. 303 ◽  
Author(s):  
Nathan M. Roberts ◽  
Charles F. Rabeni ◽  
John S. Stanovick ◽  
David A. Hamilton
Keyword(s):  
Smallmouth Bass ◽  
Lontra Canadensis ◽  
Micropterus Dolomieu ◽  
Widespread Occurrence ◽  
River Otters ◽  
Lepomis Megalotis ◽  
Rock Bass ◽  
Longear Sunfish ◽  
The Mean ◽  
Ambloplites Rupestris

The reintroduction of River Otters (Lontra canadensis) between 1982 and 1992 resulted in widespread occurrence of the species throughout the Missouri Ozarks. This study examined otter diets from the vicinity of two Ozark streams in relation to seasonal and spatial trends. Otter scats (N = 4750) were collected and analyzed from the Osage Fork River and Big Piney River during the summer and winter seasons of 2001 and 2002. During the winter (January-March), fish occurred in 86% of the samples. During the summer (June–August), occurrence of fish dropped to approximately 15% for both rivers. Seven families of fish were identified in the diets, with Centrarchidae being most common regardless of river or season. Within the Centrarchidae, the genus Lepomis (mostly Longear Sunfish, Lepomis megalotis) was most common, with Micropterus (mostly Smallmouth Bass, Micropterus dolomieu) and Rock Bass (Ambloplites rupestris) also well represented. The mean age of Ambloplites consumed (mean = 3.3 years) was consistently older than that of either Micropterus (mean = 2.54 years) or Lepomis (mean = 2.78 years). Crayfish were recovered from a mean of 85.2% of scats in the winter and 99% in the summer. Smaller fish and crayfish were more common from the upper reaches of the streams while larger fish were prevalent in the lower reaches.

scholarly journals A spectral theory for Wright’s inbreeding coefficients and related quantities

PLoS Genetics ◽  
2021 ◽  
Vol 17 (7) ◽  
pp. e1009665
Author(s):  
Olivier François ◽  
Clément Gain
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Population Genetic ◽  
Principal Component ◽  
Large Data ◽  
Population Subdivision ◽  
Adaptive Genetic Variation ◽  
Genomic Locus ◽  
Inbreeding Coefficients ◽  
Definition Of

Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

scholarly journals Genetic status of Norway spruce (Picea abies) breeding populations for northern Sweden

2013 ◽  
Vol 62 (1-6) ◽  
pp. 127-136 ◽  
Author(s):  
P. Androsiuk ◽  
A. Shimono ◽  
J. Westin ◽  
D. Lindgren ◽  
A. Fries ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Norway Spruce ◽  
Population Differentiation ◽  
Distinct Group ◽  
Null Alleles ◽  
Multilocus Genotype ◽  
Northern Sweden ◽  
High Genetic Diversity ◽  
Breeding Populations ◽  
Ssr Loci

AbstractEfficient use of any breeding resources requires a good understanding of the genetic value of the founder breeding materials for predicting the gain and diversity in future generations. This study evaluates the distribution of genetic variation and level of relatedness among and within nine breeding populations of Norway spruce for Northern Sweden using nuclear microsatellite markers. A sample set of 456 individuals selected from 140 stands were genotyped with 15 SSR loci. Over all loci each individual was identified with unique multilocus genotype. High genetic diversity (average He=0.820) and low population differentiation (FST=0.0087) characterized this material. Although low in FST, the two northernmost populations were clustered as a distinct group diverged from the central populations. The population differentiation pattern corresponds well with the post glacial migration history of Norway spruce and the current gene flow and human activity in the region. The average inbreeding coefficient was 0.084 after removal loci with high frequency of null alleles. The estimated relatedness of the trees gathered in the breeding populations was very low (average kinship coefficient 0.0077) and not structured. The high genetic variation and low and not structured relatedness between individuals found in the breeding populations confirm that the Norway spruce breeding stock for northern Sweden represent valuable genetic resources for both long-term breeding and conservation programs.

scholarly journals Profiling of ARDS pulmonary edema fluid identifies a metabolically distinct subset

2017 ◽  
Vol 312 (5) ◽  
pp. L703-L709 ◽  
Author(s):  
Angela J. Rogers ◽  
Kévin Contrepois ◽  
Manhong Wu ◽  
Ming Zheng ◽  
Gary Peltz ◽  
...  
Keyword(s):  
Pulmonary Edema ◽  
Metabolic Profiling ◽  
Metabolic Profile ◽  
Principal Component ◽  
Distinct Group ◽  
Multivariate Statistical ◽  
Clinical Criteria ◽  
Edema Fluid ◽  
Biological Heterogeneity ◽  
Physiological Heterogeneity

There is considerable biological and physiological heterogeneity among patients who meet standard clinical criteria for acute respiratory distress syndrome (ARDS). In this study, we tested the hypothesis that there exists a subgroup of ARDS patients who exhibit a metabolically distinct profile. We examined undiluted pulmonary edema fluid obtained at the time of endotracheal intubation from 16 clinically phenotyped ARDS patients and 13 control patients with hydrostatic pulmonary edema. Nontargeted metabolic profiling was carried out on the undiluted edema fluid. Univariate and multivariate statistical analyses including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were conducted to find discriminant metabolites. Seven-hundred and sixty unique metabolites were identified in the pulmonary edema fluid of these 29 patients. We found that a subset of ARDS patients (6/16, 38%) presented a distinct metabolic profile with the overrepresentation of 235 metabolites compared with edema fluid from the other 10 ARDS patients, whose edema fluid metabolic profile was indistinguishable from those of the 13 control patients with hydrostatic edema. This “high metabolite” endotype was characterized by higher concentrations of metabolites belonging to all of the main metabolic classes including lipids, amino acids, and carbohydrates. This distinct group with high metabolite levels in the edema fluid was also associated with a higher mortality rate. Thus metabolic profiling of the edema fluid of ARDS patients supports the hypothesis that there is considerable biological heterogeneity among ARDS patients who meet standard clinical and physiological criteria for ARDS.

Microgeographic genetic variation of Sitka spruce in southeastern Alaska

1989 ◽  
Vol 19 (8) ◽  
pp. 1004-1013 ◽  
Author(s):  
Robert K. Campbell ◽  
William A. Pawuk ◽  
Arland S. Harris
Keyword(s):  
Genetic Variation ◽  
Standard Deviation ◽  
Principal Components ◽  
Principal Component ◽  
Extreme Case ◽  
Common Garden ◽  
Sitka Spruce ◽  
Slope Aspect ◽  
Factor Scores ◽  
Additive Genetic Variation

Microgeographic genetic variation among populations of Sitka spruce on Mitkof Island in southeastern Alaska is described. In two common-garden environments, we evaluated genotypes of 208 parent trees from 114 locations in a 17 000-ha area. Two principal components accounted for most of the variation among locations in 11 traits measured to evaluate growth vigor and rhythm of 2-year-old seedlings. Regression analyses of factor scores derived from principal components revealed genetic gradients associated with elevation, slope, aspect, and west–east and north–south direction. Large amounts of additive genetic variation in factor scores occurred among trees within locations. When this variation within locations was used as a scale, variation among locations was also large. In an extreme case, locations differed in factor scores of the first principal component by about 3.0 units of the standard deviation of additive genetic variation in factor scores. Of the total differentiation in this case, elevational range (600 m) contributed 0.7 units of standard deviation, aspect contributed 0.9 units, and distance (16 km) from north central to southeastern parts of the island contributed 1.4 units.

Relationship of divergent ancestral genetic variation on chromosome 6p22 and racial disparities in survival in neuroblastoma.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 9516-9516
Author(s):  
Navin R. Pinto ◽  
Eric R Gamazon ◽  
Anuar Konkashbaev ◽  
Hae Kyung Im ◽  
Sharon Diskin ◽  
...  
Keyword(s):  
Genetic Variation ◽  
High Risk ◽  
Racial Disparity ◽  
African Ancestry ◽  
Principal Component ◽  
Continuous Variable ◽  
Self Report ◽  
Ancestral Population ◽  
High Risk Disease ◽  
Significant Divergence

9516 Background: An increased prevalence of high-risk disease and worse outcome are observed in children with neuroblastoma who self-report as black versus white. We sought to determine whether genetic variation would explain this racial disparity. Methods: After quality control, we analyzed 511,836 germline genetic variants in 2,709 ethnically diverse children with neuroblastoma enrolled on Children’s Oncology Group study ANBL00B1 from 2001 to 2009. Genetic variation was summarized by conducting principal components analysis. The first principal component (PC1) separated patients with African ancestry from all others. PC1 was used as a continuous variable for ordinal regression with risk group and a Cox proportional hazard model of EFS. To identify genetic mechanisms for the observed disparities, we developed a method using genome-wide variation data applied to high-risk versus non-high risk samples. We identified a comprehensive list of loci with significant divergence between the ancestral populations. We then tested each such locus for association with high-risk phenotype using logistic regression with the proportion of African ancestry estimated by ADMIXTURE as covariate. Finally, top SNPs were added to multivariate models of both risk and event-free survival to determine if any top associations could abrogate observed disparities. Results: PC1 was associated with both risk (p = 0.007) and EFS (p = 0.037). We identified 72 population-divergent SNPs nominally associated with high-risk disease (p < 0.001). The risk allele for one of the top SNPs: rs9295536 (p = 9.2x10-8) was more common in the African ancestral population, was associated with high-risk phenotype and poor outcome in all patients and validated in a Caucasian-only subanalysis. In multivariate testing, this SNP abrogated the PC1 association with EFS (p = 0.18). Conclusions: A SNP with high divergence between ancestral populations on chromosome 6p22 accounts for the observed racial disparity in survival and is also a common genetic variant associated with survival in patients derived from either European or African ancestry (Bonferroni adjusted p < 0.05). Studies to elucidate the function of this SNP are underway.

Resource Partitioning in Two Coexisting Sunfish: Pumpkinseed (Lepomis gibbosus) and Northern Longear Sunfish (Lepomis megalotis peltastes)

1980 ◽  
Vol 37 (9) ◽  
pp. 1411-1420 ◽  
Author(s):  
Dennis R. Laughlin ◽  
Earl E. Werner
Keyword(s):  
Habitat Use ◽  
Vegetation Cover ◽  
Plant Cover ◽  
Lepomis Gibbosus ◽  
Sediment Type ◽  
Vegetation Density ◽  
Sympatric Populations ◽  
Sparse Vegetation ◽  
Lepomis Megalotis ◽  
Longear Sunfish

Qualitative surveys of 22 lakes in southern Michigan indicated that relative abundances of the northern longear sunfish (Lepomis megalotis peltastes) and pumpkinseed (L. gibbosus) depended upon amount of plant cover and sediment type. The longear sunfish occurred only in lakes with marl sediments and regions of sparse vegetation cover. The pumpkinseed occurred in all lakes surveyed and increased in abundance in lakes with greater vegetation density and/or more organic sediments. Quantitative measurements of habitat and food use were made in five lakes with sympatric populations. Data from underwater transects indicated that large (> 75 mm standard length) longear sunfish occurred primarily in shallow regions containing moderate to low vegetation cover whereas large pumpkinseeds were concentrated in deeper areas with heavy vegetation cover. The smaller size-classes of both species occupied the vegetation in deeper areas of the littoral zone. Large longears consumed predominantly large, sediment-dwelling mayfly or odonate nymphs regardless of the lake or habitat types. Pumpkinseeds consumed mainly gastropods and other prey from the vegetation. Preliminary studies of seasonal food use indicated that the pumpkinseed and longear sunfish both consumed more food in the spring and exhibited greater overlap in diet during this period. The relationship between foraging behaviors of these two species and the types of prey consumed is discussed as well as the complications of assessing competition between species when food and habitat use are dependent on size.Key words: Habitat use, size-class, lake types, food overlap, competition, Lepomis, Michigan

scholarly journals Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6013 ◽  
Author(s):  
Sanja Maria Hakala ◽  
Perttu Seppä ◽  
Maria Heikkilä ◽  
Pekka Punttila ◽  
Jouni Sorvari ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Morphological Characters ◽  
Coi Gene ◽  
Species Status ◽  
Separate Species ◽  
Mitochondrial Coi ◽  
Recent Addition ◽  
Morphological Differences ◽  
Dna Microsatellite ◽  
Dna Microsatellite Markers

Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.

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