Floral and Genetic Divergence Across Environmental Gradients is Moderated by Inter-Population Gene Flow in \u3ci\u3ePlatanthera dilatata\u3c/i\u3e (Orchidaceae)

Understanding how natural selection acts on intraspecific variation to bring about phenotypic divergence is critical to understanding processes of evolutionary diversification. The orchid family is well known for pollinator-mediated selection of floral phenotypes operating among species and along environmental or geographic gradients. Its effectiveness at small spatial scales is less understood, making the geographic scale at which intraspecific floral variation is examined important to evaluating causes of phenotypic divergence. In this study, we quantified phenotypic variation in the orchid Platanthera dilatata across 26 populations in coastal Southeast Alaska and compared this to edaphic and genetic variation at microsatellite loci. We sought to determine (1) if flower morphological variation is structured at smaller geographic scales, (2) the extent of genetic divergence in relation to phenotypic divergence, (3) the scale at which inter-population gene flow occurs, and (4) the relative importance of geographic distance and abiotic factors on population genetic structure. Two morphological groups were found to separate based on lip and spur length and are restricted to different habitats. Small-flowered forms occur in muskeg bogs, whereas large-flowered forms occur in fens and meadows, and rarely in sub-alpine habitat. Genetic analyses were concordant with the morphological clusters, except for four small-flowered populations that were genetically indistinguishable from large-flowered populations and considered to be introgressed. In fact, most populations exhibited some admixture, indicating incomplete reproductive isolation between the flower forms. Pollinators may partition phenotypes but also facilitate gene flow because short-tongued Noctuidae moths pollinate both phenotypes, but longer-tongued hawkmoths were only observed pollinating the large-flowered phenotype, which may strengthen phenotypic divergence. Nevertheless, pollinator movement between habitats could have lasting effects on neutral genetic variation. At this small spatial scale, population genetic structure is only associated with environmental distance, likely due to extensive seed and pollinator movement. While this study corroborates previous findings of cryptic genetic lineages and phenotypic divergence in P. dilatata, the small scale of examination provided greater understanding of the factors that may underlie divergence

A Rare View Of Coding Mutations And Plasma Lipid Levels

A RARE VIEW OF CODING MUTATIONS AND PLASMA LIPID LEVELS. Aniruddh P. Patel, Sekar Kathiresan. Center for Human Genetics Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA and Program in Medical and Population Genetics, the Broad Institute of Harvard and MIT, Cambridge, MA (Sponsored by Richard P. Lifton, Department of Genetics, Yale University School of Medicine, New Haven, CT). Plasma low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) are quantitative, heritable risk factors for coronary heart disease. Genome-wide association screens (GWAS) of common DNA sequence variants have identified many loci associated with plasma lipid levels. Targeted re-sequencing of exons has been proposed as a strategy to pinpoint causal variants and genes based in GWAS loci. Additionally, genotyping of rare and low frequency variants in large cohorts using an exome array has been proposed as a method to assess the contribution of rare variation to plasma lipid levels at the population level. We tested the hypothesis that each genomic region identified with a significant HDL-C level association by GWA studies contains at least one gene causal for HDL-C metabolism. We performed solution-based hybrid selection of 4,118 exons at 407 genes within 47 loci associated with HDL-C and subsequently sequenced individuals drawn from the extremes of the HDL-C distribution (high HDL-C, n=385, mean=102 mg/dl or low HDL-C, n=334, mean=32 mg/dl) using next-generation sequencing technology. We tested whether rare coding sequence variants, individually or aggregated within a gene, were associated with HDL-C. To replicate findings, we performed follow-up genotyping using the Exome Array (Illumina HumanExome BeadChip) in independent participants with extremely high HDL-C (n=514, mean=98 mg/dl) or low HDL-C (n=580, mean=32 mg/dl). Through sequencing, we identified 8,138 rare (minor allele frequency \u3c 5%) missense, nonsense, or splice site variants. Across discovery sequencing and replication genotyping, we found 3 variants to be significantly associated with HDL-C. Of these, none were novel. In gene-level association analyses where rare variants within each gene are collapsed, only the CETP gene was associated with plasma HDL-C (P=2.0 x 10-6). After sequencing genes from GWAS loci in participants with extremely high or low HDL-C, we did not identify any new rare coding sequence variants with a strong effect on HDL-C. These results provide insight regarding the design of similar sequencing studies for cardiovascular traits with respect to sample size, follow-up, and analysis methodology. We then tested the hypothesis that rare coding and splice-site mutations contribute to inter-individual variability in plasma lipid concentrations in the population. We contributed to the design of a new, rare-variant genotyping array based on the sequences of the protein-coding regions of ~18,500 genes ( the exome ) in \u3e12,000 individuals. This genotyping array ( the Exome Chip ) includes approximately 250,000 non-synonymous and splice-site mutations and is estimated to capture nearly all such variation with a \u3e1:1000 allele frequency in the European population. We obtained Exome Chip genotype data in \u3e130,000 individuals from 58 studies. Within each study, we tested the association of plasma lipids with individual rare variants. To combine statistical evidence across studies, we performed meta-analysis. Top results for each trait replicated established associations in the genes APOE, CETP, and APOA5 for LDL-C, HDL-C, and TG, respectively. We identified 11 new genes associated with plasma lipid levels: ABCA6 with LDL-C (C1359R, frequency = 1:100, effect=+8.2 mg/dl, P=9.7 x 10-32, SERPINA with LDL-C (E366K, frequency = 2:100, effect = +3.1 mg/dl, P=2.3 x 10-7), REST with LDL-C (R645W, frequency = 6:10000, effect = +13.7 mg/dl, P=5.0 x 10-7), FBLN1 with LDL-C (H695R, frequency = 2:100, effect = -2.7 mg/dl, P=5.3 x 10-7), CCDC117 with LDL-C (T232I, frequency = 9:1000, effect = -4.3 mg/dl, P=7.3 x 10-7), TMED6 with HDL-C (F6L, frequency = 4:100, effect = -0.8 mg/dl, P=4.4 x 10-9), CDC25A with HDL-C (Q24H, frequency = 3:100, effect = -1.0 mg/dl, P=8.4 x 10-8), MAP1A (P2349L, frequency = 3:100) with HDL-C (effect= -1.4mg/dl, P=3.9 x 10-14) and TG (effect=+8.4mg/dl, P=3.2 x 10-26), PRRC2A with TG (S1219Y, frequency = 2:100, effect = +6.6 mg/dl, P=4.6 x 10-17), COL18A1 with TG (V125I, frequency = 1:1000, effect = +18.0 mg/dl, P=1.3 x 10-7), and EDEM3 with TG (P746S, frequency = 1:100, effect = -5.4 mg/dl, P=2.4 x 10-7). In addition, at some genes previously known to affect lipids, we identified new associations for variants: APOC3 (R19Stop, frequency = 3:10,000) with HDL (effect=+11mg/dl, P=9.9 x 10-12) and with TG (effect=-65.9mg/dl, P=5.8 x 10-23); (splicesite IVS2+1 G\u3eA, frequency = 2:1000) with HDL (effect=+10.6mg/dl, P=3.5 x 10-42) and with TG (effect=-65.2mg/dl, P=2.0 x 10-81). Using the Exome Chip rare variant genotyping array, we have discovered several new genes and variants associated with plasma lipids

Evaluation of Off-Type Grasses in Interspecific Hybrid Bermudagrass [\u3ci\u3eCynodon dactylon\u3c/i\u3e (L.) Pers. x \u3ci\u3eC. transvaalensis\u3c/i\u3e Burtt-Davy] Putting Greens

The economic impact of the golf industry in the United States (U.S.) in 2011 was estimated to be $176.8 billion. Interspecific hybrid bermudagrasses [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] are some of the most widely utilized grasses on golf courses throughout tropical, subtropical, and temperate climates. In 2007, bermudagrass was grown on 80% of putting green acreage in the southern U.S. ‘Tifgreen’ and ‘Tifdwarf’ were two of the first widely established cultivars on putting greens, but their genetic instability led to the occurrence of phenotypically different off-type (OT) grasses. Several OT grasses were selected and released as cultivars such as ‘Champion’, ‘MiniVerde’, and ‘TifEagle’. These cultivars can also be genetically unstable and OT grasses can occur in putting greens. The objectives of this research were to genetically and phenotypically characterize OT grasses and evaluate their responses to nitrogen (N) and trinexapac-ethyl (TE) applications. Off-type and desirable bermudagrass samples were collected from Champion, MiniVerde, and TifEagle golf course putting greens in 2013 and 2014. Grasses were genetically evaluated using genotyping-by-sequencing (GBS), which determined that 11% were genetically divergent from standard cultivars. Off-types were phenotypically characterized using morphology and samples clustered into three distinct morphological groups that varied in internode length and leaf length. The response of OT grasses and cultivars to six N and eight TE treatments was evaluated by measuring clippings 7, 14, 21, and 28 days after initial treatment (DAIT). The least three N rates decreased weekly clipping production 18 to 29% [percent], whereas the greatest three rates sustained growth. We observed that peak growth regulation occurred 21 DAIT for the majority of TE rates tested where clipping weights decreased 18 to 35% from 7 to 21 DAIT. We also observed a period of increased clipping production 18 to 47% from 21 to 28 DAIT for all grasses tested. It is important to maintain consistent growth among phenotypically different grasses in order to minimize any competitive growth advantage an OT grass may possess over a desirable cultivar in a golf course putting green

Microbial diversity in Swedish breeds of sheep analysed by amplicon based sequencing

The gastrointestinal tract (GIT) of ruminants have divergent type of microbiome provides favourable environment for their growth. In many species, these microbiome considered as important source of assessing animal health & welfare. A total of 18 different Swedish sheep breeds (n = 15) and Landrace Goats as an out group (n = 3) were selected to examine the faecal microbiome, i.e., Rye (n=6), Gestrike (n=4), Roslag (n=3), and Cross-breed (Suffolk + Texel) (n=2) & Goat (n=3). The replicates of 32 faecal samples were subjected to DNA extraction, the gel electrophoresis method, and amplification for PCR products and mixing. The positive replicates of all extracted DNA samples were subjected to16s amplicon metagenomics coupled with next generation sequencing (Illumina), quality control (QC), and generated processed reads of total (1799435) for all bacteria and archaea. The total of (10734) amplicon sequence variants (ASV) after the filtration were employed for the phylogeny and taxonomy analysis of bacteria at the phylum and genus level. Bioinformatics and statistical analysis was done by using DADA2 pipeline in the R software and PRISM software (Graphpad) for further visual graphical presentation of data and compare the taxonomic classification. The highest relative abundance was measured for Firmicute (66%) and Bacteriodota (29%), Fibrobacteriota (1%), Proteobacteria (1%), and Verrucomicrobiota (2%) among top 10 phyla. While, in the top 15 genera, the highest relative abundance as shown in UCG-005 (24%), Rikenellaceae RC9 gut group (13%), Christensenellaceae R-7 group (12%), Bacteroides (8%), Monoglobus (6%), Alistipes (6%), Prevotellaceae UCG-004 (6%), Ruminococcus (5%), Akkermansia (4%) and Lachnospiraceae AC2044 group (5%). Bray–Curtis distances by Breed (PCoA and NMDS) showed clear difference in the clustering of sheep from goat samples and PERMANOVA showed significance results (P<0.05) but no significance difference were seen within different Swedish sheep breeds according to ANOVA and Tukeys test. This research is the first non-culture-based study to analyse the similarities and dissimilarities of the faecal microbiome by using 16S amplicon based metagenomics coupled with NGS (next generation sequencing) in different Swedish breeds of sheep and goat (outgroup)

Relative roles of genetic and epigenetic variation on the ecology and evolution of mangrove killifishes (Kryptolebias spp.)

The field of ecological epigenetics aims to understand the implications of epigenetic modifications in adaptation, inheritance and ultimately, evolution. Many questions remain open within ecological epigenetics, in particular, how epigenetic variation is influenced by genetic background, the extent of environmentally-induced epigenetic variants, as well as its degree of heritability. This thesis used the unique diversity of mating systems present in the killifish genus Kryptolebias to investigate how genetic and environmental variation shape epigenetic variation in animals. Genetic and epigenetic structure was investigated in natural populations of K. hermaphroditus in northeast Brazil, with the species being confirmed as the second example of mixed-mating system in vertebrates. Cytosine methylation was largely influenced by genetic background. However, within-populations, when individuals were more genetically similar, DNA methylation was mostly affected by parasites. Kryptolebias ocellatus, here confirmed as an outcrossing-only androdioecious species, showed deep genetic structure in southeast Brazil. Hybridisation between K. ocellatus and the predominantly selfing K. hermaphroditus was uncovered, representing the first example of hybridisation between species with different mating systems in vertebrates. Hybrids had intermediate patterns of cytosine methylation relatively to the parental species, with important biological processes being potentially misregulated. Environmental enrichment was shown to affect brain cytosine methylation patterns in two inbred strains of K. marmoratus, however genetic background had a stronger effect than environmental variation. Commonly-affected epialleles between genotypes predominantly showed a genotype-by-environment reaction norm, suggesting that exclusively environmentally-induced epialleles may be rare. Intergenerationally, parental activity affected offspring activity, and a limited number of putative intergenerational epialleles were identified. This is the first example of behavioural parental effects induced by environmental enrichment in fish. These findings show that genetic background has a prominent effect and must be take into account when evaluating the evolutionary potential of cytosine methylation variation. In addition, inheritance of environmentally-induced cytosine methylation epialleles may be limited, with other epigenetic mechanisms, such as microRNAs, being more likely to escape epigenetic reprogramming and transmit epigenetically-induced parental effects

Complex Data Produce Better Characters

Abstract: Two studies were conducted to explore the use of complex data in character description and hybrid identification. In order to determine if complex data allow the production of better characters, eight groups of plant systematists were given two classes of drawings of plant parts, and asked to divide them into character states (clusters) in two separate experiments. The first class of drawings consisted only of cotyledons. The second class consisted of triplets of drawings: a cotyledon, seedling leaf, and inflorescence bract. The triplets were used to simulate complex data such as might be garnered by looking at a plant. Each experiment resulted in four characters (groups of clusters), one for each group of systematists. Visual and statistical analysis of the data showed that the systematists were able to produce smaller, more precisely defined character states using the more complex drawings. The character states created with the complex drawings also were more consistent across systematists, and agreed more closely with an independent assessment of phylogeny. To investigate the utility of complex data in an applied task, four observers rated 250 hybrids of Dubautia ciliolata X arborea based on the overall form (Gestalt) of the plants, and took measurements of a number of features of the same plants. A composite score of the measurements was created using principal components analysis. The correlation between the scores on the first principal component and the Gestalt ratings was computed. The Gestalt ratings and PC scores were significantly correlated, demonstrating that assessments of overall similarity can be as useful as more conventional approaches in determining the hybrid status of plants