Materials and Methods
This presentation is the property of its rightful owner.
Sponsored Links
1 / 1

Abstract PowerPoint PPT Presentation


  • 107 Views
  • Uploaded on
  • Presentation posted in: General

Materials and Methods Tissue samples from 144 individuals were collected and precisely mapped at six sites in 2012 and preserved over silica gel Total DNAs were extracted using Dneasy Plant mini kit or a modified CTAB procedure [5]

Download Presentation

Abstract

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Abstract

  • Materials and Methods

  • Tissue samples from 144 individuals were collected and precisely mapped at six sites in 2012 and preserved over silica gel

  • Total DNAs were extracted using Dneasy Plant mini kit or a modified CTAB procedure [5]

  • Total DNAs were digested with HindIII and HpaII restriction enzymes [6]

  • Sticky ends of the resulting fragments were ligated with adaptors and identifying bar codes [7]

  • Fragments were then amplified using standard PCR, and then size-sleced (250-350 bp) using a Pippin Prep

  • Fragments from all 144 individuals will then be sequenced using an unpaired-end run with the IlluminaHiSeq 2000

  • Resulting reads with be assembled into contigs, and then loci using STACKS [8]

  • Alleles will be identified as sequence variants that differ at 1-3 positions along assembled sequences

Abstract

My project is to quantify the spatial scales of gene flow and genetic structure of populations of the wildflower Maianthemum canadense, in conjunction with a larger project studying changes in other understory species. Using tissue samples collected and preserved over silica gel the previous summer, I will be isolating DNA from which I will prepare a double digest restriction size associated DNA sequencing (ddRADseq) library for Illumina HiSeq2000 sequencing. Sequence data will be compiled into a genetic library for the species, and using the programs SPAGeDI and Structure, we will assess the spatial scale of gene flow and analyze the variance within and between populations of this herb to quantify the genetic diversity of Maianthemum canadense.

Spatial scales of gene flow and genetic structure in Maianthemum canadense based on next generation sequencing dataBy Abigail Gadbois

  • Background

  • From 1948 through 1959, Dr. John T. Curtis lead a survey of Wisconsin’s plant communities, and identified Maianthemum as a the most common understory species in northern forests [1]

  • Re-surveys showed that Maianthemumhas increased density over the past fifty years, even though it lacks the traits seen in most other species that increased over that period [2]

  • Maianthemum canadense is a short, shade-loving, animal-pollinated plant with fleshy, animal-dispersed fruits, and is native to large areas of boreal and transitional forests in northern North America [3]

  • Many of the other “winning” species in northern Wisconsin over the past 50 years have been taller, exotic in origin, and/or resistant to deer herbivory[4]

Maianthemum canadense [11]

  • Analysis

  • Individual sequences will be analyzed using GENEPOP to assess genetic diversity; we will use SPAGeDiand STRUCTURE to determine the spatial scale of gene flow [9]

  • STRUCTURE permits the identification of populations that appear to be largely isolated from each other genetically [10]

  • Because Maianthemum uses biotic seed dispersal and is a winner species, we expect it to have a high degree of genetic diversity within populations, a relatively large scale of gene flow, and a relatively small number of isolated populations over distances from a few meters to 60 km

Example of STRUCTURE output from Calochortus populations [12]

  • Rationale and Hypothesis

  • Because Maianthemumhas been a “winner” species over the past 50 years and is animal-dispersed, it should have greater genetic diversity and exhibit gene flow over greater distances than declining species or those with wind-dispersed seeds

  • By analyzing population genetics of Maianthemum I hope to contribute to models designed to predict future trends in its abundance and distribution in the face of climate change.

References

[1,2,4] Weigmann and Waller 2006 Biological Conservation 129

[3] Pavek 1993 USDA

[5] Soltis 2008

[6] Peterson et. Al 2012 PLoS ONE 7

[7]Willing et. Al 2011 Bioinformatics 12

[8] Catchen et. Al 2011 Genes, Genomes, and Genetics 1

[9] Vekemans et. Al 2004 Molecular Ecology 4

[10] Hubisz et. Al 2009 Molecular Ecology 9

[11] John Perry Nuncketest

[12] Henss et. Al 2013 Ecology and Evolution

Collection sites for Maianthemum

Special thanks to Dr. Thomas Givnish, Dr. Jackson Moeller, Dimensions of Biodiversity team, National Science Foundation, and the University of Wisconsin-Madison


  • Login