Invasion Genomics and Research Proposals

Flashcards about Invasion Genomics and Research Proposal Components

Lee et al. 2018

Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States.

Jaspers et al. 2018

Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader.

Elton (1958): The Ecology of Invasions by Animals and Plants

Provided important early works in invasion biology.

Baker and Stebbins (1965): The Genetics of Colonizing Species

Provided important early works in invasion biology.

Dlugosch KM, Parker IM. 2008

Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions.

Welles and Dlugosch, 2018

Population Genomics of Colonization and Invasion

Question 1

What is the taxonomic identity of invasive species?

Question 2

How do these species manage to travel around the world?

Question 3

What are their native areas and their sources of introduction?

Question 4

What are the vectors of primary introduction and vectors of secondary spread?

Question 5

Are we dealing with single or multiple introduction events?

Question 6

How are these serendipitous voyages shaping the genetic landscape of the introduced populations?

Question 7

Are demographic bottlenecks experienced during the invasion process? (founder events)

Question 8

Are invasive populations depleted of standing genetic variation? (founder effect)

van Boheemen, et al. 2017

Multiple introductions, admixture, and bridgehead invasion characterize the introduction history of Ambrosia artemisiifolia in Europe and Australia.

Common ragweed, Ambrosia artemisiifolia

A widespread invasive species also known as noxious weed.

Areas where Common ragweed, Ambrosia artemisiifolia is Invasive

Europe; temperate Asia and the Indian subcontinent; temperate northern and southern Africa and Macaronesia; Oceania in Australia, New Zealand, and Hawaii; and Southwestern North America in California and the Southwestern United States

Impact of Ambrosia artemisiifolia

Can produce yield losses in soybeans as high as 30 percent.

Another impact of Ambrosia artemisiifolia

Its wind-blown pollen is highly allergenic.

Global Biodiversity Information Facility (www.gbif.org)

A facility that provides global biodiversity information.

Human-assisted dispersal

The movement of species around the world with human help

Introduction of A. artemisiifolia to Europe

The first known introduction of A. artemisiifolia was in France around 1850 and most likely originated from contamination of imported seeds from North America.

Later introductions of A. artemisiifolia

Major introductions have been tied to imports during the two World Wars.

Hypothesis for A. astermisifolia movement

A. astermisifolia moved from the USA à Europe, then Europe à Australia (etc.)

Aim of study by van Boheemen et al. 2017

Assess the contribution of historical admixture, multiple introductions and bridgehead invasion to the successful introductions of A. artemisiifolia into Europe and Australia.

Bridgehead invasion history (van Boheeman et al., 2017)

Two sources of introductions from the USA to Europe (bridgehead) with subsequent introduction to Australia and other places around the globe

Steps in Genotyping-by-sequencing (Elshire et al., 2011)

1. Digest genomic DNA with restriction enzyme 2. Ligate common adapters and unique barcodes for each sample 3. Pool ligated libraries 4. PCR with primers matching common adaptor 5. High throughput sequencing (Illumina) 6. Map reads to reference genome 7. Call SNPs (bioinformatics) 8. Downstream population genomic analyses

FIS

inbreeding coefficient, FIS = 1-(Ho/He), Ho = observed heterozygosity, He = expected heterozygosity under Hardy-Weinberg assumptions

AR = allelic richness

The number of alleles at a locus, corrected for population sample size

Experimental design questions

1. What is my research question and hypothesis, and how can I best address it? 2. What resources will I need? 3. How can I design a study to adequately test my hypothesis, and do so cheaply & feasibly without compromising the quality of my results? 4. Where and how will I sample populations/individuals? 5. What information is available on my proposed collecting site(s)? 6. How many samples: per population? how many populations? TOTAL? 7. Power analysis: How will I determine an adequate sample size to sufficiently address my hypothesis, a priori? 8. What genomic technique is best for my hypothesis? Enough variation? Tradeoff between # samples, # SNPs/coverage depth, cost, labor, and time! 9. How will I analyze the results such that I am addressing my hypothesis adequately? 10. What potential biases exists: in my sampling design, molecular methods, and analyses?

I. Cover sheet

1 pg; triad member info, title, etc. to fill out

III. Project summary

1 pg; an overall summary much like an abstract

IV. Project description

5 pp; A. Introduction – 1 pg; what is unknown, what is the knowledge gap and why important? B. Background – 1 pg; on the study system and what is known already C. Objective – 1/2 pg; what is your hypothesis and how will you test it? D. Research plan – 1.5-2 pp; what methods will be used? (sampling, lab work, data analyses)

II. Table of contents (1 pg)

a concise, organized “guide” to your proposal to make it easier for the reviewer to access the different parts

III. Project summary – 1 pg; an overall summary much like an abstract

A concise summary of: 1. The problem/knowledge gap 2. The significance of the problem 3. Your hypothesis 4. Your planned experimental approach 5. Your expected outcome 6. The broader impact of your research

A. Introduction Purpose

Identify the knowledge gap UP FRONT, What is known about the problem, in the big picture? What is unknown (knowledge gap – go into more detail here), What are you planning to do, and WHY?Why is it important?

B. Background Purpose

provide the necessary background and details the reviewer will need to understand your proposal, This is where you focus on your STUDY SYSTEM (e.g. Lonicera japonica), All leads to, or arcs to, your SPECIFIC HYPOTHESIS

C. Objective Purpose

clearly state your hypothesis, in specific terms

D. Research Plan Purpose

describe to the reviewers EXACTLY what you propose to do, This section MUST ABSOLUTELY link back to your original hypothesis or hypotheses., You should explicitly state this, e.g. Sample collection DNA extraction and sequencing Data analysis Timeline/schedule Expected results Expected significance

V. Expected results – 1 pg; Purpose

what do you expect to find and how will you interpret alternative findings?

VI. Significance – 1 pg; Purpose

why is this study important, how will it benefit X, Y, and Z? How will it advance science?

VII. Literature cited – Unlimited; properly formatted, peer-reviewed citations (at least 10 sources)

Author1, A. B., Author2, C. D., Author3, E. F. YEAR. Title of paper. Journal Name Volume: page-page.