Balanus diversity cline

Background

A few studies published DNA sequence data from barnacles (B. glandula) collected 15-20 years ago; the best example is here:

Download file "2004 Sotka et al.pdf"

What these studies showed is that, despite the high potential for dispersal/gene flow (the larvae are drifting in the water for many weeks), there is distinct genetic diversity dominant in southern California (the southern end of the distributional range) than in the northern part of the range. Here is a plot that includes data from the two studies with greatest spatial coverage.

The color variation (grey, black) separates data from two different time points (late 90s, early 2000s) from two papers (Sotka et al 2004, Wares and Cunningham 2005) that collected data from the same gene region (mitochondrial cytochrome oxidase I) but from different ends of that gene. So you see that in southern California (south of Point Conception), there is one 'type' that is at 100% frequency; however, the cline never goes to completion, as the southern mtDNA type can still be found at low frequency all the way into Alaska!

It has been 20 years since some of these barnacles were collected. There have been estimates that many species are moving northward (well, or following local climate velocity) at rates of 20km or more per decade. So we have a slight chance of picking up some signal on this movement. Wait, did I say movement? Of course not: they are barnacles! Our question is whether there is differential growth/fitness (reproduction) of the two primary mitochondrial lineages. If the southern type is doing better as the water warms, its frequency should increase. This means either the cline will shift northward, or will flatten out since northern sites already had a low frequency of "southern" individuals.

We will collect 50-60 Balanus from outside the FHL labs, from diverse microhabitats, and along with samples already taken at 2 other locations we will use PCR and sequencing to see how this cline looks 20 years later.

Methods

  1. Wednesday morning we will head out before paper discussion and collect some Balanus glandula into 50mL vials, they will be pickled in 95% ethanol
  2. Later in Lab 4 (ethanol is OK!), you will split into 3 teams of 2 each handling one location along the cline. Our goal is to end up with ~32 individuals successfully amplified for each location
    1. under dissecting scope, with forceps pull body of barnacle out of shell
    2. pull about half of legs (cirri) from body and put in PCR tube
    3. remainder of body goes into 1.5mL tube with 95% ethanol in it
    4. 1.5mL tubes go into small labeled bag to keep specimens separate
    5. discard shells from barnacles used; remainder leave in 50mL vial for future use
    6. each team do this for 30-32 individuals from your site
  3. In Lab 10 we will add some Chelex solution to your PCR tubes (~80µl but may change this) and heat the samples to 99° in PCR machine; DNA samples are now ready for PCR setup.
  4. In Lab 10 we will perform PCR on B. glandula
  5. Next day we can run these reactions out on agarose gels and then (hopefully) prep for sequencing.

Data are back!

A complete data set to compare your new sequence data with is contained in this file,

Download file "Balanus glandula HISTORY.geneious.zip"which is a .zip archive to be used with the software Geneious. Please download the free/trial version to your computer and check out the tutorial when you have time!

The new data are available here, JPW converted these read names using the plate input information.
Download file "BgFHL.zip"

Here is a spreadsheet for entering/sharing the data from your location:




Reading Associated

Dawson et al paper on Tetraclita moving northward

Download file "DAWSON_et_al-2010-Molecular_Ecology.pdf";

Bell et al paper on Fundulus not moving northward

Download file "J Hered-2014-Bell-jhered_esu016.pdf"; also refer to the climate velocity papers that we read and discussed in week one.

Comments

/groups/eccofhl/search/index.rss?tag=hotlist/groups/eccofhl/search/?tag=hotWhat’s HotHotListHot!?tag=hot4/groups/eccofhl/sidebar/HotListjohnwaresjohn wares2016-06-30 15:22:33+00:002016-06-30 15:22:33updated32johnwaresjohn wares2016-06-29 02:28:51+00:002016-06-29 02:28:51updated31johnwaresjohn wares2016-06-29 01:42:23+00:002016-06-29 01:42:23updated30johnwaresjohn wares2016-06-29 01:42:02+00:002016-06-29 01:42:02updated29johnwaresjohn wares2016-06-28 15:02:12+00:002016-06-28 15:02:12updated28johnwaresjohn wares2016-06-24 04:48:13+00:002016-06-24 04:48:13updated27Added tag - hotjohnwaresjohn wares2016-06-23 17:37:21+00:002016-06-23 17:37:21addTag26johnwaresjohn wares2016-06-22 23:47:31+00:002016-06-22 23:47:31updated25johnwaresjohn wares2016-06-21 18:50:55+00:002016-06-21 18:50:55updated24johnwaresjohn wares2016-06-21 02:38:03+00:002016-06-21 02:38:03updated23johnwaresjohn wares2016-06-21 02:36:50+00:002016-06-21 02:36:50updated22johnwaresjohn wares2016-06-21 02:31:29+00:002016-06-21 02:31:29updated21johnwaresjohn wares2016-06-21 02:18:48+00:002016-06-21 02:18:48updated20johnwaresjohn wares2016-06-19 16:28:21+00:002016-06-19 16:28:21updated19johnwaresjohn wares2016-06-19 16:27:22+00:002016-06-19 16:27:22updated18johnwaresjohn wares2016-06-19 05:03:34+00:002016-06-19 05:03:34updated17johnwaresjohn wares2016-06-19 00:19:10+00:002016-06-19 00:19:10updated16johnwaresjohn wares2016-06-18 19:37:20+00:002016-06-18 19:37:20updated15johnwaresjohn wares2016-06-18 18:56:54+00:002016-06-18 18:56:54updated14johnwaresjohn wares2016-06-18 16:39:15+00:002016-06-18 16:39:15updated13johnwaresjohn wares2016-06-18 15:55:16+00:002016-06-18 15:55:16updated12johnwaresjohn wares2016-06-18 10:37:56+00:002016-06-18 10:37:56updated11johnwaresjohn wares2016-06-17 05:16:48+00:002016-06-17 05:16:48updated10johnwaresjohn wares2016-06-17 05:16:30+00:002016-06-17 05:16:30updated9johnwaresjohn wares2016-06-17 05:15:18+00:002016-06-17 05:15:18updated8johnwaresjohn wares2016-06-17 05:11:21+00:002016-06-17 05:11:21updated7johnwaresjohn wares2016-06-17 05:09:25+00:002016-06-17 05:09:25updated6johnwaresjohn wares2016-06-16 19:53:48+00:002016-06-16 19:53:48updated5johnwaresjohn wares2016-06-16 19:08:22+00:002016-06-16 19:08:22updated4johnwaresjohn wares2016-06-16 19:07:35+00:002016-06-16 19:07:35updated3johnwaresjohn wares2016-06-16 19:05:26+00:002016-06-16 19:05:26updated2First createdjohnwaresjohn wares2016-06-16 18:37:09+00:002016-06-16 18:37:09created1wiki2016-06-30T15:22:33+00:00groups/eccofhl/wiki/ec337FalsePisaster Genotypes and Righting Response/groups/eccofhl/wiki/ec337/Pisaster_Genotypes_and_Righting_Response.htmljohn wares32 updatesPisaster Genotypes and Righting Response TL;DR Data! For this project, you will end up having 2-3 Pisaster ochraceus in your care; you must also keep your eyes on t...Falsejohnwares2016-06-30T15:22:33+00:00johnwaresjohn wares2016-06-29 15:51:46+00:002016-06-29 15:51:46updated15johnwaresjohn wares2016-06-29 04:26:27+00:002016-06-29 04:26:27updated14johnwaresjohn wares2016-06-28 04:28:38+00:002016-06-28 04:28:38updated13Added tag - hotjohnwaresjohn wares2016-06-24 15:41:01+00:002016-06-24 15:41:01addTag12johnwaresjohn wares2016-06-19 16:30:30+00:002016-06-19 16:30:30updated11johnwaresjohn wares2016-06-14 13:46:34+00:002016-06-14 13:46:34updated10johnwaresjohn wares2016-06-14 13:43:30+00:002016-06-14 13:43:30updated9Added tag - clinejohnwaresjohn wares2016-06-14 13:35:17+00:002016-06-14 13:35:17addTag8Added tag - phylodiversityjohnwaresjohn wares2016-06-14 13:35:16+00:002016-06-14 13:35:16addTag7Added tag - pcrjohnwaresjohn wares2016-06-14 13:35:08+00:002016-06-14 13:35:08addTag6Added tag - barnaclesjohnwaresjohn wares2016-06-14 13:35:07+00:002016-06-14 13:35:07addTag5johnwaresjohn wares2016-06-14 13:34:06+00:002016-06-14 13:34:06updated4johnwaresjohn wares2016-06-14 13:32:58+00:002016-06-14 13:32:58updated3johnwaresjohn wares2016-06-14 13:31:23+00:002016-06-14 13:31:23updated2First createdjohnwaresjohn wares2016-06-14 13:18:57+00:002016-06-14 13:18:57created1wiki2016-06-29T15:51:46+00:00groups/eccofhl/wiki/6f73aFalseBalanus diversity cline/groups/eccofhl/wiki/6f73a/Balanus_diversity_cline.htmljohn wares15 updatesBalanus diversity cline Background A few studies published DNA sequence data from barnacles (B. glandula) collected 15-20 years ago; the best example is here: ...Falsejohnwares2016-06-29T15:51:46+00:00Added tag - limpetsjohnwaresjohn wares2016-06-24 15:41:25+00:002016-06-24 15:41:25addTag10Added tag - diversityjohnwaresjohn wares2016-06-24 15:41:23+00:002016-06-24 15:41:23addTag9Added tag - distributionjohnwaresjohn wares2016-06-24 15:41:21+00:002016-06-24 15:41:21addTag8Added tag - ecologyjohnwaresjohn wares2016-06-24 15:41:20+00:002016-06-24 15:41:20addTag7Added tag - nichejohnwaresjohn wares2016-06-24 15:41:18+00:002016-06-24 15:41:18addTag6Added tag - hotjohnwaresjohn wares2016-06-24 15:41:17+00:002016-06-24 15:41:17addTag5johnwaresjohn wares2016-06-21 16:40:11+00:002016-06-21 16:40:11updated4morgankellyMorgan Kelly2016-06-20 14:33:01+00:002016-06-20 14:33:01updated3morgankellyMorgan Kelly2016-06-20 14:28:46+00:002016-06-20 14:28:46updated2First createdmorgankellyMorgan Kelly2016-06-20 14:11:36+00:002016-06-20 14:11:36created1wiki2016-06-21T16:40:11+00:00groups/eccofhl/wiki/d254bFalseTransect study/groups/eccofhl/wiki/d254b/Transect_study.htmljohn wares10 updatesTransect study In this exercise, you will use transect surveys and environmental data to create climate envelope models for a group of species of your choosing (it ...Falsejohnwares2016-06-21T16:40:11+00:00Added tag - hotmorgankellyMorgan Kelly2016-06-24 15:41:56+00:002016-06-24 15:41:56addTag5Added tag - adaptationmorgankellyMorgan Kelly2016-06-24 15:39:33+00:002016-06-24 15:39:33addTag4morgankellyMorgan Kelly2016-06-14 13:41:13+00:002016-06-14 13:41:13updated3morgankellyMorgan Kelly2016-06-14 01:37:59+00:002016-06-14 01:37:59updated2First createdmorgankellyMorgan Kelly2016-06-14 01:37:42+00:002016-06-14 01:37:42created1wiki2016-06-14T13:41:13+00:00groups/eccofhl/wiki/60339False1. Tigriopus heat tolerance/groups/eccofhl/wiki/60339/1_Tigriopus_heat_tolerance.htmlMorgan Kelly5 updates1. Tigriopus heat tolerance Background: Both genes and the environment contribute to most phenotypes. This complicates studies of local adaptation: local adaptation occurs when ...Falsemorgankelly2016-06-14T13:41:13+00:00hot/groups/eccofhl/search/index.rss?sort=modifiedDate&kind=all&sortDirection=reverse&excludePages=wiki/welcomelist/groups/eccofhl/search/?sort=modifiedDate&kind=all&sortDirection=reverse&excludePages=wiki/welcomeRecent ChangesRecentChangesListUpdates?sort=modifiedDate&kind=all&sortDirection=reverse&excludePages=wiki/welcome0/groups/eccofhl/sidebar/RecentChangesListmodifiedDateallRecent ChangesRecentChangesListUpdateswiki/welcomeNo recent changes.reverse5searchlist/groups/eccofhl/calendar/Upcoming EventsUpcomingEventsListEvents1Getting events…