Banana Slug Genomics

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====== About the slug ======
The //Ariolimax Dolicophallus// is a relatively unstudied species. Here we aim to provide concise and accurate biological information about the //Ariolimax Dolicophallus//. 

=====Banana slug biology=====
==== Presentation of John Pearse and Jan Leonard ====
Presented to the BME235 Slug Genome class on April 23, 2010, this website [[http://compbio.soe.ucsc.edu/slugGenome/|http://compbio.soe.ucsc.edu/slugGenome/]] contains a pdf "All About Banana Slugs".


====Taxonomy====
The term "banana slug" refers to any member of the genus //Ariolimax//, of which there are three species. They are part of the mollusc superfamily Arionoidea, which contains most terrestrial air-breathing slugs.  Within //Ariolimax//, there are three species: //A. columbianus//, //A. californicus//, and //A. dolichophallus//, which is the UC Santa Cruz mascot.

====Appearance and anatomy====
//Ariolimax dolichophallus//, the slender banana slug, can grow up to 7" long.  As the name suggests, banana slugs are usually bright yellow in color, although they can also be green, black, brown, or white.

Banana slugs are similar to other terrestrial species in their anatomy.  They have two sets of retractable tentacles on their head.  The top pair of larger tentacles are frequently referred to as eyestalks, and are used for light-sensing.  The smaller lower pair of tentacles provide the slug with a sense of smell.  The slug's mouth is on the underside of the head.

Directly behind the head is the slug's mantle.  The mantle is a fleshy structure that serves to protect the slug's anal and genital pores.  The pneumostome is also found in this area, and is used for gas exchange.  It connects to the banana slug's single lung.((http://oregonstate.edu/dept/nurspest/slug_anatomy.htm))

The remainder of the banana slug's body is the foot.  Banana slugs move, as do other slugs, through contraction and expansion of this foot.  Like some other terrestrial slugs, banana slugs have a backbone-like keel that runs along the foot.((http://oregonstate.edu/dept/nurspest/banana%20slug.htm))

Banana slugs are known for the thick mucous that they excrete from their skin.  This mucous performs several functions.   It keeps their skin lubricated, which is necessary for gas exchange.  During mating season, banana slugs release pheromones in their mucous that signals their location to potential mates.  In addition, the mucous provides some protection against predators, as it has anesthetic properties when it contacts a wet surface, such as the inside of a predator's mouth.((http://animaldiversity.ummz.umich.edu/site/accounts/information/Ariolimax_columbianus.html))

====Behavior and ecology====

Banana slugs are detritivorous, eating dead and decomposing plant and animal matter.  They also eat living plant material and have a special fondness for mushrooms.  Since banana slugs are prone to desiccation in hot, arid environments, they are typically nocturnal, and come out during the day only when the weather is acceptable.  During particularly dry periods of time, banana slugs can estivate by burying themselves in debris, secreting an especially thick coat of protective mucous, and going dormant until the conditions become more hospitable.((http://ic.ucsc.edu/college8core/c8wiki/index.php/Natural_History_of_UCSC))

Banana slugs have been shown to have a mutually symbiotic relationship with the redwood tree, //Sequoia sempervirens//.  The slugs do not eat the seedlings of the redwood tree, preferring even cardboard over redwood trees.  Instead, they eat plant species that compete with redwoods for light, water, and nutrients.  In exchange for this, the redwoods provide the slugs with the cool, moist habitat that they need.((http://bss.sfsu.edu/holzman/courses/fall00projects/bananaslug.html))

Banana slugs are hermaphroditic, possessing both male and female genitalia.  Though they are capable of self-fertilization, cross mating is more typical slug behavior.  When a slug is ready to mate, it will release pheromones into its slime as a signal to other slugs.  The slugs release sperm into each other and fertilize the eggs.  Sperm collected in this fashion can be stored internally for several months, to allow immature eggs to fully develop before fertilization.  After mating, one of the slugs will sometimes gnaw off the other's male genitalia to disengage (or perhaps it's own—observations are difficult), a process known as apophallation.

Many animals are predators of the banana slug, including birds, raccoons, snakes, and salamanders.  However, due to the mucous secreted by the slug, most such predators will roll the slug around in the dirt to remove the slime before eating the slug.((http://www.greatwildoutdoors.com/2007/09/10/banana-slug/))

====Search strategies ====

To find the rather sparse literature on //A. dolichophallus// requires doing sensitive literature searches, then weeding the results to get higher specificity.  This section should list searches tried, how many hits they got, and what sort of specificity they had.  The results should be collected in the Annotated Bibliography section.

  * Google Books search 
    * //dolichophallus// as the sole keyword gets 147 hits.  Many of them are not relevant (wrong genus). 
    * //dolichophallus -xenophthalmodes// reduces the hits to 129
    * //dolichophallus -xenophthalmodes -brioptera -"x dolichophallus"// reduces the hits to 125.  Not all are relevant, but it looks like at least half are.  I have not added these to the list below, but I recommend that one of the students start doing so. --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/26 13:14//
    * //ariolimax// as the sole keyword gets 739 hits---probably too many for us to process.
    * //ariolimax dolichophallus// gets 47 hits, which are probably all relevant.
  * Google scholar search
    * //ariolimax dolichophallus// gets 48 hits, which are probably all relevant.  There is most likely some overlap with the Google Books search.
    * //ariolimax// alone gets 743 hits---again too many for us.
    * //dolichiphallus// alone gets 73, some of which are wrong genus.

==== Annotated bibliography ====

Uploaded is a long bibliography by Janet Leonard {{:ariolimax_bibliography_janet_leonard.doc}}
Please extract citations from there and work them into this bibliography.
She has a lot of older works that would be difficult to find electronically, but does not include anything newer than 2002, when she created the bibliography.

=== General slug biology ===

  * **Slugs: A Guide to the Invasive and Native Fauna of California**[(cite:california_slugs>
Slugs: A Guide to the Invasive and Native Fauna of California\\
Publication Number: 8336\\
Author: RORY MC DONNELL\\
Inventory Type: PDF File\\
ISBN-13: 978-1-60107-564-2
Copyright Date: 2009\\
Length: 21 pp.\\
url: [[http://anrcatalog.ucdavis.edu/pdf/8336.pdf]].)]


  * **Field guide to the slug**[(cite:field_guide>
Field guide to the slug by David George Gordon, Western Society of Malcologists, Published in Sasquatch field guide series in 1950. ISBN 1-57061-011-8\\
url: [[http://books.google.com/books?hl=en&lr=&id=aj-5iUAjvjgC&oi=fnd&pg=PA5&dq=Ariolimax+dolichophallus&ots=wQ60VTR3fN&sig=SEzmpgFPljoPh0cvf93v0U-HICU#v=onepage&q&f=false]].)]

=== Taxonomy and anatomy for Ariolimax ===

  * **Revision of the Giant West Coast Land Slugs of the Genus Ariolimax Moerch**[(cite:giant_west_slugs_review>
Revision of the Giant West Coast Land Slugs of the Genus Ariolimax Moerch (Pulmonata: Arionidae)\\
Albert R. Mead\\
American Midland Naturalist, Vol. 30, No. 3 (Nov., 1943), pp. 675-717\\
Published by: The University of Notre Dame\\
Stable URL: [[http://www.jstor.org/stable/2421208]].)] 


  * **Heritable body size mediates apparent life-history trade-offs in a simultaneous hermaphrodite**[(cite:body_size>
Heritable body size mediates apparent life-history trade-offs in a simultaneous hermaphrodite\\
B. L. W. MILLER & B. SINERVO\\
Department of Ecology and Evolutionary Biology, University of California at Santa Cruz, Santa Cruz, CA, USA\\
Journal of Evolutionary Biology\\
Volume 20 Issue 4, Pages 1554 - 1562\\
Published Online: 16 Apr 2007\\
doi:[[http://dx.doi.org/10.1111/j.1420-9101.2007.01331.x|10.1111/j.1420-9101.2007.01331.x]].)] 

=== Sexual behavior ===

  * **The darting game in snails and slugs**[(cite:darting_game>
Menno Schilthuizen, The darting game in snails and slugs, Trends in Ecology & Evolution, Volume 20, Issue 11, November 2005, Pages 581-584, ISSN 0169-5347.\\
doi:[[http://dx.doi.org/10.1016/j.tree.2005.08.014|10.1016/j.tree.2005.08.014]].)] 

  * **Penis-biting slugs: wild claims and confusions**[(cite:penis_biting>
Heike Reise, John M. C. Hutchinson, Penis-biting slugs: wild claims and confusions, Trends in Ecology & Evolution, Volume 17, Issue 4, 1 April 2002, Page 163, ISSN 0169-5347.\\
doi:[[http://dx.doi.org/10.1016/S0169-5347(02)02453-9|10.1016/S0169-5347(02)02453-9]].)] 

  * **Sex role preferences, gender conflict and sperm trading in simultaneous hermaphrodites**[(cite:gender_conflict>
Nils Anthes, Annika Putz, Nico K. Michiels, Sex role preferences, gender conflict and sperm trading in simultaneous hermaphrodites: a new framework, Animal Behaviour, Volume 72, Issue 1, July 2006, Pages 1-12, ISSN 0003-3472.\\
doi:[[http://dx.doi.org/10.1016/j.anbehav.2005.09.017|10.1016/j.anbehav.2005.09.017]].)] 

  * **Sexual conflict and partner manipulation in the banana slug, Ariolimax dolichophallus**[(cite:partner_manipulation>
Sexual conflict and partner manipulation in the banana slug, Ariolimax dolichophallus. \\
Miller, Brooke L. W.\\
Ph.D. dissertation, University of California, Santa Cruz, United States -- California. \\
Retrieved April 22, 2010, from Dissertations & Theses @ University of California.(Publication No. AAT 3265732).\\
Document URL: [[http://proquest.umi.com/pqdlink?did=1362529141&Fmt=7&clientId=1565&RQT=309&VName=PQD]].)] 

  * **Sex and the banana slug: A comparison of courtship and copulation in Ariolimax californicus and Ariolimax dolichophallus**[(cite:sex_and_the_slug>
Sex and the banana slug: A comparison of courtship and copulation in Ariolimax californicus and Ariolimax dolichophallus
Meeting of American Malacological Society / Western Society of Malacologists 2000, pp. 18
Janet L. Leonard and John Pearse
Joseph M. Long Marine Laboratory, 100 Shaffer Rd, University of California - Santa Cruz,
Santa Cruz, California 95060, U.S.A.
Document URL: [[http://www.malacological.org/meetings/archives/2000/2000_abs.pdf]].)] 

  * **Phally polymorphism and reproductive biology in Ariolimax buttoni**[(cite:phally_polymorphism>
Phally polymorphism and reproductive biology in Ariolimax buttoni\\
American Malacological Bulletin 23(1):121-135. 2007\\
Janet L. Leonard, Jane A. Westfall, John S. Pearse\\
doi:[[http://dx.doi.org/10.4003/0740-2783-23.1.121|10.4003/0740-2783-23.1.121]].)] 

  * **Comparative reproductive biology of Ariolimax californicus and A. dolichophallus**[(cite:compar_reproductive_bio>
Comparative reproductive biology of Ariolimax californicus and A. dolichophallus\\
LEONARD Janet L. ; PEARSE John S. ; HARPER Alice Bryant ;\\
Invertebrate reproduction & development   ISSN 0792-4259 \\
2002, vol. 41, no1-3, pp. 83-93]\\
Balaban, Rehovot, ISRAEL  1989 Revue\\
Document URL: [[http://cat.inist.fr/?aModele=afficheN&cpsidt=13925818]].)] 

  * **Bateman's Principle and Simultaneous Hermaphrodites: A Paradox**[(cite:bateman_paradox>
Bateman's Principle and Simultaneous Hermaphrodites: A Paradox\\
Integrative and Comparative Biology 45(5):856-873. 2005\\
Janet L. Leonard \\
Joseph M. Long Marine Laboratory, University of California\\
doi:[[http://dx.doi.org/10.1093/icb/45.5.856|10.1093/icb/45.5.856]].)] 


  * **The Evolution of male and female reproductive traits in simultaneously hermaphroditic terrestrial gastropods**[(cite:reproductive_traits>
The Evolution of male and female reproductive traits in simultaneously hermaphroditic terrestrial gastropods.\\
Kathleen Beese, Doctoral thesis:2003-2007. Department of Environmental Sciences, University of Basel, Switzerland.\\
url: [[http://edoc.unibas.ch/577/1/DissB_7878.pdf]].)]



=== Ariolimax Columbianus and Ariolimax Californicus ===

  * **The Edibility of Polygyra and Ariolimax** A short note of a German man from Clark County Oregon who claims //Ariolimax Columbianus// has "good flavor" after proper preparation. The slug is washed in dillute vinegar to remove slime, cleaned like a fish and fried in butter. [(cite:Ariolimax_palatibility>
Allen, J.A. 1916. Edibility of Polygyra and Ariolimax. Nautilus 29, 143.\\
url: [[http://biodiversitylibrary.org/page/1815918]].)]


=== Things Banana Slugs Eat ===

== Satureja douglasii ==

    * **Palatability of monoterpenoid compositional types of Satureja douglasii to a generalist molluscan herbivore, Ariolimax dolichophallus**[(cite:palatability>
Randy L. Rice, David E. Lincoln, Jean H. Langenheim, Palatability of monoterpenoid compositional types of Satureja douglasii to a generalist molluscan herbivore, Ariolimax dolichophallus, Biochemical Systematics and Ecology, Volume 6, Issue 1, 1978, Pages 45-53, ISSN 0305-1978.\\
doi:[[http://dx.doi.org/10.1016/0305-1978(78)90023-6|10.1016/0305-1978(78)90023-6]].)]

  * **Variation of Satureja douglasii monoterpenoids in relation to light intensity and herbivory**[(cite:monoterpenoid_variation>
David E. Lincoln, Jean H. Langenheim, Variation of Satureja douglasii monoterpenoids in relation to light intensity and herbivory, Biochemical Systematics and Ecology, Volume 7, Issue 4, 26 November 1979, Pages 289-298, ISSN 0305-1978.\\
doi:[[http://dx.doi.org/10.1016/0305-1978(79)90006-1|10.1016/0305-1978(79)90006-1]].)] 

  * **A genetic approach to monoterpenoid compositional variation in Satureja douglasii**[(cite:monoterpenoid_genetic>
David E. Lincoln, Jean H. Langenheim, A genetic approach to monoterpenoid compositional variation in Satureja douglasii, Biochemical Systematics and Ecology, Volume 9, Issues 2-3, 10 November 1981, Pages 153-160, ISSN 0305-1978.\\
doi:[[http://dx.doi.org/10.1016/0305-1978(81)90033-8|10.1016/0305-1978(81)90033-8]].)] 

  * **The effect of moisture stress on monoterpenoid yield and composition in Satureja douglasii**[(cite:moisture_stress>
Jonathan Gershenzon, David E. Lincoln, Jean H. Langenheim, The effect of moisture stress on monoterpenoid yield and composition in Satureja douglasii, Biochemical Systematics and Ecology, Volume 6, Issue 1, 1978, Pages 33-43, ISSN 0305-1978.\\
doi:[[http://dx.doi.org/10.1016/0305-1978(78)90022-4|10.1016/0305-1978(78)90022-4]].)] 

  * **Effect of light and temperature on monoterpenoid yield and composition in Satureja douglasii**[(cite:monoterenoid_yield>
David E. Lincoln, Jean H. Langenheim, Effect of light and temperature on monoterpenoid yield and composition in Satureja douglasii, Biochemical Systematics and Ecology, Volume 6, Issue 1, 1978, Pages 21-32, ISSN 0305-1978.\\
doi:[[http://dx.doi.org/10.1016/0305-1978(78)90021-2|10.1016/0305-1978(78)90021-2]].)] 

== Hymenaea courbaril ==

  * **Effect of moisture stress on composition and yield in leaf resin of Hymenaea courbaril**[(cite:moister_stress2>
Jean H. Langenheim, Will H. Stubblebine, Craig E. Foster, Effect of moisture stress on composition and yield in leaf resin of Hymenaea courbaril, Biochemical Systematics and Ecology, Volume 7, Issue 1, 1979, Pages 21-28, ISSN 0305-1978.\\
doi:[[http://dx.doi.org/10.1016/0305-1978(79)90036-X|10.1016/0305-1978(79)90036-X]].)] 

  * **Variation in terpenes and phenolics through leaf development in Hymenaea and its possible significance to herbivory**[(cite:terpene_variation>
David R. Crankshaw, Jean H. Langenheim, Variation in terpenes and phenolics through leaf development in Hymenaea and its possible significance to herbivory, Biochemical Systematics and Ecology, Volume 9, Issues 2-3, 10 November 1981, Pages 115-124, ISSN 0305-1978.\\
doi:[[http://dx.doi.org/10.1016/0305-1978(81)90029-6|10.1016/0305-1978(81)90029-6]].)] 

==== References ====
<refnotes>notes-separator: none</refnotes>
~~REFNOTES cite~~


===== Heterozygosity and slug selfing =====
Every animal has a genome, and almost every genome is stored in multiple copies.  Some plants keep as many as 100 different copies of their genome (with small changes between each) but many animals are diploid,  meaning they have two copies of their genome.  Heterozygosity is a term that describes the difference between the two copies of the genome. Most diploid organisms are heterozygous since they get one copy of their genome from each parents.  While the ploidy of the banana slug is unknown, we suspect that it is diploid. At the end of the spring 2015 class professor [[https://www.soe.ucsc.edu/people/ed | Ed Green ]] performed a heterozygosity analysis on the kolossus Discovar //de novo// banana slug assembly. The result showed that the slug that was sequenced was entirely homozygous.  

This is very strange, normally organisms are heterozygous because they get a copy of their genome from each parent. While the level of heterozygosity changes between organisms, it is very odd to see an organism that has no heterozygosity at all. The lack of variation in the slug can be explained by one of their odder behaviors, 'selfing'. It has been proven that the banana slug can 'self', a process in which the organism impregnates itself.  By repeating this process over many generations, a homozygous slug would be born.  

Our findings suggest that the slugs do indeed self in nature, and it may be their preferred way of reproducing.  Our project sequenced a wild caught slug, and the fact that this wild caught slug was homozygous heavily implies that it is the result of several generations of selfing.
Banana Slug Genomics

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