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On patterns of coevolution
across cophylogenies
Mark Merilo, Sarah J. Adamowicz, R. Ayesha Ali
1
Evolution 2013 Snowbird, Utah Monday, June 24th, 2013
Species interactions
wormwould, (2010), Parasitic Wasp [ONLINE]. Available at: http://www.flickr.com/photos/onthespiral [Accessed 20 January 13]
Fir0002/Flagstaffotos, (2007), Leaf Hopper nymph of the Common Jassid (Eurymela fenestrata) [ONLINE]. Available at:
http://en.wikipedia.org/wiki/File:Common_jassid_nymphs_and_ants02.jpg [Accessed 20 January 13].
Dr Graham Beards, (2009), Electron micrograph of Bacteriophages [ONLINE]. Available at: http://commons.wikimedia.org/wiki/File:Phage.jpg [Accessed 20 January 13].
John Severns, (2006), Honey bee [ONLINE]. Available at: http://en.wikipedia.org/wiki/File:European_honey_bee_extracts_nectar.jpg [Accessed 20 January 13].
Richard Naylor, (2009), Parasitoid wasps [ONLINE]. Available at: http://news.bbc.co.uk/local/sheffield/hi/people_and_places/nature/newsid_8370000/8370816.stm [Accessed 20
January 13].
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Symbiotic relationships
Persistent, recurring biological
interactions
Mutualism, commensalism, parasitism
Obligate and facultative relationships
Shared phylogenetic topology
Reciprocal speciation between the two
associated lineages; cospeciation
But what about when they don’t match?
Phylogenetic reconstruction
Superimpose phylogenies, explain
differences with events
Jan Derk, (2002), Common Clownfish [ONLINE]. Available at: http://en.wikipedia.org/wiki/File:Common_clownfish_curves_dnsmpl.jpg [Accessed 20 January 13].
Rafael Barbizan Sühs, (2006), Wasp [ONLINE]. Available at: http://en.wikipedia.org/wiki/File:Hymenoptera,_Vespidae,_Polistinae,_Mischocyttarus_rotundicollis_.jpg
[Accessed 20 January 13].
Brian Valentine, (2006), Small wasp parasitising aphids [ONLINE]. Available at: http://www.flickr.com/photos/lordv/2869916160/ [Accessed 20 January 13].
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Coevolutionary Events
Event types
Cospeciation
Sorting
Duplication
Host switch
Cospeciation Sorting
Duplication Host switch
Host
Symbiont
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Past research
Specific, small scale studies
Mostly single cophylogeny comparison
Tested individually for congruence
No direct comparisons between phylogenies
5
Questions
Is the symbiont phylogeny dependent on the
host phylogeny?
How can the coevolutionary history of
symbiotic species be quantified & compared
across groups?
How do profiles of coevolutionary events
differ across cophylogeny classifications?
Latitude, transmission (horizontal, vertical),
association (ecto, endo, intracellular), etc.
6
Overview of analysis
Co-phylogeny collection
Single, standardized Web of Science search
Both symbiont phylogenies, and associations
Transfer of cophylogenies to digital format
Co-phylogenetic history reconstruction
Core-PA (cost-based: fixed, parameter adaptive)
Develop permutation test
Use dirmult package in R
7
Symbiont categories
0
5
10
15
20
25
30
Josh Grosse, (2002), Roundworm [ONLINE]. Available at: http://en.wikipedia.org/wiki/File:Roundworm.jpg [Accessed 20 January 13].
CDC/Vector Ecology & Control Laboratory, (2007), Flea [ONLINE]. Available at: http://static.ddmcdn.com/gif/flea-1.jpg [Accessed 20 January 13].
Thomas Splettstoesser, (2012), Cowpea mosaic virus [ONLINE]. Available at: http://www.scistyle.com [Accessed 20 January 13].
Rafael Barbizan Sühs, (2006), Wasp [ONLINE]. Available at: http://en.wikipedia.org/wiki/File:Hymenoptera,_Vespidae,_Polistinae,_Mischocyttarus_rotundicollis_.jpg [Accessed 20 January
13].
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Overview of analysis
Co-phylogeny collection
Single, standardized Web of Science search
Both symbiont phylogenies, and associations
Transfer of cophylogenies to digital format
Co-phylogenetic history reconstruction
Core-PA (cost-based: fixed, parameter adaptive)
Develop permutation test
Use dirmult package in R
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Dirichlet distribution
How to compare cophylogeny event profiles?
Given total number of coevolutionary events,
event counts follow a multinomial distribution
Extension of binomial distribution for binary data
Assume event proportions among host-symbiont
pairs within a group (e.g. latitude zone) are similar
Expect variance within these groups
A Dirichlet distribution provides a model for how
these proportions vary
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2
8
4
1
Calculate LLRT
“Tropical” “Temperate”
2
1
2
1
Cospeciation Sorting Duplication Host-switch
Dirichlet model & permutation test
X 999 2
8
4
1
Cospeciation Sorting Duplication Host-switch
Calculate LLRT statistic
Tropical Temperate
2
1
2
1
11
2
8
4
1
Calculate LLRT
“Tropical” “Temperate”
2
1
2
1
Cospeciation Sorting Duplication Host-switch
2
8
4
1
Calculate LLRT statistic
“Tropical” “Temperate”
2
1
2
1
Cospeciation Sorting Duplication Host-switch
Fit Dirichlet distribution model to event counts
Log Likelihood Ratio Test (LLRT) statistic
Randomized permutations to build distribution
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LLRT statistic
Exploratory biological results (α = 0.2)
Of interest for further study
Ecto-endo symbionts (expected)
Innate-adaptive immune system (vert/invert)
Tropical vs. temperate
Not significant
Horizontal/vertical transmission (unexpected!)
Parasites/mutualist symbionts
Presence/absence of secondary hosts
Tropical-subtropical
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Parameter Adaptive results:
Ratios of Proportions Speciation Event
Comparison Cospeciation Sorting Duplication Host-switch p
Tropical vs
Temperate 0.96 1.08 0.90 0.54 0.10
Ecto- vs Endo-
symbiont 1.06 0.95 1.03 1.63 0.16
Adaptive vs
Innate *
1.31 0.90 0.98 4.53 0.03
14
* Vertebrate vs Invertebrate immune system
Less host-switching in the tropics
Parameter Adaptive results:
Ratios of Proportions Speciation Event
Comparison Cospeciation Sorting Duplication Host-switch p
Tropical vs
Temperate 0.96 1.08 0.90 0.54 0.10
Ecto- vs Endo-
symbiont 1.06 0.95 1.03 1.63 0.16
Adaptive vs
Innate *
1.31 0.90 0.98 4.53 0.03
15
* Vertebrate vs Invertebrate immune system
Less host-switching in the tropics
Parameter Adaptive results:
Ratios of Proportions Speciation Event
Comparison Cospeciation Sorting Duplication Host-switch p
Tropical vs
Temperate 0.96 1.08 0.90 0.54 0.10
Ecto- vs Endo-
symbiont 1.06 0.95 1.03 1.63 0.16
Adaptive vs
Innate *
1.31 0.90 0.98 4.53 0.03
16
* Vertebrate vs Invertebrate immune system
More host switching in ecto-symbionts
Parameter Adaptive results:
Ratios of Proportions Speciation Event
Comparison Cospeciation Sorting Duplication Host-switch p
Tropical vs
Temperate 0.96 1.08 0.90 0.54 0.10
Ecto- vs Endo-
symbiont 1.06 0.95 1.03 1.63 0.16
Adaptive vs
Innate *
1.31 0.90 0.98 4.53 0.03
17
* Vertebrate vs Invertebrate immune system
More cospeciation and host-switching in hosts with adaptive immune systems
Conclusions & future directions
Conducted meta-analysis of cophylogenies
Developed statistical test to compare event
profiles from several copylogenies
Identified knowledge gaps requiring study
Repeat comparisons within specific taxa
Perform Dirichlet regression test to
simultaneously include several factors into
one parsimonious model
18
Acknowledgements
Jinzhong Fu, Alex Smith
Nicolas Wieseke
Adamowicz, Hebert labs
19