On patterns of coevolution across cophylogenies 2013.pdf · On patterns of coevolution across cophylogenies Mark Merilo, Sarah J. Adamowicz, R. Ayesha Ali 1 Evolution 2013 Snowbird,

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

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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.

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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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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


Calculate LLRT statistic

Tropical Temperate

2

1

2

1

11

2

8

4

1

Calculate LLRT


2

1

2

1


2

8

4

1

Calculate LLRT statistic


2

1

2

1


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

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* Vertebrate vs Invertebrate immune system

Less host-switching in the tropics




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


Less host-switching in the tropics




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

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More host switching in ecto-symbionts




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

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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

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Acknowledgements

Jinzhong Fu, Alex Smith

Nicolas Wieseke

Adamowicz, Hebert labs

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On patterns of coevolution across cophylogenies 2013.pdf · On patterns of coevolution across cophylogenies Mark Merilo, Sarah J. Adamowicz, R. Ayesha Ali 1 Evolution 2013 Snowbird,

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