8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Increased taxon sampling with short DNAsequences -

John James WilsonDepartment of Integrative Biology

University of Guelph

 jwilso04@uoguelph.ca

does it support or collapse “deep” monophyly?

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Lepidoptera phylogeny

more genes? more taxa? better models?

Introduction Methods Results Discussion

(Regier et al. 2008)

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Introduction Methods Results Discussion

- 24 nuclear genes- exemplar taxa

- resolve deep nodes

- COI only- every species

- global ID system

lots of data?

- Lists priority gene regions

- COI and EF-1a

more genes? more taxa? better models?

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

more taxa?

X2

Hillis et al. (1998, 2003)

- limited amount of time and

money for data assembly

- phylogenetic estimatesimprove with more taxa even if #

of characters remains unchanged

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

more taxa?

X2

Hillis et al. (1998, 2003)

- limited amount of time and

money for data assembly

- phylogenetic estimatesimprove with more taxa even if #

of characters remains unchanged

objective (i)test this hypothesis

using macrolepidoptera

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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ancient rapid radiation?

Introduction Methods Results Discussion

(Rokas & Carroll 2006)

- difficult to reconstruct- taxon sampling

may not help

(Whitfield & Kjer 2006)

a

b

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ancient rapid radiation?

Introduction Methods Results Discussion

(Rokas & Carroll 2006)

- difficult to reconstruct- taxon sampling

may not help

(Whitfield & Kjer 2006)

objective (ii)

explore effect of 

tree-shape withsimulated

sequences

a

b

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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empirical sequences

Introduction Methods Results Discussion

Mimallonidae

Geometridae

Hesperiidae

Hedylidae

Nymphalidae Papilionidae

Megalopygidae

Pieridae

Noctuidae

Sphingidae

Notodontidae

Lasiocampidae

Saturniidae

97

Drepanidae 5 sampling levels

(species per 

family):

- 100- 200

- 300

- 400

- 500

Cytochrome c 

oxidase I (650bp)

Uraniidae

Bombycidae

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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simulated sequences

Introduction Methods Results Discussion

X1 X2 X4

- simulated along NJ tree of empirical sequences- constrained families as clades, and deeper 

phylogeny of Pogue (2009)

2 sampling levels:

- 1000 species (~80 species per family)

- 150 species (~10 species per family)

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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phylogenetic analysis

Introduction Methods Results Discussion

- maximum parsimony analysis using TNT- tree and character scores measured in PAUP

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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evaluating phylogenies

Introduction Methods Results Discussion

1. Proportion of monophyletic taxa

# of monophyletic taxa/number of taxa

2. Taxon consistency index = m/s

m = minimum # of clades a taxon can exhibit on any cladogram

s = minimum # of clades a taxon exhibits on actual cladogram

3. Taxon retention index = (g-s)/(g-m)

g = greatest # of clades a taxon can exhibit on any cladogram

‘concordance’ groups - 16 families

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

increasing taxon number in empirical datasets

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

100 200 300 400 500

# species per family

Proportion of monophyletictaxa

Taxon

consistencyindex

Taxonretentionindex

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

increasing taxon number in empirical datasets

#spp. ave. p-dist. #spp. ave. p-dist.

MI 13 0.109 13 0.109LA 69 0.123 69 0.123

BO 29 0.121 29 0.121

SA 100 0.131, 0.133 166 0.132

SP 100 0.106, 0.106 457 0.106

HE 17 0.098 17 0.098

HP 100 0.122, 0.120 500 0.122, 0.122

PA 100 0.119, 0.119 209 0.119

PI 100 0.144, 0.142 211 0.142

LY 100 0.101, 0.094 404 0.098

NY 100 0.132, 0.129 500 0.134, 0.133

DR 5 0.098 5 0.098

UR 6 0.109 6 0.109

GE 100 0.112, 0.114 500 0.115, 0.115

NO 100 0.122, 0.121 372 0.12

NC 100 0.109, 0.111 500 0.109, 0.109All 1139 0.138, 0.138 3958 0.137, 0.137

CI 1139 0.024, 0.024 3958 0.010, 0.010

RI 1139 0.498, 0.501 3958 0.500, 0.580

Homoplasy measures

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

increasing taxon number in empirical datasets

#spp. ave. p-dist. #spp. ave. p-dist.

MI 13 0.109 13 0.109LA 69 0.123 69 0.123

BO 29 0.121 29 0.121

SA 100 0.131, 0.133 166 0.132

SP 100 0.106, 0.106 457 0.106

HE 17 0.098 17 0.098

HP 100 0.122, 0.120 500 0.122, 0.122

PA 100 0.119, 0.119 209 0.119

PI 100 0.144, 0.142 211 0.142

LY 100 0.101, 0.094 404 0.098

NY 100 0.132, 0.129 500 0.134, 0.133

DR 5 0.098 5 0.098

UR 6 0.109 6 0.109

GE 100 0.112, 0.114 500 0.115, 0.115

NO 100 0.122, 0.121 372 0.12

NC 100 0.109, 0.111 500 0.109, 0.109All 1139 0.138, 0.138 3958 0.137, 0.137

CI 1139 0.024, 0.024 3958 0.010, 0.010

RI 1139 0.498, 0.501 3958 0.500, 0.580

Homoplasy measures

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

increasing tree-like shape in simulated datasets

Proportion of monophyletictaxa

Taxon

consistencyindex

Taxonretentionindex

100 speciesper family

10 speciesper family

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70

0.80

0.90

1.00

X1 X2 X4 X8 X16

branch length empirical values

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

results summary

(i) increasing taxon number in empirical datasets- doesn’t increase # monophyletic families- doesn’t break long branches- adds homoplasy to the dataset

(ii) increasing tree-like shape in simulated datasets- does increase # monophyletic families- but not substantially

- increased taxon sampling doesn’t help

I d i M h d R l Di i

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

improving phylogenies

I t d ti M th d R lt Di i

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

improving phylogenies

more genes? may not help- Regier et al’s 5 genes generally recovered families

- other studies show varying success (wg, Ef-1a, period )

- few exemplars increase the a priori probability of speciesappearing together 

I t d ti M th d R lt Di i

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

improving phylogenies

more genes? may not help

more taxa? may not help- sequence information to increase taxon sampling for other 

genes is non-existent- additional taxon sampling must improve the stability of the

classification?

I t d ti M th d R lt Di i

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

improving phylogenies

more genes? may not help

more taxa? may not help

better models? may not help- unfeasible in terms of computer time

- global parsimony still represents the boldest test of 

monophyly (Goloboff et al. 2009)

-do we really know how molecules evolve?

I t d ti M th d R lt Di i

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

improving phylogenies

more genes? may not help

more taxa? may not help

better models? may not help

I t d ti M th d R lt Di i

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

The recovery of short internodes is likely to vary even

with small perturbations of gene choice, taxon sampling

and analytical assumptions 

improving phylogenies

Introduction Methods Results Discussion

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

The recovery of short internodes is likely to vary even

with small perturbations of gene choice, taxon sampling

and analytical assumptions 

Increased taxon sampling with short

molecular sequences - does it support or 

collapse “deep” monophyly?

improving phylogenies

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

http://slidepdf.com/reader/full/increased-taxon-sampling-with-short-molecular-sequences-does-it-support-or 24/26

 

Laboratory 

Database & Analysis

Funding &Support 

Megan Milton, Brianne Hebert, Riadul

Mannan & Sujeevan Ratnasingham

Paul Hebert,

Bob Hanner, João Lima

Listed on the Canadian Centre for 

DNA Barcoding website:

www.dnabarcoding.ca

 Area de

Conservación

GuanacasteDan Janzen, Winnie Hallwachs & ACG

Parataxonomists

Study design

Acknowledgments

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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 Thank you!

Introduction Methods Results Discussion

8/6/2019 Increased taxon sampling with short molecular sequences - does it support or collapse deep monophyly in the macrolepidopteran phylogeny?

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Introduction Methods Results Discussion

Effect of gene length and gene choice

0

150

300

450

0 25 50 75

# of Taxa

Sum

ofB

ootstrap

SupportValues(

>50)

forMono p

hyleticSubfami li

es

25 50 75

# of Taxa

EF-1a

wingless

COI1 gene

2 genes

3 genes

Maximum Parsimony

Maximum LikelihoodNymphalidae