analysis of evolutionary divergences

Genes to Geoscience Research Enrichment Program 2011Mark Westoby, Ian Wright

is this relationship

due to phylogeny?

Seed mass (mg) [log scale]

0.1 1 10 100

See

d ou

tput

per

m2 c

anop

y ou

tline

101

102

103

104

105

Myrtaceae

Proteaceae

Fabaceae

Rutaceae

Other

Henery & Westoby 2001

seed output (number) per

m2 per yr

Seed mass (mg) [log scale]

0.1 1 10 100

Se

ed

ou

tpu

t p

er

m2 c

an

op

y o

utli

ne

101

102

103

104

105

it is associated with phylogeny (to some extent)- phylogenetic history and present-day

adaptation aren’t “either-or” alternative explanations

ideally, would think of evolution as a tree rather than as categories- families may be very different ages- no resolution inside families

AcmenaSyzygium

OsborniaBackhousia

EugeniaMetrosideros

Tristania

Darwinia

AngophoraCorymbia

EucalyptusMelaleucaSyncarpia

LophostemonXanthostemon

Qualea (outgroup)

merging trait data across species with phylogenetic tree

combined account of historical process through evolutionary time with present-day ecological adaptation

repeated, consistent ecological divergences vs single divergences giving rise to a pattern

main aims of the module

logic of questions that can be asked- continuing dispute about interpretations

quantification short of significance-testing- graph-types- not much emphasis on significance testing- especially, how to phrase interpretations

help with software and tools for people who have examples that need them

not about deducing trees or

reconstructing ancestral characters

other topics touched briefly

polytomies

branch lengths

scaling up to whole radiations

species selection designs

phrasing interpretations

community structure, phylogenetic overdispersion or underdispersion

provisional schedule

Mon 10th Oct 2-5 pm

lecture-type explanations

exercises in building figures and phrasing interpretations

Fri 14th Oct 9:30-12:30 am

continuing with lecture-type explanations (depending how far we get on Monday)

working through real datasets

EXERCISE A: Growth patterns of Acer (maple) species

rapid height

extension

allocation to spread rather than height

make a graph

please!(leader

growth as x)

suggest biological mechanisms that might give rise to

negative correlation between leader extension and relative lateral growth

positive correlation between leader extension and negative annual growth

it’s always a good idea to envisage possible data-patterns beforehand

and work out what they might mean

are they correlated, across present-

day species?

phylogenetic tree of 4 Acer spp

draw on the graph lines

connecting D to E and F to G

these are separate cases of evolutionary divergence

(phylogenetically independent contrasts or PICs)

PIC-stick graph

Growth patterns of Acer (maple) species

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0 10 20 30 40 50Leader growth (cm/yr)

Rel

ativ

e la

tera

l gro

wth

(as

fr

acti

on

of

lead

er g

row

th)

count the consistency: in

2/2 PICs increased

leader growth was

associated with reduced lateral growth

PIC-stick graph

8/11 PICs show the same positive relationship as across all species

Saverimuttu & Westoby 1996

Seedling survival following 95% cotyledon surgery

large-seed advantage in 14/16 PICs

no overall cross-species pattern- implies diffs

between genera and families swamp within-genus pattern

Armstrong & Westoby 93

tracing the phylo tree

Growth patterns of Acer (maple) species

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0 10 20 30 40 50Leader growth (cm/yr)

Rel

ativ

e la

tera

l gro

wth

(as

fr

acti

on

of

lead

er g

row

th)

earlier divergence

later divergences

later divergences

in summary of the acer example

one divergence was between faster and slower growing lineages (or habitats). The faster-growing lineage has more lateral spread as well as faster vertical extension

other divergences (within each sublineage) were between allocation to vertical vs lateral growth

in these 4 species one sort of divergence came before the other; but in the larger phylogeny they were more interspersed

Ackerly and Donoghue 1996

“hanging on the tree” step 1: calculate past nodes

can be done in excel

hanging on the tree step 2: new dataset of divergences

set up a new

worksheet

rows are divergences (nodes), not

species

cells are calculated as differences (=(C2-C3) from other worksheet)

usually can “fill right” to enter

formula for other variables

make a graph of divergences

divergence in terminal extension per yr

divergence in relative lateral

growth

+ve

+ve

-ve

-ve

Q1: where will the datapoints lie for divergences where

increased terminal extension is associated with narrower

lateral growth?

make a graph of divergences

divergence in terminal extension per yr

divergence in relative lateral

growth

+ve

+ve

-ve

-ve

Q2: where will the datapoints lie for divergences where

increased terminal extension is associated with wider

lateral growth?

make the graph and interpret it

1. earlier divergence where faster leader growth was positively associated with

wider spread

2. earlier divergence could also have been

here

3. later divergences where faster leader growth was associated with narrower

spread

3. later divergences where faster leader growth was associated with narrower

spread

New dataset of divergences Rows (replicates) are divergences (= nodes, radiations,

branchpoints)

Columns (variables) are divergence for a trait, rather than trait value

Q: Has divergence in trait A been consistently correlated with divergence in trait B?- considered across replicate divergence events during evolutionary

history

+, +

-,-

-, +

+, -

Divgnce in A

Divgnce in B

correlated-divergence graph

Issue is which quadrants the dots are in, not whether the cloud has a distinct axis- regression forced through (0, 0)

sometimes “folded”, all Divg(A) are +ve

Divgnce in A

Divgnce in B

marsupials (selected)

adult female

body mass (g) litter size

days between

litters

reproductive potential

yr-1

log10 adult

female body mass

log10 reproducti

ve potential

diet (1=mainly foliage,

2= mainly

animals, nectar, or fruit)

1=arboreal,

2=terrestrial

Dasyuridae Antechinus stuartii 20 6.8 365 6.80 1.30 0.83 2 2

Dasyuridae Dasyurus viverrinus 880 6 365 6.00 2.94 0.78 2 2

Myrmecobiidae Myrmecobius fasciatus 459 4 365 4.00 2.66 0.60 2 2

Phascolarctidae Phascolarctos cinereus 5100 1 383 0.95 3.71 -0.02 1 1

Vombatidae Vombatus ursinus 26000 1 730 0.50 4.41 -0.30 1 2

Potoroidae Bettongia penicillata 1300 1 102 3.58 3.11 0.55 2 2

Macropodidae Dendrolagus lumholtzii 6475 1 435 0.84 3.81 -0.08 1 1

Macropodidae Macropus agilis 11000 1 220 1.66 4.04 0.22 1 2

Macropodidae Macropus robustus 15600 1 256 1.43 4.19 0.15 1 2

Phalangeridae Wyulda squamicaudata 1675 1 365 1.00 3.22 0.00 1 2

Phalangeridae Trichosurus vulpecula 2300 1 274 1.33 3.36 0.12 1 1

Burramyidae Burramys parvus 42 3.6 365 3.60 1.62 0.56 2 2

Burramyidae Cercartetus caudatus 30 3 183 5.98 1.48 0.78 2 1

Pseudocheiridae Petauroides volans 1700 1 521 0.70 3.23 -0.15 1 1

PetauridaeGymnobelideus leadbeateri 133 1.6 183 3.19 2.12 0.50 2 1

Tarsipedidae Tarsipes rostratus 9 2.5 122 7.48 0.95 0.87 2 1

questions about marsupials

do we expect reproductive potential to be related to adult body mass? in what way?

how do we expect folivory vs omnivory to relate to body size and reproductive potential?

cross-spp graph for log reproductive potential vs log body mass

larger species have lower reproductive potential

folivores tend to be larger and to have lower reproductive potential

marsupials (…. cont)

what are some alternative phylogenetic histories by which the 3-way relationships among body size, reproductive potential and diet might have come about?

so should the correlation between body size and reproductive potential be interpreted as resulting from diet divergence?

Handout 1: Find the evol divergences between folivory and omnivory, indicate

these on the cross-species graph. Indicate also other divergences within diet

categories.

Handout 2: Divergences dataset with graph showing correlation of divergences

folivore-omnivore divergences are big contributors to –ve correlation

but other divergences also contribute, 12/15 being consistent

What about arboreal vs terrestrial? Go back to cross-species graph, draw arrows from terrestrial to arboreal

sides of divergences

divergences between arboreal and terrestrial?

mixed picture

5 terrestrial have bigger body mass at given reprod potential

but the arb-terr divergences don’t clearly run in that direction

(for categories -- not all nodes give a clean divergence)

comments from Wright on software and data sources

Ackerly 1999

Interpreting phylogeny and cross-species correlation: 3 patterns

Evol divgnce weaker than cross-spp

Evol divgnce similar to cross-spp

Evol divgnce stronger than cross-spp

Cross-species graphs

Ack

erly

& R

eich

199

9Species data Independent contrasts

1.21.00.80.60.40.20.0-0.6

-0.4

-0.2

0.0

0.2

0.4

Leaf life span (mo, log)

Leaf

siz

e (c

m2, l

og)

2101

2

3

R = -0.42

210-2

-1

0

1

2

3

R = 0.0

1.21.00.80.60.40.20.0-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

Leaf life span contrasts

Leaf

siz

e co

ntra

sts

Spe

cific

leaf

are

a (c

m2/g

, log

) Conifers

Angiosperm/conifer contrast

Angiosperms

Spe

cific

leaf

are

a co

ntra

sts

R = -0.75 R = -0.64

a

b

c

d

+, +

+, +

-, -

-, -

central question about interpretation

if the difference between folivory and omnivory were underlain by a single evolutionary divergences, would it then be wrong to say that folivores tended to be larger-bodied?

argument that it would be wrong (Ackerly 2009): “from a comparative perspective … closely related species are not statistically independent, and nonindependence enhances the probability of Type I error (rejecting a true null hypothesis)”

this quote from what is supposed to be an authoritatative review shows continuing misconception, 15 years after I thought it had been cleared up- 3-round Forum in J Ecol 1995, Westoby et al 1995a, b, c, Harvey et al

1995 a, b, Rees 1995

what’s correct about Ackerly quote?

relationship between leaf lifespan and leaf size (or folivory and body size) might arise via some third variable rather than via a direct mechanism

traits that are phylogenetically conservative and differ systematically between gymnos and angios could be candidates for third variables

what’s misleading about Ackerly quote?

you can only guarantee independence from third variables when V1 is applied randomly to replicates and V2 is the outcome- i.e. in a true controlled experiment- the only situation where probability of a given correlation arising by

chance ((type I error) can be estimated reliably

but evolution is not a controlled experiment- lineages have particular traits, these make them good at particular

ways of life, they tend to persist in those ways of life, and therefore tend to keep the same traits

- “phylogenetic niche conservatism”- evolutionary datasets are rife with cross-correlations

so you need to remember from the outset that correlation does not prove causation- and the concept of “independence” doesn’t help

phylogenetic niche conservatism: a pervasive evolutionary process

potential niches (ecol competent trait-combos) are correlated

niches are more likely to be colonized from clades already occupying nearby niches

observed trait-correlation results both from evolutionary history and from present-day ecology

process is measured by cross-species corr’n at least as well as by divergence corr’n- (Westoby et al 1995, Price 1997,

Harvey & Rambaut 2000)

Trait A

Tra

it B

underlying issue . . . Do evolutionary paths give rise to niches?

- Divergences should be items of evidence

Or do niches draw evolutionary paths towards them? - Present-day species should be items of evidence

These alternatives are not resolvable from trait patterns across present-day species- because niche and lineage have been entwined during

evolutionary history, and therefore are confounded in present-day datasets

- statistical partialling-out (as in evol divergence calculations) doesn’t solve the problem, it just arbitrarily chooses one interpretation over the other

correct view : two distinct questions

what trait-combos are successful in present day?- Species is the item of evidence --> cross-species

correlation (plus physiology and field experiments)

how has evolutionary history distributed clades into niches?- Evolutionary divergence is the item of evidence -->

correlation of divergences

asking these questions in combination is the best research style in evolution and ecology

Ackerly & Donoghue 1996

Evo

l div

erge

nce

corr

elat

ion

-1.01.00.0-1.0

-0.5

0.0

0.5

1.0

0.5-0.5

Cross-species correlation

Usually, trait-pairs are correlated both as evolutionary divergences and cross-species. But this

is worth investigating in each case, because it’s interesting where one but not the other is significant

Ackerly 1999

Ackerly 1999

Interpreting phylogeny and cross-species correlation: 3 patterns

Evol divgnce weaker than cross-spp

Evol divgnce similar to cross-spp

Evol divgnce stronger than cross-spp

Cross-species graphs

Ackerly 1999

Other cases: correlated cross-species but not (or weakly) as divergences

Evol divgnce weaker than cross-spp

Evol divgnce similar to cross-spp

Evol divgnce stronger than cross-spp

signifies the cross-species correlation has been produced by one or a few divergences, deep in the phylogenetic tree

Ackerly 1999

Evol divgnce weaker than cross-spp

Evol divgnce similar to cross-spp

Evol divgnce stronger than cross-spp

Other cases: correlated as divergences but not (or weakly) cross-species

signifies consistent divergence pattern between closely-related species

but tends to be overridden by other large differences when comparing

between genera or families

FAQ1: when related species tend to be similar, should this be attributed to phylogenetic constraint?

No. It shows phylo conservatism or phylo signal. Phylo constraint or inertia implies the trait has been under directional selection but has failed to respond. This is not proven for two reasons:- other mechanisms involving continuing stabilizing

selection (niche conservatism) produce phylo conservatism, and are known to be very common

- failure to respond to directional selection over millions of years is a VERY strong claim what sort of trait wouldn’t have selectable mutants? needs a definite proposed mechanism, should not be

invoked as an explanation that should be accepted in absence of other explanations

FAQ2: Is it obligatory to correct for effects of phylogeny?

No (when concerned with present-day function), because- tests for correlated evol divergences (phylo correction)

do NOT reliably control for all potentially confounding third variables

- phylo correction DOES remove from consideration any trait-variation that has been phylogenetically conservative, and much of that may well be concerned with present-day function also

Unfortunately it’s quite common to get mss back from journals with reviews insisting on phylo-corrected analysis.

Difficult to decide when to just give in and do it, versus when to dispute the principle.

how should one approach cross-correlated data?

what’s the difference in correlation pattern between these two pathways of causation?

V1 V

3

V2

V1 V

3

V2

cross-correlated data?

- V1-V2 corr- V1-V3 no corr- V3-V2 no corr

- V1-V2 corr- V1-V3 corr- V3-V2 corr

V1 V

3

V2

V1 V

3

V2

cross-correlated data (…cont)

what’s the difference in correlation pattern between these three pathways of causation?

V1 V

3

V2

V1 V

3

V2

V1 V

3

V2

cross-correlated data (…cont)- V1-V2 corr- V3-V2 corr- V1-V3 uncorr

- V1-V2 weak corr- V3-V2 corr- V1-V3 corr

- V1-V2 corr- V3-V2 corr- V1-V3 weak corr

V1 V

3

V2

V1 V

3

V2

V1 V

3

V2

cross-correlated data (…cont)

is there a difference in correlation pattern between these three pathways of causation?

V1 V

3

V2

V1 V

3

V2

V1 V

3

V2

cross-correlated data (…cont)

all 3 variables are correlated in each case

removing effect of V3 should:- demolish V1-V2

correlation in cases 2 and 3

- possibly (but not certainly) leave some V1-V2 correlation intact in case 1

V1 V

3

V2

V1 V

3

V2

V1 V

3

V2

partial correlations

regress V2 on V3, take residuals

correlate residuals in V2 with V1

partialling out effect of V3 should definitely remove significance from V1-V2 correlation in case 2; possibly in case 1

V1 V

3

V2

V1 V

3

V2

partial correlations suppose V2 is correlated both

with V1 and V3

our question is whether V1 or V3 is the true cause of V2 variation

suppose V1-V2 uncorrelated after partialling out effect of V3- does that mean V3 is the true

cause?

No, because V1 could equally be the true cause and V3 an incidental correlate

V1

V3

V2

?

?

phylogenetic correlations suppose seed size is correlated both with

height and genus

our question is whether height or genus is the true cause of seed size variation

suppose height and seed size are uncorrelated after partialling out effect of genus- does that mean genus is the true cause?

No, because height could equally be the true cause and genus an incidental correlate

more fundamentally, it makes no sense to treat height and genus as mutually exclusive when they have evolved together

height

genus

seed

size

?

?

phrasing interpretati

on

the following examples give some alternative phrasings for

discussion about which are good and which are not so good

1. cell size was positively correlated with genome size (phylogenetically corrected r2 = 0.74)

2. cell size was positively correlated with genome size both before (r2 = 0.76) and after (r2 = 0.74) phylogenetic correction

3. increased genome size was associated with increased cell size across 12/14 evolutionary divergences, both older and more recent. Correspondingly there was strong positive correlation (r2 = 0.76) across all present-day species

1. after correction for phylogeny, there was no significant relationship between body size and geographical range

2. There was a strong correlation across species between body size and geographical range. It arose almost entirely from the evolutionary divergence between clade A (smaller body size and geographical range) and clade B (larger body size and wider geographical range). Correlations were not significant within either clade A or clade B.

3. The correlation between body size and geographical range arose from a single evolutionary divergence. Consequently it was likely to be a chance correlation.

4. The correlation between body size and geographical range arose from a single evolutionary divergence. Consequently it may have been caused by some third variable connected to phylogeny.

1. Divergence in core temperature has been positively correlated with divergence in % muscle tissue across most evolutionary divergences within each of clades A and B, but clade B operates at lower temperature at a given % muscle tissue.

2. Core temperature and % muscle tissue showed significant positive correlation after phylogenetic correction.

3. Core temperature was only very weakly correlated with % muscle tissue across all species, but the correlation became stronger when expressed as evolutionary divergences.

Species data Independent contrasts

1.21.00.80.60.40.20.0-0.6

-0.4

-0.2

0.0

0.2

0.4

Leaf life span (mo, log)

Leaf siz

e (cm

2, lo

g)

2101

2

3

R = -0.42

210-2

-1

0

1

2

3

R = 0.0

1.21.00.80.60.40.20.0-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

Leaf life span contrasts

Leaf siz

e contrasts

Specific

le

af area (cm

2/g, lo

g)

Conifers

Angiosperm/conifer contrast

Angiosperms

Specific

le

af area contrasts

R = -0.75 R = -0.64

a

b

c

d

1. after phylogenetic correction, specific leaf area was negatively correlated with leaf lifespan (r = -0.64)

2. specific leaf area was negatively correlated with leaf lifespan both across present-day species (r = -0.75) and across the majority of evolutionary divergences (r = -0.64)

3. decreasing specific leaf area was associated with increasing leaf lifespan both at the oldest evolutionary divergence (conifers vs angiosperms) and at the majority of subsequent divergences. The outcome has been a consistent negative correlation across all present-day species (r = -0.75).

Species data Independent contrasts

1.21.00.80.60.40.20.0-0.6

-0.4

-0.2

0.0

0.2

0.4

Leaf life span (mo, log)

Le

af

siz

e (

cm

2,

log

)

2101

2

3

R = -0.42

210-2

-1

0

1

2

3

R = 0.0

1.21.00.80.60.40.20.0-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

Leaf life span contrasts

Le

af

siz

e c

on

tra

sts

Sp

ecific

le

af

are

a (

cm

2/g

, lo

g)

Conifers

Angiosperm/conifer contrast

Angiosperms

Sp

ecific

le

af

are

a c

on

tra

sts

R = -0.75 R = -0.64

a

b

c

d

1. After phylogenetic correction there was no correlation between leaf lifespan and leaf size. Consequently the tendency of conifers to have narrow evergreen leaves should not be interpreted as an ecological adaptation.

2. The cross-species tendency for long leaf lifespan to be associated with smaller leaf size arose from the divergence between conifers and angiosperms, and was not evident within either clade.

gap requirement (1 no gap, 2 small gap, 3 large gap)

log10 s

eed m

ass (

mg)

1. this data set does not support the hypothesis that large-seeded species are more likely to establish in small gaps or shade than are small-seeded species

2. species found in large gaps were more likely to have smaller seed sizes than species found in small gaps. However, within this dataset only a small number of evolutionary divergences underpinned this pattern and they did not show a consistent downshift in seed size in large gaps

3. species with seeds larger than 10 mg established in both large and small gaps, but species with seeds smaller than 10 mg established only in large gaps. In 3 of the 5 independent evolutionary divergences among these species, the large-gap species had smaller seeds

data originally from Foster SA, Janson CH (1985) The relationship between seed size and establishment conditions in tropical woody plants. Ecology 66:773-780; phylogenetic reanalysis by Kelly CK, Purvis A (1993) Seed size and establishment conditions in tropical trees. Oecologia 94:356-360

principles of good interpretation

Describe the pattern across present-day species. - quantify it, e.g. indicate strength via r2 or similar measure. - avoid implying it is causation rather than correlation.

Describe history of evolutionary divergences lying behind the pattern across present-day species- quantify strength (e.g. r2) or consistency (e.g. fraction of PICs in

same direction as cross-species pattern)- be as concrete as possible, e.g. dates of divergence

good interpretation (….2)

Discuss evidence about mechanisms- correlation does not prove causation whether also related

to phylogeny or not- phylogeny can be a guide to likely third variables- both traits a response to physical environment?

within-site vs across-site relations

- evidence from manipulative experiments?- physiological mechanism understood?

you feel confidence about mechanisms when correlative evidence and known physiological mechanism and manipulative experiments all line up together

lizard gripSpecies Body

mass (g)

Pad area

(mm2)

Clinging ability

(newtons)

Anolis sagrei 4.4 21 1.3

Anolis grahami 6.9 36 2.5

Anolis leachi 18.1 61 4.9

Hemidactylus frenatus 3 25 1

Hemidactylus turcicus 2.1 22 0.8

Gehyra oceanica 7.9 69 4.7

Gehyra mutilata 1.7 18 0.8

Gekko gecko 43.4 227 20.1

Lipinia leptosoma 1.3 9.1 0.2

Prasinohaema virens 3.1 19 0.4

Prasinohaema prehensicauda 7.1 21 0.2

Prasinohaema flavipes 23.9 53 0.8

biology of lizard clinging isometric expectations are for foot area to increase

to 2/3 power of body mass, and for clinging ability to be proportional to foot area - in which case larger lizards would fall off more easily

or does clinging ability increase in proportion to body mass? - so large species can cling on just as well as small species- and if so, is that achieved by having relatively bigger feet,

or by having more clinging power per unit foot surface?

and how do differences relate to the phylogeny?- 3 main groups, Anolis, geckos and skinks

lizard analysis 1

plot provided of log10(clinging ability) vs log10(body mass), with different symbols for 3 main groups- assess by eye whether slopes are closer to 1 or 2/3

draw lines having slopes of 1 and of 2/3 assess for each main group as well as across all species

plot log10(footpad area) vs log10(body mass)- symbols and reference lines as before

plot log10(clinging ability) vs log10(footpad area)- symbols and reference lines as before

1. in Anolis and geckos, clinging ability does increase 1:1 with body mass

2. in skinks it doesn’t (and also clinging ability is generally lower)

footpad area vs

body mass

in skinks, footpad area scales ~2/3 with body mass

in anolis and geckos, scales shallower than 1, though maybe a bit steeper than 2/3

footpad area contributes somewhat to clinging ability keeping up with body mass in anolis and geckos, but doesn’t fully explain

anolis are as clingy as geckos per footpad area; skinks less so

within anolis and geckos (but not skinks) clinginess increases somewhat faster than footpad area- the other contributor to clinging ability keeping up with body mass

calculate evolutionary divergences

as differences of log10(variable)- this is equivalent to ratio of the arithmetic quantity, thus a

divergence of 1.0 means one side of the divergence is 10-fold bigger than the other

graph divergences of clinging ability vs divergences of footpad area- put reference line of slope 1 passing through 0, 0- identify divergences as within geckos, within anolis,

between geckos and skinks, etc

except for within skinks, divergences in clinging ability were generally somewhat wider than divergences in pad area- meaning that heavier lizards have stickier footpads

and the divergences between major groups especially so

-1.00 -0.80 -0.60 -0.40 -0.20 0.00 0.20 0.40 0.60 0.80

-1.50

-1.00

-0.50

0.00

0.50

1.00

1.50

c_lg_Cling vs c_lg_padarea

geckos vs

skinksanolids vs

others

other topics touched briefly

polytomies

branch lengths

scaling up to whole radiations

species selection designs

phrasing interpretations

community structure, phylogenetic overdispersion or underdispersion

polytomies

in principle, all phylogenies are dichotomous- because species form by splitting from one other

population

but in practice, we often are not sure in exactly what sequence species separated- hence polytomies

handling of polytomies varies between applications

for measuring divergence in a single trait, use SD across however many species there are

AOT (in phylocom) splits the branches into above-the-median vs below-the-median on an ‘X’ trait- then calculates a 2-group divergence on traits Y1, Y2 etc

glm-like programs calculate a regression coefficient between the two traits across n branches- for two branches, the slope of the regression fit to them

would be divg(A)/divg(B)

Branch lengths

most mathematical theory assumes branch lengths are important: but there are issues with this at two levels

practical issues: how can we estimate branch lengths? - most models ask for branch lengths to be provided;

some provide ways of filling in estimates based on little or no data

conceptual issues: should divergences be adjusted for branch length?

concepts about branch length

adjusting for branch length has the effect of measuring the rate of evolutionary divergence rather than the amount

amount of divergence is the same, but rate is

much slower

are divergences decided by time elapsed or by destination? difference is in time since divergence,

not time needed for divergence

adjusting divergences for branch lengths

assumes trait values are still changing- present values are temporary- under directional (not convergent) selection

assumes present-day trait values are determined by past changes, as opposed to past changes being determined by the niche to which natural selection is “aiming”

in my opinion it’s at least as sensible not to adjust for branch length

scaling up to whole evolutionary radiations

Seed mass is the ecological trait with widest coverage so far- ~12,000 angiosperm spp, combining our datasets with Kew

Phylogenetic tree populated densely enough to locate evolutionary divergences fairly closely

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Allocasuarina torulosa (Casuarinaceae)

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20 divergences making largest contribution to variation across present day spp

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20 widest divergences

Moles et al (2005) A brief history of seed size

an important divergence

wide divergence between means (435-fold)

many spp on each side

big contribution to SS across all present-day spp

Arecaceae

Zingiberales

Commelinales

Poales

Provisional molec date

~95 Ma (Wikstrom et al 2001)

Correlates of seed mass divergence

In the 11 dichotomous widest divergences in seed mass, smaller seeds were associated with divergence in:

GROWTH FORM: 9 smaller, 2 same, 0 larger

DISPERSAL: 6 shift to abiotic, 4 no shift, 1 shift to biotic

LATITUDE: 7 further from equator, 3 no shift, 1 nearer equator

Most consistent pattern by far was divergence of seed mass associated with divergence of growth form- Also true in the full correlated divergence analysis across all 2223

nodes

Seed mass mapped onto phylogeny is an early specimen of a new

fusion of ecology with evolution

Old fusion was population biology- population genetics + population dynamics

survivorships and fecundities are common language

New fusion is evolutionary trees and dates + ecol trait datasets worldwide + cost-benefit evidence- explain the spread of ecological strategies across present-

day species, hand-in-hand with narrative history of radiations

species-selection design

Often you have no choice, you are working with whatever data are available. But sometimes you may be collecting fresh data, and then the question what species to work on becomes important

there is no single best design- it depends on the question- tough choices need to be faced

species selection for experiments: within-clade studies

e.g. Ackerly’s study of Acer

advantage is to have species that are fairly similar

disadvantage is that there is no way to tell whether the patterns observed within Acer generalize to other clades- unreplicated with respect to clades

traditional, but actually a poor design- better to have several clades, fewer species within each

species-pairs chosen as phylo independent contrasts (PICs) if selected for wide divergence on the “index” trait

or environment (A), gets a strong test of how A divergence correlates with B divergence, replicated across clades

however gives biased estimates of mean trait values within each clade

value of trait A

because extreme species are more likely to be chosen

phylogenetic community structure

for Genes to Geoscience masterclass on Evolutionary

Divergence AnalysisMark Westoby, Ian Wright,

October 2011

phylogeny of communities

foundation-stone review paper: Webb, C. O., D. D. Ackerly, M. A. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33:475–505.

phylocom software- manuals and downloads at http

://www.phylodiversity.net/phylocom/

very fashionable type of analysis currently

reason for being interested “As species of the same genus have

usually, though by no means invariably, some similarity in

habits and constitution, and

always in structure, the struggle will

generally be more severe between

species of the same genus, when they

come into competition with each other, than between species of

distinct genera” (Darwin 1859)

are species within communities overdispersed phylogenetically?- if species that are phylogenetically

closer are more likely to competitively exclude each other

- and if competitive exclusion is a major influence on community composition ….

species/genus ratios in communities- Elton 1946, Williams 1948 and

subsequently- new methods are essentially a

modern version of this same analysis

measurement and sig testing

indices calculated within each community- phylo distance to nearest neighbour (MNND)- mean phylo distance to all other species within

community (MPD)

significance test against 1000 random communities- species drawn from some larger pool at random with

respect to phylogeny- gives frequency distributions of “expected” MNND and

MPD

phylogenetic distance means how far back down the tree to last common ancestor

fundamental problem with MPD and MNND sig tests

two opposite processes- tendency of clades to have preferred habitat

underdispersion- competitive exclusion of phylogenetically similar

overdispersion

MPD and MNND measures are the resultant of these two opposite processes- when a measure is not significantly different from random, is

that because there is no competitive overdispersion, or because it is cancelled out by habitat-preference underdispersion?

- (when MPD or MNND shows significant overdispersion, that probably does mean something)

fundamental problems (cont)

What to take as the “source pool” of species for assembling random communities?- other plots in the same study? everything within 100 km?

rainforest flora of the Amazon? whole world biota?

the wider the range of habitats included in the source pool, the stronger will be the effect of phylogenetic underdispersion-due-to-habitat-preference in each community

summary of main points 1

evol divergence analysis IS NOT obligatory as a correction to cross-species analysis- but it’s a good thing to do asking complementary

questions to cross-species correlations- and you may find it being demanded (wrongly) by

reviewers: then you have to decide whether to just do it anyhow, or rather to explain why they are wrong

evol divergence analysis CAN BE an elegant and powerful way of looking at the history that led up to present-day species- complementary to understanding ecology across

present-day species

main points 2

Approach the history aiming to understand the actual events- graphs more than significance tests

what (and when) were the biggest divergences?

did some kinds of divergences happen before others?

how consistent were the divergences?

some key referencesAckerly DD. 1999. Comparative plant ecology and the role of phylogenetic information. In: Press MC, Scholes J., Barker MG, eds. Physiological Plant Ecology. Blackwell Science, 391-413.Ackerly D. 2009. Colloquium Papers: Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. Proceedings of the National Academy of Sciences 106: 19699-19706.Felsenstein J. 1985. Phylogenies and the comparative method. American Naturalist 125: 1-15.Harvey PH. 1996. Phylogenies for ecologists. Journal of Animal Ecology 65: 255–263.Harvey PH, Pagel MD. 1991. The Comparative Method in Evolutionary Biology (RM May and PH Harvey, Eds.). Oxford: Oxford University Press.Harvey PH, Read AF, Nee S. 1995a. Why ecologists need to be phylogenetically challenged. J. Ecol. 83: 535-536.Harvey PH, Read AF, Nee S. 1995b. Further remarks on the role of phylogeny in comparative ecology. J. Ecol. 83: 733-734.Westoby M. 1999. Generalization in functional plant ecology: the species sampling problem, plant ecology strategies schemes, and phylogeny. In: Pugnaire F, Valladares F, eds. Handbook of Functional Plant Ecology. New York: Marcel Dekker, 847-872.Westoby M. 2006. Phylogenetic ecology at world scale, a new fusion between ecology and evolution. Ecology 87: S163-S166.Westoby M, Leishman MR, Lord JM. 1995. On misinterpreting the “phylogenetic correction.” J. Ecol. 83: 531-534.Westoby M, Leishman M, Lord JM. 1995. Further remarks on phylogenetic correction. J. Ecol. 83: 727-734.Westoby M, Leishman MR, Lord JM. 1995. Issues of interpretation after relating comparative datasets to phylogeny. J. Ecol. 83: 892-893.