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3/26/17
Biogeography expands:
• Phylogeography (done)
PhyloEcoBiogeography:
Biome Relationships
Jeannine Cavender-Bares et al. 2009
• PhyloEcoBiogeography
PhyloEcoBiogeography:
Biome Relationships
Phylogenetics can
inform ecological
processes at many scales
PhyloEcoBiogeography:
Biome Relationships
Examined speciation events
within Southern Hemisphere
continental biome types
Examined speciation events
within Southern Hemisphere
continental biome types
1. Most speciation events of trees
(and herbs) occur within same
biome type OR between similar
biome types
2. Most transoceanic
colonizations occur within same
biome type
3. Niche conservatism NOT
adaptive radiation is seen in S.
Hemisphere diversification
Michael Crisp et al. (2009) Nature
Michael Crisp et al. (2009) Nature
Only 356 shifts occurred in
10,800 speciation events
within same biome
between two biomes
1
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PhyloEcoBiogeography:
Biome Relationships
• Most species are of recent
origin
• Speciation events involve
daughter species in similar
communities in similar
geographical area
— niche conservatism
Examined phylogenetic and
biogeographical relationships
within Seasonally Dry Tropical
Forests
Toby Pennington et al.
(2009) Ann Rev Ecol Syst
Toby Pennington et al.
(2009) Ann Rev Ecol Syst
Chronogram of legume tribe
PhyloEcoBiogeography:
Biome Relationships
PhyloEcoBiogeography:
Evolution of Niche
• Climatic niche evolution in California Clarkia
• Strong correlation of
geographic distance and
phylogenetic distance!
• Do related species share similar
climatic/elevation niches? (niche
conservatism)
• Do related species show significant
disparity in climatic/elevation niches?
(adaptive radiation)
Toby Pennington et al.
(2009) Ann Rev Ecol Syst
Mantel test
2
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PhyloEcoBiogeography:
Evolution of Niche
Chronogram of 35 diploid Clarkia species
C. breweri
C. concinna
10mya
PhyloEcoBiogeography:
Evolution of Niche
Mean annual temp
Mean temp coldest
quarter
Mean diurnal temp
range
Annual precipitation
• Temperature and elevation
variables show more disparity
among close relatives in
speciation - adaptive radiation
Isothermality
Precipitation wettest
month
Temperature
seasonality
Precipitation driest
month
Max temp warmest
month
Precipitation
seasonality
Min temp coldest
month
Precipitation wettest
quarter
Temp annual range
Precipitation driest
quarter
Mean temp wettest
quarter
Precipitation warmest
quarter
Mean temp driest
quarter
Precipitation coldest
quarter
Mean temp warmest
quarter
Elevation
• Precipitation shows
phylogenetic conservatism –
close species are more similar
in precipitation niche
Downloaded from
from rstb.royalsocietypublishing.org
rstb.royalsocietypublishing.org on
on October
October 22,
22, 2010
2010
Downloaded
(a)
(a)
pre-warming
pre-warming
• Temperature shows significant
disparity through time < 5mya
- adaptive radiation
others, which
which has
has been
been shown
shown to
to result
result in
in ecological
ecological
others,
mismatches that
that can
can have
have negative
negative fitness
fitness conseconsemismatches
quences (Stenseth
(Stenseth &
& Mysterud
Mysterud 2002;
2002; Stenseth
Stenseth et
et al.
al.
quences
2002; Visser
Visser &
& Both
Both 2005;
2005; Both
Both et
et al.
al. 2006).
2006). Under
Under
2002;
these circumstances,
circumstances, not
not only
only is
is the
the inclusion
inclusion of
of phylophylothese
geny an
an important
important analytical
analytical tool
tool for
for more
more properly
properly
geny
assessing statistical
statistical trait
trait correlations,
correlations, but
but itit is
is vital
vital for
for
assessing
understanding the
the pattern
pattern of
of differential
differential species’
species’
understanding
response to
to climate
climate change.
change.
response
Willis et
et al.
al. (2008,
(2008, 2009)
2009) recently
recently demonstrated
demonstrated the
the
Willis
value of
of applying
applying aa phylogenetic
phylogenetic approach
approach to
to examine
examine
value
the impacts
impacts of
of climate
climate change
change using
using aa long-term
long-term
the
phenological dataset
dataset from
from Concord,
Concord, MA
MA (USA)
(USA) that
that
phenological
was initiated
initiated by
by the
the naturalist
naturalist and
and conservationist
conservationist
was
Henry David
David Thoreau
Thoreau (Miller-Rushing
(Miller-Rushing &
& Primack
Primack
Henry
2008;
Primack
et
al.
2009).
They
analysed
these
floris2008; Primack et al. 2009). They analysed these floristic data
data using
using statistical
statistical methods
methods that
that incorporate
incorporate
tic
phylogenetic history
history and
and discovered
discovered that
that clades
clades that
that
phylogenetic
have been
been less
less able
able to
to respond
respond to
to climate
climate change
change by
by
have
adjusting
their
flowering
time
have
significantly
adjusting their flowering time have significantly
declined in
in abundance.
abundance. These
These results
results can
can help
help predict
predict
declined
which species
species face
face aa greater
greater risk
risk of
of regional
regional extinction
extinction
which
as climate
climate change
change is
is exacerbated.
exacerbated. For
For example,
example, they
they
as
indicate that
that we
we should
should be
be particularly
particularly concerned
concerned
indicate
about the
the continued
continued regional
regional loss
loss of
of species
species in
in the
the
about
Liliaceae and
and Orchidaceae
Orchidaceae clades,
clades, but
but perhaps
perhaps less
less so
so
Liliaceae
of species
species in
in the
the Brassicaceae
Brassicaceae and
and Fabaceae.
Fabaceae. The
The
of
latter
two
clades
contain
species
that
have
been
far
latter two clades contain species that have been far
better able
able to
to adjust
adjust their
their phenology
phenology to
to climate
climate
better
change, and
and contain
contain fewer
fewer species
species that
that have
have declined
declined
change,
in abundance.
abundance. However,
However, the
the extent
extent to
to which
which these
these
in
regional results
results are
are more
more broadly
broadly applicable
applicable to
to other
other
regional
geographically disjunct
disjunct plant
plant communities,
communities, or
or to
to other
other
geographically
groups of
of species
species in
in the
the Tree
Tree of
of Life,
Life, remains
remains unexaunexagroups
mined. In
In particular,
particular, do
do closely
closely related
related species
species in
in
mined.
different geographical
geographical regions,
regions, and
and in
in different
different parts
parts
different
of the
the Tree
Tree of
of Life,
Life, share
share similar
similar phenological
phenological responses
responses
of
to climate
climate change?
change? And
And is
is phenological
phenological response
response simisimito
larly associated
associated with
with changes
changes in
in species’
species’ abundance?
abundance?
larly
To address
address these
these questions,
questions, we
we extend
extend the
the approach
approach
To
of Willis
Willis et
et al.
al. (2008)
(2008) to
to test
test for
for similar
similar trends
trends in
in plant
plant
of
and bird
bird communities
communities in
in the
the United
United States
States and
and the
the
and
UK. First,
First, we
we compare
compare the
the phylogenetic
phylogenetic distribution
distribution
UK.
of phenological
phenological response
response traits
traits between
between the
the geographicgeographicof
ally disjunct
disjunct temperate
temperate plant
plant communities
communities of
of Concord,
Concord,
ally
USA and
and Chinnor,
Chinnor, UK.
UK. Second,
Second, we
we examine
examine how
how
USA
phenological response
response traits
traits contribute
contribute to
to the
the phylogephylogephenological
netic pattern
pattern of
of non-native
non-native plant
plant species’
species’ success
success
netic
within each
each of
of these
these communities.
communities. And
And third,
third, we
we test
test
within
for the
the influence
influence of
of climate
climate change
change on
on the
the pattern
pattern of
of
for
Consequences of global warming? do all
species have ability to track climate
change to their species niche?
• if different lineages of plants and
animals have different adaptations to
temperature . . .
(b)
(b)
post-warming
post-warming
mean
mean temperature
temperature
• Precipitation shows no
significant disparity through
time - phylogenetic
conservatism
PhyloEcoBiogeography:
is especially
especially relevant
relevant because
because climate
climate change
change has
has
is
Climate
Change
greatly altered
altered
the phenology
phenology of
of some
some species
species but
but not
not
greatly
the
mean
mean temperature
temperature
PhyloEcoBiogeography:
Evolution of Niche
3202 C.
C. C.
C. Davis
Davis et
et al.
al. Phylogeny
Phylogeny and
and phenology
phenology
3202
extinct
extinct
• then there may be clade specific
extinction with global warming
Davis et al. 2010 – Importance of phylogeny to
the study of phenological response to global
climate change
Figure 1.
1. Phylogenetic
Phylogenetic bias
bias in
in the
the pattern
pattern of
of species
species decline
decline
Figure
owing to
to climate
climate change.
change. A
A hypothetical
hypothetical phylogeny
phylogeny of
of organorganowing
isms is
is depicted
depicted during
during prepre- and
and post-warming
post-warming intervals.
intervals. The
The
isms
red vertical
vertical bars
bars over
over each
each species
species represent
represent aa climatically
climatically relrelred
evant trait
trait that
that is
is linked
linked to
to species
species success
success (e.g.
(e.g. ‘species
‘species
evant
thermal tolerance’).
tolerance’). This
This trait
trait exhibits
exhibits phylogenetic
phylogenetic
thermal
signal—i.e. closely
closely related
related species
species share
share similar
similar thermal
thermal toltolsignal—i.e.
erances. An
An environmental
environmental temperature
temperature regime,
regime, mean
mean
erances.
annual temperature,
temperature, is
is depicted
depicted by
by the
the yellow
yellow shading
shading in
in
annual
the background.
background. Following
Following warming,
warming, some
some clades
clades of
of species
species
the
remain within
within their
their thermal
thermal tolerance
tolerance range,
range, whereas
whereas other
other
remain
clades are
are now
now well
well outside
outside their
their range
range and
and become
become locally
locally
clades
extirpated. This
This results
results in
in aa phylogenetically
phylogenetically biased
biased pattern
pattern
extirpated.
of species
species loss
loss (i.e.
(i.e. phylogenetic
phylogenetic selectivity).
selectivity).
of
3
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PhyloEcoBiogeography:
Climate Change
PhyloEcoBiogeography:
Climate Change
wild geranium
Consequences of global warming? do all
species have ability to track climate
change to their species niche?
Downloaded from rstb.royalsocietypublishing.org on October 22, 2010
• used flowering phenology (& migratory
bird arrival) data from Thoreau’s Woods
in Concord, MA from 1851-2010
3206 C. C. Davis et al. Phylogeny and phenology
(a)
Chinnor, UK
2
Orchidaceae
1
Araili-/Apiaceae
e.g. Daucus 22
Dipsacales p.p.
e.g. Ranunculus
e.g. Campanulaa
e.g. Acer, Aseculus
3
2
e.g. Arabidopsis, Brassica
22
Asterales 18
4
19
e.g. Campanula,
Circisum
Thoreau Woods
1851 - 2010
4 Brassicaceae
20
Asteralaceae p.p. 19
e.g. Solidago
red-eyed vireo
3 Sapindaceae
1
e.g. Scabiosa, Vallerianella 21
Camanulaceae
e.g. Ophrys
Ranunculaceae p.p.
5 Onagraceae
5
e.g. Oenothera, Epilobium
6 Rosaceae p.p.
e.g. Prunus, Pyrus
6
18
7 Rosaceae p.p.
e.g. Geum, Rosa
7
8
8 Betulaceae
e.g. Betula,
Corylus
17 species from the Concord flora depicting changes in abundance
Fig. 1. Composite phylogeny of 429 flowering plant
from
1900 to 2007. Change in abundance
9
ranged on an integer scale from Boraginaceae
!5 to "4, and
17 was calculated as the difference in abundance for each taxon in 1900 and 2007 based on 7 abundance categories
Myosotis
9 Fabaceae
(0 to 6; see Materials and Methods).e.g.Branch
color indicates
parsimony
character
state
reconstruction
of
change
in
abundance.
For simplicity, we have indicated
16
e.g. Lotus, Trifolium
this reconstruction by using 4 colors: Rubiaceae
red (major
16 decline, !5 to !3),
14 pink (moderate decline, !2), gray (little to no change, !1 to "1), and blue (increase, "2 to
10
e.g. Galium
Chinnor
versus
Concord
"4). For the complete character reconstruction
and taxon
for all internal
nodes
as the
mean
15 labels see Fig. S1. Average decline in abundance was calculated (c)
13 ascertained from 10
change in abundance of descendant nodes weighted with branch length information
divergence
time estimates. An average decline
of 2.5 Time
or Tracking
Euphorbiaceae
Rel. Flowering
e.g.using
Euphorbia
Plantaginaceace
p.p.50%
15 or greater, based on our most conservative scoring
greater corresponds to a decline in
abundance of
6 abundance categories (0 to 5; see0Materials
0.5
1.0
1.5
11
e.g. Veronica
in Methods). Clades exhibiting these major declines are indicated with black dots. Each of the most inclusive clades exhibiting these declines are
indicated in pink
Chinnor/
Lamiales 14
12
Concord
and referenced numerically to their clade
name.Verbascum
Subclades in major decline that are nested within more widely recognized clades are labeled
with the more
e.g. Mentha,
11 Saxifragales p.p.
Rubiaceae/
familiar name followed by pro parte (p.p.). These clades include some of the most charismatic
wildflower
as anemones and
e.g. Ribes,
Saxifraga species in New England, such
Rubiaceae
Caryophyllaceae
p.p. bedstraws and bluets (Rubiaceae p.p.), bladderworts
buttercups (Ranunculaceae p.p.), asters, campanulas, goldenrods, pussytoes, and12thistles
(Asterales),
Rosaceae p.p. (Prunus, Malus/Sorbus)/
e.g. Stellaria
(Lentibulariaceae), dogwoods (Cornaceae), lilies (Liliales), louseworts and Indian paintbrushes
(Orobanchaceae), mints (Lamiaceae
p.p.), orchids
(Orchidaceae),
Rosaceae p.p. (Prunus,
Amelanchier)
13 Caryophyllales
Rosaceae
p.p. (Geum,
Rosa)/
primroses (Onograceae p.p.), roses (Rosaceae p.p.), saxifrages (Saxifragales), Indian pipes
(Ericales
violets
(Malpighiales).
e.g. Silene,
Rumexp.p.), and St. John’s worts and
***
PhyloEcoBiogeography:
Climate Change
Rosaceae p.p. (Rosa, Potentilla)
Ranunculaceae p.p. (Ranuculus)/
Ranunculaceae p.p. (Ranunculus)
Ranunculaceae (Clematis, Ranuculus)/
Ranunculaceae e.g. Ranunculus
3
Ranuculaceae (Clematis, Ranuculus)
e.g. Anemone, Aquilegia
Asparagales p.p. 18
Papaveraceae
Onagraceae/
e.g. Iris, Maianthemum
e.g. Corydalis
Onagraceae
Onagraceae
4
Lamiales/
2
e.g.
Epilobium
3
18
Lamiales
1
4
Fabaceae p.p. (Trifolium)/
Fabaceae p.p. (Trifolium)
Campanulaceae/
Campanulaceae
Asteraceae p.p. 17
phylogenetic
conservatism
and trait correlations with change in abundanceAsteraceae p.p. (Senecio, Solidago)/
e.g. Solidago
17
Asteraceae p.p. (Senecio, Solidago)
Trait
correlation
5
Apiales/
5 Fabaceae p.p.
Phylogenetic
Apiaceae
e.g. Desmodium
(b)
2
Concord, USA
Results and Discussion
Our results (Fig. 1 and Table 1) indicate that change in
abundance and f lowering-time response traits were phylogenetically conserved, which indicates that species evolutionary
history is important to understanding community response to
Table 1. Statistical tests of
1
• strong
phylogenetic
signalare
climate change. Species that
are declining
in abundance
more closely related than
by chance.
Similarly,
forexpected
which families
of plants
species that exhibit similar f lowering-time responses to temtracked or could not track
perature are more closely related than expected by chance. In
warmer springs
contrast, latitudinal range increasingly
was not phylogenetically
conserved
Campanulacae
conservatism
16
e.g. Campanula,
Lobelia
15
15
Flowering time tracking of seasonal temperature
Apiaceae
Shift in flowering time 1850–1900 e.g.
Daucus
Shift in flowering time 1900–2006
Shift in flowering time 1850–2006
Mean latitudinal range
Lamiales 14
Change in abundance 1900–2006
e.g. Mentha,
Verbascum
n
175
319
303
271
14
414
429
Model 1
Observed rank
19
2
2,120
340
3,705
1
13
**
***
—
†
12
***
Consequences of global warming? do all
species have ability to track climate
change to their species niche?
Ranunculaceae p.p.
n
175
319
303
271
414
—
Model 2
6
Estimate
7
!0.48
!0.02
0.04
0.04
9
!0.10
—
6 Fabaceae p.p.
n
Estimate
e.g. Trifolium, Vicia
7 Rosaceae p.p.
*
166
!0.62
*
e.g. Prunus, Spiraea
*** 8 311
!0.01
*
8
Rosaceae p.p.
***
296
0.03
***
e.g. Rosa
***
253
0.03
***
9 Sapindales,
***
362
!0.08
***
Malvales
— e.g. Hibiscus,
— Toxicodendron
—
—
*
***
trackers
16
Trait
PhyloEcoBiogeography:
Climate Change
Model 3
non-trackers
Chinnor
n
140
140
140
140
140
—
honeysuckle
• invasive species were more responsive
to tracking and even shifting their
flowering phenology
Concord
Estimate
difference between
!1.00community
*** average
*0.03
* * significant
***
* marginally significant
0.02
***
—
—
!0.09
***
—
—
10
Tests used a phylogeny with branch lengths adjusted for time. The significance of phylogenetic
conservatism was tested by comparing the rank of the observed
11
standard deviation (SD) of descendent trait meansRubiaceae
to a null13
model based on 9,999 random iterations of trait distributions across the composite phylogeny. The
10 Cornaceae
observed rank is compared with a 2-tail test
significance,
a P value of 0.05. Trait correlations were tested by using the
e.g.of
Galium,
Cephalntus i.e., an observed rank of 250
11 equals
e.g. Cornus
comparative methods of generalized estimating equations (GEE). Estimates12describe the Primulaceae
direction and magnitude of the correlation (e.g., a negative estimate
Ericaceae
e.g. Lysimachia
#!0.1$ of mean latitude with change in abundance suggests that species
from more
southerly
latitudes are increasing in abundance). Model 1 (univariate model),
e.g. Rhododendron,
Vaccinium
correlation of change in abundance with each trait; Model 2 (multivariate model), correlation of change in abundance with each trait and habitat, abundance
2. Composite status
phylogenies
of 167Model
and 323
flowering plant
species
fromof
(a)
Chinnor,
UK and with
(b) Concord,
USA. Red
(ca. 1900), flowering season, Figure
and native/introduced
as covariates;
3 (multivariate
model),
correlation
change
in abundance
all traits and
habitat, abundance (ca. 1900),
flowering
season,
and native/introduced
status
as covariates
(shift inresponsive
flowering-time
response
1850 –2006
was on
excluded
due to to track
and
blue dots
at nodes
represent less and
more
phenologically
clades,
respectively,
based
their ability
its high correlation with the their
other flowering
flowering-time
†, Ptemperature
% 0.1; *, P % 0.05;
0.01; ***, P % 0.001;
n % sample
size.clades that have demonstrated a
timesshift
to traits).
seasonal
variation.
Solid-coloured
dots indicate
those
**, P %
significant tracking response. A null distribution of mean flowering time tracking for each node in the phylogeny was generated
by 9999 randomizations (‘node.mn’ in PHYLOCOM). Observed clade values that ranked less than or equal to 250 (p ! 0.05)
Willis et al.
indicated significantly strong trackers while values that ranked greater than or equal to 9750 (p ! 0.05) indicated significantly
weak trackers. Open dots indicate marginally significant tracking clades (p ! 0.10). Each of the clades exhibiting these tracking
responses is further highlighted in pink and blue and referenced numerically to its clade name. Subclades of interest are
labelled with the more familiar, and more inclusive, clade to which they belong followed by pro parte (p.p.). See the electronic
supplementary material, figure S1 for full taxon labels. Bar graphs (c) depict phylogenetically corrected mean differences
between tracking and non-tracking clades between Chinnor and Concord. These results are normalized against the community
17030 ! www.pnas.org"cgi"doi"10.1073"pnas.0806446105
4