Evolution of ecological communities - Barcodes to...
Transcript of Evolution of ecological communities - Barcodes to...
Evolution of ecological communities
through the lens of an island
chronosequence
NSF Dimensions of Biodiversity
Rosemary Gillespie, Henrik Krehenwinkel, Andy RomingerJun Ying Lim, Kari Goodman, Dan Gruner, John Harte
University of California, Berkeley, USA nature.berkeley.edu/evolab
nature.berkeley.edu/hawaiidimensions
Evolution of ecological communities through
the lens of an island chronosequence
Henrik
Krehenwinkel
Andy Rominger, Henrik Krehenwinkel, Dan Gruner, Jun Ying
Lim, Kari Goodman, Ellie Armstrong, Gordon Bennett, Michael
Brewer, Darko Cotoras, Curtis Ewing, Diana Percy, Patrick
O’Grady, Don Price, George Roderick, Kerry Shaw
Microevolution Macroevolution
Fit
nes
s
Fitn
ess
Biodiversity Dynamics
Evolution Ecology
Fit
nes
s
Biodiversity dynamics
Fit
nes
s
Processes occur over different scales, so how to assess dynamics?
Island chronosequence
5.1 my
2.6-3.7 my
0.7-1.8 my
0-0.4 my
Neontological &
paleontological data
Fritz et al 2013. Diversity in time and space... TREE 28, 509-516
Species diversity through time
extant lineages (blue line)
Extant & extinct
lineages (brown line)
Circles - true & reconstructed trait value
for the most recent common ancestor
brown - extant & extinct lineages.
blue- extant lineages only
Dynamics of trait evolution
Geographic space Environmental space
Tim
e
Environmental factor 1
Species shifts from orange to
blue environment that appears
only after T1
Temporal dynamics in niche interactions
5 million years ago
Kauai
Niihau
Nihoa
Necker
1 million years ago
KauaiNiihau
Oahu
Maui Nui
2.5 million years ago
Kauai
Niihau
Nihoa
Oahu
Chronosequence
5 million years ago
Kauai
Niihau
Nihoa
Necker
0.5 million years ago
Kauai
NiihauOahu
Maui Nui
Hawaii
PresentKauai
Niihau
OahuMaui Nui
Hawaii
2.5 million years ago
Kauai
Niihau
Nihoa
Oahu
1 million years ago
KauaiNiihau
Oahu
Maui Nui
Can read chrono-sequence
as a fossil record to look
at: • Dynamics of trait evolution
• Species diversity through
time
• Temporal dynamics in niche
interactions.
Island chronosequence
1. Microevolution 2 macroevolution
1. Evolutionary dynamics over time
•Repetition of evolutionary process
2. Species diversity through time
•How communities come together
over time
3. Ecological interactions
•Measurement of ecological metrics
(space for time)
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
1. Micro- to macro-evolution
• the early stages
Youngest island …..
Carson et al. 1990 PNAS 87, pp. 7055-7057,
Dynamics on
Hawaii Island
as the “crucible
of evolution”
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Forest
habitat
specialist
Habitat fragmentation clearly limits gene flow
Vandergast et al. 2004. Mol Ecol 13: 1729-1743
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Photograph by J.D. Griggs
Isolation separates populations
Fusion injects diversity
Balance between isolation & time
How does this play out over time?
2. Evolutionary dynamics
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
brown - extant & extinct lineages.
blue- extant lineages only
5.1 my
2.6-3.7 my
0.7-1.8 my
0-0.4 my
Progression rule
Evolutionary Dynamics
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Hormiga, Arnedo & Gillespie 2003.
Systematic Biology 52: 70-88
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
M. kanakana Kauai
M. anguliventris Kauai
M. discreta Kauai
M. cavata Necker
M. nigrofrenata Kauai
M. anguliventris Hawaii
M. naevigera Hawaii
M. kanakana Hawaii
M. cavata Hawaii
M. nigrofrenata Hawaii
M. facunda Hawaii
M. anguliventris Maui
M. naevigera Maui
M. kanakana Maui
M. discreta Molokai
M. arida MauiM. sp Maui
M. hiatus Maui
M. anguliventris Oahu
M. naevigera Oahu
M. kanakana Oahu
M. rufithorax Oahu
M. imbricataOahu
M. spinosa Oahu
M. perkinsi Oahu
M. edita Oahu
Diversification
early in radiation• Adaptive
• Populations diverge
in allopatry
Garb & Gillespie, 2009.
Molecular Ecology
Radiation of long-jawed spiders, Tetragnatha, in Hawaii
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Based on mtDNA, minisatellites, & allozymes …..
Independent evolution of ecomorphs
KauaiOahuMaui NuiHawaii
….. general progression down island chain
Gillespie 2004, Science; Pons & Gillespie
2004. J. Mol Evolution 59: 632-641
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Rhomphaea metaltissima
A. huinakolu Kauai
A. kahili Kauai
A. uwepa Oahu
A. makue Oahu
A. sp (white) Oahu
A. melekalikimaka Maui
A. sp (black) MolokaiA. sp (gold) Molokai
A. sp Molokai(like mele- kalikimaka)
A. poele Molokai
A. laau MauiA. alepe Maui
A. corniger Maui
A. waikula Hawaii
A. hiwa Hawaii
Spintharus flavidus
Ariamnes attenuata
Argyrodes trigonum
Repeated evolution
Evolution of
“ecomorphs”
Gene-tree (mt
COI &
nuclear EF1
seqs); output
by Beast.
Posterior
probabilities
above nodes
Gold – under leaves
White –
on lichen
Brown – bark/ rock
2. Evolutionary dynamics
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
brown - extant & extinct lineages.
blue- extant lineages only
“Onset” of diversification
in a given lineage is reset
on each island
Ariamnes spiders
Therefore, we know that:
• Taxa differ in
• The interplay between ecological &
genetic shifts during diversification
• …. Can now look at patterns of
diversity over time; whole
communities1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
3. Species Diversity
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
extant lineages (blue line)
Extant & extinct
lineages (brown line)
0
1
2
3
4
5
6
7
8
Hawaii Maui Nui Oahu Kauai
Mecaphesa
0
0.5
1
1.5
2
2.5
3
3.5
4
Hawaii Maui Nui Oahu Kauai
Orsonwelles
No
. sp
ecie
s/ a
rea
Youngest -- Island age -- Oldest Youngest -- Island age -- Oldest
Insights from chronosequence
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
0
1
2
3
4
5
6
7
8
Hawaii Maui Nui Oahu Kauai
Mecaphesa
0
0.5
1
1.5
2
2.5
3
3.5
4
Hawaii Maui Nui Oahu Kauai
Orsonwelles
0
0.5
1
1.5
2
2.5
3
3.5
4
4.5
Hawaii Maui Nui Oahu Kauai
Ariamnes
0
0.5
1
1.5
2
2.5
3
Hawaii Maui Nui Oahu Kauai
Tetragnatha – spiny leg clade
No
. sp
ecie
s/ a
rea
No.
spec
ies/
are
a
Youngest -- Island age -- Oldest Youngest -- Island age -- Oldest
Insights from chronosequence
R2 = 0.8238
R2 = 0.8088
R2 = 0.9951
R2 = 0.9575
R2 = 0.9641
R2 = 0.996
R2 = 0.8403
R2 = 0.96
R2 = 0.9917
0
0.005
0.01
0.015
0.02
0.025
0 1 2 3 4 5 6
Island Age
No
. sp
ecie
s/ a
rea
Gillespie & Baldwin 2009
No
. S
pec
ies/
Are
a
Island Age (My)
Insights from chronosequence
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Chronosequence
extant lineages (blue line)
Extant & extinct
lineages (brown line)
Species diversity over time
Therefore, we know that:
• Taxa differ in
• The interplay between ecological &
genetic shifts during diversification
• Rate of accumulation of species
• Patterns of diversity over time
• Highlights how different groups perceive
the chronosequence
• …. and ecological theory can give us
a guide as to what’s novel
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
4. Ecological Interactions• Measurement of ecological metrics
• Space for time
Geographic space Environmental space
Tim
e
Environmental factor 1
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Species (*) shifts from
orange to blue environment
that appears only after T1
Different environmental
conditions (colors)
Harte (2011) Oxford University Press.
Maximum Entropy Theory of Ecology
EnergyIndividualsSpecies
• Community-wide genetic
divergence across space,
environment and time
(chronosequence)
• Testing novel theory
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Deviation from predictions
on youngest substrates
may indicate that
community has not yet
reached steady state
Fitting species abundance data to METE predictions
Rominger et al. 2015 Global Ecology and Biogeography
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Interaction Networks
Modularity - degree to which species interact in semi-
autonomous modules
Nestedness - degree of asymmetry in interaction between
specialists and generalists Rominger et al. 2015 Global Ecology and Biogeography
• Modularity increases, likely
due to coevolution
• Nestedness decreases with site
age. Perhaps due to high
immigration of new species with
high probabilities to eat / be
eaten by generalist species
already present
More
….s
pec
iali
zati
on …
Les
s
De
gre
e
11
0
●
●
● ●
Age (mya)
No
rma
lize
d d
eg
ree
0.001 0.010 0.100 1.000
0.1
● Cosmopolitans
Endemics
Top panels show that networks deviate most from MaxEnt on youngest
and oldest sites. Deviation on Koh is not different than expected by
chance. Koh shows minimal modularity, and maximal connectance.
Bottom panel shows number of links for island endemics versus island
cosmopolitans. Endemics show lower linkage overall, but significantly
increase on the middle aged site Hal. Koh shows increased linkage
overall. When looking at links to plant genera this pattern holds except that
endemics on Hal no long show a difference in generality, indicating that
the pattern is driven in part by plant diversity.
Kilauea Kohala Maui Kauai
Lin
kag
e
Rominger et al. 2015 Global Ecology and Biogeography
• ecological theory can give us a guide as to what’s novel
Networks deviate most from METE predictions on youngest & oldest sites
ecol
specialization Incomplete
assembly
Lin
kag
e
Bennett & O’Grady
2012 Mol. Phylo. Evol.
Across the chronosequence we’ve found:
• Different arthropod groups perceive, colonize and diverge
across evolving landscapes differently
• Results in different patterns of species accumulation over
time
• Deviation from statistical steady state varies across groups
and substrate ages.
• Interaction of ecological & evolutionary strategies,
isolation & mixing, likely interact to produce patterns
1. Micro-macro evolution 2. Evolutionary dynamics 3.Species diversity 4. Ecological interactions
Biodiversity Dynamics Across a Chronosequence
Looking at sites of similar elevation,
precipitation; all in Metrosideros
forest and accessible in reserves
Research Underway ……
Intensive ecological sampling
Biodiversity Dynamics Across a Chronosequence
Metagenomics across the chronosequence
Changes in Community
Structure & Dynamics• Rapid identification of taxa & cryptic
diversity
• Relative abundances
• Using metabarcoding of whole predators to
identify
• prey-predator interactions
• food plants of herbivores
Changes in Evolutionary Dynamics• Genetic structure of all lineages in the
ecosystem
• Which factors drive divergence of lineages
Henrik Krehenwinkel
Zhou et al 2013. Ultra-deep sequencing enables high fidelity recovery of biodiversity
for bulk arthropod samples without PCR amplification. GigaScience 2: 4.
Pinol, J. et a. 2013. A progmatic approach to the analysis of diets of generalist
predators …. Mol Ecol Resources 14: 18-26
Kozich et al. 2012 Applied & Environmental Microbiology
Metagenomics across the chronosequence
• 16s based taxon identification
• Molecular community studies
• Also functional genomic studies
• Initially on 454, now on MiSeq or
HiSeq
• ITS in fungi
• COI in animals
• MiSeq protocol developed for
microbiome sequencing
• Applicable to any other PCR fragment; ~
400 microbiome samples /run;
sequencing right after PCR
Cost-effective mass-multiplexing
Gibson, J. et al. 2014 Simultaneous assessment of the macrobiome & microbiome in a
bulk sample of tropical arthropods. PNAS 111: 8007–8012
Ji, Y. Et al. 2013. Reliable, verifiable, and efficient … Ecology Letters 16:1245-1257
Yu, DW et al. Biodiversity soup ..2012. Methods in Ecology & Evolution 3: 613-623
Leray, M. & Knowlton, N. 2014. DNA barcoding & metabarcoding …. PNAS
nature.berkeley.edu/hawaiidimensions
Visualization by Thorsten Andresen, Nils Sparwasser, S Reiniger & R Meisner; data from DLR, NGDC, GLCF & USGS
Mahalo! Thank you!