Download Oaks: a ‘worst case scenario for the biological species

Who am I this time?
The affinities and [mis]behaviors of
Hill’s oak (Quercus ellipsoidalis)
Andrew Hipp
Jaime Weber
Alka Srivastava
The Morton Arboretum
Oaks: a ‘worst case scenario for the biological
species concept’1
1Jerry
Coyne and H. Allen Orr
“Hybridization and introgression in Quercus alba
James W. Hardin (1975) J. Arnold Arboretum 56: 336–363
Distribution of cytoplasmic haplotypes by species
Dumolin-Lapegue et al. (1997) Evolution 53: 1406-1413
Gonzalez-Rodriguez, A. et al. (2004) Morphological and RAPD analysis of hybridization between Quercus affinis and Q. laurina ,
two Mexican red oaks. American Journal of Botany 91:401-409.
Quercus petraea – Sessile oak
source: www.habitas.org.uk/flora/
Quercus robur – Pedunculate oak
Source: http://www.bomengids.nl/
“Species status of hybridizing oaks”
Muir et al. (2000) Nature 405:1016
Scotti-Saintagne et al. (2004) Genetics 168: 1615–1626.
A potent issue in the Great Lakes region is whether the endemic Hill’s oak (Q.
A second issue is how and to what extent these species are mixed up with black
ellipsoidalis) and the Appalachian scarlet oak (Q. coccinea) represent two biological
oak (Q. velutina).
entities or just endpoints on a morphological continuum.
Q. ellipsoidalis
Q. velutina
Q. coccinea
Genetic (AFLP) data have
previously been used to
demonstrate that scarlet oak
is cleanly separated from Hill’s
oak and black oak, which are
themselves largely
distinguishable from one
another, but less cleanly
separated.
NMDS on a Jaccard’s
pairwise distance matrix, AFLP
data.
Final stress = 30.40305
Final instability = 0.01349
Number of iterations = 100 R2 =
0.216 (axis 1) + 0.287 (axis 2) =
0.503.
MCMC clustering (STRUCTURE),
admixture model, allele freq’s
correlated, flat prior on id’s.
Q. coccinea
Q. ellipsoidalis
Hipp and Weber (2008) Syst. Bot. 33: 148–158.
Q. velutina
Sampling for the current study:
851 individuals from six species – black
oak, Hill’s oak, scarlet oak, pin oak, red
oak, and Shumard’s oak – from 58 sites,
including 803 individuals from the three
focal species and 24 from red oak.
Questions driving this study
General questions (the ones biologists all have):
• How does the ecological and morphological coherence we
observe in oak species persist in the face of introgression?
• What do oak species look like when we tease apart shared
ancestry and ongoing gene flow?
Particulars (questions that keep at least some IOS members
awake at night, but probably not all biologists):
• What are the genetic disjunctions among Hill’s oak, scarlet
oak, and black oak?
• What are the evolutionary (phylogenetic) relationships among
black oak members of eastern North America?
• What is the pattern of hybridization / local gene flow among
Hill’s oak, scarlet oak, and black oak?
The New World black
oak group (Quercus
section Lobatae) has
proven particularly
challenging in previous
molecular work, and at
the outset of our study,
it wasn’t at all clear
that we would be able
to distinguish species
from one another.
Aldrich et al. (2003) Can J. For Res 33: 2228–2237
AFLP Methods:
1. Double digestion with
MseI and EcoRI
2. Adapter ligation
3. Amplification with
unlabelled 1-base
selective primers
4. Amplification with 3-base
selective primers, one of
which is fluorescently
labelled
5. Product is run out on ABI
sequencers (capillary or
slab) with internal lane
standard
For this project we screened
128 primer pairs and
selected one.
Each individual is scored as having (1) or not having (0) an allele at
each position; that is, as having or not having a band of a particular
size.
Polyacrilimide gel showing AFLP
banding patterns for two primer
pairs (blue and yellow) with an
internal lane standard (red)
What kind of data do you get out of this process?
Each ID indicates a single individual sampled in the field.
Each number indicates the size of a genetic marker, an AFLP band
that indicates the presence (1) or absence (0) of a specific gene copy
at a specific region of the genome.
50
52
55
57
58
59
62
63
64
65
vel2406
1
1
1
1
0
0
0
1
1
1
rub2407
1
1
1
1
0
0
0
1
1
1
vel2416
1
1
1
1
0
1
0
1
1
1
vel2418
1
0
1
1
0
1
0
1
1
1
ell2422
1
1
1
1
0
0
0
1
1
1
ell2424
1
1
1
1
0
0
0
1
1
1
eXr2426
1
1
1
1
0
0
1
1
1
1
ell2431
1
1
1
1
0
0
0
1
1
1
ell2438
1
1
1
1
1
0
0
1
1
1
ell2439
1
1
1
1
0
0
0
1
1
1
ell2442
1
1
1
1
0
0
0
1
1
1
rub2447
1
1
1
1
0
0
0
1
0
1
eXv2450
1
1
1
1
0
0
0
1
1
1
These data are good for estimating genetic
distances between individuals
vel2406
vel2418
ell2422
ell2424
ell2431
ell2438
ell2439
ell2442
eXv2450
Interspecific D = 0.0503 ± 0.0011
Intraspecific D = 0.0476 ± 0.0021
vel2406
0.0000
vel2418
0.0485
0.0000
ell2422
0.0514
0.0467
0.0000
ell2424
0.0493
0.0474
0.0385
0.0000
ell2431
0.0517
0.0471
0.0389
0.0478
0.0000
ell2438
0.0455
0.0559
0.0527
0.0539
0.0657
0.0000
ell2439
0.0575
0.0489
0.0489
0.0305
0.0589
0.0457
0.0000
ell2442
0.0474
0.0544
0.0428
0.0462
0.0460
0.0548
0.0415
0.0000
eXv2450
0.0635
0.0646
0.0401
0.0465
0.0522
0.0458
0.0449
0.0508
0.0000
Methods
•
•
•
•
Plants were collected from the three target
species (Q. coccinea, Q. ellipsoidalis, Q. velutina)
from populations throughout the Great Lakes
region, along with examplars of co-occurring,
related species (Q. palustris, Q. rubra, Q.
shumardii).
Individuals were classified to species using
morphological and genetic methods and
assigned to populations based on locality.
AFLP data were collected for all individuals.
Analyses:
a. Ordination, ME trees, Bayesian clustering
approach, and linear regression used to
visualize patterns
b. Permutation tests used to test the significance
of gene flow relative to a null model of no
gene flow.
Scarlet oak: Quercus coccinea
Scarlet oak, Chemung Co., NY
Black oak, Chemung Co., NY
Black oak, Taltree Arboretum
Black oak, Taltree Arboretum
Hill’s oak, Taltree Arboretum
Black oak, Quercus velutina
Hill’s oak, Quercus ellipsoidalis
Finding 1:
As we throw more data
at the problem, it
becomes clear that
Q. coccinea and
Q. ellipsoidalis are sister
species, and
populations of each
species form discrete
clusters.
Minimum evolution (ME) tree of
populations based on pairwise
distance matrix of AFLP data
(Nei’s unbiased D for populations)
Dataset:
259 AFLPs (2 primer pairs)
718 ind’ls in 81 populations
80% genetic threshold
Minimum evolution (ME) tree of
populations based on pairwise
distance matrix of AFLP data (Jaccard’s
distance); nonparametric bootstraps
above branches
Dataset:
2228 AFLPs (10 primer pairs)
This sister species relationship
between Hill’s oak and scarlet oak
is satisfying given the difficulty of
distinguishing the two species in
the northeastern Illinois /
northwestern Indiana area.
Quercus coccinea is limited to
perhaps a single site in the region
(Tinley Creek FP, Cook Co., IL).
This result is also satisfying in light of
the variety in acorn morphology of
Q. ellipsoidalis, which is almost
dazzling.
“Though the extremes under which
the acorns of Quercus ellipsoidalis
occur pass into one another so that
the recognition of forms based on
them is scarcely more than a
convenient way of ensuring their
reference to this alliance, the fruit of
a given tree is fairly uniform.... So far
as I know, each of the fruit forms
may be expected wherever the
species occurs.”
William Trelease, 1919
In a recent issue of the International Oak Journal,
Dave Shepherd has published a long-overdue
reinvestigation of morphological variation in
Quercus ellipsoidalis and Q. coccinea. One of the
many observations in this study is the
morphological similarity between certain Q.
coccinea populations of northeastern North
America and Q. ellipsoidalis of the Great Lakes
region.
Shepard (2009) International Oak Journal 20 [Figure 4, Discriminate functions analysis].
Our findings on the relationships among populations
within the species are consistent with Shepard’s
morphological work, demonstrating a close genetic
similarity between Q. ellipsoidalis and the Q. coccinea
populations we sampled in New York state. It is still
striking how broad the genetic disjuncture between
these taxa is.
Scarlet oak
Black oak
Nonmetric multidimensional scaling (NMDS)
ordination of populations based on pairwise
distance matrix of AFLP data (Nei’s unbiased D
for populations)
Dataset:
259 AFLPs (2 primer pairs)
728 ind’ls in 75 populations
65% genetic threshold
Hill’s oak
Finding 2:
Analyzed at the individual (rather than population) level, the species separate out
pretty cleanly, though with some remarkable misclassifications between black oak and
Hill’s oak – i.e., incongruence between our identifications based on morphology and
the population assignments based on genetic data. The incorporation of genes from
one species into another is the definition of genetic introgression, and the presence of
such individuals supports the hypothesis of gene flow between the two species.
Finding 3:
Of the three species, Quercus ellipsoidalis exhibits the greatest genetic variance
(among-population). This might be a sampling bias – we sampled more Q.
ellipsoidalis than other species – but our geographic range in Q. coccinea and Q.
velutina was greater than in Q. ellipsoidalis, so the potential to detect regional
genetic variants in those species was also good.
NW IN
Michigan
We can correlate spatial data – pairwise geographic distances – with genetic data
– pairwise genetic distances – to investigate whether this genetic variance has a
geographic pattern.
If there a positive correlation between geographic distance and genetic distance
within a species, then we can conclude that genetic variance is spatially
autocorrelated: populations that are near one another are also genetically similar,
due either to gene flow or geographic dispersal patterns.
We can also use spatial data to investigate whether sympatric species share
alleles. We can detect localized gene flow between species either by comparing
genetic similarity among paired populations of the focal species…
… or by correlating pairwise geographic distances with pairwise genetic distances
on among-species (rather than within-species) comparisons. A significant positive
correlation tells us that the species are or were recently sharing genes locally.
Finding 4:
There appears to be
allele sharing (gene
flow) between Q.
ellipsoidalis and Q.
velutina in the upper
Great Lakes region,
where the two occur in
sympatry. The effect
persists even when
only individuals with
95% assignment to one
species are include in
analysis.
However, this effect is
not very strong and
bears further study.
Pin oak – Q. palustris
Hill’s oak – Q. ellipsoidalis
Red oak – Q. rubra
Black oak – Q. velutina
Scarlet oak – Q. coccinea
Jensen 1977. Taxon 26: 399—407.
Conclusions
1. Hill’s oak and scarlet oak are sister species, and their morphological
similarity is therefore a consequence of shared ancestry, not
convergence or gene flow. Variance in the morphology of both
species, such that they overlap morphologically, may be reflected in
their population genetic structure. However, the strong genetic
disjuncture between the two is consistent with recognition at the
species level.
2. Within Hill’s oak, there is substantial geographically-structured
genetic variation that is not present in the other two species.
3. There appears to be local allele-sharing as well as introgression
between Hill’s oak and black oak; however, the effect is not strong
and bears further study.
Upshot: Oak species—even the worst of them—are genetically cohesive
even in the face of ongoing local gene flow, and the nuclear genome
bears the stamps of both phylogeny and introgression.
Jaime Weber, Research Assistant
Q. velutina 2521
Q. ellipsoidalis 2528
Q. ellipsoidalis 2532
Q. velutina 2544
Alka Srivastava, Volunteer
Jason Sturner, Herbarium Assistant
Acknowledgements
Selected collaborators on this project: Jeannine Cavender-Bares, Paul Manos,
Anton Reznicek.
Field and Lab assistance: J. Sturner, K. Feldheim, E. Sackett-Hermann, L.
Anderson, D. Bassett, G. Fewless, M. Bowles, R. Ewert, A. Gapinski, J. Hitz, C.
Kirschbaum, D. Ladd, J. Mendelson, M. Nee, B. Olker, J. Wibbenmeyer, J.
Yunger, the Forest Preserve Districts of Cook, Lake, DuPage Counties, Illinois,
Albany Pine Bush Preserve, Indiana DNR, and numerous others.
Funding: The Morton Arboretum, Michigan Botanical Club, and
The American Philosophical Society.
And thank you!