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1/19/2016
Population Structure: An Evolutionary Perspective
Genomics and Speciation: The New World
Mallard Complex
• Need to consider sampling schemes when studying population
structure of wild populations
• Do sampling schemes capture the “true” evolutionary relationships?
• Better conservation and management practices by
understanding evolutionary drivers along with a landscape
genomics approach
• What are the explaining mechanisms (selection, gene flow, genetic drift)
behind contemporary population structure?
• Causes of morphological and genetic discordance
Philip Lavretsky
• Recent divergence (ILS) vs. hybridization (gene flow)
• Differentiating between historical vs. contemporary gene flow to
understand the effects of introgression
A Genomics Approach Towards the NW Clade’s
Evolutionary History and Population Structure
History of the Study System
•
Monochromats endemic to North America and largely allopatric
(Johnsgard 1978)
•
Dichromatic Mallard has a Holarctic distribution with little to no
nuclear differentiation across this range (Kraus et al. 2013)
•
• Sampled 166 samples (22–43 per taxon)
Once found west of the Mississippi River, environmental degradation (Livezey
1991; Green 1996; Johnson and Sorenson 1999; Mank et al. 2004) and release programs (Heusmann 1974; Soutiere
1986; Hepp et al. 1988) caused an expansion of the Mallard’s range in the 1960s across
North America
Lavretsky et al. 2014. The Auk
•
Increased interspecific competition and hybridization with mallards
caused concern over extinction via introgressive hybridization for
monochromats
• However, genetic studies have largely been inconclusive in:
• Genetically identifying hybrids
• Unable to distinguish between zero and moderate gene flow
What is the cause of this apparent morpho-genetic discord?
Methods
•
Obtain pseudo-random genomic sampling  ddRAD
sequencing
• Sequences were de-multiplexed by barcode, quality-filtered, and
assembled using a pipeline following DaCosta and Sorenson (2014, Plos
ONE)
 3,026 Autosomal and 198 Z-linked markers
Population Structure
• Overall pair-wise ΦST and absolute divergence (i.e., dXY; Nei and Li
1979 estimated in R package, PopGenome (Pfeifer et al. 2014)
• Visualizing Population structure:
• Principal component analysis (PCA) in R (i.e., “prcomp”) program
• ADMIXTURE (Alexander et al. 2009; Alexander and Lange 2011)
• NeighborNet phylogenetic tree based on concatenating unphased data
as implemented in SplitsTree4 program (Huson and Bryant 2006)
• Testing between positive/diversifying and purifying/balancing
selection in BayeScan v. 2.1
(Foll and Gaggiotti 2008)
• Z-linked markers were manually aligned by comparing mallard and
chicken positions using Narcisse Release 2.3.2-duck-20100216Beta
(Courcelle et al. 2008)
Lavretsky. in prep. Evolution
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1/19/2016
Autosomes vs Z Sex Chromosome
Population Structure
• Supports divergence with gene
flow scenario where selection is
stronger then gene flow (Cruickshank
Lavretsky et al. 2015a.Mol. Eco.
and Hahn 2014)
Lavretsky. in prep. Evolution
• Consistent with positive selection
within mallards
• Ducks fit 3/4ths expectations: (Lavretsky et al. 2015a & b. Mol. Eco)
•
•
•
Seasonal monogamy + long term pair bonds = expected NE(z): NE(Aut) = 0.75
forced extra-pair copulation by males = expected NE(z): NE (Aut) > 0.75
elevated female mortality during nesting = expected NE(z): NE(Aut) < 0.75
3-5% of Z-linked versus <1% of autosomal markers putatively under positive selection
 The whole Z chromosome is at a later stage of divergence (Lavretsky et al. 2015a. Mol. Eco.)
Selection is playing an important role in the divergence of the Z sex chromosome
(Lavretsky
et al. 2015a. Mol. Eco.)
Lavretsky. in prep. Evolution
Population Structure
A Picture is Forming: Speciation via Sex Chromosome
SplitsTree
• Monochromats and mallards = Incipient Forms
• Autosomal divergence = Genetic drift
Nucleotide Diversity
• Diagnosability
thousands of loci (small frequency differences)
Autosomal requires
Z-Chromosome
Mallard ( > 10 million)
0.0061
0.0030
American Black Duck
0.0062
0.0025
(~400,000)
• Largely0.0061
distinguishes
between dichromatic and monochromatic taxa
Mexican Duck
0.0026
• Z sex chromosome = Positive Selection in Mallards
•
(~50,000)
WGC Mottled Duck
•
(~110-165,000)
FL Mottled Duck (~ 35-
Region of importance has been noted in other sister pairs (Dhami et al. 2015)
0.0059
0.0021
Post-zygotic isolation via Haldane’s Rule
0.0057
0.0021
55,000)
• Genetic similarity due to ancestry not gene flow
Star-like nuDNA = Rapid Radiation
• Mallard-like traits (i.e., green in head, black in rump) are vestigial
characteristics from the mallard
•
•
•
Black duck breeding experiments were unable to breed out mallard traits even with
selecting for “pure” mallard parents for 3 generations (Kirby et al 2004; pers. comm. Heusmann)
Mexican ducks had varying degrees of mallard traits yet none were genetically
identified as hybrid
First year Hawaiian duck males display mallard traits that are lost as adults
Lavretsky. in prep. Evolution
Is hybridization a serious concern? ---- Perhaps not as
big as onceBlack
thought,
BUT…
Duck
Duck
Duck
X
Duck
Mallard
Duck
If divergence is proceeding in a few genes/regions, then I
hypothesize that backcrossing can reestablish “purity” in only
a couple generations
Duck
ABDU
MALL
Duck
X
Duck
Black Duck
Duck
Simulations in scaup suggest that hybrid ancestry can
be essentially lost after 4 generations of backcrossing
(>F5) (Lavretsky et al. 2015b. Mol. Eco)
Duck
Black Duck
Duck
Does it matter where the genetic diversity that is already
present in the species comes from if there are no
outbreeding effects?
• Funding:
Acknowledgements
• National Science Foundation (NSF DEB-0926162)
• Ducks Unlimited Richard H. G. Bonnycastle Fellowship in Wetland and Waterfowl
Biology
• American Museum of Natural History
• Ohio Waterfowl Association Graduate fellowship
• Wright State University
• U.C. Davis Museum of Wildlife and Fish Biology
• Wright State University
• University of Miami Florida
• Miami University of Ohio and Project Dragonfly
• Samples:
• USFWS Flyway Wing Bee (Ken Richkus)
• Ruben Del Castillo, Todd Scott and Wingshooters Lodge-Mexico, Mexico
• Eduardo Carrera & DU-Mexico
• Patricio Gaudiano
• Blanca E. Hernández-Baños
• John Eadie and Andy Engilis Jr. at the UC-Davis Museum of Wildlife and Fish Biology
• Kevin McCracken
• Graeme Cumming
• Leo Joseph
• Burke Museum, Bell Museum, Museum of the North
• Evangeline Shank, Michaela Woods, Jonathan Bowers, & Brittany Bowers
• Bio-informatics
• Jeffrey M. DaCosta & Michael D. Sorenson, Boston University
• Kevin Hawkins Wright State University
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