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Population Genomic Data Delineate Conservation Units In Mottled Ducks (Anas Fulvigula)

J. L. Peters, P. Lavretsky, Jeffrey M. DaCosta, Jeffrey M. DaCosta, Ronald R. Bielefeld, Jamie C. Feddersen, Jamie C. Feddersen, M. Sorenson
Published 2016 · Biology

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Large multi-locus data sets provide an unprecedented opportunity for detecting fine-scale population structure and identifying populations that warrant independent conservation and management. In this study, we used 3161 polymorphic loci obtained from double-digest restriction-site associated DNA sequencing (ddRAD-seq) to examine genetic differentiation between populations of mottled ducks (Anas fulvigula) and their close relative, the mallard (A. platyrhynchos). Florida (FL) and western gulf coast (WGC) mottled ducks group into discrete populations in ordination analyses and can be assigned unambiguously to their population of origin based on multi-locus genotypes. Moreover, we find limited evidence of recent admixture between populations, and the range gap separating them is a significant barrier to gene flow. We found no evidence of diversifying selection in the sample of loci we analyzed; instead, the genome-wide pattern of differentiation between mottled duck populations is consistent with historical isolation and divergence by neutral genetic drift. Thus, our results indicate that FL and WGC mottled ducks are discrete populations on separate evolutionary pathways and should be managed as independent conservation units, and perhaps recognized as distinct subspecies given observed differences in plumage and morphology. In contrast, the recently established South Atlantic coastal zone population is indistinguishable from the WGC population but shows evidence of a small amount of admixture from FL mottled ducks. Our study demonstrates a quantitative, operational approach for delineating discrete populations for conservation using ddRAD-seq data; multi-locus genotypes allow for a robust test of historical isolation and evolutionary independence on much shorter evolutionary timescales than the overly conservative standard of reciprocal monophyly in mtDNA.
This paper references
10.1016/J.TREE.2007.09.008
Adaptation from standing genetic variation.
R. Barrett (2008)
10.1371/journal.pone.0003376
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
Nathan A. Baird (2008)
THE HOWARD AND MOORE COMPLETE CHECKLIST OF THE BIRDS OF THE WORLD. 4 th EDITION VOLUME 2 (2014)
E. Dickinson (2003)
10.1642/0004-8038(2002)119[0026:DVMDOS]2.0.CO;2
DIAGNOSABILITY VERSUS MEAN DIFFERENCES OF SAGE SPARROW SUBSPECIES
M. Patten (2002)
10.1186/s13059-015-0652-y
The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver
L. Lu (2015)
The Clements Checklist of Birds of the World. By James F. Clements .:The Clements Checklist of Birds of the World
J. A. Bates (2008)
10.1086/271270
Notes Upon American Water Birds
R. Ridgway (1874)
10.1186/1471-2156-12-99
Evolution and connectivity in the world-wide migration system of the mallard: Inferences from mitochondrial DNA
R. H. Kraus (2011)
10.1111/j.1365-294X.2008.03946.x
Divergent selection and heterogeneous genomic divergence
P. Nosil (2009)
10.1016/j.tig.2012.03.009
The genomics of speciation-with-gene-flow.
J. Feder (2012)
Waterbird population estimates
S. Delany (2002)
10.1111/mec.13402
Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards
P. Lavretsky (2015)
10.1016/S0022-2836(05)80360-2
Basic local alignment search tool.
S. Altschul (1990)
10.1642/AUK-15-1.1
Subspecies and the philosophy of science
M. Patten (2015)
10.1111/j.1365-294X.2005.02553.x
Detecting the number of clusters of individuals using the software structure: a simulation study
G. Evanno (2005)
10.18637/JSS.V007.I10
zt: A Sofware Tool for Simple and Partial Mantel Tests
E. Bonnet (2002)
10.1016/j.tree.2012.05.012
Harnessing genomics for delineating conservation units.
W. Funk (2012)
10.1146/annurev-animal-022513-114217
Recent advances in primate phylogenomics.
J. Pecon-Slattery (2014)
Avian Subspecies: Summary and Prospectus
S. Haig (2010)
10.1016/S0169-5347(00)01876-0
Considering evolutionary processes in conservation biology.
Crandall (2000)
ML-RELATE: a computer program
S. Kalinowski (2006)
10.1111/eva.12149
Using genomics to characterize evolutionary potential for conservation of wild populations
K. Harrisson (2014)
Mottled duck (Anas fulvigula) movements in the Texas Chenier Plain Region
Jena A. Moon (2015)
10.1146/annurev.es.18.110187.001413
EVOLUTION OF ANIMAL MITOCHONDRIAL DNA: RELEVANCE FOR POPULATION BIOLOGY AND SYSTEMATICS
C. Moritz (1987)
Handbook of North American birds
R. S. Palmer (1962)
10.1525/auk.2013.12241
Phylogeography of the California Gnatcatcher (Polioptila californica) Using Multilocus Dna Sequences and Ecological Niche Modeling: Implications for Conservation
R. Zink (2013)
STRUCTURE: a simulation study
L. Excoffier (2011)
10.1007/s10592-013-0557-9
Interspecific hybridization contributes to high genetic diversity and apparent effective population size in an endemic population of mottled ducks (Anas fulvigula maculosa)
J. Peters (2013)
10.1016/j.tig.2010.01.001
Conservation genetics in transition to conservation genomics.
N. Ouborg (2010)
10.1046/J.1471-8286.2002.00305.X
spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels
O. Hardy (2002)
DNA (RAD) markers
J.A (2015)
leucocephalos) (Aves: Passeriformes)
T. Jombart (2010)
10.1371/journal.pgen.1003905
Robust Demographic Inference from Genomic and SNP Data
L. Excoffier (2013)
[Book review] The A.O.U. Check-list of North American Birds, 6th edition, by American Ornithologists' Union
C. Robbins (1983)
10.1642/0004-8038(2005)122[0712:R]2.0.CO;2
The Howard and Moore Complete Checklist of the Birds of the World
A. Kratter (2005)
10.5860/choice.28-6265
A Supplement To Distribution And Taxonomy Of Birds Of The World
C. Sibley (1952)
10.1642/AUK-14-184.1
Interpreting negative results with taxonomic and conservation implications: Another look at the distinctness of coastal California Gnatcatchers
J. McCormack (2015)
virus reservoir species
D.E (2009)
10.1534/genetics.108.092221
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective
M. Foll (2008)
10.1186/1471-2148-14-153
Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, northwestern Costa Rica, the skipper butterfly named Urbanus belli (family Hesperiidae) comprises three morphologically cryptic species
Claudia Bertrand (2014)
10.1007/s10592-005-4978-y
A Comparison of Hybridization between Mottled Ducks (Anas fulvigula)and Mallards (A. platyrhynchos) in Florida and South Carolina using Microsatellite DNA Analysis
C. L. Williams (2005)
The eBird/Clements Checklist of Birds of the World: Version 6.9. (Downloaded from http://www.birds.cornell.edu/clementschecklist/download/)
J. F. Clements (2014)
10.1093/molbev/msu136
PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R
B. Pfeifer (2014)
10.1111/mec.12796
Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow
Tami E Cruickshank (2014)
10.1111/J.1523-1739.2007.00685.X
Population adaptive index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation.
A. Bonin (2007)
10.1016/j.ympev.2013.08.008
Phylogenetics of a recent radiation in the mallards and allies (Aves: Anas): inferences from a genomic transect and the multispecies coalescent.
P. Lavretsky (2014)
10.1016/j.ympev.2014.10.023
Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow.
M. Harvey (2015)
10.1642/AUK-13-164.1
Rapid radiation and hybridization contribute to weak differentiation and hinder phylogenetic inferences in the New World Mallard complex (Anas spp.)
P. Lavretsky (2014)
10.1016/j.ympev.2011.10.012
Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences.
J. McCormack (2012)
10.1111/mec.12049
Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex
E. M. O'Neill (2013)
10.1111/J.1471-8286.2006.01256.X
ml‐relate: a computer program for maximum likelihood estimation of relatedness and relationship
S. Kalinowski (2006)
10.1098/rspb.2003.2617
The role of subspecies in obscuring avian biological diversity and misleading conservation policy
R. Zink (2004)
10.1650/7566
EVALUATION OF ALLOZYME AND MICROSATELLITE VARIATION IN TEXAS AND FLORIDA MOTTLED DUCKS
C. L. Williams (2005)
10.1111/j.1365-294X.2006.02890.x
INVITED REVIEW: What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity
R. Waples (2006)
10.1007/s12686-012-9622-9
Fifty-nine microsatellite markers for hybrid classification studies involving endemic Florida Mottled Duck (Anas fulvigula fulvigula) and invasive Mallards (A. platyrhynchos)
S. Seyoum (2012)
Ecology and Population Genetics of Mottled Ducks within the South Atlantic Coastal Zone
G. Weng (2006)
10.1098/rspb.2005.3425
Are subspecies useful in evolutionary and conservation biology?
A. Phillimore (2006)
10.1080/10635150252899752
Strategies to protect biological diversity and the evolutionary processes that sustain it.
C. Moritz (2002)
10.1371/journal.pone.0037135
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
Brant K. Peterson (2012)
Inference of population structure using multilocus genotype data.
J. Pritchard (2000)
10.1642/AUK-15-232.1
Willet be one species or two? A genomic view of the evolutionary history of Tringa semipalmata
Jessica A Oswald (2016)
10.1007/s10592-015-0796-z
Conservation genomics reveals multiple evolutionary units within Bell’s Vireo (Vireo bellii)
Luke B. Klicka (2015)
Rapid and cost-ef
Conserv. Genet (2007)
10.1038/ng.2657
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species
Y. Huang (2013)
10.1111/j.1365-294X.2008.03737.x
Mitochondrial DNA under siege in avian phylogeography
R. Zink (2008)
10.1525/OM.2010.67.1.172
Chapter 14: Avian Subspecies: Summary and Prospectus
S. Haig (2010)
10.1016/B978-0-12-398760-0.50026-2
PHYLOGENETIC RELATIONSHIPS OF MITOCHONDRIAL DNA UNDER VARIOUS DEMOGRAPHIC MODELS OF SPECIATION
J. Neigel (1986)
10.1111/mec.13314
Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation
L. Campagna (2015)
10.1098/rspb.2012.0813
Genomic consequences of multiple speciation processes in a stick insect
P. Nosil (2012)
10.5860/choice.190117
Ducks, Geese, and Swans of North America
G. Baldassarre (2014)
10.1002/JWMG.734
Movements and seasonal use of habitats by rural and urban female mottled ducks in southeast Florida
Dana M. Varner (2014)
10.1111/j.1558-5646.1995.tb02308.x
INFERRING PHYLOGENIES FROM mtDNA VARIATION: MITOCHONDRIAL‐GENE TREES VERSUS NUCLEAR‐GENE TREES
W. Moore (1995)
Conservation genetics of snowy plovers
W. C. 977–993. Funk (2007)
Avian subspecies: summary and prospectus. Ornithol
S. M. Haig (2010)
10.1093/NAR/GKH340
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
R. Edgar (2004)
10.1038/nature07331
Genes mirror geography within Europe
J. Novembre (2008)
10.1046/J.1523-1739.1999.98193.X
The importance of systematic biology in defining units of conservation
W. W. Dimmick (1999)
10.1046/J.1523-1739.1997.96109.X
Critique of the evolutionarily significant unit as a definition for distinct population segments und
David S. Pennock (1997)
10.1098/rstb.2011.0263
Genomic divergence during speciation: causes and consequences
P. Nosil (2012)
10.1111/j.1365-294X.2005.02827.x
Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax)
K. E. Omland (2006)
World Mallard complex (Anas spp.)
P. Lavretsky (2014)
2006.What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity
R. Waples (2006)
10.1111/j.1558-5646.2008.00372.x
Multilocus Phylogeography of a Holarctic Duck: Colonization of North America from Eurasia by Gadwall (Anas strepera)
J. L. Peters (2008)
10.1186/gb-2010-11-6-r68
Molecular evolution of genes in avian genomes
K. Nam (2010)
10.1016/J.BIOCON.2014.03.010
Evidence for two subspecies of Gunnison’s prairie dogs (Cynomys gunnisoni), and the general importance of the subspecies concept
Loren C. Sackett (2014)
10.1642/AUK-13-246.1
Genetic and morphometric diversity in the Lark Sparrow (Chondestes grammacus) suggest discontinuous clinal variation across major breeding regions associated with previously characterized subspecies
J. D. Ross (2014)
Harnessing genomics
W.C (2012)
10.1007/s10592-006-9278-7
Conservation genetics of snowy plovers (Charadrius alexandrinus) in the Western Hemisphere: population genetic structure and delineation of subspecies
W. Funk (2006)
10.1371/journal.pone.0106713
Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol
Jeffrey M. DaCosta (2014)
10.1038/nature03030
A physical map of the chicken genome
J. Wallis (2004)
10.1101/GR.5681207
Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.
M. R. Miller (2007)
10.1371/journal.pgen.1000862
Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
Paul A Hohenlohe (2010)
10.1111/mec.12769
Parallel signatures of selection in temporally isolated lineages of pink salmon
L. Seeb (2014)
10.1023/A:1011858312115
Molecular population genetics, phylogeography, and conservation biology of the mottled duck (Anas fulvigula)
K. McCracken (2004)
10.1007/s12686-011-9548-7
STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method
D. Earl (2011)
10.1017/S0016672300033620
Estimators for pairwise relatedness and individual inbreeding coefficients
K. Ritland (1996)
10.1016/0169-5347(94)90057-4
Defining 'Evolutionarily Significant Units' for conservation.
C. Moritz (1994)
10.1186/1471-2164-15-275
Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti
G. Rašić (2013)
10.1007/S12686-011-9548-7
The interplay between habitat availability and population differentiation
Y. Verkuil (2012)
10.1098/rstb.2011.0197
Genome-wide patterns of divergence during speciation: the lake whitefish case study
S. Renaut (2012)
Taxonomic considerations
E. Smith (2006)
Conservation genomics reveals multiple
L. B. 576–579. Klicka (2016)
10.1093/bioinformatics/btr124
Fastsimcoal: a Continuous-time Coalescent Simulator of Genomic Diversity under Arbitrarily Complex Evolutionary Scenarios
L. Excoffier (2011)
10.1525/OM.2010.67.1.6
Chapter 1: Subspecies Represent Geographically Partitioned Variation, A Gold Mine of Evolutionary Biology, and a Challenge for Conservation
K. Winker (2010)
10.1534/genetics.116.196493
Molecular Population Genetics
S. Casillas (2017)
10.1111/J.1095-8312.2009.01282.X
Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes)
D. Irwin (2009)
10.1111/J.1523-1739.2006.00530.X
Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act.
Susan M. Haig (2006)
10.1111/evo.12209
GENETIC DIVERGENCE ALONG THE SPECIATION CONTINUUM: THE TRANSITION FROM HOST RACE TO SPECIES IN RHAGOLETIS (DIPTERA: TEPHRITIDAE)
T. H. Powell (2013)
10.1093/bioinformatics/btq461
Search and clustering orders of magnitude faster than BLAST
R. Edgar (2010)
10.1186/1471-2156-11-94
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
T. Jombart (2010)



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10.1111/mec.15343
Assessing changes in genomic divergence following a century of human‐mediated secondary contact among wild and captive‐bred ducks
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10.1650/CONDOR-17-18.1
Hybridization between Mottled Ducks (Anas fulvigula maculosa) and Mallards (A. platyrhynchos) in the western Gulf Coast region
R. Ford (2017)
10.1007/s12686-019-01082-2
Improving our conservation genetic toolkit: ddRAD-seq for SNPs in snow leopards
S. Janjua (2019)
10.1002/ece3.5538
Old divergence and restricted gene flow between torrent duck (Merganetta armata) subspecies in the Central and Southern Andes
Luis Alza (2019)
10.1038/s41437-020-0315-y
Phylogeography of the iconic Australian red-tailed black-cockatoo (Calyptorhynchus banksii) and implications for its conservation
Kyle M. Ewart (2020)
10.1002/ece3.4981
Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America
P. Lavretsky (2019)
10.1111/eva.12569
Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation
S. Flanagan (2018)
10.1111/mec.15091
ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America
P. Lavretsky (2019)
10.1017/S0959270918000205
Birds of different feather flock together - genetic structure of Taiga Bean Goose in Central Scandinavia
A. D. Jong (2019)
10.1007/13836_2020_76
Population Genomics Provides Key Insights into Admixture, Speciation, and Evolution of Closely Related Ducks of the Mallard Complex
P. Lavretsky (2020)
10.1007/s10592-018-1079-2
Considering evolutionary processes in cycad conservation: identification of evolutionarily significant units within Dioon sonorense (Zamiaceae) in northwestern Mexico
José Said Gutiérrez-Ortega (2018)
10.1007/978-3-030-16477-5_8
Population Genomics and Phylogeography
Jente Ottenburghs (2019)
10.1071/WR18170
Evaluating the use of risk assessment frameworks in the identification of population units for biodiversity conservation
Erin Liddell (2020)
10.1002/jwmg.21951
Variation in Survival and Harvest Rates in Florida Mottled Duck
Ronald R. Bielefeld (2020)
10.1007/s10592-020-01256-8
Population differentiation and historical demography of the threatened snowy plover Charadrius nivosus (Cassin, 1858)
Josephine D’Urban Jackson (2020)
10.1101/2020.11.14.383240
Inherent population structure determines the importance of filtering parameters for reduced representation sequencing analyses
D. Selechnik (2020)
Unearthing the Past and Present of a Semi-fossorial Lizard: Conservation Genetics, Phylogeography, and Taxonomy of Plestiodon egregius
Kathryn Mercier (2020)
10.1111/1755-0998.13082
Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species
Kyle M. Ewart (2019)
10.1093/BIOLINNEAN/BLZ050
Conservation genomics of range disjunction in a global biodiversity hotspot: a case study of Banksia biterax (Proteaceae) in southwestern Australia
D. Bradbury (2019)
10.1007/13836_2018_56
Landscape Genomics for Wildlife Research
B. Forester (2018)
10.1186/s12864-018-4615-z
New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)
J. M. Doyle (2018)
10.1007/978-3-030-16477-5_10
The Contribution of Genomics to Bird Conservation
Loren Cassin-Sackett (2019)
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