title: Empty Niches after Extinctions Increase Population Sizes of Modern Corals.
abstract: Large environmental fluctuations often cause mass extinctions, extirpating species and transforming communities [1, 2]. While the effects on community structure are evident in the fossil record, demographic consequences for populations of individual species are harder to evaluate because fossils reveal relative, but not absolute, abundances. However, genomic analyses of living species that have survived a mass extinction event offer the potential for understanding the demographic effects of such environmental fluctuations on extant species. Here, we show how environmental variation since the Pliocene has shaped demographic changes in extant corals of the genus Orbicella, major extant reef builders in the Caribbean that today are endangered. We use genomic approaches to estimate previously unknown current and past population sizes over the last 3 million years. Populations of all three Orbicella declined around 2-1 million years ago, coincident with the extinction of at least 50% of Caribbean coral species. The estimated changes in population size are consistent across the three species despite their ecological differences. Subsequently, two shallow-water specialists expanded their population sizes at least 2-fold, over a time that overlaps with the disappearance of their sister competitor species O. nancyi (the organ-pipe Orbicella). Our study suggests that populations of Orbicella species are capable of rebounding from reductions in population size under suitable conditions and that the effective population size of modern corals provides rich standing genetic variation for corals to adapt to climate change. For conservation genetics, our study suggests the need to evaluate genetic variation under appropriate demographic models.
authors.affiliation: Department of Biology, The Pennsylvania State University, 208 Mueller Lab, State College, PA 16802, USA; Smithsonian Tropical Research Institute, Smithsonian Institution, 9100 Panama City PL, Washington, DC 20521, USA. Electronic address: pradac@si.edu.
authors.forename: Carlos
authors.initials: C
authors.lastname: Prada
authors.affiliation: Department of Biology, The Pennsylvania State University, 208 Mueller Lab, State College, PA 16802, USA.
authors.forename: Bishoy
authors.initials: B
authors.lastname: Hanna
authors.affiliation: Department of Earth and Environmental Sciences, University of Iowa, 115 Trowbridge Hall, Iowa City, IA 52242, USA.
authors.forename: Ann F
authors.initials: AF
authors.lastname: Budd
authors.affiliation: CCEHBR, Hollings Marine Laboratory, NCCOS, National Ocean Service, US National Oceanic and Atmospheric Administration, 331 Fort Johnson Road, Charleston, SC 29412, USA.
authors.forename: Cheryl M
authors.initials: CM
authors.lastname: Woodley
authors.affiliation: HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: Department of Biology, The Pennsylvania State University, 208 Mueller Lab, State College, PA 16802, USA; Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Prol. Av. Niños Héroes, Puerto Morelos C.P. 77580, Q. Roo, Cancún, Mexico.
authors.forename: Roberto
authors.initials: R
authors.lastname: Iglesias-Prieto
authors.affiliation: Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, Brisbane, 4072, Queensland, Australia; School of Biological Sciences, The University of Queensland, Brisbane, 4072, Queensland, Australia.
authors.forename: John M
authors.initials: JM
authors.lastname: Pandolfi
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
authors.forename: Don
authors.initials: D
authors.lastname: Levitan
authors.affiliation: Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
authors.forename: Kenneth G
authors.initials: KG
authors.lastname: Johnson
authors.affiliation: Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10(th) and Constitution Avenue, NW Washington, DC 20560-0163, USA.
authors.forename: Nancy
authors.initials: N
authors.lastname: Knowlton
authors.affiliation: The Systems Biology Institute, Falcon Building 5F, Shirokanedai, Minato, Tokyo 108-0071, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
authors.affiliation: Department of Biology, The Pennsylvania State University, 208 Mueller Lab, State College, PA 16802, USA. Electronic address: mxd60@psu.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: DeGiorgio
authors.affiliation: Department of Biology, The Pennsylvania State University, 208 Mueller Lab, State College, PA 16802, USA; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10(th) and Constitution Avenue, NW Washington, DC 20560-0163, USA; Smithsonian Tropical Research Institute, Smithsonian Institution, 9100 Panama City PL, Washington, DC 20521, USA. Electronic address: mum55@psu.edu.
authors.forename: Mónica
authors.initials: M
authors.lastname: Medina
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000502:physiology*; D057894:Coral Reefs; D053476:Extinction, Biological; D005580:Fossils; D011158:Population Growth; D013997:Time Factors
keywords: ESA threatened; Pleistocene; Pliocene; coral reefs; empty niche; genome; niche partitioning; population expansion; sea level change