title: Inferences of population structure and demographic history for Taxodium distichum, a coniferous tree in North America, based on amplicon sequencing analysis.
abstract: OBJECTIVE
  Studies of natural genetic variation can elucidate the genetic basis of phenotypic variation and the past population structure of species. Our study species, Taxodium distichum, is a unique conifer that inhabits the flood plains and swamps of North America. Morphological and ecological differences in two varieties, T. distichum var. distichum (bald cypress) and T. distichum var. imbricarium (pond cypress), are well known, but little is known about the level of genetic differentiation between the varieties and the demographic history of local populations.
  
  
  METHODS
  We analyzed nucleotide polymorphisms at 47 nuclear loci from 96 individuals collected from the Mississippi River Alluvial Valley (MRAV), and Gulf Coastal populations in Texas, Louisiana, and Florida using high-throughput DNA sequencing. Standard population genetic statistics were calculated, and demographic parameters were estimated using a composite-likelihood approach.
  
  
  RESULTS
  Taxodium distichum in North America can be divided into at least three genetic groups, bald cypress in the MRAV and Texas, bald cypress in Florida, and pond cypress in Florida. The levels of genetic differentiation among the groups were low but significant. Several loci showed the signatures of positive selection, which might be responsible for local adaptation or varietal differentiation.
  
  
  CONCLUSIONS
  Bald cypress was genetically differentiated into two geographical groups, and the boundary was located between the MRAV and Florida. This differentiation could be explained by population expansion from east to west. Despite the overlap of the two varieties' ranges, they were genetically differentiated in Florida. The estimated demographic parameters suggested that pond cypress split from bald cypress during the late Miocene.
authors.affiliation: Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
authors.forename: Yuka
authors.initials: Y
authors.lastname: Ikezaki
authors.affiliation: Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan.
authors.forename: Yoshihisa
authors.initials: Y
authors.lastname: Suyama
authors.affiliation: Wetland and Aquatic Research Center, U.S. Geological Survey, Lafayette, Louisiana 70506 USA.
authors.forename: Beth A
authors.initials: BA
authors.lastname: Middleton
authors.affiliation: Faculty of Life & Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Tsumura
authors.affiliation: Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
authors.forename: Kousuke
authors.initials: K
authors.lastname: Teshima
authors.affiliation: Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
authors.forename: Hidenori
authors.initials: H
authors.lastname: Tachida
authors.affiliation: Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan jkusumi@scs.kyushu-u.ac.jp.
authors.forename: Junko
authors.initials: J
authors.lastname: Kusumi
mesh_terms: D003710:Demography; D005431:Florida; D014644:Genetic Variation; D005843:Geography; D059014:High-Throughput Nucleotide Sequencing; D016013:Likelihood Functions; D008145:Louisiana; D008922:Mississippi; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D032489:Taxodium / Q000235:genetics* / Q000502:physiology; D013781:Texas; D014197:Trees
keywords: Cupressaceae; Taxodium distichum; amplicon sequencing; genetic differentiation