Inferences of population structure and demographic history for Taxodium Distichum, a coniferous tree in North America, based on Amplicon sequencing analysis

Yuka Ikezaki, Yoshihisa Suyama, Beth A. Middleton, Yoshihiko Tsumura, Kosuke Teshima, Hidenori Tachida, Junko Kusumi

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

PREMISE OF THE STUDY: 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. KEY 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.

Original languageEnglish
Pages (from-to)1937-1949
Number of pages13
JournalAmerican Journal of Botany
Volume103
Issue number11
DOIs
Publication statusPublished - Nov 1 2016

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Taxodium
Taxodium distichum
demographic history
North America
coniferous tree
population structure
demographic statistics
pond
Demography
valley
genetic differentiation
Cupressus
history
Mississippi River
Mississippi
river
Population
Rivers
valleys
local adaptation

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Plant Science

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Inferences of population structure and demographic history for Taxodium Distichum, a coniferous tree in North America, based on Amplicon sequencing analysis. / Ikezaki, Yuka; Suyama, Yoshihisa; Middleton, Beth A.; Tsumura, Yoshihiko; Teshima, Kosuke; Tachida, Hidenori; Kusumi, Junko.

In: American Journal of Botany, Vol. 103, No. 11, 01.11.2016, p. 1937-1949.

Research output: Contribution to journalArticle

Ikezaki, Yuka ; Suyama, Yoshihisa ; Middleton, Beth A. ; Tsumura, Yoshihiko ; Teshima, Kosuke ; Tachida, Hidenori ; Kusumi, Junko. / Inferences of population structure and demographic history for Taxodium Distichum, a coniferous tree in North America, based on Amplicon sequencing analysis. In: American Journal of Botany. 2016 ; Vol. 103, No. 11. pp. 1937-1949.
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abstract = "PREMISE OF THE STUDY: 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. KEY 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.",
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AU - Tsumura, Yoshihiko

AU - Teshima, Kosuke

AU - Tachida, Hidenori

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