Genetic Diversity and Phylogeography in a Tasmanian Rainforest Vonifer (Lagarostrobos franklinii (Hook f.) Quinn Podocarpaceae

coalescence;nucleotide diversity;genetic diversity;Huon pine;RAPDs;chloroplast nucleotide diversity

Clark, Catherine M. ; Ronald Sederoff, Committee Co-Chair,Thomas R. Wentworth, Committee Co-Chair,Bruce S. Weir, Committee Member,Henry Amerson, Committee Member,Clark, Catherine M. ; Ronald Sederoff ; Committee Co-Chair ; Thomas R. Wentworth ; Committee Co-Chair ; Bruce S. Weir ; Committee Member ; Henry Amerson ; Committee Member

University:North Carolina State University

关键词: coalescence;    nucleotide diversity;    genetic diversity;    Huon pine;    RAPDs;    chloroplast nucleotide diversity;   

Others  :  https://repository.lib.ncsu.edu/bitstream/handle/1840.16/5054/etd.pdf?sequence=1&isAllowed=y

美国|英语

来源: null

【 摘 要 】

Genetic variation in Huon pine (Lagarostrobos franklinii), a Tasmanian rainforest conifer, was estimated using several marker systems and two spatial scales. Genealogy based methods were used to infer population history of eight Huon pine stands based on chloroplast DNA variation. Chloroplast nucleotide diversity (pi) was low (0.00093) in a multilocus haplotype generated by three universal chloroplast primers (trnS-trnT, trnD-trnT, psbC-trnS). Five haplotypes were identified; two were widely distributed but the most frequently occurring haplotype was found only in trees in the western portion of the range. Genetic differentiation among populations was significant and showed a high degree of structure (GST = 0.26077). Pairwise comparisons between populations revealed significant structure between the southeastern and northwestern watersheds and significant isolation by distance (p < 0.02). Nucleotide variation was also assessed in segments of three nuclear genes, 4Cl (4-coumarate: coenzyme A ligase), ITS2 (intergenic spacer region of ribosomal DNA) and G3pdh (glyceraldehyde 3-phosphate dehydrogenase). A total of 1,154 base pairs were sequenced from 79 individuals (158 alleles) representing seven geographic locations. Estimates of nucleotide diversity (pi = 0.00089) and theta (0.00061) were low for the combined loci and similar to chloroplast estimates. There was a higher level of variation at the 4Cl locus (pi = 0.00167) associated with recombination. Nucleotide diversity for nuclear loci was highest in the subalpine Mt. Read population, previously described as a putative clonal stand. Population differentiation (FST = 0.0130) was lower than estimated in chloroplast DNA, or in a previous allozyme investigation (FST = 0.095). Multilocus genotypes based on RAPD markers (random amplified polymorphic DNA) were generated to further investigate genetic diversity in the Huon pine stand at Mt. Read. DNA was analyzed from 63 trees from Mt. Read and genetic diversity compared to 33 Huon pine samples from a wide geographic range. Twelve random decanucleotide primers amplified a total of 35 alleles. Only three of the alleles (8.6%) from the Mt. Read population were polymorphic in contrast to 18 (51.4%) polymorphic alleles in the reference population. Gene diversity at Mt. Read (0.0316) was six-fold lower than that found in the reference sample (0.1973). Only four unique DNA fingerprints were revealed at Mt. Read and these were spatially clustered in the stand. Each of the 33 isolates in the wide geographic sample exhibited a unique genotype.The three marker systems of this study, along with a previous allozyme survey, are concordant in indications of a low level of diversity in a Southern Hemisphere conifer. The low level of nucleotide diversity, star-like phylogeny and haplotype distribution of chloroplast DNA suggest that Huon pine has experienced a series of population bottlenecks and colonization events from refugial areas. This is congruent with paleoecological data that suggest that there were major refugial areas on the western coast of Tasmania in addition to small, isolated refugia in other portions of the current range. The low level of variation found in nuclear loci is also compatible with a history of demographic events related to Pleistocene and Holocene environmental variability and long-term range reduction. The limited genetic variation in the Mt. Read population may be related to minimal gene flow into this stand due to geographic isolation, and extensive vegetative reproduction in a harsh environment.