Abstract:Phylogeography (Avise et al., 1987) is a branch of historical biogeography that involves determining the history of taxa in space and time by integrating the phylogenetic and geographical patterns. This is carried out especially at the level of species complex or intraspecific populations to reveal how the present distribution patterns of taxa have been shaped by geological events or other factors. As the taxon is at species level, the scale in time and space is much shorter and smaller than the study of gener… Show more
“…glauca (Huang et al 2002;Lee et al 2006;Shih et al 2006), T. aralioides (Huang et al 2004), Cunninghamia konishii , Cas. carlesii (Cheng et al 2005), Machilus thunbergii (Wu et al 2006), M. kusanoi (Wu et al 2006), Abies kawakamii (Shih et al 2007), and C. kanehirae (this study).…”
Section: Two Divergence Centers Are Common For Vascular Plants In Taiwanmentioning
confidence: 99%
“…4), and includes the Hsuehsahan, Shiouhluan, Ssuyan, Hakannishan, Lishan, Tahu, Tashueshan, and Huisun populations for the seven respective tree species. Species here include several temperate species: T. aralioides (Huang et al 2004), Cu. konishii (Chung et al 2004), Cas.…”
Section: Two Divergence Centers Are Common For Vascular Plants In Taiwanmentioning
confidence: 99%
“…Using a similar strategy, Huang et al (2004) inferred that the north-central region, west of the central mountain range (CMR) was a potential refugium for Trochodendron aralioides, a temperate species, during the last glaciation. Cheng et al (2005) proposed that the above regions might have been potential refugia for Castanopsis carlesii, another widespread species in Taiwan according to the average F ST values of individual populations compared to the remaining populations, which means where the most-divergent populations are located.…”
Cinnamomum kanehirae Hayata (Lauraceae), the most valuable subtropical and temperate broadleaf timber tree in Taiwan, is rapidly disappearing from the wild. Taking advantage of a scion garden established by the Taiwan Forestry Research Institute, we examined patterns of chloroplast DNA (cpDNA) variations in 19 populations including 94 individuals. By sequencing two cpDNA fragments using universal primers (the trnL-trnF and petG-trnP intergenic spacers), we found eight polymorphic sites, six haplotypes, and extremely low nucleotide diversity (p = 0.00016) from 792 bp aligned sequences. The ancestral haplotype is widely distributed. Among the populations studied, three separated populations, at Yungfeng, Fuli, and Tahu have high nucleotide diversity. No phylogeographical structures of haplotypes were revealed because the tests of N ST -G ST for populations did not differ from zero in any situations; a 'star-like' genealogy is characteristic when all haplotypes rapidly coalesce and is a general outcome of population expansion. The neutrality test also suggested demographic expansion. The genetic divergence and diversity analyses suggested that two potential refugia existed during the last glaciation with a major one located in southeastern Taiwan and a minor one located in Tahu in north-central Taiwan in the Hsuehshan Range, west of the Central Mountain Range.
“…glauca (Huang et al 2002;Lee et al 2006;Shih et al 2006), T. aralioides (Huang et al 2004), Cunninghamia konishii , Cas. carlesii (Cheng et al 2005), Machilus thunbergii (Wu et al 2006), M. kusanoi (Wu et al 2006), Abies kawakamii (Shih et al 2007), and C. kanehirae (this study).…”
Section: Two Divergence Centers Are Common For Vascular Plants In Taiwanmentioning
confidence: 99%
“…4), and includes the Hsuehsahan, Shiouhluan, Ssuyan, Hakannishan, Lishan, Tahu, Tashueshan, and Huisun populations for the seven respective tree species. Species here include several temperate species: T. aralioides (Huang et al 2004), Cu. konishii (Chung et al 2004), Cas.…”
Section: Two Divergence Centers Are Common For Vascular Plants In Taiwanmentioning
confidence: 99%
“…Using a similar strategy, Huang et al (2004) inferred that the north-central region, west of the central mountain range (CMR) was a potential refugium for Trochodendron aralioides, a temperate species, during the last glaciation. Cheng et al (2005) proposed that the above regions might have been potential refugia for Castanopsis carlesii, another widespread species in Taiwan according to the average F ST values of individual populations compared to the remaining populations, which means where the most-divergent populations are located.…”
Cinnamomum kanehirae Hayata (Lauraceae), the most valuable subtropical and temperate broadleaf timber tree in Taiwan, is rapidly disappearing from the wild. Taking advantage of a scion garden established by the Taiwan Forestry Research Institute, we examined patterns of chloroplast DNA (cpDNA) variations in 19 populations including 94 individuals. By sequencing two cpDNA fragments using universal primers (the trnL-trnF and petG-trnP intergenic spacers), we found eight polymorphic sites, six haplotypes, and extremely low nucleotide diversity (p = 0.00016) from 792 bp aligned sequences. The ancestral haplotype is widely distributed. Among the populations studied, three separated populations, at Yungfeng, Fuli, and Tahu have high nucleotide diversity. No phylogeographical structures of haplotypes were revealed because the tests of N ST -G ST for populations did not differ from zero in any situations; a 'star-like' genealogy is characteristic when all haplotypes rapidly coalesce and is a general outcome of population expansion. The neutrality test also suggested demographic expansion. The genetic divergence and diversity analyses suggested that two potential refugia existed during the last glaciation with a major one located in southeastern Taiwan and a minor one located in Tahu in north-central Taiwan in the Hsuehshan Range, west of the Central Mountain Range.
“…Chloroplast DNA is thought to evolve slowly, with low mutation and recombination rates, and is known to be maternally inherited in most angiosperms. Maternally inherited DNA markers generally reveal much greater genetic structure in comparison with biparentally inherited nuclear markers (Petit et al, 1993a,b) and these markers have been successfully applied to identify possible glacial refugia and species migration routes of many plant species (Huang et al, 2004;Cheng et al, 2005;Fjellheim et al, 2006;Shephard et al, 2007). In principle, the geographical origin of wood samples can be checked with the cpDNA markers that show enough geographical structure.…”
“…NCPA has been advantageous for disentangling contributions of historical processes and current gene flow to the observed patterns of haplotype composition. This method has been instrumental in phylogeographical research of humans (Hammer et al, 1998), reptiles (Paulo et al, 2002;Amato et al, 2008), fishes (Weiss et al, 2002), insects (Contreras-Díaz et al, 2003), mollusks (Turner et al, 2000;Wilke and Pfenninger, 2002), coelenterates (Márquez et al, 2002), and plants (Huang and Lin, 2006).…”
ABSTRACT. The finless porpoise (Neophocaena phocaenoides) is a small cetacean whose survival is largely affected by human activity. The characteristics and structures of 3 populations in China and 4 to 5 populations in Japan have been well documented, although their history and origins remain poorly understood. In this study, nested clade phylogeographical analysis was applied to mtDNA sequences from finless porpoises to delineate the historical factors shaping the divergence pattern of this species. The sampling range covered most habitats of the finless porpoise, including the Chinese and Japanese coasts and the Yangtze River. A nested cladogram was constructed, and all 3 (2-step) clades were linked together without interior or tip status. Our data indicated that haplotype C was the most common among most individuals and populations, which could be the most ancient haplotype among all of the sampled types. As populations expanded to reside in different areas, ancient types with haplotype C mutated to other haplotypes, which were kept endemic by geological barriers that changed during glacial cycles that retarded gene flow. Populations in Japanese Pacific coasts and inland sea and post-arc marginal seacoasts NCPA of the finless porpoise and the Yangtze River were formed by the residual individuals left when allopatric fragmentation occurred in the ancestral population. The existence of highly endemic haplotypes and high genetic diversity from the Ariake Sound, Tachibana Bay, and the Yellow Sea indicated a relatively isolated state in these areas during the evolutionary history of the finless porpoise. The phylogenetic pattern revealed in the present study provided a better understanding of the biogeographical events that affected the finless porpoise within this region.
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