Recolonization and radiation in Larix (Pinaceae): evidence from nuclear ribosomal DNA paralogues

Abstract

Gene paralogy frequently causes the conflict between gene tree and species tree, but sometimes the coexistence of a few paralogous copies could provide more markers for tracing the phylogeographical process of some organisms. In the present study, nrDNA ITS paralogues were cloned from all but one species of Larix, an Eocene genus having two sections, Larix and Multiserialis, with a huge circumboreal distribution and an Eastern Asia-Western North America disjunction, respectively. A total of 96 distinct clones, excluding five putative pseudogenes or recombinants, were obtained and used in the gene genealogy analysis. The clones from all Eurasian species of section Larix are mixed together, suggesting that recolonization and recent morphological differentiation could have played important roles in the evolution of this section. In contrast, the species diversification of the Eurasian section Multiserialis may result from radiation in the east Himalayas and its vicinity, considering extensive nrDNA founder effects in this group. Our study also suggests that the distribution pattern analysis of members of multiple gene family would be very useful in tracking the evolutionary history of some taxa with recent origin or rapid radiation that cannot be resolved by other molecular markers.

Species-diagnostic markers in Larix spp. based on RAPDs and nuclear, cpDNA, and mtDNA gene sequences, and their phylogenetic implications

“…The same trend could be seen for the North Eurasian group, where no clear phylogenetical structure could be supported systematically by the various data sets analyzed herein or previously published. Such a lack of congruent phylogenetic structure across data sets might not be surprising, given the multiple evidences for incomplete reproductive isolation and natural hybridization between parapatric Larix taxa in this region (e.g., Wei and Wang 2004b).…”

Phylogeography of Larix sukaczewii Dyl. and Larix sibirica L. inferred from nucleotide variation of nuclear genes

“…However, some authors have argued that for various reasons such as, e.g., the presence of multiple copies, compensatory base changes, and difficulties in alignment, the use of ITS for such studies is problematic (Alvarez and Wendel 2003;Bailey et al 2003;Campbell et al 2005;Gernandt and Liston 1999). Indeed, the presence of multiple copies of the ITS region was reported for some Larix species (Gernandt and Liston 1999;Gernandt et al 2001;Wei and Wang 2004b). Yet, there is also evidence suggesting that different multiple copies of the ITS region were not amplified in our study.…”

“…Therefore, geographic isolation has been considered as a barrier to gene flow among Larix populations (Lewandowski et al 1994;Young and Young 1992). Yet, most previous studies on Larix revealed low population differentiation (Larionova et al 2004;Lewandowski 1997;Semerikov and Lascoux 2003;Timerjanov 1997;Wei and Wang 2004b). Recent divergence of extant populations was suggested as the cause of the low genetic differentiation within and among Eurasian species from the genus Larix (Semerikov and Lascoux 2003;Wei and Wang 2004b).…”

“…Yet, most previous studies on Larix suggested relatively simple pictures, such as low levels of genetic differentiation at both inter and intraspecific levels. Recent speciation on the geological time scale, lack of reproductive isolation, and recent divergence of extant populations were given as explanations for such low differentiation (Gros-Louis et al 2005;Larionova et al 2004;Lewandowski 1997;Semerikov and Lascoux 2003;Timerjanov 1997;Wei and Wang 2004b).…”

Climate Variability and Associated Response of <i>Larix griffithii</i> in Kanchenjunga Conservation Area of Nepal

“…is the least studied species in the context of Nepal. It is mainly because these species are confined to 24 Applied Ecology and Environmental Sciences the eastern Himalayas, especially south and east [11] and distribution of some species appears to have a very restricted range being recorded from only two localities one in Tibet and another in Nepal [12]. Understanding past climate variation and its effects on forests help us to anticipate the potential effects of global warming.…”