Molecular Evolution And Biogeography Of Larix (Pinaceae)

Inheritance pathways of the three genomes in the pine family (Pinaceae) are strikingly different, i.e., the chloroplast, mitochondrial, and nuclear genomes are paternally, maternally, and biparentally inherited, respectively. In comparison to the relatively simple nuclear genomes of angiosperms, the pine family is characterized by a large nuclear genome and highly complex gene families. Besides, the nuclear ribosomal DNA ITS region has extensive intra- and (or) inter- genomic length heterogeneity and sequence polymorphism in Pinaceae, this family, however, all have a diploid chromosome number of 2n=24 except Pseudotsuga menziesii and Pseudolarix amabilis. Therefore, the pine family provides ideal materials not only for the study of gene tree/species tree but also for the investigation of mechanisms of molecular and genome evolution. In addition, the family Pinaceae has a very long evolutionary history, of which many taxa experienced some huge geological changes, e.g., the collision of India with Asia and subsequent uplift of the Himalayas and Tibetan Plateau, its phylogenetic reconstruction would be very helpful to elucidate some important biogeography issues.In this study, we sampled all species and most varieties of Larix except L. lyallii to reconstruct the evolutionary history of the genus based on PCR direct sequencing of the chloroplast trnT-trnF region and cloning analyses of the nrDNA ITS region and low copy nuclear 4-coumarate: coenzyme A ligase (4CL) gene. Also, the evolutionary dynamics of the two nuclear gene families was investigated. The main results are summarized as follows:1. The phylogenies of the cpDNA trnT-trnF and nrDNA ITS regions are highlycongruent, suggesting that the North American Larix is a monophyletic group sister to the Eurasian larches and that the divergence time between the Eurasian long-bracted and short-bracted species is nearly as early as that between the North American and the Eurasian ones. The Beringian Bridge is most probably the passage for the intercontinental dispersal of Larix ancestor, and bract length divergence might have occurred independently in different continents considering that L. laricina and L. occidentalis, two North American species with very different bracts, have identical sequence of the trnT-trnF region.2. The 4CL gene exists as a small gene family with two to four distinct members in each Larix species sampled except that L. gmelinii var. principis-rupprechtii includes as many as seven members. Phylogenetic analysis of the 44 distinct clones obtained, excluding some putative recombinants, showed that an ancient gene duplication in the common ancestor of Larix resulted in the paralogous genes 4clA and 4clB and a further duplication of 4clA gave rise to 4clA1 and 4clA2. The paralogous genes from gene duplication differ greatly in their evolutionary rate due to a reduction in the selective constraint on at least one duplicate copy or function divergence. In addition, lineage sorting was observed in the Larix 4CL gene tree and great difference in the evolutionary dynamics was found between Larix and Pinns. Frequent gene duplication could be an important mechanism responsible for the unusually large nuclear genome sizes of conifers.3. 101 distinct nrDNA ITS clones were obtained and sequenced. The entire ITS region length of Larix ranges from 1653 bp to 1773 bp. Excluding several putative pseudogenes or recombinant, the other ones from the same genome are very conserved in length and nucleotide sequence. That is to say, the concerted evolution rate of nrDNA family is faster in Larix than in some old genera of Pinaceae such as Pinus and Picea, which may be attributed to the less complexity of nrDNA organization and the young history of Larix. Some unique ITS paralogues are likely from the minor loci or representorphons given their chimeric structure and high sequence divergence. This study also shows that the distribution pattern analysis of nrDNA ITS paralogues are very useful in tracking the evolutionary history of Larix. In the ITS phylogeny, clones fr...