Tracing the geographic origin of endangered plant species using transcriptome-derived SNPs: An example of Cathaya argyrophylla.

Genetic markers have emerged as one of the most promising tools for species identification and geographic traceability in biodiversity conservation and international trade of biological products. However, traditional molecular markers rarely have sufficient resolution at lower taxonomic levels, especially for discriminating closely related forest tree species and their populations. In this study, we developed a panel of RNA-Seq based single nucleotide polymorphism (SNP) markers for tracing the geographic origin of an endangered conifer, Cathaya argyrophylla, which is a paleoendemic restricted to four mountain regions in subtropical China. A total of 69 individuals from five populations (DLS, SHS, HP, BMS, and DYS) covering the entire range were used for transcriptome sequencing. Based on these transcriptomic data, we evaluated genetic variation and population structure of C. argyrophylla, and found extremely low nucleotide diversity but strong population differentiation. We also screened 113 population-specific SNP loci, including 96 for BMS, eight for DYS, six for SHS, two for HP, and one for one of the three subpopulations from DLS. According to these geographically diagnostic SNPs, we designed four population-specific molecular barcodes for PCR amplification. To test the utility and efficiency of the four markers in geographic discrimination, double-blind experiment was performed using 157 individuals labelled without any locality information. We found that almost all tested individuals could be successfully assigned to their geographic localities. Our study not only sheds some new light on the genetic profile of C. argyrophylla, but also provides a practical and cost-efficient solution for geographic traceability using transcriptome-derived SNPs.

Phylotranscriptomics reveals the evolutionary history of subtropical East Asian white pines: further insights into gymnosperm diversification.

Floristic composition within a geographic area is driven by a wide array of factors from local biotic interactions to biogeographical processes. Subtropical East Asia is a key biodiversity hotspot of the world, and harbors the most families of extant gymnosperms and a large number of endemic genera with ancient origins, but rare phylogenetic studies explored whether it served as a diversification center for gymnosperms. Here, we investigated the evolutionary and biogeographical history of subtropical East Asian white pines using an integrative approach that combines phylotranscriptomic and ecological analyses. Using 2,606 orthologous nuclear genes, we reconstructed a fully resolved and dated phylogeny of these species. Two main clades first diverged in the early Miocene, and by the late Miocene, all species appeared. Two white pines endemic to Taiwan Island experienced independent colonization events and regional extinction, which resulted in the present disjunctive distribution from mainland China. Ecological and biogeographical analyses indicate that the monsoon-driven assembly of evergreen broadleaved forests (EBLFs) might have significantly affected the diversification of subtropical East Asian white pines. Our study highlights the interactions of biotic and abiotic forces in the diversification and speciation of subtropical East Asian white pines. These findings indicate that subtropical East Asia is not only a floristic museum, but also a diversification center for gymnosperms. Our study also demonstrates the importance of phylotranscriptomics on species delimitation and biodiversity conservation, particularly for closely related species.

Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines.

How coniferous forests evolved in the Northern Hemisphere remains largely unknown. Unlike most groups of organisms that generally follow a latitudinal diversity gradient, most conifer species in the Northern Hemisphere are distributed in mountainous areas at middle latitudes. It is of great interest to know whether the midlatitude region has been an evolutionary cradle or museum for conifers and how evolutionary and ecological factors have driven their spatiotemporal evolution. Here, we investigated the macroevolution of Pinus, the largest conifer genus and characteristic of northern temperate coniferous forests, based on nearly complete species sampling. Using 1,662 genes from transcriptome sequences, we reconstructed a robust species phylogeny and reestimated divergence times of global pines. We found that ∼90% of extant pine species originated in the Miocene in sharp contrast to the ancient origin of Pinus, indicating a Neogene rediversification. Surprisingly, species at middle latitudes are much older than those at other latitudes. This finding, coupled with net diversification rate analysis, indicates that the midlatitude region has provided an evolutionary museum for global pines. Analyses of 31 environmental variables, together with a comparison of evolutionary rates of niche and phenotypic traits with a net diversification rate, found that topography played a primary role in pine diversification, and the aridity index was decisive for the niche rate shift. Moreover, fire has forced diversification and adaptive evolution of Pinus Our study highlights the importance of integrating phylogenomic and ecological approaches to address evolution of biological groups at the global scale.

Cryptic speciation in the Chinese white pine (Pinus armandii): Implications for the high species diversity of conifers in the Hengduan Mountains, a global biodiversity hotspot.

Conifers are the largest and ecologically and economically most important component group of the gymnosperms. Despite their slow rate of molecular evolution, rapid and recent diversification was unexpectedly prevalent in this ancient group in the Hengduan Mountains, a world's biodiversity hotspot and gymnosperm diversity center in Southwest China. In this study, we investigated the underlying mechanisms and disentangled the interactions of geography and ecology in speciation and evolution in Pinus armandii, an important forest tree species endemic to China, by integrating analyses of population transcriptomics, population genetics and ecological niche modeling. Many lines of evidence suggest that cryptic speciation has occurred in P. armandii. During the process, geologically induced formation of Mount Gongga and other massive peaks might trigger the initial vicariance isolation of the northern and southern subdivisions, and ecologically based selection then reinforced their differentiation and local adaptation. Our ecological niche analysis and earlier reciprocal transplant experiments in P. armandii provided convincing evidences for the critical role of ecology in the process of speciation. These findings suggest that both geography and ecology contributed significantly to the abundance of very recent and rapid species divergences, which promoted the rising of the extremely high conifer diversity in the Hengduan Mountains.

Long-distance dispersal or postglacial contraction? Insights into disjunction between Himalaya-Hengduan Mountains and Taiwan in a cold-adapted herbaceous genus, Triplostegia.

Current disjunct patterns can result from long-distance dispersal or postglacial contraction. We herein investigate the evolutionary history of Triplostegia to elucidate the disjunction between the Himalaya-Hengduan Mountain region (HHM) and Taiwan (TW). Genetic structure of Triplostegia was investigated for 48 populations using sequences from five chloroplast loci and the ribosomal nuclear internal transcribed spacer. Divergence time estimation, ancestral area reconstruction, and species distribution modeling (SDM) were employed to examine the biogeographic history of Triplostegia. Substantial genetic differentiation among populations from southwestern China (SW), Central China (CC), and TW was detected. Triplostegia was inferred to have originated in SW, and diversification began during the late Miocene; CC was colonized in the mid-Pliocene, and TW was finally colonized in the early Pleistocene. SDM suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last interglacial in Triplostegia. Disjunction between HHM and TW in Triplostegia is most likely the consequence of topographic isolation and postglacial contraction. The potential climatic suitability areas for Triplostegia by 2070s (2061-2080) are predicted to slightly shrink and move northward. With continued global warming and human-induced deforestation, extinction risk may increase for the cold-adapted species, and appropriate strategies should be employed for ecosystem conservation.

Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics.

Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants. Our review of the published data suggests that, although many gene families are conserved among herbaceous and tree species, some gene families, such as those involved in resistance to biotic and abiotic stresses and in the synthesis and transport of sugars, are often expanded in tree genomes. As the genomes of more tree species are sequenced, comparative genomics will further elucidate the complexity of tree genomes and how this relates to traits unique to trees.

Revisiting the phosphatidylethanolamine-binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution.

Angiosperms and gymnosperms are two major groups of extant seed plants. It has been suggested that gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction. Expression patterns in three gymnosperm taxa and heterologous expression in Arabidopsis were studied to investigate the functions of gymnosperm FT-like and TERMINAL FLOWER 1 (TFL1)-like genes. Phylogenetic reconstruction suggests that an ancient gene duplication predating the divergence of seed plants gave rise to the FT and TFL1 genes. Expression patterns indicate that gymnosperm TFL1-like genes play a role in the reproductive development process, while GymFT1 and GymFT2, the FT-like genes resulting from a duplication event in the common ancestor of gymnosperms, function in both growth rhythm and sexual development pathways. When expressed in Arabidopsis, both spruce FT-like and TFL1-like genes repressed flowering. Our study demonstrates that gymnosperms do have FT-like and TFL1-like genes. Frequent gene and genome duplications contributed significantly to the expansion of the plant PEBP gene family. The expression patterns of gymnosperm PEBP genes provide novel insight into the functional evolution of this gene family.

Molecular phylogenetics and evolutionary history of sect. Quinquefoliae (Pinus): implications for Northern Hemisphere biogeography.

Climatic changes and tectonic events in the Cenozoic have greatly influenced the evolution and geographic distribution of the temperate flora. Such consequences should be most evident in plant groups that are ancient, widespread, and diverse. As one of the most widespread genera of trees, Pinus provides a good model for investigating the history of species diversification and biogeographic disjunction in the Northern Hemisphere. In this study, we reconstructed the phylogeny and investigated the evolutionary and biogeographic history of sect. Quinquefoliae (Pinus), a species-rich lineage disjunctly distributed in Asia, Europe and North America, based on complete taxon sampling and by using nine DNA fragments from chloroplast (cp), mitochondrial (mt) and nuclear genomes. The monophyly of the three subsections, Krempfianae, Gerardianae, and Strobus, is well-supported by cpDNA and nuclear gene phylogenies. However, neither subsect. Gerardianae nor subsect. Strobus forms a monophyletic group in the mtDNA phylogeny, in which sect. Quinquefoliae was divided into two major clades, one consisting of the North American and northeastern Asian species as well as the European P. peuce of subsect. Strobus, and the other comprising the remaining Eurasian species belonging to three subsections. The significant topological incongruence among the gene trees, in conjunction with divergence time estimation and ancestral area reconstruction, indicates that both ancient and relatively recent introgressive hybridization events occurred in the evolution of sect. Quinquefoliae, particularly in northeastern Asia and northwestern North America. In addition, the phylogenetic analysis suggests that the species of subsect. Strobus from subtropical eastern Asia and neighboring areas may have a single origin, although species non-monophyly is very widespread in the nuclear gene trees. Moreover, our study seems to support a Tethyan origin of sect. Quinquefoliae given the distributions and phylogenetic positions of subsects. Krempfianae and Gerardianae, and also highlights the importance of active mountain buildings and climatic changes during the Late Neogene in shaping the species diversity and geographic distribution of Pinus.

Phylogeography of Pinus armandii and its relatives: heterogeneous contributions of geography and climate changes to the genetic differentiation and diversification of Chinese white pines.

Geographic barriers and Quaternary climate changes are two major forces driving the evolution, speciation, and genetic structuring of extant organisms. In this study, we used Pinus armandii and eleven other Asian white pines (subsection Strobus, subgenus Pinus) to explore the influences of geographic factors and Pleistocene climatic oscillations on species in South China, a region known to be centers of plant endemism and biodiversity hotspots. Range-wide patterns of genetic variation were investigated using chloroplast and mitochondrial DNA markers, with extensive sampling throughout the entire range of P. armandii. Both cpDNA and mtDNA revealed that P. armandii exhibits high levels of genetic diversity and significant population differentiation. Three geographically distinct subdivisions corresponding to the Qinling-Daba Mountains (QDM), Himalaya-Hengduan Mountains (HHM) and Yungui Plateau (YGP) were revealed in mainland China by cpDNA. Their break zone was located in the southeastern margin of the Qinghai-Tibetan Plateau (QTP). A series of massive mountains, induced by the QTP uplift, imposed significant geographic barriers to genetic exchange. The disjunct distribution patterns of ancestral haplotypes suggest that a large continuous population of the white pines may have existed from southwest to subtropical China. Repeated range shifts in response to the Pleistocene glaciations led to the isolation and diversification of the subtropical species. The two Taiwanese white pines share a common ancestor with the species in mainland China and obtain their chloroplasts via long-distance pollen dispersal from North Asian pines. Distinct genetic patterns were detected in populations from the Qinling-Daba Mountains, Yungui Plateau, Himalaya-Hengduan Mountains, and subtropical China, indicating significant contributions of geographic factors to the genetic differentiation in white pines. Our study depicts a clear picture of the evolutionary history of Chinese white pines and highlights the heterogeneous contributions of geography and Pleistocene climatic fluctuations to the extremely high plant species diversity and endemism in South China.

Molecular phylogeny and biogeography of Pseudotsuga (Pinaceae): insights into the floristic relationship between Taiwan and its adjacent areas.

Climatic oscillations and geological events play major roles in shaping species diversity and the distribution of plants. The mechanisms underlying the high level of plant species diversity in eastern Asia are hotly debated. In this study, five cpDNA regions, two mtDNA fragments and one nuclear gene (LEAFY) were employed to investigate species diversification and the historical biogeography of Pseudotsuga (Pinaceae), a genus with a typical eastern Asia and western North America disjunct distribution. Both the nuclear LEAFY gene and cpDNA phylogenies strongly suggest that eastern Asian and North American species are monophyletic, respectively. Within the eastern Asia clade, the cpDNA tree placed P. japonica as sister to the rest of the Asian species, but the LEAFY gene tree showed a sister relationship between P. japonica-P. sinensis-P. gaussenii and P. brevifolia-P. forrestii. Molecular dating indicated that the Asian species last shared a common ancestor 20.26+/-5.84 mya and the species diversification of Pseudotsuga was correlated with the Tertiary climatic and tectonic changes. These results, together with the fossil evidence, suggest that Pseudotsuga might have originated from North America and then migrated to eastern Asia by the Bering land bridge during the early Miocene. The Taiwanese species P. wilsoniana harbored two divergent types of LEAFY sequences, which implies that this species might have originated by hybridization between P. brevifolia or its ancestor and the ancestor of P. japonica-P. sinensis-P. gaussenii. Our study also suggests that Taiwan is closely related to both southwest and east China in flora.

Molecular phylogeny and biogeography of Picea (Pinaceae): implications for phylogeographical studies using cytoplasmic haplotypes.

The center of diversity is not necessarily the place of origin, as has been established by many plant molecular phylogenies. Picea is a complicated but very important genus in coniferous forests of the Northern Hemisphere, with a high species diversity in Asia. Its phylogeny and biogeography were investigated here using sequence analysis of the paternally inherited chloroplast trnC-trnD and trnT-trnF regions and the maternally inherited mitochondrial nad5 intron 1. We found that the North American P. breweriana and P. sitchensis were basal to the other spruces that were further divided into three clades in the cpDNA phylogeny, and that the New World species harbored four of five mitotypes detected, including two ancestral ones and three endemics. These results, combined with biogeographic analyses using DIVA and MacClade and fossil evidence, suggest that Picea originated in North America, and that its present distribution could stem from two times of dispersal from North America to Asia by the Beringian land bridge, and then from Asia to Europe. Most of the northeastern Asian species and the European P. abies could arise from a recent radiation given the very low interspecific genetic differentiation and pure mitotype of them. Considering that the ancestral mtDNA polymorphism can be preserved in many descendant species, even distantly related ones, we suggest that more species, at least the closely related ones, should be sampled in the phylogeographical study using cytoplasmic haplotypes if possible. In addition, we also discussed the evolution and phylogenetic utility of morphological characters in Picea.

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

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.

Evolution of 4-coumarate:coenzyme A ligase (4CL) gene and divergence of Larix (Pinaceae).

The evolutionary dynamics of the 4CL gene encoding 4-coumarate:coenzyme A ligase was investigated in the genus Larix (Pinaceae) by comparing copy number, GC content and codon usage, sequence divergence, and phylogenetic analysis. All 4CL clones of Larix formed a strongly supported monophyletic group, in which two robust clades (4clA and 4clB) derived from an ancient gene duplication event in the common ancestor of Larix were identified. Further gene duplication in the 4clA clade gave rise to two subclades 4clA(1) and 4clA(2). Frequent duplication/deletion appears to be a common evolutionary phenomenon in the 4CL gene family and paralogous genes differ greatly in their evolution rate. The existence of L. speciosa in subclades 4clA(1) and 4clA(2) suggests that this species may represent a primitive form of Larix or the closest relative of the common ancestor of the Eurasian Sect. Multiserialis. In addition, cpDNA and nrDNA ITS analyses support the hypothesis of an early separation of Larix into a North American and a Eurasian clade, which is congruent with the results of previous allozyme and very recent AFLP analyses. The unexpected close relationship between North American larches and the short-bracted species L. gmelinii in East Asia, based on the 4CL gene tree, may stem from lineage sorting.

Marked intragenomic heterogeneity and geographical differentiation of nrDNA ITS in Larix potaninii (Pinaceae).

Nuclear ribosomal DNA (nrDNA) of gymnosperms, especially Pinaceae, is characterized by slow concerted evolution and exhibits substantial ITS-region length variation (975-3663 bp), in sharp contrast to the narrow range (565-700 bp) in angiosperms. Here we examined intra- and intergenomic heterogeneity of the nrDNA internal transcribed spacer (ITS) region in four varieties of Larix potaninii, a species from the mountainous areas of western China. Two clones with more than a 100-bp deletion in ITS1 were detected in L. potaninii var. chinensis and L. potaninii var. australis, respectively. The deletion resulted in the loss of most part, including the motif sequence, of subrepeat 1 (SR1). Sequence divergence and phylogenetic analyses showed that some clones would be pseudogenes given their low GC content, high substitution rates, unique positions in the phylogenetic trees, or significant length variation. These clones might represent orphons or paralogues at minor loci resulting from large-scale gene or chromosome reorganization. Some recombinants characterized by chimeric structure and discordant phylogenetic positions in partitioned sequence analyses indicate that unequal crossing-over plays an important role in the process of nrDNA concerted evolution. In addition, some varieties of L. potaninii might have experienced an nrDNA founder effect parallel to their geographical isolation.