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—Amblyanthus chenii (Primulaceae; Myrsinoideae) is a new species discovered growing in the understory of primeval forests in Medog County, southeast Xizang, China and is described based on morphological evidence. This is the first generic record of Amblyanthus in China. The new species is most morphologically similar to A. multiflorus. Amblyanthus chenii can be easily distinguished from other congeneric species by various morphological differences. A phylogenetic analysis based on nuclear ribosomal ITS and six plastid markers indicated that A. chenii and Amblyanthopsis burmanica form a clade that is nested within the large pantropical genus Ardisia and is sister to Ardisia subgenus Crispardisia. The close relationship among Amblyanthus, Amblyanthopsis, and Ardisia subg. Crispardisia is strongly supported by their shared synapomorphy of crenulate leaves with marginal glands.

Significance Crucihimalaya himalaica is a close relative of Arabidopsis with typical Qinghai–Tibet Plateau (QTP) distribution. Here, by combining short- and long-read sequencing technologies, we provide a de novo genome sequence of C. himalaica. Our results suggest that the quick uplifting of the QTP coincided with the expansion of repeat elements. Gene families showing dramatic contractions and expansions, as well as genes showing clear signs of natural selection, were likely responsible for C. himalaica’s specific adaptation to the harsh environment of the QTP. We also show that the transition to self-pollination of C. himalaica might have enabled its occupation of the QTP. This study provides insights into how plants might adapt to extreme environmental conditions., Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai–Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica’s adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.

Crucihimalaya himalaica , a close relative of Arabidopsis and Capsella , grows on the Qinghai–Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata , from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica ’s adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica , might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.

Euclidieae, a morphologically diverse tribe in the family Brassicaceae (Cruciferae), consists of 29 genera and more than 150 species distributed mainly in Asia. Prior phylogenetic analyses on Euclidieae are inadequate. In this study, sequence data from the plastid genome and nuclear ribosomal DNA of 72 species in 27 genera of Euclidieae were used to infer the inter- and intra-generic relationships within. The well-resolved and strongly supported plastome phylogenies revealed that Euclidieae could be divided into five clades. Both Cymatocarpus and Neotorularia are polyphyletic in nuclear and plastome phylogenies. Besides, the conflicts of systematic positions of three species of Braya and two species of Solms-laubachia s.l. indicated that hybridization and or introgression might have happened during the evolutionary history of the tribe. Results from divergence-time analyses suggested an early Miocene origin of Euclidieae, and it probably originated from the Central Asia, Pamir Plateau and West Himalaya. In addition, multiple ndh genes loss and pseudogenization were detected in eight species based on comparative genomic study.

The taxonomic treatment within the unigeneric tribe Yinshanieae (Brassicaceae) is controversial, owing to differences in generic delimitation applied to its species. In this study, sequences from nuclear ITS and chloroplast trnL-F regions were used to test the monophyly of Yinshanieae, while two nuclear markers (ITS, ETS) and four chloroplast markers (trnL-F, trnH-psbA, rps16, rpL32-trnL) were used to elucidate the phylogenetic relationships within the tribe. Using maximum parsimony, maximum likelihood, and Bayesian inference methods, we reconstructed the phylogeny of Brassicaceae and Yinshanieae. The results show that Yinshanieae is not a monophyletic group, with the taxa splitting into two distantly related clades: one clade contains four taxa and falls in Lineage I, whereas the other includes all species previously placed in Hilliella and is embedded in the Expanded Lineage II. The tribe Yinshanieae is redefined, and a new tribe, Hillielleae, is proposed based on combined evidence from molecular phylogeny, morphology, and cytology.

Aim The Himalaya-Hengduan Mountain (HHM) biodiversity hotspot including the 'sky islands' of Southwest China harbour exceptional plant diversity and endemicity at subnival summits (most of them exceeding 4300 m a.s.l.). This study is the first using a comparative phylogeographical framework to gain insights into the temporal origin of this highly fragmented subnival flora, and the historical factors shaping its genetic architecture as exemplified by four perennial herbs.

The recent finding of the tryptophan aminotransferase (TAA)/flavin monooxygenase (YUC) pathway as the principal route of auxin production in plants provides an opportunity to revisit the origin of plant auxin biosynthesis. Phylogenetic analyses of the TAA and YUC gene families provide very little evidence for the production of indole-3-acetic acid (IAA) in algae. Instead, horizontal gene transfer of YUCs from bacteria to the ancestral land plant suggests that the TAA/YUC pathway is a land plant innovation. In this Opinion article we postulate that the origin of tryptophan-dependent IAA biosynthesis in land plants might have evolved in response to interactions with microbes, particularly bacteria, allowing plants to counteract bacterial activities and control their own auxin signaling.

The discovery of horizontal gene transfer (HGT) has challenged the Darwinian “tree of life” concept and, at the same time, has provided new insights into biological evolution. HGT is not only frequent in prokaryotes and unicellular eukaryotes, but also occurs in multicellular eukaryotes. In this article, we review the occurrence and evolutionary significance of HGT in the three major groups of multicellular eukaryotes (animals, plants, and fungi). We also briefly discuss HGT detection methods and possible transfer mechanisms, and offer some predictions about the overall trend of HGT occurrence in multicellular eukaryotes.

Stellera chamaejasme L. is a perennial weed of the family Thymelaeaceae, has wide geographical range, from Altai of eastern Russia, northern China and Mongolia towards south as far as the dry regions of the western Himalaya, the Tibetan plateau and south-western China (Wang and Gilbert 2007). S. chamaejasme is poisonous and thus, is harmful to browsing animals. In overgrazed areas, this species proliferate rapidly due to the open habitat and lack of competition (Grey-Wilson 1995). In recent years, S. chamaejasme has caused severe damage to many ecosystems and has brought great economic loss in Inner Mongolia, Qinghai, Xizang and Sichuan of China (Liu et al. 2004). However, its population genetics is largely unknown. Here, we developed 12 polymorphic microsatellite markers from S. chamaejasme which will be used to investigate the population genetics of this species, and to trace its invasive history in the future study.

Horizontal gene transfer (HGT) may not only create genome mosaicism, but also introduce evolutionary novelties to recipient organisms. HGT in plastid genomes, though relatively rare, still exists. HGT-derived genes are particularly common in unicellular photosynthetic eukaryotes and they also occur in multicellular plants. In particular, ancient HGT events occurring during the early evolution of primary photosynthetic eukaryotes were probably frequent. There is clear evidence that anciently acquired genes played an important role in the establishment of primary plastids and in the transition of plants from aquatic to terrestrial environments. Although algal genes have often been used to infer historical plastids in plastid-lacking eukaryotes, reliable approaches are needed to distinguish endosymbionts-derived genes from those independently acquired from preferential feeding or other activities.

In photosynthetic eukaryotes, many genes were transferred from plastids or algal endosymbionts to nuclear genomes of host cells. These transferred genes are often considered genetic footprints of plastids. However, genes of algal origin have also been detected in some plastid-lacking eukaryotes, and these genes are often cited as evidence of historical plastids. In this paper, we discuss two recent publications about algal genes in plastid-lacking eukaryotes. Both studies highlight the point that algal genes are not exclusively derived from historical plastids. Instead, the findings show that gene acquisition through feeding activities is a plausible explanation.

Solms-laubachia tianbaoshanensis, a new species from the scree slopes and alpine meadows of Hengduan Mountains of NW Yunnan, China, is described and illustrated. It resembles S. linearifolia and S. pulcherrima in gross morphology but differs in having crisped simple subhirsute trichomes to 2 mm long, persistent sepals, pink petals, and longer fruit. In addition, molecular phylogentic analyses based on sequences of nuclear ITS and chloroplast matK, petN-psbM, and trnL-F clearly showed that the new species is distinct from the other congeners.

The Hengduan Mountains region of south-west China is a noted biodiversity hotspot, but the geographic origins and historical assembly of its rich endemic flora, including the sky-island species of Solms-laubachia Muschl. (Brassicaceae), have been little studied. Previous molecular studies on the phylogeny of Solms-laubachia showed it to be paraphyletic, leading to considerable expansion not only of its taxonomic limits, but also its geographic range, with the inclusion of taxa from outside the Hengduan region. However, these studies provided little resolution of interspecific relationships, preventing inferences about historical biogeography within the clade. In the present study, new sequence data from two nuclear genes (LEAFY and G3pdh) and two chloroplast intergenic spacers (petN-psbM and psbM-trnD) were combined with existing markers to increase phylogenetic signals. Phaeonychium villosum (Maxim.) Al-Shehbaz was found to be nested within Solms-laubachia s.l. In general, phylogenetic relationships appear to be a good predictor of geography, with the Hengduan Mountain endemics embedded in a paraphyletic grade of species from the western Himalayas and central Asia, but they also imply morphological homoplasy. Incongruence was detected between the nuclear and chloroplast gene trees, perhaps resulting from incomplete lineage sorting of ancestral polymorphisms. The crown age of Solms-laubachia s.l. was estimated to be approximately 1.42-3.68 mya, using Bayesian relaxed molecular clock analysis. Historical biogeographic analysis using a parametric dispersal-extinction-cladogenesis model inferred central Asia and the western Himalayas as most probable ancestral range of Solms-laubachia s.l., and estimated higher rates of eastward expansion than westward during the diversification of descendant lineages. In summary, our results suggest that Solms-laubachia s.l. originated during the Pliocene in central Asia, and subsequently migrated eastward into the Hengduan Mountains, colonizing sky-island, alpine scree-slope habitats that may have provided novel ecological opportunity and accelerated speciation, ultimately establishing this region as the present center of diversity of the genus.

Sequence data from the nuclear ribosomal ITS region and the chloroplast truL-F were used to examine the generie delimitations of Solms-laubachia Musehl., Christolea Cambess., Desideria Pamp., Leiospora (C. A. Mey) F. Dvorak and Phaeonychium O. E. Schulz. Solms-laubachia. Desideria. and P.jafrii Al-Shehbaz formed a well-supported monophyletie clade, with Christolea as sister group. However, both Solms-laubachia and Desideria were polyphyletie as they appeared in more than two positions in that clade within which P. jafrii was embedded. The results are consistent with those based on sequences of plastid malurase (matK) and the nuclear chalcone synthase (Chs). SEM survey further reveals that the seed epidermis micromorphology of D. baiogoinensis (K. C. Kuan & C. H. An) Al-Shehbaz is most similar to that S. lanata Botsch. Based on these findings, compreshensive synopsis of an expanded Solms-laubachia with 26 species is presented: all species of Desideria and P. jafrii are transferred to Solms-laubachia resulting in 12 new combinations: S. baiogoinensis (K. C. Kuna & C. H. An) J. P. Yue. Al-Shehbaz & H. Sun. S. flabellata (Regel)) J. P. Yue, Al-Shehbaz & H. Sun. S. haranensis (Al-Shehbaz) J. P Yue , Al-Shehbaz & H. Sun. S. flabellata (Regel) J. P. Yue. Al-Shehbaz &H. Sun . S. haranensis (Al-Shehbaz) J. P. Yue . Al-Shehbaz & H. Sun . S. himalayenis (Cambess) J. P. Yue, Al-Shehbaz & H. Sun, S.incana (Ovez.) J. P. Yue, Al-Shehbaz & H. Sun, S. jafrri (Al-Shehbaz) J. P. Yue, Al-Shehbaz & H. Sun. S. mirabilis (Pamp) J. P. Yue, Al-Shehbaz & H. Sun. S. nepalensis (H. Hara) J. P. Yue, Al-Shehbaz & H. Sun. S. prolifera (Maxim) J. P. Yue, Al-Shehbaz & H. Sun and S. Stewartii(T. Anderson) J. P. Yue, Al-Shehbaz & H. Sun. Furthermore four new species of Solms-laubachia are described from western China. S. angustifolia J. P. Yue, Al-Shehbaz & H. Sun. S. grandiflora J. P. Yue, Al-Shehbaz & H. Sun. and S. sunhangiana J. P. Yue, Al-Shehbaz (all from Sichuan Province and S. calcicola J. P. Yue, Al-Shehbaz & H. Sun(from Xizang). Both S. linearifolia (W. W. Sui) O.E. Sehulz and S. mirabilis are lectolypified.

Sequences of the plastid maturase (matK) and nuclear chalcone synthase (Chs) were analyzed separately and in combination to assess phylogenetic relationships of Solms-laubachia Muschl. (all nine known species and two undescribed ones) to the genera Baimashania Al-Shehbaz, Parrya R. Br., Desideria Pamp., Leiospora (C. A. Mey.) Dvorak, Christolea Cambess., and Phaeonychium O. E. Sschulz (Brassicaceae). Baimashania is clustered with Aubrieta deltoidea(L.) DC. and Arabis blepharophylla Hook. & Arn. Solms-laubachia, Desideria, Leiospora, Christolea. and Phaeonychium are more closely related to Matthiola R. Br. than to Parrya, and they form a Well-supported clade. Within this clade. Leiospora is sister to a subclade containing the sister groups Christolea and Solms-laubachia s.l. The Solms-laubachia s.l. group contains Solms-laubachia, Desideria, and a species of Phaeonychium. Neither Solms-laubachia nor Desideria is monophyletic, whereas Phaeonychium jafrii Al-Shehbaz is embedded within the group. Therefore, our results suggest that Solms-laubachia he expanded to include Desideria and P. jafrii. Nevertheless, more species of Desideria. Parrya, and Phaeonychium are needed to further test our findings.

Chromist algae include diverse photosynthetic organisms of great ecological and social importance. Despite vigorous research efforts, a clear understanding of how various chromists acquired photosynthetic organelles has been complicated by conflicting phylogenetic results, along with an undetermined number and pattern of endosymbioses, and the horizontal movement of genes that accompany them. We apply novel statistical approaches to assess impacts of endosymbiotic gene transfer on three principal chromist groups at the heart of long-standing controversies. Our results provide robust support for acquisitions of photosynthesis through serial endosymbioses, beginning with the adoption of a red alga by cryptophytes, then a cryptophyte by the ancestor of ochrophytes, and finally an ochrophyte by the ancestor of haptophytes. Resolution of how chromist algae are related through endosymbioses provides a framework for unravelling the further reticulate history of red algal-derived plastids, and for clarifying evolutionary processes that gave rise to eukaryotic photosynthetic diversity., The chromalveolate hypothesis proposes that chromist algae became photosynthetic through a single endosymbiosis in a common ancestor. Here, Stiller et al. use a novel statistical approach to propose that instead, the major chromist algae arose as a result of three specific serial plastid transfers.

Cytological studies were carried out on eight species of five genera (Anisodus, Atropanthe, Hyoscyamus, Mandragora and Przewalskia) in the tribe Hyoscyameae (Solanaceae). First chromosome counts were reported in six species: Anisodus luridus, A. acutangulus, A. tanguticus, A. carniolicoides, Atropanthe sinensis and Mandragora caulescens, all with 2n = 8x = 48. Two records, for Hyoscyamus niger (2n = 2x = 34) and Przewalskia tangutica (2n = 4x = 44), were also confirmed. All species studied showed the proximal type of mitotic prophase chromosome condensation pattern. Three types of interphase nuclei were recognized: the round prochromosome type for Anisodus, Atropanthe and Mandragora, the rod prochromosome type for Przewalskia and the complex chromocentre type for Hyoscyamus. The cytological data supported the close relationship of all four species of Anisodus. Evidence from the interphase nuclei and chromosome base numbers supported the traditional classification of Hyoscyameae into two groups, i.e. Physochlaina praealta + Hyoscyamus (complex interphase type and x = 7, 14, 17) and Przewalskia + Atropanthe + Anisodus + Scopolia + Atropa + Mandragora (prochromosome type and x = 6, 11). Polyploidy is found in most species of the tribe in the Himalayan-Hengduan Mountains, as well as in the Mediterranean region, west-central Asia and eastern Asia. It seems that it probably occurred very early in Hyoscyameae evolution, before the uplift of the Himalayan-Hengduan Mountains. The Himalayan orogeny might have played a minor role in the polyploid evolution of plants in this tribe. (c) 2005 The Linnean Society of London. Botanical Journal of the Linnean Society.

The karyotypes of six species of Solms-laubachia and one each of Parrya and Desideria (Brassicaceae) from the Himalayan-Hengduan Mountains (Tibet, Sichuan and Yunnan provinces) were investigated. Chromosome counts of S. xerophyta, S. lanata, S. platycarpa and D. baiogoinensis are reported for the first time and found to be diploid with 2n = 14. Diploid counts were also made of S. retropilosa, a species previously known to be a tetraploid. The karyotype formulae of D. baiogoinensis, S. eurycarpa, S. pulcherrima, S. retropilosa, S. xerophyta and S. platycarpa are 2n = 14 = 6 m + 6sm + 2st, whereas those of S. lanata and P. nudicaulis are 2n = 14 = 6 in + 2sm + 6st and 2n = 14 = 8 in + 4sm + 2st, respectively. Karyotypes and counts of S. eurycarpa and S. pulcherrima are in agreement with prior studies. The relationships within Solms-laubachia and among the three genera are discussed. Speciation within Solms-laubachia may have been the result of primarily intrachromosomal variation at the diploid level, and the genus probably evolved within the Himalayan-Hengduan Mountains instead of migrating from other regions. (C) 2004 The Linnean Society of London.

Background It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms remain largely unknown. Results Choanoflagellates are phagotrophs and the closest living relatives of animals. In this study, we performed phylogenomic analyses to investigate the scale of HGT and the evolutionary importance of horizontally acquired genes in the choanoflagellate Monosiga brevicollis. Our analyses identified 405 genes that are likely derived from algae and prokaryotes, accounting for approximately 4.4% of the Monosiga nuclear genome. Many of the horizontally acquired genes identified in Monosiga were probably acquired from food sources, rather than by endosymbiotic gene transfer (EGT) from obsolete endosymbionts or plastids. Of 193 genes identified in our analyses with functional information, 84 (43.5%) are involved in carbohydrate or amino acid metabolism, and 45 (23.3%) are transporters and/or involved in response to oxidative, osmotic, antibiotic, or heavy metal stresses. Some identified genes may also participate in biosynthesis of important metabolites such as vitamins C and K12, porphyrins and phospholipids. Conclusions Our results suggest that HGT is frequent in Monosiga brevicollis and might have contributed substantially to its adaptation and evolution. This finding also highlights the importance of HGT in the genome and organismal evolution of phagotrophic eukaryotes.

Background Besides gene duplication and de novo gene generation, horizontal gene transfer (HGT) is another important way of acquiring new genes. HGT may endow the recipients with novel phenotypic traits that are important for species evolution and adaption to new ecological niches. Parasitic systems expectedly allow the occurrence of HGT at relatively high frequencies due to their long-term physical contact. In plants, a number of HGT events have been reported between the organelles of parasites and the hosts, but HGT between host and parasite nuclear genomes has rarely been found. Results A thorough transcriptome screening revealed that a strictosidine synthase-like (SSL) gene in the root parasitic plant Orobanche aegyptiaca and the shoot parasitic plant Cuscuta australis showed much higher sequence similarities with those in Brassicaceae than with those in their close relatives, suggesting independent gene horizontal transfer events from Brassicaceae to these parasites. These findings were strongly supported by phylogenetic analysis and their identical unique amino acid residues and deletions. Intriguingly, the nucleus-located SSL genes in Brassicaceae belonged to a new member of SSL gene family, which were originated from gene duplication. The presence of introns indicated that the transfer occurred directly by DNA integration in both parasites. Furthermore, positive selection was detected in the foreign SSL gene in O. aegyptiaca but not in C. australis. The expression of the foreign SSL genes in these two parasitic plants was detected in multiple development stages and tissues, and the foreign SSL gene was induced after wounding treatment in C. australis stems. These data imply that the foreign genes may still retain certain functions in the recipient species. Conclusions Our study strongly supports that parasitic plants can gain novel nuclear genes from distantly related host species by HGT and the foreign genes may execute certain functions in the new hosts.

In complex multicellular eukaryotes such as animals and plants, horizontal gene transfer is commonly considered rare with very limited evolutionary significance. Here we show that horizontal gene transfer is a dynamic process occurring frequently in the early evolution of land plants. Our genome analyses of the moss Physcomitrella patens identified 57 families of nuclear genes that were acquired from prokaryotes, fungi or viruses. Many of these gene families were transferred to the ancestors of green or land plants. Available experimental evidence shows that these anciently acquired genes are involved in some essential or plant-specific activities such as xylem formation, plant defence, nitrogen recycling as well as the biosynthesis of starch, polyamines, hormones and glutathione. These findings suggest that horizontal gene transfer had a critical role in the transition of plants from aquatic to terrestrial environments. On the basis of these findings, we propose a model of horizontal gene transfer mechanism in nonvascular and seedless vascular plants., Although horizontal gene transfer is prevalent in microorganisms, such sharing of genetic information is thought to be rare in land plants. Focusing on the sequenced moss species, Physcomitrella patens, these authors report genes acquired from microorganisms, which might have facilitated early evolution of land plants.

The 'Tanaka-Kaiyong Line' (TKL) is a major phytogeographic boundary in Southwest China, separating East Asia's Sino-Himalayan and Sino-Japanese Floras. However, little is known about the importance of this boundary in promoting intraspecific phylogeographic subdivision and divergence. Using chloroplast (cpDNA) and nuclear-intron (nDNA) sequence data, we reconstructed the population history of Sophora davidii, a drought-tolerant riparian shrub widely distributed on either side of the TKL. Specifically, we aimed at testing two long-standing explanations for possible vicariant events across the TKL: (i) Late Pliocene (c. 3 Ma) geological uplift of the eastern Qinghai-Tibetan Plateau (QTP) or (ii) a sharp environmental gradient associated with the establishment of different monsoon regimes on either side of the TKL during the (Late) Pleistocene. Our genealogical analyses detected a major west-east split in cpDNA, geographically largely consistent with the TKL, and dated to c. 1.28 Ma (95% HPD: 0.21-2.96 Ma), hence postdating the latest phase of eastern QTP uplift. Furthermore, integrating cpDNA phylogeographic patterns with mismatch analyses, we found multiple refugial isolation and long-term demographic stability of populations in the west (Hengduan Mountain Range) compared with extensive range expansions in the east, possibly during the last glacial period(s) and followed by differentiation into regional sublineages (southeast: Yunnan-Guizhou Plateau vs. northeast: Qinling Mts./Loess Plateau). Although nuclear differentiation was less marked, the geographical pattern of nDNA haplotypes provided some further indication of the species' eastward expansion, possibly from source populations located just east of the TKL (lower Jinshajiang region). Overall, the present data reject the geological (tectonic) explanation for the TKL and, instead, provide supportive evidence for its role as a climatically driven barrier to present-day plant dispersal. In addition, our study highlights changing temperatures and vegetation types during the last glacial period(s), along with aspects of regional topography, to be important determinants of the glacial eastward expansion of S. davidii. In consequence, our study lends support to a 'glacial out-of-Hengduan Mts'. hypothesis for the xerophytic-riparian flora of Southwest China, which in turn is inconsistent with the traditional view of the TKL as a 'classical' vicariant-biogeographic boundary.

Solms-laubachia eurycarpa is a medicinal herb endemic to the Hengduan Mountains region of south-central China. We screened a partial genomic library enriched for microsatellites and characterized 10 polymorphic loci for S. eurycarpa. The number of alleles per locus ranged from five to 15, with an average of 9.6. The observed and expected heterozygosities ranged from 0.2 to 0.725 and from 0.585 to 0.871, respectively. Amplification in closely related taxa was successful for most loci. The results indicate significant potential for the utility of these markers in studying the population genetics of S. eurycarpa and related species.

Draba dongchuanensis is described, illustrated, and compared with several, primarily Himalayan and Tibetan species, including D. amplexicaulis, D. draboides, D. mongolica, D. polyphylla, D. setosa, and D. surculosa. From these, it is readily distinguished from all of the Himalayan species of Draba by a combination of strongly dilated filament bases, setose basal leaves, and auriculate middle cauline leaves.

Horizontal gene transfer (HGT) has been well documented in prokaryotes and unicellular eukaryotes, but its role in plants and animals remains elusive. In a recent study, we showed that at least 57 families of nuclear genes in the moss Physcomitrella patens were acquired from prokaryotes, fungi or viruses and that HGT played a critical role in plant colonization of land. In this paper, we categorize all acquired genes based on their putative functions and biological processes, and further address the importance of HGT in plant innovation and evolution.

Background Horizontal gene transfer (HGT) is traditionally considered to be rare in multicellular eukaryotes such as animals. Recently, many genes of miscellaneous algal origins were discovered in choanoflagellates. Considering that choanoflagellates are the existing closest relatives of animals, we speculated that ancient HGT might have occurred in the unicellular ancestor of animals and affected the long-term evolution of animals. Results Through genome screening, phylogenetic and domain analyses, we identified 14 gene families, including 92 genes, in the tunicate Ciona intestinalis that are likely derived from miscellaneous photosynthetic eukaryotes. Almost all of these gene families are distributed in diverse animals, suggesting that they were mostly acquired by the common ancestor of animals. Their miscellaneous origins also suggest that these genes are not derived from a particular algal endosymbiont. In addition, most genes identified in our analyses are functionally related to molecule transport, cellular regulation and methylation signaling, suggesting that the acquisition of these genes might have facilitated the intercellular communication in the ancestral animal. Conclusions Our findings provide additional evidence that algal genes in aplastidic eukaryotes are not exclusively derived from historical plastids and thus important for interpreting the evolution of eukaryotic photosynthesis. Most importantly, our data represent the first evidence that more anciently acquired genes might exist in animals and that ancient HGT events have played an important role in animal evolution.