Selection of candidate coding DNA barcoding regions for use on land plants

An in silico screen of 41 of the 81 coding regions of the Nicotiana plastid genome generated a shortlist of 12 candidates as DNA barcoding loci for land plants. These loci were evaluated for amplification and sequence variation against a reference set of 98 land plant taxa. The deployment of multiple primers and a modified multiplexed tandem polymerase chain reaction yielded 85–94% amplification across taxa, and mean sequence differences between sister taxa of 6.1 from 156 bases of accD to 22 from 493 bases of matK. We conclude that loci should be combined for effective diagnosis, and recommend further investigation of the following six loci: matK, rpoB, rpoC1, ndhJ, ycf5 and accD.

Land plants and DNA barcodes: short-term and long-term goals

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL, trnL-F, etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the 'genetic gaps' that are useful in assessing species limits.

delta13Corg of Paleozoic land plants

Based on the evaluation of 1323 carbon isotope values for Silurian to Permian terrestrial organic carbon, measured on plant fossils, cuticules, humic coals and bulk terrestrial organic matter (TOM), we conclude that the temporal trend in d13CTOM records variations in the global carbon cycle, notably an increase in the fractional burial of light (terrestrial) organic matter in Late Palaeozoic sediments. d13CTOM values suggest that the Late Palaeozoic pO2 peak could have been restricted to a time frame of ca. 40 Ma. Carbon isotope data from four taxonomic groups reveal small differences that could be a consequence of habitat conditions. No significant differences in organic carbon isotopic composition in relation to variable climatic conditions are discernible. The carbon isotopic composition solely reflects C3 plant metabolism.

A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants

Post-print version of the article.

Meiosis in flowering plants and other green organisms.

Sexual eukaryotes generate gametes using a specialized cell division called meiosis that serves both to halve the number of chromosomes and to reshuffle genetic variation present in the parent. The nature and mechanism of the meiotic cell division in plants and its effect on genetic variation are reviewed here. As flowers are the site of meiosis and fertilization in angiosperms, meiotic control will be considered within this developmental context. Finally, we review what is known about the control of meiosis in green algae and non-flowering land plants and discuss evolutionary transitions relating to meiosis that have occurred in the lineages giving rise to the angiosperms.

Phytochrome diversity in green plants and the origin of canonical plant phytochromes.

Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades. Surprisingly, the phytochrome portions of algal and land plant neochromes, a chimera of phytochrome and phototropin, appear to share a common origin. Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives.

Pasture Degradation and Recovery in Australia's Rangelands : Learning from History

"The extended drought periods in each degradation episode have provided a test of the capacity of grazing systems (i.e. land, plants, animals, humans and social structure) to handle stress. Evidence that degradation was already occurring was identified prior to the extended drought sequences. The sequence of dry years, ranging from two to eight years, exposed and/or amplified the degradation processes. The unequivocal evidence was provided by: (a) the physical 'horror' of bare landscapes, erosion scalds and gullies and dust storms; (b) the biological devastation of woody weeds and animal suffering/deaths or forced sales, and; (c) the financial and emotional plight of graziers and their families due to reduced production in some cases leading to abandonment of properties or, sadly, deaths (e.g. McDonald 1991, Ker Conway 1989)."--Publisher website

The function of the RNA-binding protein TEL1 in moss reveals ancient regulatory mechanisms of shoot development

The shoot represents the basic body plan in land plants. It consists of a repeated structure composed of stems and leaves. Whereas vascular plants generate a shoot in their diploid phase, non-vascular plants such as mosses form a shoot (called the gametophore) in their haploid generation. The evolution of regulatory mechanisms or genetic networks used in the development of these two kinds of shoots is unclear. TERMINAL EAR1-like genes have been involved in diploid shoot development in vascular plants. Here, we show that disruption of PpTEL1 from the moss Physcomitrella patens, causes reduced protonema growth and gametophore initiation, as well as defects in gametophore development. Leafy shoots formed on ΔTEL1 mutants exhibit shorter stems with more leaves per shoot, suggesting an accelerated leaf initiation (shortened plastochron), a phenotype shared with the Poaceae vascular plants TE1 and PLA2/LHD2 mutants. Moreover, the positive correlation between plastochron length and leaf size observed in ΔTEL1 mutants suggests a conserved compensatory mechanism correlating leaf growth and leaf initiation rate that would minimize overall changes in plant biomass. The RNA-binding protein encoded by PpTEL1 contains two N-terminus RNA-recognition motifs, and a third C-terminus non-canonical RRM, specific to TEL proteins. Removal of the PpTEL1 C-terminus (including this third RRM) or only 16–18 amino acids within it seriously impairs PpTEL1 function, suggesting a critical role for this third RRM. These results show a conserved function of the RNA-binding PpTEL1 protein in the regulation of shoot development, from early ancestors to vascular plants, that depends on the third TEL-specific RRM.

Structure and vascular tissue expression of duplicated TERMINAL EAR1-like paralogues in poplar

TERMINAL EAR1-like (TEL) genes encode putative RNA-binding proteins only found in land plants. Previous studies suggested that they may regulate tissue and organ initiation in Poaceae. Two TEL genes were identified in both Populus trichocarpa and the hybrid aspen Populus tremula × P. alba, named, respectively, PoptrTEL1-2 and PtaTEL1-2. The analysis of the organisation around the PoptrTEL genes in the P. trichocarpa genome and the estimation of the synonymous substitution rate for PtaTEL1-2 genes indicate that the paralogous link between these two Populus TEL genes probably results from the Salicoid large-scale gene-duplication event. Phylogenetic analyses confirmed their orthology link with the other TEL genes. The expression pattern of both PtaTEL genes appeared to be restricted to the mother cells of the plant body: leaf founder cells, leaf primordia, axillary buds and root differentiating tissues, as well as to mother cells of vascular tissues. Most interestingly, PtaTEL1-2 transcripts were found in differentiating cells of secondary xylem and phloem, but probably not in the cambium itself. Taken together, these results indicate specific expression of the TEL genes in differentiating cells controlling tissue and organ development in Populus (and other Angiosperm species).

Importance of carbon dioxide physiological forcing to future climate change

An increase in atmospheric carbon dioxide (CO2) concentration influences climate both directly through its radiative effect (i.e., trapping longwave radiation) and indirectly through its physiological effect (i.e., reducing transpiration of land plants). Here we compare the climate response to radiative and physiological effects of increased CO2 using the National Center for Atmospheric Research (NCAR) coupled Community Land and Community Atmosphere Model. In response to a doubling of CO2, the radiative effect of CO2 causes mean surface air temperature over land to increase by 2.86 ± 0.02 K (± 1 standard error), whereas the physiological effects of CO2 on land plants alone causes air temperature over land to increase by 0.42 ± 0.02 K. Combined, these two effects cause a land surface warming of 3.33 ± 0.03 K. The radiative effect of doubling CO2 increases global runoff by 5.2 ± 0.6%, primarily by increasing precipitation over the continents. The physiological effect increases runoff by 8.4 ± 0.6%, primarily by diminishing evapotranspiration from the continents. Combined, these two effects cause a 14.9 ± 0.7% increase in runoff. Relative humidity remains roughly constant in response to CO2-radiative forcing, whereas relative humidity over land decreases in response to CO2-physiological forcing as a result of reduced plant transpiration. Our study points to an emerging consensus that the physiological effects of increasing atmospheric CO2 on land plants will increase global warming beyond that caused by the radiative effects of CO2.

湖北中泥盆世一植物新属的研究

植物自晚志留世登陆以来，经过对恶劣的陆生环境长期而艰难的适应，在泥盆纪，特别是中上泥盆世开始其大规模的演化发展。在此其间，石松类、楔叶类、前蕨类、真蕨类以及前裸子植物等相继出现，使得陆生植物进入其第一个空前繁盛时期。 但是，也正是在这个介于陆地植物起源及其大规模发展的阶段，植物分类以及各植物之间的亲缘关系很不清楚。特别是前蕨类，它起源于三枝蕨类，并且被认为是真蕨类和前裸子植物的祖先，但目前对它是如何从三枝蕨类进化到真蕨类和前裸子植物却几乎一无所知。就如同一个黑匣子，有一个入口和两个出口，我们的任务就是打开这个黑匣子，弄清楚前蕨类中各植物的自然分类位置以及他们之间的亲缘关系。那么，有关早期陆地植物进化的一些悬而未决的问题也便迎刃而解了。 本论文正是为此目的而作。并且，植物新属变枝蕨的发现将无疑为最终达到这个目的做出很大的贡献。

陆地植物对环境变化的响应

陆地植物起源以后，地球上的环境发生了巨大的变化。大气CO2浓度自泥盆纪早期的2000-4OOOμml•mol_1下降至石炭一二叠纪的300μml•mol_1左右，02浓度在泥盆纪至石炭一二叠纪时期，由20-30μml•mol_1上升到70-80μml•mol_1，随后又下降到目前的水平。陆地植物登陆后，形态结构也发生了显著的改变，气生部分表而分化出了通气结构--气孔器和保护结构--角质层。泥盆纪首选标志植物刺镰蕨（Drelpanophycus spinaefrmis）在整个泥盆纪，广布全世界。刺镰蕨的气孔器类型一直存在两种观点，一种认为刺镰蕨的气孔器是平列型，即气孔器山两个保卫细胞和两个副卫细胞组成：另一观点认为刺镰蕨的气孔器为不规则型，即气孔器仅有两个保卫细胞构成，不具副卫细胞。我们借助于扫描电镜、石蜡制片技术和叶表皮离析法，细致地研究了现代石松（Lycopodium japonicum）叶的横切而、表皮及气孔器的内外表面结构，并同刺镰蕨的表皮和气孔器进行了对比。认为刺镰蕨的气孔器和所有的化石石松类及现代石松类的气孔器一样，均属于不规则型。从而解决了关于刺镰蕨气孔器类型的长期争论的关键性科学问题。 胡桃科青钱柳属植物起源于晚白垩世的环北太平洋沿岸，化石植物最早发现于北美古新世和早始新世的Motana,，Wyoming，North Dakota，north Colorado地区，欧亚地区仅出现在渐新世至上新世的Kazakhstan、Germany、Romnania、Russia、Japan、中国云南远谋和四川米易地区。我们将采于吉林省珲春组始新世的叶化石鉴定为一青钱柳相似种，该化石成为东亚地区出现最早的青钱柳属植物，这一发现也支持晚白垩至早第三纪时期环北太平洋两岸曾经相连的观点，青钱柳属在晚白垩由北美起源，在始新世经东亚向欧亚大陆扩散，由于环境变迁，第四纪以后，青钱柳属仪剩一种植物分布于中国的亚热带地区。文中还利用共存分析方法估测出始新世吉林省珲春地区属于暖温带至亚热带气候。 统万城遗址位于我国黄土高原向毛乌素沙漠过渡地带的北缘，属于暖温带森林草原向温带干草原、温带荒漠草原过渡的地区，同时又是东部季风区向西北干旱区过渡的生态环境敏感带。今天统万城地区的自然景观属于沙漠，仅存稀疏的次生灌丛和草本群落。但是，通过对统万城城墙内的孢粉和木材进行的综合研究表明，在约1600年前，当地为温带草原，在塬面或山丘上分布有侧柏林，沟谷、河岸边生长喜温湿的乔木，河流、湖泊、沼泽中水生植物繁盛，在丘间低洼处或盐碱土上分布有灌木和草本植物。当时该地区的年均温为7.8 ℃-9.3℃，最热月平均温度23.0℃-24.9℃，最冷月平均温度-12℃-5.6℃，年较差28.5℃-3 8.2℃，年降雨量403.4-550．Omm，最大月降雨量83.8-123.9mm，最少月降雨量4.4-12.2mm，当时气候比现在温暖湿润，年均温比现在高出0.2-0.7℃，年降雨量也高出60--lOOmm。而如此的历史景观今天已经向南迁移，侧柏林或森林草原退缩至延安以南地区。在此近1600年的时间里，毛乌素沙漠分布范围不断扩大，其南部边缘推进了约200 km，推测沙漠扩展的速率达到平均125m/a。

中国二叠纪—三叠纪陆生植物多样性变化的研究

本文基于华南、华北地区二叠纪—三叠纪陆生植物大化石和孢粉的数据库， 对中国二叠纪—三叠纪陆生植物的多样性变化进行了统计分析研究，并重点探讨了在二叠纪—三叠纪界线（Permian-Triassic Boundary，PTB ）陆生植物是否与同期的海洋动物一样发生了同步的集群灭绝事件。 统计分析表明，华南、华北陆生植物大化石的分异度穿过PTB 均显示了较长时续（约37.8Ma）的下降和残存阶段，而孢粉化石在早三叠世的分异度则是上升的。总体上，陆生植物分异度穿过PTB 的变化较同期的海洋动物平稳缓慢。华南地区陆生植物大化石在晚二叠世末长兴期（Changhsingian）虽然伴随着最高的属灭绝率85.94% 和最低的属新生率28.12%，发生了最大的灭绝事件，但在晚二叠世早期和早三叠世的属的灭绝率也较高，分别为61.02% 和66.67% 。种的灭绝率在晚二叠世早期从早二叠世晚期的39%大幅度上升到80.36%，晚二叠世晚期达峰值97%，早三叠世稍降为93%，显然高于其它时段灭绝率范围（30—70%）。种和属的灭绝率呈现了同样的高峰阶段，从晚二叠世早期至早三叠世，时续为20.8 百万年（Ma）。基于更替率分析，华南地区陆生植物的高更替率事件分别发生在早二叠世晚期（93.75%）、早三叠世（90.92%）和晚三叠世（91.38%），但陆生植物在穿越早二叠世晚期—晚三叠世的整个过程中，更替率波动不大、比较平稳。华北地区陆生植物大化石穿越PTB 的灭绝率比华南地区低，属级高灭绝率事件集中在晚二叠世早期（67.31%）和晚二叠世晚期（63.89%）， 时续为14.8Ma，种级高灭绝率事件与华南地区类似，集中在晚二叠世早期（85.67%）、晚二叠世晚期（90.86%）和早三叠世（80.28% ）三个阶段，时续为20.8Ma 。显而易见，这比同期海洋动物集群灭绝的时续（3—11Ma ）要长。 本文基于这些分析结果，仔细考虑了集群灭绝的4 个特点（即量值、广度、幅度和时续），认为华南、华北陆生植物在PTB 并未发生集群灭绝事件，而是发生了演化替代，即陆生植物穿过PTB 经历了大的植物群重组和新种的演化。总体上，中国二叠纪—三叠纪陆生植物中选择性灭绝非常明显，古生代占优势的种子蕨、真蕨类、木本石松类和楔叶类逐渐被早中生代比较进化的裸子植物和真蕨类植物所替代，陆生植物穿过PTB 显示了危机（灭绝）—残存—复苏—辐射的宏演化式样。

Decadal patterns in atmospheric carbon dioxide as indicators of changing growth and decay of terrestrial vegetation [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): Large-scale changes in the growth and decay of land plants can be deduced from trends in the concentration of atmospherics [sic] carbon dioxide, after removing signals in the recorded data caused by oceanic and industrial disturbances to the concentration.