Nystroemiaceae,a new family of Permian gymnosperms from China with an unusual combination of features

Nystroemiaceae is proposed as a new family of gymnosperms from the Permian of Cathaysia that adds to the diversity of gymnosperms known from this critical time in seed plant evolution. This family is characterized by bifurcating and highly branched pinnate ovuliferous organs bearing bicornute ovules (seeds) and entire leaves with anastomozing veins that are born on complex and modern-looking branching systems with clear axillary branching. The reconstruction is based on numerous large specimens from two localities in North China, in which the different plant parts are attached to each other. The ovulate structures show some apparently plesiomorphic (primitive) character states more typical of early seed plants, whereas the leaves and branches show the clearly apomorphic (derived) character states of broad-leaved gymnosperms.     

Energy–water and seasonal variations in climate underlie the spatial distribution patterns of gymnosperm species richness in China

Studying the pattern of species richness is crucial in understanding the diversity and distribution of organisms in the earth. Climate and human influences are the major driving factors that directly influence the large‐scale distributions of plant species, including gymnosperms. Understanding how gymnosperms respond to climate, topography, and human‐induced changes is useful in predicting the impacts of global change. Here, we attempt to evaluate how climatic and human‐induced processes could affect the spatial richness patterns of gymnosperms in China. Initially, we divided a map of the country into grid cells of 50 × 50 km² spatial resolution and plotted the geographical coordinate distribution occurrence of 236 native gymnosperm taxa. The gymnosperm taxa were separated into three response variables: (a) all species, (b) endemic species, and (c) nonendemic species, based on their distribution. The species richness patterns of these response variables to four predictor sets were also evaluated: (a) energy–water, (b) climatic seasonality, (c) habitat heterogeneity, and (d) human influences. We performed generalized linear models (GLMs) and variation partitioning analyses to determine the effect of predictors on spatial richness patterns. The results showed that the distribution pattern of species richness was highest in the southwestern mountainous area and Taiwan in China. We found a significant relationship between the predictor variable set and species richness pattern. Further, our findings provide evidence that climatic seasonality is the most important factor in explaining distinct fractions of variations in the species richness patterns of all studied response variables. Moreover, it was found that energy–water was the best predictor set to determine the richness pattern of all species and endemic species, while habitat heterogeneity has a better influence on nonendemic species. Therefore, we conclude that with the current climate fluctuations as a result of climate change and increasing human activities, gymnosperms might face a high risk of extinction.     

Evolution of seed storage protein genes: Legumin genes of Ginkgo biloba

Legumin-like seed storage proteins have been intensively studied in crop plants. However, little is known about the molecular evolution of these proteins and their genes and it was assumed that they originated from an ancestral gene that already existed at the beginning of angiosperm evolution. We have evidence for the ubiquitous occurrence of homologous proteins in gymnosperms as well. We have characterized the major seed storage globulin from Ginkgo biloba by amino acid sequencing, which reveals clear homology to legumin-like proteins from angiosperms. The Ginkgo legumin is encoded by a gene family; we describe two of its members. The promoter regions contain sequence motifs which are known to function as regulatory elements involved in seed-specific expression of angiosperm legumins, although the tissues concerned are different in gymnosperms and angiosperms. The Ginkgo legumin gene structure is divergent from that of angiosperms and suggests that the evolution of legumin genes implicated loss of introns. From our data and from functional approaches recently described it becomes obvious that the posttranslational processing site of legumin precursors is less conserved than hitherto assumed. Finally, we present a phylogenetic analysis of legumin encoding sequences and discuss their utility as molecular markers for the reconstruction of seed plant evolution.Correspondence to: K.-P. Häger     

Trait syndromes among North American trees are evolutionarily conserved and show adaptive value over broad geographic scales

Adaptive syndromes and their evolutionary constraints represent a powerful construct for understanding plant distributions. However, it is unclear how the species requirements to face multiple stressors promotes syndrome formation and to which abiotic stressors these syndromes show adaptive value over broad geographic scales. We combined local occurrence data from the U.S. Forest Inventory and Analysis (FIA) of 219 angiosperm and 85 gymnosperm species living across the conterminous US with phylogenies and trait data to identify tree syndromes, their evolutionary conservatism, and their adaptive value over broad scales. Factor analyses and evolutionary model selection revealed that trees possess functional trait syndromes that are strongly conserved. Major syndromes at the species level differed between angiosperms and gymnosperms. While the two main syndromes in angiosperms were related to cold and drought‐waterlogging tolerance, in gymnosperms a trade‐off between shade and drought tolerance was the main syndrome followed by a growth‐fire resistance syndrome. Additional RLQ and fourth‐corner approaches revealed that trait syndromes at the community level were broadly similar to those observed at the species level for angiosperms, although this was less clear for gymnosperms. This suggests that syndrome evolution has played an important role on angiosperm distributions, whereas additional ecological factors explain gymnosperm distributions. Importantly, syndromes show adaptive value, as they were geographically associated with several environmental variables showing structure from continental to local scales, being temperature the main abiotic stressor. Our results indicate that across the conterminous US tree species possess clear syndromes that are subjected to strong evolutionary constraints driving tree species and forest community distribution.     

Ecological and genetic factors linked to contrasting genome dynamics in seed plants

The large-scale replacement of gymnosperms by angiosperms in many ecological niches over time and the huge disparity in species numbers have led scientists to explore factors (e.g. polyploidy, developmental systems, floral evolution) that may have contributed to the astonishing rise of angiosperm diversity. Here, we explore genomic and ecological factors influencing seed plant genomes. This is timely given the recent surge in genomic data. We compare and contrast the genomic structure and evolution of angiosperms and gymnosperms and find that angiosperm genomes are more dynamic and diverse, particularly amongst the herbaceous species. Gymnosperms typically have reduced frequencies of a number of processes (e.g. polyploidy) that have shaped the genomes of other vascular plants and have alternative mechanisms to suppress genome dynamism (e.g. epigenetics and activity of transposable elements). Furthermore, the presence of several characters in angiosperms (e.g. herbaceous habit, short minimum generation time) has enabled them to exploit new niches and to be viable with small population sizes, where the power of genetic drift can outweigh that of selection. Together these processes have led to increased rates of genetic divergence and faster fixation times of variation in many angiosperms compared with gymnosperms.     

Time for a rethink: time sub‐sampling methods in disparity‐through‐time analyses

Disparity‐through‐time analyses can be used to determine how morphological diversity changes in response to mass extinctions, or to investigate the drivers of morphological change. These analyses are routinely applied to palaeobiological datasets, yet, although there is much discussion about how to best calculate disparity, there has been little consideration of how taxa should be sub‐sampled through time. Standard practice is to group taxa into discrete time bins, often based on stratigraphic periods. However, this can introduce biases when bins are of unequal size, and implicitly assumes a punctuated model of evolution. In addition, many time bins may have few or no taxa, meaning that disparity cannot be calculated for the bin and making it harder to complete downstream analyses. Here we describe a different method to complement the disparity‐through‐time tool‐kit: time‐slicing. This method uses a time‐calibrated phylogenetic tree to sample disparity‐through‐time at any fixed point in time rather than binning taxa. It uses all available data (tips, nodes and branches) to increase the power of the analyses, specifies the implied model of evolution (punctuated or gradual), and is implemented in R. We test the time‐slicing method on four example datasets and compare its performance in common disparity‐through‐time analyses. We find that the way we time sub‐sample taxa can change our interpretations of the results of disparity‐through‐time analyses. We advise using multiple methods for time sub‐sampling taxa, rather than just time binning, to gain a better understanding disparity‐through‐time.     

Ecological and evolutionary determinants of a key plant functional trait: wood density and its community-wide variation across latitude and elevation

Wood density is an important trait in trees indicative of their life history and mechanical and physiological strategies. The following examines the evolutionary ecology of wood density using a large database for seed plants. In particular, we focused on the geographic and phylogenetic variation in wood density for both gymnosperms and angiosperms. A phylogenetic supertree was constructed for over 4600 taxa, allowing for comprehensive analyses of divergences across the seed plant phylogeny. Community-wide means and variances for wood densities were quantified for 171 standardized forest communities. Wood density was generally highly conserved across the entire seed plant phylogeny, yet large divergences were found within the rosid clade. Geographic and community variation in wood density, however, was significantly lower in temperate and high elevation communities, dominated by gymnosperms, than in tropical lowland communities, dominated by angiosperms, suggesting an increase in trait and, to some extent, clade filtering with latitude and elevation. Together, our results support the notion that both biotic and abiotic forces have been important in the evolution of wood density as well as in controlling the observed trait mean and variance across geographic gradients.     

The origin of Darwin’s “abominable mystery”

The phrase “Darwin’s abominable mystery” is frequently used with reference to a range of outstanding questions about the evolution of the plant group today known as the angiosperms. Here, I seek to more fully understand what prompted Darwin to coin the phrase in 1879, and the meaning he attached to it, by surveying the systematics, paleobotanical records, and phylogenetic hypotheses of his time. In the light of this historical research, I argue that Darwin was referring to the origin only of a subset of what are today called angiosperms: a (now obsolete) group equivalent to the “dicotyledons” of the Hooker and Bentham system. To Darwin and his contemporaries, the dicotyledons’ fossil record began abruptly and with great diversity in the Cretaceous, whereas the gymnosperms and monocotyledons were thought to have fossil records dating back to the Carboniferous or beyond. Based on their morphology, the dicotyledons were widely seen by botanists in Darwin’s time (unlike today) as more similar to the gymnosperms than to the monocotyledons. Thus, morphology seemed to point to gymnosperm progenitors of dicotyledons, but this hypothesis made the monocotyledons, given their (at the time) apparently longer fossil record, difficult to place. Darwin had friendly disagreements about the mystery of the dicotyledons’ abrupt appearance in the fossil record with others who thought that their evolution must have been more rapid than his own gradualism would allow. But the mystery may have been made “abominable” to him because it was seen by some contemporary paleobotanists, most notably William Carruthers, the Keeper of Botany at the British Museum, as evidence for divine intervention in the history of life. Subsequent developments in plant systematics and paleobotany after 1879 meant that Darwin’s letter was widely understood to be referring to the abrupt appearance of all angiosperms when it was published in 1903, a meaning that has been attached to it ever since.     

种子植物抗细胞凋亡DAD基因的演化

抗细胞凋亡基因(DAD)是一个高度保守的细胞凋亡抑制基因,在植物生长发育中承担重要功能。为全面了解DAD基因在种子植物中的分布和演化规律,该文利用31种植物的全基因组数据,通过生物信息学手段,深入探讨和分析了不同植物类群中DAD基因的拷贝数目、基因结构和染色体定位,并综合另外7种裸子植物的转录组数据探讨了其在种子植物中的演化趋势。结果表明,DAD基因属于低拷贝基因,在不同种子植物中只具有1–3个拷贝;不同DAD基因编码的氨基酸长度在108–170 aa之间变动。同线性和系统发育分析进一步表明,种子植物DAD基因的演化具有明显的谱系特异性。随机复制和染色体大片段复制及其随后的基因丢失可能是其维持低拷贝的重要方式。     

The Evolution of euAPETALA2 Genes in Vascular Plants: From Plesiomorphic Roles in Sporangia to Acquired Functions in Ovules and Fruits

The field of evolutionary developmental biology can help address how morphological novelties evolve, a key question in evolutionary biology. In Arabidopsis thaliana, APETALA2 (AP2) plays a role in the development of key plant innovations including seeds, flowers, and fruits. AP2 belongs to the AP2/ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR family which has members in all viridiplantae, making it one of the oldest and most diverse gene lineages. One key subclade, present across vascular plants is the euAPETALA2 (euAP2) clade, whose founding member is AP2. We reconstructed the evolution of the euAP2 gene lineage in vascular plants to better understand its impact on the morphological evolution of plants, identifying seven major duplication events. We also performed spatiotemporal expression analyses of euAP2/TOE3 genes focusing on less explored vascular plant lineages, including ferns, gymnosperms, early diverging angiosperms and early diverging eudicots. Altogether, our data suggest that euAP2 genes originally contributed to spore and sporangium development, and were subsequently recruited to ovule, fruit and floral organ development. Finally, euAP2 protein sequences are highly conserved; therefore, changes in the role of euAP2 homologs during development are most likely due to changes in regulatory regions.     

Evolution of DNA amounts across land plants (embryophyta)

BACKGROUND AND AIMS: DNA C-values in land plants (comprising bryophytes, lycophytes, monilophytes, gymnosperms and angiosperms) vary approximately 1000-fold from approx. 0.11 to 127.4 pg. To understand the evolutionary significance of this huge variation it is essential to evaluate the phylogenetic component. Recent increases in C-value data (e.g. Plant DNA C-values database; release 2.0, January 2003; http://www.rbgkew.org.uk/cval/homepage.html) together with improved consensus of relationships between and within land plant groups makes such an analysis timely. METHODS: Insights into the distribution of C-values in each group of land plants were gained by superimposing available C-value data (4119 angiosperms, 181 gymnosperms, 63 monilophytes, 4 lycophytes and 171 bryophytes) onto phylogenetic trees. To enable ancestral C-values to be reconstructed for clades within land plants, character-state mapping with parsimony and MacClade was also applied. KEY RESULTS AND CONCLUSIONS: Different land plant groups are characterized by different C-value profiles, distribution of C-values and ancestral C-values. For example, the large ( approximately 1000-fold) range yet strongly skewed distribution of C-values in angiosperms contrasts with the very narrow 12-fold range in bryophytes. Further, character-state mapping showed that the ancestral genome sizes of both angiosperms and bryophytes were reconstructed as very small (i.e. < or =1.4 pg) whereas gymnosperms and most branches of monilophytes were reconstructed with intermediate C-values (i.e. >3.5, <14.0 pg). More in-depth analyses provided evidence for several independent increases and decreases in C-values; for example, decreases in Gnetaceae (Gymnosperms) and heterosperous water ferns (monilophytes); increases in Santalales and some monocots (both angiosperms), Pinaceae, Sciadopityaceae and Cephalotaxaceae (Gymnosperms) and possibly in the Psilotaceae + Ophioglossaceae clade (monilophytes). Thus, in agreement with several focused studies within angiosperm families and genera showing that C-values may both increase and decrease, it is apparent that this dynamic pattern of genome size evolution is repeated on a broad scale across land plants.     

New Insights into Evolution of the ABC Transporter Family in Mesostigma viride,a Unicellular Charophyte Algae

ATP-binding cassette (ABC) transporters play an important role in driving the exchange of multiple molecules across cell membranes. The plant ABC transporter family is among the largest protein families, and recent progress has advanced our understanding of ABC classification. However, the ancestral form and deep origin of plant ABCs remain elusive. In this study, we identified 59 ABC transporters in Mesostigma viride, a unicellular charophyte algae that represents the earliest diverging lineage of streptophytes, and 1034 ABCs in genomes representing a broad taxonomic sampling from distantly related plant evolutionary lineages, including chlorophytes, charophytes, bryophytes, lycophytes, gymnosperms, basal angiosperms, monocots, and eudicots. We classified the plant ABC transporters by comprehensive phylogenetic analysis of each subfamily. Our analysis revealed the ancestral type of ABC proteins as well as duplication and gene loss during plant evolution, contributing to our understanding of the functional conservation and diversity of this family. In summary, this study provides new insight into the origin and evolution of plant ABC transporters.     

The Use (and Misuse) of Phylogenetic Trees in Comparative Behavioral Analyses

Phylogenetic comparative methods play a critical role in our understanding of the adaptive origin of primate behaviors. To incorporate evolutionary history directly into comparative behavioral research, behavioral ecologists rely on strong, well-resolved phylogenetic trees. Phylogenies provide the framework on which behaviors can be compared and homologies can be distinguished from similarities due to convergent or parallel evolution. Phylogenetic reconstructions are also of critical importance when inferring the ancestral state of behavioral patterns and when suggesting the evolutionary changes that behavior has undergone. Improvements in genome sequencing technologies have increased the amount of data available to researchers. Recently, several primate phylogenetic studies have used multiple loci to produce robust phylogenetic trees that include hundreds of primate species. These trees are now commonly used in comparative analyses and there is a perception that we have a complete picture of the primate tree. But how confident can we be in those phylogenies? And how reliable are comparative analyses based on such trees? Herein, we argue that even recent molecular phylogenies should be treated cautiously because they rely on many assumptions and have many shortcomings. Most phylogenetic studies do not model gene tree diversity and can produce misleading results, such as strong support for an incorrect species tree, especially in the case of rapid and recent radiations. We discuss implications that incorrect phylogenies can have for reconstructing the evolution of primate behaviors and we urge primatologists to be aware of the current limitations of phylogenetic reconstructions when applying phylogenetic comparative methods.     

Characterization of the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in female and male cones of the conifer genera Picea, Podocarpus, and Taxus: implications for current evo-devo hypotheses for gymnosperms

The identity of genes causally implicated in the development and evolutionary origin of reproductive characters in gymnosperms is largely unknown. Working within the framework of plant evolutionary developmental biology, here we have cloned, sequenced, performed phylogenetic analyses upon and tested the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in reproductive structures from selected species of the conifer genera Picea, Podocarpus, and Taxus. Contrary to expectations based on previous assessments, expression of LFY/FLO and NLY in cones of these taxa was found to occur simultaneously in a single reproductive axis, initially overlapping but later in mutually exclusive primordia and/or groups of developing cells in both female and male structures. These observations directly affect the status of the "mostly male theory" for the origin of the angiosperm flower. On the other hand, comparative spatiotemporal patterns of the expression of these genes suggest a complex genetic regulatory network of cone development, as well as a scheme of functional divergence for LFY/FLO with respect to NLY homologs in gymnosperms, both with clear heterochronic aspects. Results presented in this study contribute to the understanding of the molecular-genetic basis of morphological evolution in conifer cones, and may aid in establishing a foundation for gymnosperm-specific, testable evo-devo hypotheses.     

Nucleotide distribution in gymnosperm nuclear sequences suggests a model for GC-content change in land-plant nuclear genomes

Nuclear protein coding sequences from gymnosperms are currently scarce. We have determined 4 kb of nuclear protein coding sequences from gymnosperms and have collected and analyzed >60 kb of nuclear sequences from gymnosperms and nonspermatophytes in order to better understand processes influencing genome evolution in plants. We show that conifers possess both biased and nonbiased genes with respect to GC content, as found in monocots, suggesting that the common ancestor of conifers and monocots may have possessed both biased and nonbiased genes. The lack of biased genes in dicots is suggested to be a derived character for this lineage. We present a simple but speculative model of land-plant genome evolution which considers changes in GC bias and CpG frequency, respectively, as independent processes and which can account for several puzzling aspects of observed nucleotide frequencies in plant genes.Abbreviations GC guanosine plus cytosine - GapC glycolytic glyceraldehyde-3-phosphate dehydrogenase, EC 1.2.1.12 - GapA Calvin cycle glyceraldehyde-3-phosphate dehydrogenase, EC 1.2.1.13 - O/E ratio of observed-to-expected dinucleotide frequencies Correspondence to: W. Martin     

Divergence in structure and function of tau class glutathione transferase from Pinus tabulaeformis,P. yunnanensis and P. densata

Glutathione transferases (GSTs) are a family of enzymes that play important roles in stress tolerance and detoxification in plants. The plant GSTs are divided into four classes (phi, tau, zeta and theta), among which tau is the most numerously represented. To date, studies on GSTs in plants have focused largely on crop species. There is extremely little information on the molecular characteristics of GSTs in gymnosperms. Generalization on GST characteristics unique to gymnosperms and the patterns of GST evolution in plants cannot be made before more members of the gene family in conifers are described. In this study we report three new GSTs from Pinus tabulaeformis, Pinus densata and Pinus yunnanensis. Structural and phylogenetic analyses placed these three GSTs in tau class. The tau GST class is subdivided into three clades and this subdivision seems an ancient event that may have pre-dated the gymnosperm and angiosperm split. Sequence analysis revealed a highly conserved N-terminal domain in contrast to a highly variable C-terminal domain. Mutations even outside the critical glutathione-binding site in N-terminal domain can have pronounced effect on GST catalytic property. Thus, sequence similarity does not parallel functional specificity. The high diversity in C-terminal domain determines a wide range of substrate selectivity and specificity among tau GSTs. Thus the a few conserved residues in C-terminal domain seem essential to maintain the structure of the domain and the protein dimer. More extensive data on GST family organization and a thorough gene-by-gene analysis in conifers are needed to advance our understanding of the true diversity and evolution of GST in structure and function in plants.     

Sensory Perception: Lessons from Synesthesia: Using Synesthesia to Inform the Understanding of Sensory Perception

Synesthesia, the conscious, idiosyncratic, repeatable, and involuntary sensation of one sensory modality in response to another, is a condition that has puzzled both researchers and philosophers for centuries. Much time has been spent proving the condition’s existence as well as investigating its etiology, but what can be learned from synesthesia remains a poorly discussed topic. Here, synaesthesia is presented as a possible answer rather than a question to the current gaps in our understanding of sensory perception. By first appreciating the similarities between normal sensory perception and synesthesia, one can use what is known about synaesthesia, from behavioral and imaging studies, to inform our understanding of “normal” sensory perception. In particular, in considering synesthesia, one can better understand how and where the different sensory modalities interact in the brain, how different sensory modalities can interact without confusion ― the binding problem ― as well as how sensory perception develops.