Different facets of alpha and beta diversity of benthic diatoms along stream watercourse in a large near-natural catchment.

Understanding the processes and mechanisms that shape the distribution patterns and variations of biodiversity along spatial gradients continues to be a priority for ecological research. We focused on the biodiversity of benthic diatom communities within a large near-natural watershed. The objectives are: (1) to explore the overall spatial patterns of benthic diatom biodiversity; (2) to investigate the effects associated with watercourse position and environmental variables, as well as both common and rare species on two facets (i.e., taxonomic and functional) of alpha and beta diversity; and (3) to unveil the mechanisms underlying their spatial variations. Alpha diversity indices along the stream watercourse showed a clear increasing trend from upstream to downstream sites. Results of random forest regression identified conductivity as the primary factor influencing functional alpha diversity, while elevation emerged as the predominant factor for taxonomic alpha diversity. Beta diversity partitioning revealed that taxonomic beta diversity generally exceeded functional beta diversity. These diversity measures exhibited different patterns along the watercourse position: taxonomic beta diversity remained relatively consistent along the watercourse, whereas functional total beta diversity and its two components of middle stream sites were lower than those of upstream and downstream sites. Functional beta diversity was sustained by dominant and common species, while rare species made significant contributions to taxonomic beta diversity. Both taxonomic and functional beta diversity and its components displayed a stronger influence from spatial factors than from local environmental, geo-climatic, and nutrient variables. Collectively, taxonomic and functional alpha and beta diversity demonstrated distinct responses to the main environmental gradients and spatial factors within our catchment, highlighting their different insights into diatom diversity. Furthermore, research is required to assess the generalizability of our findings to similar ecosystems. In addition, this study presents opportunities for expansion to include other taxa (e.g., macroinvertebrates and fish) to gain a comprehensive understanding of the driving mechanisms behind stream biodiversity.

Three cassava A20/AN1 family genes, Metip3 (5, and 7), can bestow on tolerance of plants to multiple abiotic stresses but show functional convergence and divergence.

A20/AN1 zinc-finger domain-containing genes are very promising candidates in improving plant tolerance to abiotic stresses, but considerably less is known about functions and mechanisms for many of them. In this study, Metip3 (5, and 7), cassava (Manihot esculenta) A20/AN1 genes carrying one A20 domain and one AN1 domain, were functionally characterized at different layers. Metip3 (5, and 7) proteins were all located in the nucleus. No interactions were found between these three proteins. Metip3 (5, and 7)-expressing Arabidopsis was more tolerant to multiple abiotic stresses by Na, Cd, Mn, Al, drought, high temperature, and low temperature. Metip3- and Metip5-expressing Arabidopsis was sensitive to Cu stress, while Metip7-expressing Arabidopsis was insensitive. The H2O2 production significantly decreased in all transgenic Arabidopsis, however, O2·- production significantly decreased in Metip3- and Metip5-expressing Arabidopsis but did not significantly changed in Metip7-expressing Arabidopsis under drought. Metip3 (5, and 7) expression-silenced cassava showed the decreased tolerance to drought and NaCl, presented significant decreases in superoxide dismutase and catalase activities and proline content, and displayed a significant increase in malondialdehyde content under drought. Taken together with transcriptome sequencing analysis, it is suggested that Metip5 gene can not only affect signal transduction related to plant hormone, mitogen activated protein kinases, and starch and sucrose metabolism, DRE-binding transcription factors, and antioxidants, conferring the drought tolerance, but also might deliver the signals from DREB2A INTERACTING PROTEIN1, E3 ubiquitin-protein ligases to proteasome, leading to the drought intolerance. The results are informative not only for further study on evolution of A20/AN1 genes but also for development of climate resilient crops.

CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species.

Living species vary significantly in phenotype and genomic content. Sophisticated statistical methods linking genes with phenotypes within a species have led to breakthroughs in complex genetic diseases and genetic breeding. Despite the abundance of genomic and phenotypic data available for thousands of species, finding genotype-phenotype associations across species is challenging due to the non-independence of species data resulting from common ancestry. To address this, we present CALANGO (comparative analysis with annotation-based genomic components), a phylogeny-aware comparative genomics tool to find homologous regions and biological roles associated with quantitative phenotypes across species. In two case studies, CALANGO identified both known and previously unidentified genotype-phenotype associations. The first study revealed unknown aspects of the ecological interaction between Escherichia coli, its integrated bacteriophages, and the pathogenicity phenotype. The second identified an association between maximum height in angiosperms and the expansion of a reproductive mechanism that prevents inbreeding and increases genetic diversity, with implications for conservation biology and agriculture.

Phylogenetic analysis and interactomics study unveil gene co-optive evolution of LysR-type transcription regulators across non-pathogenic, opportunistic, and pathogenic mycobacteria.

Mycobacterial species is known for inhabiting various niches ranging from soil to harsh intracellular environment of animal hosts and their survival through constant changes. For survival and persistence, these organisms must quickly adapt by bringing shift in their metabolism. Metabolic shifts are brought by sensing the environmental cues usually by membrane localized sensor molecules. These signals are transmitted to regulators of various metabolic pathways leading to post-translational modifications of regulators ultimately resulting in altered metabolic state of the cell. Multiple regulatory mechanisms have been unearthed so far that play crucial role in adapting to these situations, and among them, the signal-dependent transcriptional regulators mediated responses are integral for the microbes to perceive environmental signals and generate appropriate adaptive responses. LysR-type transcriptional regulators (LTTRs) form the largest family of transcriptional regulators, which are present in all kingdoms of life. Their numbers vary among bacterial genera and even in different mycobacterial species. To understand the evolutionary aspect of pathogenicity based on LTTRs, we performed phylogenetic analysis of LTTRs encoded by several mycobacterial species representing non-pathogenic (NP), opportunistic (OP), and totally pathogenic (TP) mycobacteria. Our results showed that LTTRs of TP clustered separately from LTTRs of NP and OP mycobacteria. In addition, LTTRs frequency per Mb of genome was reduced in TP when compared with NP and OP. Further, the protein-protein interactions and degree-based network analysis showed concomitant increased interactions per LTTRs with increase in pathogenicity. These results suggested the increase in regulon of LTTRs during evolution of TP mycobacteria.

Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome.

The gut microbiomes of non-human primates have received a great deal of attention due to their close relationship to humans. In recent years, these studies have mainly focused on the gut microbiome of wild primates, which will be helpful to understanding the evolution of primates and their gut microbiomes (e.g., gut microbiome plasticity and diet flexibility). However, there is still a lack of basic information on the gut microbiomes from wild populations. Here, we investigated the gut microbial composition (16S rRNA gene) and function (metagenome and metagenome-assembled genomes (MAGs)) of Yunnan snub-nosed monkey populations in Weixi County, Yunnan Province, China, that had diets either completely based on wild-foraging or were regularly supplemented with human provisioned food. We found a significant difference in the gut microbiome between these two populations: the gut microbiome of the wild-foraging (no food provision) population was enriched genes involved in the detoxification of bamboo cyanide (high proportion of bamboo shoot intake) and chitin (from insect diet) digestion, while the gut microbiome of the food provisioned (e.g., fruits) wild populations were enriched genes involved in carbohydrate metabolism. Moreover, the gut microbiome of the wild-foraging population shared a putatively functional convergence with the gut microbiome of wild bamboo-eating pandas: such as microbes and genes involved in the cyanide detoxification. Therefore, the gut microbiome of the Yunnan snub-nosed monkey displayed the potential plasticity in response to diet flexibility. Long-term food-provisioning of the wild population has led to dramatic changes in gut microbial composition, function, and even antibiotic resistance. The antibiotic resistance profile for the wild Yunnan snub-nosed monkey population could be considered the baseline and an important piece of information for conservation.

Contrasting responses to soil and water salinity in stomata and canopy traits produced convergence of water-use in tomatoes (Solanum esculentum) and okra (Abelmoschus esculentus): application to water management.

BACKGROUND: Salinity constrains agricultural sustainability and crops differ in their response. We tested the hypothesis that contrasting responses in canopy and stomatal traits to salinity will cause convergence of water-use in okra and tomato. RESULTS: Stomata were found almost exclusively (>90%) on the lower leaf surface of tomato, but okra produced ~30% of stomata on the upper leaf surface. While salinity reduced the magnitudes of canopy and stomata traits in tomato, stomata traits were either unaffected or enhanced in okra. Salinity reduced the rates and duration of stomatal conductance (gs ) in both crops, more severely in tomato, in which gs was restricted to early mornings in contrast to its bell-shape trend in okra. The superiority of okra in its stomata traits was compensated by the larger plant canopies in tomato, resulting in both daytime canopy transpiration and total plant water-use within 17% and 28%, respectively, of each other for the two crops. A tight stomatal control of transpiration that minimised use of water and its uptake from the soil conferred a superior salinity tolerance on tomato over okra. In both crops, stomata density (D) was inversely correlated with stomata area (A), while water-use was positively correlated with plant leaf area, in addition to D and A in tomato; gs was also correlated with stomata area index in tomato. CONCLUSION: Differences in water-use for both crops were relatively narrow, despite the several-fold differences in their canopy and stomata traits. Under saline conditions, irrigation intervals should be long for tomato but short for okra. © 2021 Society of Chemical Industry.

Insights into the Evolution of Spermatogenesis-Related Ubiquitin-Proteasome System Genes in Abdominal Testicular Laurasiatherians.

During embryonic development in mammals, the testicles generally descend into the scrotum, making the testicular temperature 2-4 °C lower than the core temperature via heat exchange and clearance, and thus more beneficial for normal spermatogenesis. Failure to descend, known as cryptorchidism, carries a series of risks such as infertility and testicular cancer. However, some mammals have evolved abdominal testes while maintaining healthy reproduction. To explore the underlying molecular mechanism, we conducted comparative genomic analyses and functional assays on the spermatogenesis-related ubiquitin-proteasome system (UPS) genes essential to sperm formation in representative laurasiatherians. Here, positive selection and rapid evolution of spermatogenesis-related UPS genes were identified in the abdominal testicular laurasiatherians. Moreover, potential convergent amino acids were found between distantly related species with similar abdominal testicles and functional analyses showed RNF8 (V437I) in abdominal testicular species (437I) has a stronger ubiquitination ability, which suggests that the mammals with abdominal testes might exhibit enhanced sperm cell histone clearance to maintain sperm formation. This evidence implies that, in response to "cryptorchidism injury", spermatogenesis-related UPS genes in the abdominal testicular species might have undergone adaptive evolution to stabilize sperm formation. Thus, our study could provide some novel insights into the reproductive adaptation in abdominal testicular mammals.

Convergent Phenotypic Evolution of Rhodopsin for Dim-Light Sensing across Deep-Diving Vertebrates.

Rhodopsin comprises an opsin attached to a retinal chromophore and is the only visual pigment conferring dim-light vision in vertebrates. On activation by photons, the retinal group becomes detached from the opsin, which is then inactive until it is recharged. Of all vertebrate species, those that dive face unique visual challenges, experiencing rapid decreases in light level and hunting in near darkness. Here, we combine sequence analyses with functional assays to show that the rhodopsin pigments of four divergent lineages of deep-diving vertebrates have undergone convergent increases in their retinal release rate. We compare gene sequences and detect parallel amino acids between penguins and diving mammals and perform mutagenesis to show that a single critical residue fully explains the observed increases in retinal release rate in both the emperor penguin and beaked whale. At the same time, we find that other shared sites have no significant effect on retinal release, implying that convergence does not always signify adaptive significance. We propose that accelerated retinal release confers rapid rhodopsin recharging, enabling the visual systems of diving species to adjust quickly to changing light levels as they descend through the water column. This contrasts with nocturnal species, where adaptation to darkness has been attributed to slower retinal release rates.

Elevated nitrate simplifies microbial community compositions and interactions in sulfide-rich river sediments.

Excessive nitrate in water systems is prevailing and a global risk of human health. Polluted river sediments are dominated by anaerobes and often the hotspot of denitrification. So far, little is known about the ecological effects of nitrate pollution on microbial dynamics, especially those in sulfide-rich sediments. Here we simulated a nitrate surge and monitored the microbial responses, as well as the changes of important environmental parameters in a sulfide-rich river sediment for a month. Our analysis of sediment microbial communities showed that elevated nitrate led to (i) a functional convergence at denitrification and sulfide oxidation, (ii) a taxonomic convergence at Proteobacteria, and (iii) a significant loss of biodiversity, community stability and other functions. Two chemolithotrophic denitrifiers Thiobacillus and Luteimonas were enriched after nitrate amendment, although the original communities were dominated by methanogens and syntrophic bacteria. Also, serial dilutions of sediment microbial communities found that Thiobacillus thiophilus dominated 18/30 communities because of its capability of simultaneous nitrate reduction and sulfide oxidation. Additionally, our network analysis indicated that keystone taxa seemed more likely to be native auxotrophs (e.g., syntrophic bacteria, methanogens) rather than dominant denitrifiers, possibly because of the extensive interspecific cross-feeding they estabilished, while environment perturbations probably disrupted that cross-feeding and simplified microbial interactions. This study advances our understanding of microbial community responses to nitrate pollution and possible mechanism in the sulfide-rich river sediment.

Convergent spectral shifts to blue-green vision in mammals extends the known sensitivity of vertebrate M/LWS pigments.

Daylight vision in most mammals is mediated predominantly by a middle/long wavelength-sensitive (M/LWS) pigment. Although spectral sensitivity and associated shifts in M/LWS are mainly determined by five critical sites, predicted phenotypic variation is rarely validated, and its ecological significance is unclear. We experimentally determine spectral tuning of M/LWS pigments and show that two highly divergent taxa, the gerbil and the elephant-shrew, have undergone independent dramatic blue-green shifts to 490 nm. By generating mutant proteins, we identify additional critical sites contributing to these shifts. Our results, which extend the known range of spectral tuning of vertebrate M/LWS, provide a compelling case of functional convergence, likely related to parallel adaptive shifts from nocturnal to brighter light conditions in similar habitats.

Duplications and Functional Convergence of Intestinal Carbohydrate-Digesting Enzymes.

Vertebrate diets and digestive physiologies vary tremendously. Although the contribution of ecological and behavioral features to such diversity is well documented, the roles and identities of individual intestinal enzymes shaping digestive traits remain largely unexplored. Here, we show that the sucrase-isomaltase (SI)/maltase-glucoamylase (MGAM) dual enzyme system long assumed to be the conserved disaccharide and starch digestion framework in all vertebrates is absent in many lineages. Our analyses indicate that independent duplications of an ancestral SI gave rise to the mammalian-specific MGAM, as well as to other duplicates in fish and birds. Strikingly, the duplicated avian enzyme exhibits similar activities to MGAM, revealing an unexpected case of functional convergence. Our results highlight digestive enzyme variation as a key uncharacterized component of dietary diversity in vertebrates.

Cross-Regional View of Functional and Taxonomic Microbiota Composition in Obesity and Post-obesity Treatment Shows Country Specific Microbial Contribution.

Gut microbiota has been shown to have an important influence on host health. The microbial composition of the human gut microbiota is modulated by diet and other lifestyle habits and it has been reported that microbial diversity is altered in obese people. Obesity is a worldwide health problem that negatively impacts the quality of life. Currently, the widespread treatment for obesity is bariatric surgery. Interestingly, gut microbiota has been shown to be a relevant factor in effective weight loss after bariatric surgery. Since that the human gut microbiota of normal subjects differs between geographic regions, it is possible that rearrangements of the gut microbiota in dysbiosis context are also region-specific. To better understand how gut microbiota contribute to obesity, this study compared the composition of the human gut microbiota of obese and lean people from six different regions and showed that the microbiota compositions in the context of obesity were specific to each studied geographic location. Furthermore, we analyzed the functional patterns using shotgun DNA metagenomic sequencing and compared the results with other obesity-related metagenomic studies, we observed that microbial contribution to functional pathways were country-specific. Nevertheless, our study showed that although microbial composition of obese patients was country-specific, the overall metabolic functions appeared to be the same between countries, indicating that different microbiota components contribute to similar metabolic outcomes to yield functional redundancy. Furthermore, we studied the microbiota functional changes of obese patients after bariatric surgery, by shotgun metagenomics sequencing and observed that changes in functional pathways were specific to the type of obesity treatment. In all, our study provides new insights into the differences and similarities of obese gut microbiota in relation to geographic location and obesity treatments.

Community divergence and convergence along experimental gradients of stress and disturbance.

We created 24 mesocosms containing mixtures of herbaceous species arranged along experimentally maintained gradients of stress (external abiotic constraints limiting biomass production) and disturbance (events causing partial or total live biomass destruction) in order to determine the degree to which community assembly is deterministic or historically contingent during succession. In this 7-yr experiment, we found taxonomic divergence and functional convergence during the last 3 yr. Although communities became more functionally dissimilar as the difference in the level of stress increased, they were equally taxonomically different irrespective of the amount of difference between them in terms of stress and disturbance. In addition, comparing communities experiencing the same conditions, taxonomic community structure was more dissimilar as the levels of stress and disturbance decreased. Therefore, community assembly was largely deterministic from a functional perspective but more historically contingent from a taxonomic perspective, and the relative importance of taxonomic historical contingency decreased as the levels of stress and disturbance frequency increased.

Occupancy and overlap in trait space along a successional gradient in Mediterranean old fields.

PREMISE OF THE STUDY: Secondary succession is a worldwide phenomenon affecting plant communities. Studying functional variation during succession aids in understanding the mechanisms through which environmental shifts drive succession. We investigated changes in the functional space occupied by herbaceous communities during succession. Furthermore, since different traits are differently affected by environmental conditions, we asked how considering different sets of plant traits impacts those changes. METHODS: Using a chronosequence of Mediterranean old fields (2-42 yr after abandonment), we analyzed shifts of the occupied functional space during succession, how the volume of occupied functional space varies compared with null expectations, and the functional overlap between communities of different successional status. We repeated these analyses considering (1) the leaf-height-seed functional dimensions separately and together and (2) different sets of traits representing those dimensions. KEY RESULTS: From early to late succession, a shift toward nutrient conservative-light competitive species occurred. Functional strategies of mid-successional communities appeared more diverse than expected by chance and less diverse than expected for early and late communities. Early and middle stages overlapped the most. These patterns were generally robust to the choice of functional axes, though important trait-specific exceptions occurred. CONCLUSIONS: We showed evidence for a well-defined history of successive dominance of different assembly mechanisms along succession, resulting in a generally stronger functional diversification in mid-succession. We also demonstrated that different traits typically grouped under one functional dimension can substantially affect the results, discouraging the use of surrogate traits from the same dimension.

QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically.

Transcription Activator-Like (TAL) effectors from Xanthomonas plant pathogenic bacteria can bind to the promoter region of plant genes and induce their expression. DNA-binding specificity is governed by a central domain made of nearly identical repeats, each determining the recognition of one base pair via two amino acid residues (a.k.a. Repeat Variable Di-residue, or RVD). Knowing how TAL effectors differ from each other within and between strains would be useful to infer functional and evolutionary relationships, but their repetitive nature precludes reliable use of traditional alignment methods. The suite QueTAL was therefore developed to offer tailored tools for comparison of TAL effector genes. The program DisTAL considers each repeat as a unit, transforms a TAL effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. The program FuncTAL is aimed at finding TAL effectors with similar DNA-binding capabilities. It calculates correlations between position weight matrices of potential target DNA sequence predicted from the RVD sequence, and builds trees based on these correlations. The programs accurately represented phylogenetic and functional relationships between TAL effectors using either simulated or literature-curated data. When using the programs on a large set of TAL effector sequences, the DisTAL tree largely reflected the expected species phylogeny. In contrast, FuncTAL showed that TAL effectors with similar binding capabilities can be found between phylogenetically distant taxa. This suite will help users to rapidly analyse any TAL effector genes of interest and compare them to other available TAL genes and should improve our understanding of TAL effectors evolution. It is available at http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi.

Extending the generality of leaf economic design principles in the cycads, an ancient lineage.

Cycads are the most ancient lineage of living seed plants, but the design of their leaves has received little study. We tested whether cycad leaves are governed by the same fundamental design principles previously established for ferns, conifers and angiosperms, and characterized the uniqueness of this relict lineage in foliar trait relationships. Leaf structure, photosynthesis, hydraulics and nutrient composition were studied in 33 cycad species from nine genera and three families growing in two botanical gardens. Cycads varied greatly in leaf structure and physiology. Similarly to other lineages, light-saturated photosynthetic rate per mass (Am ) was related negatively to leaf mass per area and positively to foliar concentrations of chlorophyll, nitrogen (N), phosphorus and iron, but unlike angiosperms, leaf photosynthetic rate was not associated with leaf hydraulic conductance. Cycads had lower photosynthetic N use efficiency and higher photosynthetic performance relative to hydraulic capacity compared with other lineages. These findings extend the relationships shown for foliar traits in angiosperms to the cycads. This functional convergence supports the modern synthetic understanding of leaf design, with common constraints operating across lineages, even as they highlight exceptional aspects of the biology of this key relict lineage.

Functional convergence spasm.

Convergence spasm (CS) means intermittent episodes of convergence, miosis and accommodation with disconjugate gaze mimicking abducens palsy. The organic causes range from metabolic to host of neurological and ophthalmic diseases that we describe. It was first described as a presentation of psychogenic disorders by von Graefe as early as in 1856. Nonetheless, patients exhibiting this sign are often subjected to plethora of unnecessary, sophisticated and invasive diagnostic procedures. Such functional cases were treated with either cycloplegic/placebo eye drop or amytal abreaction. Though epidemiological studies suggest that conversion disorder is equally prevalent in industrialized nations and developing countries, a few cases of functional CS are reported from West including Asia, that to, decade(s) before and none from India, to the best of our knowledge. We illustrate a case of functional CS with photograph after consent from patient and its successful treatment.

Sustained periodic terrestrial locomotion in air-breathing fishes.

While emergent behaviours have long been reported for air-breathing osteichthyians, only recently have researchers undertaken quantitative analyses of terrestrial locomotion. This review summarizes studies of sustained periodic terrestrial movements by air-breathing fishes and quantifies the contributions of the paired appendages and the axial body to forward propulsion. Elongate fishes with axial-based locomotion, e.g. the ropefish Erpetoichthys calabaricus, generate an anterior-to-posterior wave of undulation that travels down the axial musculoskeletal system and pushes the body against the substratum at multiple points. In contrast, appendage-based locomotors, e.g. the barred mudskipper Periophthalmus argentilineatus, produce no axial bending during sustained locomotion, but instead use repeated protraction-retraction cycles of the pectoral fins to elevate the centre of mass and propel the entire body anteriorly. Fishes that use an axial-appendage-based mechanism, e.g. walking catfishes Clarias spp., produce side-to-side, whole-body bending in co-ordination with protraction-retraction cycles of the pectoral fins. Once the body is maximally bent to one side, the tail is pressed against the substratum and drawn back through the mid-sagittal plane, which elevates the centre of mass and rotates it about a fulcrum formed by the pectoral fin and the ground. Although appendage-based terrestrial locomotion appears to be rare in osteichthyians, many different species appear to have converged upon functionally similar axial-based and axial-appendage-based movements. Based on common forms observed across divergent taxa, it appears that dorsoventral compression of the body, elongation of the axial skeleton or the presence of robust pectoral fins can facilitate effective terrestrial movement by air-breathing fishes.

The evolution of floral nectaries in Disa (Orchidaceae: Disinae): recapitulation or diversifying innovation?

BACKGROUND AND AIMS: The Orchidaceae have a history of recurring convergent evolution in floral function as nectar production has evolved repeatedly from an ancestral nectarless state. However, orchids exhibit considerable diversity in nectary type, position and morphology, indicating that this convergence arose from alternative adaptive solutions. Using the genus Disa, this study asks whether repeated evolution of floral nectaries involved recapitulation of the same nectary type or diversifying innovation. Epidermis morphology of closely related nectar-producing and nectarless species is also compared in order to identify histological changes that accompanied the gain or loss of nectar production. METHODS: The micromorphology of nectaries and positionally equivalent tissues in nectarless species was examined with light and scanning electron microscopy. This information was subjected to phylogenetic analyses to reconstruct nectary evolution and compare characteristics of nectar-producing and nectarless species. KEY RESULTS: Two nectary types evolved in Disa. Nectar exudation by modified stomata in floral spurs evolved twice, whereas exudation by a secretory epidermis evolved six times in different perianth segments. The spur epidermis of nectarless species exhibited considerable micromorphological variation, including strongly textured surfaces and non-secreting stomata in some species. Epidermis morphology of nectar-producing species did not differ consistently from that of rewardless species at the magnifications used in this study, suggesting that transitions from rewardlessness to nectar production are not necessarily accompanied by visible morphological changes but only require sub-cellular modification. CONCLUSIONS: Independent nectary evolution in Disa involved both repeated recapitulation of secretory epidermis, which is present in the sister genus Brownleea, and innovation of stomatal nectaries. These contrasting nectary types and positional diversity within types imply weak genetic, developmental or physiological constraints in ancestral, nectarless Disa. Such functional convergence generated by morphologically diverse solutions probably also underlies the extensive diversity of nectary types and positions in the Orchidaceae.

PIRSF family classification system for protein functional and evolutionary analysis.

The PIRSF protein classification system (http://pir.georgetown.edu/pirsf/) reflects evolutionary relationships of full-length proteins and domains. The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). PIRSF families are curated systematically based on literature review and integrative sequence and functional analysis, including sequence and structure similarity, domain architecture, functional association, genome context, and phyletic pattern. The results of classification and expert annotation are summarized in PIRSF family reports with graphical viewers for taxonomic distribution, domain architecture, family hierarchy, and multiple alignment and phylogenetic tree. The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution. Domain or fold-based searches allow identification of evolutionarily related protein families sharing domains or structural folds. Functional convergence and functional divergence are revealed by the relationships between protein classification and curated family functions. The taxonomic distribution allows the identification of lineage-specific or broadly conserved protein families and can reveal horizontal gene transfer. Here we demonstrate, with illustrative examples, how to use the web-based PIRSF system as a tool for functional and evolutionary studies of protein families.