FReD: The floral reflectance spectra database

Floral reflectance measurements are of great value to researchers who need consider the real colour of flowers, for example in the context of how the flowers appear to their pollinators. We have thus developed the Floral Reflectance Database (FReD) to assist these researchers, gathering together floral reflectance data in a publicly available, searchable online database. The first version of the database is now available online at "http://www.reflectance.co.uk":http://www.reflectance.co.uk. We anticipate that this resource will be of interest to researchers working on flower colour and animal vision

Diversification of land plants: insights from a family-level phylogenetic analysis

<p>Abstract</p> <p>Background</p> <p>Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic.</p> <p>Results</p> <p>We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate.</p> <p>Conclusions</p> <p>This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.</p

Genomic profiling of plastid DNA variation in the Mediterranean olive tree

<p>Abstract</p> <p>Background</p> <p>Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (<it>Olea europaea </it>L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs) of cpDNA haplotypes in the Mediterranean olive tree.</p> <p>Results</p> <p>Eight complete cpDNA genomes of <it>Olea </it>were sequenced <it>de novo</it>. The nucleotide divergence between olive cpDNA lineages was low and not exceeding 0.07%. Based on these sequences, markers were developed for studying two single nucleotide substitutions and length polymorphism of 62 regions (with variable microsatellite motifs or other indels). They were then used to genotype the cpDNA variation in cultivated and wild Mediterranean olive trees (315 individuals). Forty polymorphic loci were detected on this sample, allowing the distinction of 22 haplotypes belonging to the three Mediterranean cpDNA lineages known as E1, E2 and E3. The discriminating power of cpDNA variation was particularly low for the cultivated olive tree with one predominating haplotype, but more diversity was detected in wild populations.</p> <p>Conclusions</p> <p>We propose a method for a rapid characterisation of the Mediterranean olive germplasm. The low variation in the cultivated olive tree indicated that the utility of cpDNA variation for forensic analyses is limited to rare haplotypes. In contrast, the high cpDNA variation in wild populations demonstrated that our markers may be useful for phylogeographic and populations genetic studies in <it>O. europaea</it>.</p

Assessing Calibration Uncertainty in Molecular Dating: The Assignment of Fossils to Alternative Calibration Points

Although recent methodological advances have allowed the incorporation of rate variation in molecular dating analyses, the calibration procedure, performed mainly through fossils, remains resistant to improvements. One source of uncertainty pertains to the assignment of fossils to specific nodes in a phylogeny, especially when alternative possibilities exist that can be equally justified on morphological grounds. Here we expand on a recently developed fossil cross-validation method to evaluate whether alternative nodal assignments of multiple fossils produce calibration sets that differ in their internal consistency. We use an enlarged Crypteroniaceae-centered phylogeny of Myrtales, six fossils, and 72 combinations of calibration points, termed calibration sets, to identify (i) the fossil assignments that produce the most internally consistent calibration sets and (ii) the mean ages, derived from these calibration sets, for the split of the Southeast Asian Crypteroniaceae from their West Gondwanan sister clade (node X). We found that a correlation exists between s values, devised to measure the consistency among the calibration points of a calibration set (Near and Sanderson, 2004), and nodal distances among calibration points. By ranking all sets according to the percent deviation of s from the regression line with nodal distance, we identified the sets with the highest level of corrected calibration-set consistency. These sets generated lower standard deviations associated with the ages of node X than sets characterized by lower corrected consistency. The three calibration sets with the highest corrected consistencies produced mean age estimates for node X of 79.70, 79.14, and 78.15 My. These timeframes are most compatible with the hypothesis that the Crypteroniaceae stem lineage dispersed from Africa to the Deccan plate as it drifted northward during the Late Cretaceou

Towards the completion of speciation : the evolution of reproductive isolation beyond the first barriers

y Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.Peer reviewe

A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park as a model system (South Africa)

A DNA barcode consists of a standardized short sequence of DNA (400-800bp) used to identify the taxonomic species a small organic fragment belongs to. Even though it has been easy to discriminate animal species by using the mitochondrial gene cox1, this is still difficult for plants seeing that the mitochondrial genome is not variable enough on the species level. During the Second International Barcode of Life Conference in Tapei (September 2007), different plastid regions were proposed as potential plant DNA barcodes, such as atpF-atpH and psbK-psbI, but no consensus on which region to use was reached during the meeting. The largest plant DNA barcoding study to date proposed matK as the best candidate and suggested that in combination with trnH-psbA a slight increase in performance could be achieved. However, no study has tested the suitability of the newly proposed psbK-psbI and atpF-atpH for plant barcoding purposes. Four potential DNA barcodes, matK, trnH-psbA, atpF-atpH, and psbK-psbI, were amplified and sequenced for a selective sampling including mainly trees and shrubs of the flora of the Kruger National Park Africa (South Africa). The performance of each region and also each possible combination of these were tested by applying a battery of metrics and statistical tests. Our results confirm that the second half (5’ end) of matK is the best candidate in a single locus barcoding approach reaching 87.5% of species correctly identified. Combining matK with trnH-psbA and psbK-psbI increased only slightly the performance in discriminating species. The results from this study show that the use of a ‘three-region barcode’ does not significantly outperform matK in a single-locus barcoding approach. We therefore argue against the ‘multiple barcode approach’ proposed by the plant working group, and instead propose to keep barcoding plants in line with the approach taken for animals, i.e. using one barcode: cox1 for animals and matK for plants

Elasmobranch diversity across a remote coral reef atoll revealed through environmental DNA metabarcoding

As elasmobranchs are becoming increasingly threatened, efficient methods for monitoring the distribution and diversity of elasmobranch populations are required. Environmental DNA (eDNA) metabarcoding is a progressively applied technique that enables mass identification of entire communities and is an effective method for the detection of rare and elusive species. We performed an eDNA metabarcoding survey for fish communities around a coral reef atoll in the Chagos Archipelago (Central Indian Ocean) and assessed the diversity and distribution of elasmobranch species detected within these communities. Our eDNA survey detected 353 amplicon sequence variants (ASVs) attributed to fishes, 12 of which were elasmobranchs. There were no differences in fish communities based on the presence and absence of ASVs between sample depth (surface and 40 m) or sampling habitat, but communities based on read abundance were significantly different between habitats. The dominant elasmobranch species were grey reef (Carcharhinus amblyrhynchos) and silvertip (C. albimarginatus) sharks, and elasmobranch communities were significantly different between sampling depth and habitat. Overall, we find that eDNA metabarcoding can be used to reveal the diversity of elasmobranchs within broader taxonomic assays, but further research and development of targeted metabarcoding primers may be required before it can be integrated into a toolkit for monitoring these species

Phylogeny of Iridaceae Subfamily Crocoideae Based on a Combined Multigene Plastid DNA Analysis

The phylogeny of Crocoideae, the largest of four subfamilies currently recognized in Tridaceae, has eluded resolution until sequences of two more plastid DNA regions were added here to a previously published matrix containing sequences from four DNA plastid regions. Sister to the core Nivenioideae, the woody Klattia, Nivenia, and Witsenia, Crocoideae are a climax group in lridaceae, comprising some 995 species, slightly more than half of the total in the family. Synapomorphies of Crocoideae include pollen exine perforate, pollen aperture operculate, ovule campylotropous (or hypotropous), root xylem vessels with simple perforations, cormous rootstock, inflorescence a spike, and plants deciduous. The six DNA region analysis here that includes examples of 27 of the 28 genera of the subfamily shows the southern African Tritoniopsis sister to the remaining genera, which resolve into four well-supported clusters (bootstrap support \u3e85%). Each of these major clades is treated as a tribe, the synapomorphies of which are discussed in light of the molecular phylogenetic analyses. Original embryological and seed developmental studies largely support the tribal classification. Tritoniopsideae alone has the inner floral bracts not forked apically, and a hypotropous ovule, while this tribe and Watsonieae have axillary corm development. The remaining three tribes have apical corm development, and together with Watsonieae have a campylotropous ovule, and the inner layer of the inner integument crushed at maturity

Assembling the Tree of Life in Europe (AToLE)

A network of scientists under the umbrella of &#x27;Assembling the Tree of Life in Europe (AToLE)&#x27; seeks funding under the FP7-Theme: Cooperation - Environment (including Climate Change and Biodiversity Conservation) programme of the European Commission.&#xd;&#xa