Descriptions and diagnoses are alternative choices in all Codes of Nomenclature because Linnaeus relied diagnoses, not descriptions, to name ca. 13,400 animals, plants, and fungi. A diagnosis names ...characters in which a new taxon differs from the most similar known taxon; a description mixes taxonomically informative and uninformative features, usually without indicating which is which. The first formal diagnoses of new taxa that included DNA-based characters came out in 2001, and by November 2015, at least 98 names of species of acoels, lichens, angiosperms, annelids, alveolates, arachnids, centipedes, turtles, fishes, butterflies, mollusks, nematodes, and pathogenic fungi have been published based on diagnostic mitochondrial, plastid, or nuclear DNA substitutions, indels, or rarely genetic distances, with or without additional morphological features. Authors have found diverse ways to specify the diagnostic traits (all published studies are here tabulated). While descriptions try to "cover" within-species variation, a goal rarely accomplished because of (i) the stochastic nature of specimen availability (thousands of species are known from single collections) and (ii) the subjective circumscription of species, the purpose of diagnoses was and is speedy identification. Linnaeus tried to achieve this by citing images, geographic occurrence, and previous literature. The renewed attention to sharp diagnosis now coincides with worldwide barcoding efforts, may speed up formal naming, and matches the increasing reliance on DNA for both classification and identification. I argue for DNA-based diagnoses of new species becoming a recommendation in all Codes, not just the bacterial code.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Premise
The proportion of woody dicots with toothed leaves increases toward colder regions, a relationship used to reconstruct past mean annual temperatures. Recent hypotheses explaining this ...relationship are that (1) leaves in colder regions are thinner, requiring thick veins for support and water supply, with the resulting craspedodromous venation leading to marginal teeth (support–supply hypothesis) or that (2) teeth are associated with the packing of leaf primordia in winter buds (bud‐packing hypothesis).
Methods
We addressed these hypotheses by examining leaf thickness, number of primordia in buds, growing season length (mean annual temperature, MAT), and other traits in 151 deciduous woody species using georeferenced occurrences and a Bayesian model controlling for phylogeny. We excluded evergreen species because longer leaf life spans correlate with higher leaf mass per area, precluding the detection of independent effects of leaf thickness on leaf‐margin type.
Results
The best model predicted toothed leaves with 94% accuracy, with growing season length the strongest predictor. Neither leaf thickness nor number of leaves preformed in buds significantly influenced margin type, rejecting the support–supply and bud‐packing hypotheses.
Conclusions
A direct selective benefit of leaf teeth via a carbon gain early in the spring as proposed by Royer and Wilf (2006) would match the strong correlation between toothed species occurrence and short growing season found here using Bayesian hierarchical models. Efforts should be directed to physiological work quantifying seasonal photosynthate production in toothed and nontoothed leaves.
The three bryophyte lineages have long-lived gametophytes that are either bisexual, producing both male- and female gametes, or sexually specialized and then producing only one type of gamete. ...Phylogenies suggest repeated evolutionary switches between these systems, implying that bryophyte sex chromosomes may have been gained and lost repeatedly. How this occurred is poorly understood, even though plant sex chromosomes were first discovered in liverworts. We explain how the sex chromosomes of haploid-dominant organisms are distinct from the better-studied X-Y and Z-W systems in the tree of life, summarise what is known about their distribution and genetic composition, and present new cytogenetic data for Frullania dilatata and Plagiochila asplenioides, the former with two U chromosomes and one V chromosome, the latter with one U chromosome and two V chromosomes; male and female C-values in F. dilatata are correspondingly asymmetric （the C-value of P. asplenioides is only known for female nuclei）. So far, there is a lack of high-throughput sequencing, quantification, and in situ study of the repetitive DNA, organellar DNA, and transposable elements, and it is therefore not known what causes the size difference of U and V chromosomes from the autosomes or each other. Heterochromatin was also first discovered in bryophytes, but its function in their sex regulation has not been addressed. Studies of bryophyte sex chromosomes with combined cytogenetic and genomic approaches are fundamental for a fuller understanding of sex chromosome evolution across the tree of life.
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•Spatiotemporal analysis of prevalence of avian assemblage in urban greenspace.•Prevalence decreases as distance to water sources increases, for some bird species.•Higher ...Leucocytozoon prevalence in the unvisited section of the forest.•Infection responses to biotic and abiotic factors were species specific.
Prevalence responses to anthropic factors differ across hosts and parasite species. We here analyzed the spatiotemporal variation of avian haemosporidian prevalence in bird assemblages of the Mooswald forest (i.e., urban greenspace; Freiburg, Germany), in response to local environmental features (e.g., water sources, human presence (visited)/absence (unvisited)) and bird-level traits (e.g., body condition, age, sex) in 2 years. We used a nested PCR protocol (mitochondrial (mt)DNA cytochrome b (cyt b) gene) and microscopy to determine haemosporidian infections. Prevalence was analyzed using a general linear multi-model (glmulti) approach with Akaike information criterion corrected for small samples (AICc), with subsequent model inferences using a GLMM on the best selected model, considering bird species as a random factor. Analyses were conducted for the main understory bird species (Blackcap – Sylvia atricapilla, Chaffinch – Coereba flaveola, Great Tit – Parus major, Blue Tit – Cyanistes caeruleus, European Robin – Erithacus rubecula, Blackbird – Turdus merula, Song Thrush – Turdus philomelos). We further conducted spatial autocorrelation analyses for all haemosporidian infections, and classification and regression trees (CARTs) for focal species. We analyzed a total of 544 samples of seven bird species. In 2011 prevalence for Haemoproteus/Plasmodium was 25.8% and 11.7% for Leucocytozoon. In 2013 prevalence for Haemoproteus/Plasmodium was 26.5% and 35.5% for Leucocytozoon. Haemosporidian prevalence was significantly different between some focal species. There was a negative association between distance to the nearest water source and prevalence in the year 2011, and the opposite pattern for the year 2013. However, when analyzed for the six focal species separately, such a relationship could change from a negative to a positive one, or there could be no relationship at all. For Leucocytozoon there was higher prevalence in the section of the forest visited by humans. We did not find spatial autocorrelation for prevalence across the study site, but there were statistically significant local spatial clusters in the visited section. Although there were similar responses of prevalence to some factors, infection patterns were generally bird species-specific. Thus, prevalence is a labile epidemiological parameter, varying spatiotemporally in an idiosyncratic way.
We analysed phylogenetic relationships in the order Cucurbitales using 14 DNA regions from the three plant genomes: the mitochondrial nadl b/c intron and matR gene, the nuclear ribosomal 18S, ...ITS1-5.8S-ITS2, and 28S genes, and the plastid rbcL, matK, ndhF, atpB, trnL, trnL-trnF, rpl20-rps12, trnS-trnG and trnH-psbA genes, spacers, and introns. The dataset includes 664 ingroup species, representating all but two genera and over 25% of the ca. 2600 species in the order. Maximum likelihood analyses yielded mostly congruent topologies for the datasets from the three genomes. Relationships among the eight families of Cucurbitales were: (Apodanthaceae, Anisophylleaceae, (Cucurbitaceae, ((Coriariaceae, Corynocarpaceae), (Tetramelaceae, (Datiscaceae, Begoniaceae))). Based on these molecular data and morphological data from the literature, we recircumscribe tribes and genera within Cucurbitaceae and present a more natural classification for this family. Our new system comprises 95 genera in 15 tribes, five of them new: Actinostemmateae, Indofevilleeae, Thladiantheae, Momordiceae, and Siraitieae. Formal naming requires 44 new combinations and two new names in Cucurbitaceae.
Context.
Neptune’s incomplete ring arcs have been stable since their discovery in 1984 by stellar occultation. Although these structures should be destroyed within a few months through differential ...Keplerian motion, imaging data over the past couple of decades have shown that these structures remain stable.
Aims.
We present the first SPHERE near-infrared observations of Neptune’s ring arcs taken at 2.2 μm (broadband
Ks
) with the IRDIS camera at the Very Large Telescope (VLT) in August 2016.
Methods.
The images were aligned using the ephemerides of the satellite Proteus and were suitably co-added to enhance ring and satellite signals.
Results.
We analyse high-angular-resolution near-infrared images of Neptune’s ring arcs obtained in 2016 at the ESO VLT-UT3 with the adaptive-optics-fed camera SPHERE-IRDIS. We derive accurate mean motion values for the arcs and the nearby satellite Galatea. The trailing arcs Fraternité and Égalité have been stable since they were last observed in 2007. Furthermore, we confirm the fading away of the leading arcs Courage and Liberté. Finally, we confirm the mismatch between the arcs’ position and the 42:43 inclined and eccentric corotation resonances with Galatea, thus demonstrating that no 42:43 corotation model works to explain the azimuthal confinement of the arcs’ materiel.
The independent evolution of heteromorphic sex chromosomes in 19 species from 4 families of flowering plants permits studying X/Y divergence after the initial recombination suppression. Here, we ...document autosome/Y divergence in the tropical Cucurbitaceae Coccinia grandis, which is ca. 3 myr old. Karyotyping and C-value measurements show that the C. grandis Y chromosome has twice the size of any of the other chromosomes, with a male/female C-value difference of 0.094 pg or 10% of the total genome. FISH staining revealed 5S and 45S rDNA sites on autosomes but not on the Y chromosome, making it unlikely that rDNA contributed to the elongation of the Y chromosome; recent end-to-end fusion also seems unlikely given the lack of interstitial telomeric signals. GISH with different concentrations of female blocking DNA detected a possible pseudo-autosomal region on the Y chromosome, and C-banding suggests that the entire Y chromosome in C. grandis is heterochromatic. During meiosis, there is an end-to-end connection between the X and the Y chromosome, but the X does not otherwise differ from the remaining chromosomes. These findings and a review of plants with heteromorphic sex chromosomes reveal no relationship between species age and degree of sex chromosome dimorphism. Its relatively small genome size (0.943 pg/2C in males), large Y chromosome, and phylogenetic proximity to the fully sequenced Cucumis sativus make C. grandis a promising model to study sex chromosome evolution.
Phenological mismatch results when interacting species change the timing of regularly repeated phases in their life cycles at different rates. We review whether this continuously ongoing phenomenon, ...also known as trophic asynchrony, is becoming more common under ongoing rapid climate change. In antagonistic trophic interactions, any mismatch will have negative impacts for only one of the species, whereas in mutualistic interactions, both partners are expected to suffer. Trophic mismatch is therefore expected to last for evolutionarily short periods, perhaps only a few seasons, adding to the difficulty of attributing it to climate change, which requires long-term data. So far, the prediction that diverging phenologies linked to climate change will cause mismatch is most clearly met in antagonistic interactions at high latitudes in the Artic. There is limited evidence of phenological mismatch in mutualistic interactions, possibly because of strong selection on mutualists to have co-adapted phenological strategies. The study of individual plasticity, population variation, and the genetic bases for phenological strategies is in its infancy. Recent work on woody plants revealed the large imprint of historic climate change on temperature, chilling, and day-length
thresholds used by different species to synchronize their phenophases, which in the Northern Hemisphere has led to biogeographic phenological regions in which long-lived plants have adapted to particular interannual and intermillennial amplitudes of climate change.
The important question of taxonomy and its impact on conservation efforts was brought to general attention by Robert May in 1990 with a
News and Views article in
Nature entitled “Taxonomy as ...destiny.” Taxonomy, however, has built-in instabilities that result in name changes, raising the question of whether name changes have a consistent impact on conservation efforts. Our review investigates three possible outcomes of taxonomic change, namely a positive impact on protection efforts, a hampering impact, or no measurable impact. We address these cases with a review of the relevant literature: specifically, government and conservation agency reports, scientific papers, and the general press, as well as correspondence with biologists active in plant and animal conservation. We found no evidence of a consistent effect of taxonomic change on conservation, although splitting taxa may tend to increase protection, and name changes may have the least effect where they concern charismatic organisms.
Melon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. ...hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F), adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis.
Analyses of combined chloroplast sequences (4,375 aligned nucleotides) for 123 of the 130 genera of Cucurbitaceae indicate that the genera Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce are embedded within Cucumis. Phylogenetic trees from nuclear sequences for these taxa are congruent, and the combined data yield a well-supported phylogeny. The nesting of the five genera in Cucumis greatly changes the natural geographic range of the genus, extending it throughout the Malesian region and into Australia. The closest relative of Cucumis is Muellerargia, with one species in Australia and Indonesia, the other in Madagascar. Cucumber and its sister species, C. hystrix, are nested among Australian, Malaysian, and Western Indian species placed in Mukia or Dicaelospermum and in one case not yet formally described. Cucumis melo is sister to this Australian/Asian clade, rather than being close to African species as previously thought. Molecular clocks indicate that the deepest divergences in Cucumis, including the split between C. melo and its Australian/Asian sister clade, go back to the mid-Eocene.
Based on congruent nuclear and chloroplast phylogenies we conclude that Cucumis comprises an old Australian/Asian component that was heretofore unsuspected. Cucumis sativus evolved within this Australian/Asian clade and is phylogenetically far more distant from C. melo than implied by the current morphological classification.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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