Chromosome-level genome assembly of the European green woodpecker Picus viridis.

The European green woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here, we assembled a highly contiguous genome assembly for this species using a combination of short- and long-read sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37 Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a ∼30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the P. viridis genome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers. Five historical and seven contemporary samples have been resequenced and may give insights on the population history of this species.

A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata).

The spotted flycatcher (Muscicapa striata) forms with the Mediterranean flycatcher (Muscicapa tyrrhenica) a newly recognized species pair of trans-Saharan migratory passerines. These flycatchers present a nested peripatric distribution, a pattern especially unusual among high dispersal species that questions the eco-evolutionary factors involved during the speciation process. Here, we present a genome assembly for M. striata assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.08 Gb long and consists of 4,779 contigs with an N50 of 3.2 Mb. The completeness of our M. striata genome assembly is supported by the number of BUSCO (95%) and ultraconserved element (UCE) (4889/5041; 97.0%) loci retrieved. This assembly showed high synteny with the Ficedula albicollis reference genome, the closest species for which a chromosome-scale reference genome is available. Several inversions were identified and will need to be investigated at the family level.

Impact of the Difluoromethylene Group in the Organocatalyzed Acylative Kinetic Resolution of α,α-Difluorohydrins.

Due to the omnipresence of chiral organofluorine compounds in pharmaceutical, agrochemical, and material chemistry, the development of enantioselective methods for their preparation is highly desirable. In the present study, the enantioselective organocatalyzed acylation of α,α-difluorohydrins using a commercially available chiral isothiourea is reported through a kinetic resolution (KR) process. It reveals that the difluoromethylene moiety (C(sp3 )F2 ) can serve as a directing group through electrostatic fluorine-cation interactions, greatly improving the enantioselectivity of the KR. In this context, a broad range of fluorinated alcohols such as valuable 4,4-difluoro-1,3-diols could be synthesized with exquisite enantiocontrol (typically >99:1 er). Turning to 2,2-difluoro-1,3-diols, we also demonstrated that aromatic and fluorinated groups were mutually compatible to provide the expected enantioenriched adducts with >99:1 er.

Indirect Tertiary Alcohol Enantiocontrol by Acylative Organocatalytic Kinetic Resolution.

The stereocontrol of tertiary alcohols represents a recurrent challenge in organic synthesis. In the present paper, we describe a simple, efficient, and indirect method to enantioselectively prepare tertiary alcohols through a chiral isothiourea catalyzed selective acylation of adjacent secondary alcohols. This transformation enables the kinetic resolution (KR) of easily prepared racemic diastereoenriched secondary/tertiary diols providing both monoesters and starting diols in highly enantioenriched forms (s-value >200).

Desert crossing strategies of migrant songbirds vary between and within species.

Each year, billions of songbirds cross large ecological barriers during their migration. Understanding how they perform this incredible task is crucial to predict how global change may threaten the safety of such journeys. Earlier studies based on radar suggested that most songbirds cross deserts in intermittent flights at high altitude, stopping in the desert during the day, while recent tracking with light loggers suggested diurnal prolongation of nocturnal flights and common non-stop flights for some species. We analyzed light intensity and temperature data obtained from geolocation loggers deployed on 130 individuals of ten migratory songbird species, and show that a large variety of strategies for crossing deserts exists between, but also sometimes within species. Diurnal stopover in the desert is a common strategy in autumn, while most species prolonged some nocturnal flights into the day. Non-stop flights over the desert occurred more frequently in spring than in autumn, and more frequently in foliage gleaners. Temperature recordings suggest that songbirds crossed deserts with flight bouts performed at various altitudes according to species and season, along a gradient ranging from low above ground in autumn to probably >2000 m above ground level, and possibly at higher altitude in spring. High-altitude flights are therefore not the general rule for crossing deserts in migrant songbirds. We conclude that a diversity of migration strategies exists for desert crossing among songbirds, with variations between but also within species.

FragSAD: A database of diversity and species abundance distributions from habitat fragments.

Habitat destruction is the single greatest anthropogenic threat to biodiversity. Decades of research on this issue have led to the accumulation of hundreds of data sets comparing species assemblages in larger, intact, habitats to smaller, more fragmented, habitats. Despite this, little synthesis or consensus has been achieved, primarily because of non-standardized sampling methodology and analyses of notoriously scale-dependent response variables (i.e., species richness). To be able to compare and contrast the results of habitat fragmentation on species' assemblages, it is necessary to have the underlying data on species abundances and sampling intensity, so that standardization can be achieved. To accomplish this, we systematically searched the literature for studies where abundances of species in assemblages (of any taxa) were sampled from many habitat patches that varied in size. From these, we extracted data from several studies, and contacted authors of studies where appropriate data were collected but not published, giving us 117 studies that compared species assemblages among habitat fragments that varied in area. Less than one-half (41) of studies came from tropical forests of Central and South America, but there were many studies from temperate forests and grasslands from all continents except Antarctica. Fifty-four of the studies were on invertebrates (mostly insects), but there were several studies on plants (15), birds (16), mammals (19), and reptiles and amphibians (13). We also collected qualitative information on the length of time since fragmentation. With data on total and relative abundances (and identities) of species, sampling effort, and affiliated meta-data about the study sites, these data can be used to more definitively test hypotheses about the role of habitat fragmentation in altering patterns of biodiversity. There are no copyright restrictions. Please cite this data paper and the associated Dryad data set if the data are used in publications.

Double Catalytic Kinetic Resolution (DoCKR) of Acyclic anti-1,3-Diols: The Additive Horeau Amplification.

The concept of a synergistic double catalytic kinetic resolution (DoCKR) as described in this article was successfully applied to racemic acyclic anti-1,3-diols, a common motif in natural products. This process takes advantage of an additive Horeau amplification involving two successive enantioselective organocatalytic acylation reactions, and leads to diesters and recovered diols with high enantiopurities. It was first developed with C2 -symmetrical diols and then further extended to non-C2 -symmetrical anti diols to prepare useful chiral building blocks. The protocol is highly practical as it only requires 1 mol % of a commercially available organocatalyst and leads to easily separable products. This procedure was applied to the shortest reported total synthesis of (+)-cryptocaryalactone, a natural product with anti-germinative activity.

Tapping the woodpecker tree for evolutionary insight.

Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships within specific clades or have sampled sparsely across the family. We compared DNA sequences of six loci from 203 of the 217 recognized species of woodpeckers to construct a comprehensive tree of intrafamilial relationships. We recovered many known, but also numerous unknown, relationships among clades and species. We found, for example, that the three picine tribes are related as follows (Picini, (Campephilini, Melanerpini)) and that the genus Dinopium is paraphyletic. We used the tree to analyze rates of diversification and biogeographic patterns within the family. Diversification rate increased on two occasions during woodpecker history. We also tested diversification rates between temperate and tropical species but found no significant difference. Biogeographic analysis supported an Old World origin of the family and identified at least six independent cases of New World-Old World sister relationships. In light of the tree, we discuss how convergence, mimicry, and potential cases of hybridization have complicated woodpecker taxonomy.

Biogeography and diversification dynamics of the African woodpeckers.

The dynamics of species accumulation of African terrestrial vertebrates over time remains underexplored in comparison with those in the New World, despite Africa hosting about 25% of the world's avian diversity. This lack of knowledge hampers our understanding of the fundamental processes that drive biodiversity and the dynamics of speciation. To begin to address this gap, we reconstructed species-level phylogenies of two unrelated clades of African woodpeckers (12 species of Geocolaptes/Campethera and 13 species of Chloropicus/Mesopicos/Dendropicos/Ipophilus) that diverged from their closest Indo-Malayan relatives at similar times. Our results demonstrate that the current taxonomy is misleading: three (Campethera, Dendropicos and Mesopicos) out of four polytpic genera/subgenera are not monophyletic. Our results also show that current estimates of diversity at the species level are significantly understated, as up to 18 species for the 'Campethera clade' and 19 for the 'Dendropicos clade' could be recognized. The first splits within both clades involve species that are largely restricted to the Guineo-Congolian biogeographic regions, followed by later adaptations to particular habitats (forest versus savannah) and colonization of other regions (e.g. Southern Africa), each of which occurred multiple times in both clades. Assuming a conservative species delimitation scheme, our results indicate that diversification rates are decreasing through time for both clades. Applying a more extreme species recognition scheme (18 and 19 species for the Campethera and Dendropicos clades, respectively), our results support a decrease in diversification rates only for the Dendropicos clade and thus underline the importance of the number of species included in our diversification analyses. Greater ecological diversity of the Campethera clade where multiple species exhibit either an arboreal or terrestrial foraging strategy might explain the constant diversification rates through time we found under the eighteen species scheme.

Recurrent hybridization and recent origin obscure phylogenetic relationships within the 'white-headed' gull (Larus sp.) complex.

Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.

Complete mitochondrial genomes of the white-browed piculet (Sasia ochracea, Picidae) and pale-billed woodpecker (Campephilus guatemalensis, Picidae).

The mitochondrial genome of the white-browed piculet Sasia ochracea (Piciformes, Picidae) and the pale-billed woodpecker Campephilus guatemalensis (Piciformes, Picidae) were sequenced using a mixed strategy of Sanger and next-generation sequencing methods. The size of the circular mitochondrial genomes were 16 908 and 16 856 bp, respectively, and include 13 protein-coding genes, 22 transfer tRNAs, 2 ribosomal RNAs, a control region and a reduced pseudo control region. The functional control region was located between the tRNAThr and tRNAPro, as found in the two other Piciformes for which complete mtDNA data are available. The length of the pseudo-control region in the white-browed piculet (103 bp) and pale-billed woodpecker (87 bp) is similar to the size of that region in Dryocopus pileatus (60 bp) and much shorter that the length of this region in Pteroglossus azara (1493 bp), suggesting that size reduction occurred before the last common ancestor of the piculets and woodpeckers.

Highly Enantioselective Acylation of Acyclic Meso 1,3-Diols through Synergistic Isothiourea-Catalyzed Desymmetrization/Chiroablative Kinetic Resolution.

A general and highly efficient organocatalyzed desymmetrization of acyclic meso 1,3-diols through acyl transfer using chiral isothioureas is described. The introduction of π-systems in the acyclic substrates provided new opportunities in terms of reactivity, enantioselectivity and synthetic potential. To reach this high level of enantioselectivity (up to er >99:1), the reaction proceeds through a synergistic mechanism involving a desymmetrization reaction and a chiroablative kinetic resolution process. This methodology was used with success as the sole enantioselective catalytic step (developed on a gram scale) to achieve the total synthesis of the antiosteoporotic diarylheptanoid (-)-diospongin A (7 steps).

A new classification of the Pied Woodpeckers assemblage (Dendropicini, Picidae) based on a comprehensive multi-locus phylogeny.

The pied woodpecker assemblage historically included the widespread genera Picoides and Dendrocopos. The assignment of species to either of these two genera has for long puzzled systematists due to their overall plumage similarity. Recent molecular studies not only suggested that both of these genera are not monophyletic, but also that four other genera, the African Dendropicos the South American Veniliornis and two Asian monospecific genera (Hypopicus and Sapheopipo) are nested within the Dendrocopos-Picoides clade. Yet, our current understanding of the phylogeny and taxonomy of this group is still very partial because several distinctive Old World species that have been assigned to different genera throughout their taxonomic history have not been sampled yet. Here, using DNA sequence data gathered from four loci, we reconstructed a species level phylogeny of the Indo-Malayan and Palearctic Pied Woodpeckers to understand the phylogenetic relationships and biogeographic history of the Eurasian species with respect to African and New World lineages. Our phylogenetic analyses revealed nine strongly supported clades within the Dendropicini. Noticeably, two species that had disputed affinities at the genus level clustered in clades with species from the same biogeographical region: the Brown-backed Woodpecker (D. obsoletus) is nested in Dendropicos and the Arabian Woodpecker (D. dorae) is related to two Eurasian species, the Brown-fronted (D. auriceps) and Middle-spotted woodpeckers (D. medius). The nine clades have a strong biogeographic component and very few dispersal event among bioregions occurred. For example, the African species formed a clade, suggesting that only one dispersal event is needed to explain the presence of Dendropicini in Africa. Based on our phylogenetic results, we propose a new classification of the Dendropicini that recognizes nine genera.

Species undersampling in tropical bat surveys: effects on emerging biodiversity patterns.

Undersampling is commonplace in biodiversity surveys of species-rich tropical assemblages in which rare taxa abound, with possible repercussions for our ability to implement surveys and monitoring programmes in a cost-effective way. We investigated the consequences of information loss due to species undersampling (missing subsets of species from the full species pool) in tropical bat surveys for the emerging patterns of species richness (SR) and compositional variation across sites. For 27 bat assemblage data sets from across the tropics, we used correlations between original data sets and subsets with different numbers of species deleted either at random, or according to their rarity in the assemblage, to assess to what extent patterns in SR and composition in data subsets are congruent with those in the initial data set. We then examined to what degree high sample representativeness (r ≥ 0·8) was influenced by biogeographic region, sampling method, sampling effort or structural assemblage characteristics. For SR, correlations between random subsets and original data sets were strong (r ≥ 0·8) with moderate (ca. 20%) species loss. Bias associated with information loss was greater for species composition; on average ca. 90% of species in random subsets had to be retained to adequately capture among-site variation. For nonrandom subsets, removing only the rarest species (on average c. 10% of the full data set) yielded strong correlations (r > 0·95) for both SR and composition. Eliminating greater proportions of rare species resulted in weaker correlations and large variation in the magnitude of observed correlations among data sets. Species subsets that comprised ca. 85% of the original set can be considered reliable surrogates, capable of adequately revealing patterns of SR and temporal or spatial turnover in many tropical bat assemblages. Our analyses thus demonstrate the potential as well as limitations for reducing survey effort and streamlining sampling protocols, and consequently for increasing the cost-effectiveness in tropical bat surveys or monitoring programmes. The dependence of the performance of species subsets on structural assemblage characteristics (total assemblage abundance, proportion of rare species), however, underscores the importance of adaptive monitoring schemes and of establishing surrogate performance on a site by site basis based on pilot surveys.

Stereocontrol of all-carbon quaternary centers through enantioselective desymmetrization of meso primary diols by organocatalyzed acyl transfer.

The symmetry breaking of meso primary diols bearing a tetrahydropyran ring was employed, using catalytic asymmetric acyl transfer, to control all-carbon quaternary stereocenters. The planar chiral Fu DMAP catalyst was used in this reaction to reach a high degree of enantioselectivity (up to 97:3 e.r.) through a synergic effect combining a desymmetrization step and a kinetic resolution. Moreover, a beneficial effect was exhibited by C6F6 solvent, yielding the first example of an organocatalyzed asymmetric acyl transfer. The desymmetrized monoesters were then used to obtain, after a straightforward ring opening sequence, complex polyketide building blocks bearing all-carbon quaternary stereocenters.

A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves: Picidae).

The ever increasing number of analysed loci in phylogenetics has not only allowed resolution of some parts of the Tree of Life but has also highlighted parts of the tree where incongruent signals among loci were detected. Previous molecular studies suggested conflicting relationships for the New World genus Campephilus, being either associated to the Megapicini or Dendropocini. Yet, the limited number of analysed loci and the use of the concatenation approach to reconstruct the phylogeny prevented the disentanglement of lineage sorting and introgression as causal explanation of this topological conflict. We sequenced four mitochondrial, nine autosomal and three Z-linked loci and used a method that incorporates population level processes into the phylogenetic framework to understand which process (lineage sorting of genetic polymorphism or hybridization/introgression) best explains this conflict. Our analyses revealed that the autosomal FGB intron-7 and to a lesser extent the Z-linked loci have a different phylogenetic history from the mitochondrial loci and some other nuclear loci we analysed. We suggest that this conflicting pattern is the result of introgression consecutive to a hybridization event at the time when members of the Campephilus and melanerpine (Melanerpes and Sphyrapicus) lineages colonized the New World. The case of Campephilus highlights that the mitochondrial genome does not always carry the 'wrong' phylogenetic signal after a past hybridization event. Indeed, we here emphasise that the signature of such event can also be detected in the nuclear genome. With the ongoing increase in the number of loci analysed in phylogenetic studies, it is very likely that further cases will be discovered. Our current results indicate that (1) the genus Campephilus is related to the Asian genera Blythipicus, Chrysocolaptes and Reinwardtipicus, in accordance with morphological data and (2) that the nuclear genome of Campephilus is likely the mixture of two unrelated lineages. Yet, further work with a denser sampling of loci is necessary to evaluate the extant of the Sphyrapicus/Melanerpes lineage nuclear genome that introgressed into the Campephilus genome.

A convergent approach to (-)-callystatin†A based on local symmetry.

The key is symmetry! A convergent synthetic approach of the highly cytotoxic natural product (-)-callystatin A was developed assembling three fragments through Julia-Kocienski olefination and Stille cross-coupling. The new strategy relies on a pivotal local symmetry of the target molecule. In this preliminary study, particular attention was devoted to facilitate the catalytic enantiocontrol of strategic stereogenic centers present in each of the fragments (see scheme).

Total synthesis of (+)-crocacin C using hidden symmetry.

A highly convergent and protecting-group-free synthesis of (+)-crocacin C, featuring an enzymatic enantioselective desymmetrization of a meso-diol, a base-induced ring opening of a THP ring, and a one-pot hydrostannylation/Stille coupling as the key steps, is reported. The natural product was obtained in 11 steps and 22.3% overall yield starting from readily available oxabicycle 1. Finally, a unique enantioselective step, an enzymatic desymmetrization, revealed four stereogenic centers and created one in C4 of the THP furnishing the dense building block 4 with high enantioselectivity (ee >98%).

Michael addition initiated carbocyclization sequences with nitroolefins for the stereoselective synthesis of functionalized heterocyclic and carbocyclic systems.

The synthesis of various heterocycles and carbocycles (tetrahydrofurans, pyrrolidines, cyclopentanes) has been achieved by using new and efficient ionic addition/cyclization sequences. Nitroolefins play an important role in the Michael addition induced ring-closing reactions (MIRC) reported in the present article, with various substituted alcohols, amines, Grignard reactants, or malonate derivatives acting as the nucleophile partner. The optimized cascade reactions were high yielding in most cases and highly stereoselective, creating up to three stereogenic centers starting from achiral substrates.