Systematics of the avian family Alaudidae using multilocus and genomic data

The family Alaudidae,larks,comprises 93-100 species(depending on taxonomy)that are widely distributed across Africa and Eurasia,with single species extending their ranges to North and northernmost South America and Australia.A decade-old molecular phylogeny,comprising~80%of the species,revealed multiple cases of parallel evolution and large variation in rates of morphological evolution,which had misled taxonomists into creating many non-monophyletic genera.Here,we reconstruct the phylogeny of the larks,using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species(in total 133 taxa;not all loci available for all species).We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling(in total 51 samples of 44 taxa across 40 species).Our results confirm the previous findings of rampant morphological convergence and divergence,and reveal new cases of paraphyletic genera.We propose a new subfamily classification,and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae.Our study supports recently proposed species splits as well as some recent lumps,while also questioning some of the latter.This comprehensive phylogeny will form an important basis for future studies,such as comparative studies of lark natural history,ecology,evolution and conservation.

贡嘎山东坡的鸟类多样性和区系

经过7年5次野外系统调查并综合有关文献,贡嘎山东坡分布有鸟类336种,其中,留鸟204种(60.7%),夏候鸟89种(26.5%),冬候鸟18种(5.4%),旅鸟25种(7.4%);东洋界物种205种(61.0%),古北界物种105种(31.3%),广布种26种(7.7%);雀形目Passeriformes鸟类245种(72.9%);繁殖鸟类293种(87.2%)。本地区有国家Ⅰ级重点保护鸟类3种,国家Ⅱ级重点保护鸟类29种;横断山-喜马拉雅地区特有鸟类53种;CITES附录Ⅰ鸟类3种,附录Ⅱ鸟类25种;世界自然保护联盟濒危物种红色名录濒危鸟类1种,易危鸟类2种。研究发现,东洋界物种的海拔分布下限平均、上限平均、中点平均和海拔跨度平均都低于古北界物种,但仅海拔分布中点平均和上限平均差异有统计学意义(P<0.05),体现了东洋界和古北界物种对高海拔环境适应能力的不同可能与其不同的生物地理演化历史有关;东洋界占优势的特有种(51/53)海拔分布下限平均、中点平均和上限平均显著高于非特有物种,体现出东洋界特有种对高山环境的适应也许与其特有化过程有关。贡嘎山东坡鸟类丰富度在中海拔1 800~2 800 m的落叶阔叶混交林和针阔叶混交林中最高,在高海拔和低海拔物种丰富度较低,物种丰富度呈中峰模式,鸟类生态群落随植物群落结构变化而呈现一定的垂直生态替代规律。

An overview of the phylogeny and diversity of eukaryotes

Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eu-karyotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predomi-nantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the pro-posed relationships of these groups to each other.

Integrative taxonomy of the Plain-backed Thrush(Zoothera mollissima)complex(Aves,Turdidae)reveals cryptic species,including a new species

Background: The Plain-backed Thrush Zoothera mollissima breeds in the Himalayas and mountains of central China. It was long considered conspecific with the Long-tailed Thrush Zoothera dixoni, until these were shown to be broadly sympatric.Methods: We revise the Z. mollissima–Z. dixoni complex by integrating morphological, acoustic, genetic(two mitochondrial and two nuclear markers), ecological and distributional datasets.Results: In earlier field observations, we noted two very different song types of "Plain-backed" Thrush segregated by breeding habitat and elevation. Further integrative analyses congruently identify three groups: an alpine breeder in the Himalayas and Sichuan, China("Alpine Thrush"); a forest breeder in the eastern Himalayas and northwest Yunnan(at least), China("Himalayan Forest Thrush"); and a forest breeder in central Sichuan("Sichuan Forest Thrush"). Alpine and Himalayan Forest Thrushes are broadly sympatric, but segregated by habitat and altitude, and the same is probably true also for Alpine and Sichuan Forest Thrushes. These three groups differ markedly in morphology and songs. In addition, DNA sequence data from three non-breeding specimens from Yunnan indicate that yet another lineage exists("Yunnan Thrush"). However, we find no consistent morphological differences from Alpine Thrush, and its breeding range is unknown. Molecular phylogenetic analyses suggest that all four groups diverged at least a few million years ago, and identify Alpine Thrush and the putative "Yunnan Thrush" as sisters, and the two forest taxa as sisters. Cytochrome b divergences among the four Z. mollissima sensu lato(s.l.) clades are similar to those between any of them and Z. dixoni, and exceed that between the two congeneric outgroup species. We lectotypify the name Oreocincla rostrata Hodgson, 1845 with the Z. mollissima sensu stricto(s.s.) specimen long considered its type. No available name unambiguously pertains to the Himalayan Forest Thrush.Conclusions: The Plain-backed Thrush Z. mollissima s.l. comprises at least three species: Alpine Thrush Z. mollissima s.s., with a widespread alpine breeding distribution; Sichuan Forest Thrush Z. griseiceps, breeding in central Sichuan forests; and Himalayan Forest Thrush, breeding in the eastern Himalayas and northwest Yunnan(at least), which is described herein as a new species. "Yunnan Thrush" requires further study.

Elevational patterns of bird species richness on the eastern slope of Mt.Gongga,Sichuan Province,China

Background:In biological systems,biological diversity often displays a rapid turn-over across elevations.This defining feature has made mountains classic systems for studying the spatial variation in diversity.Because patterns of elevational diversity can vary among lineages and mountain systems it remains difficult to extrapolate findings from one montane region to another,or among lineages.In this study,we assessed patterns and drivers of avian diversity along an elevational gradient on the eastern slope of Mt.Gongga,the highest peak in the Hengduan Mountain Range in central China,and a mountain where comprehensive studies of avian diversity are still lacking.Methods:We surveyed bird species in eight 400-m elevational bands from 1200 to 4400 m a.s.l.between 2012 and 2017.To test the relationship between bird species richness and environmental factors,we examined the relative importance of seven ecological variables on breeding season distribution patterns:land area(LA),mean daily temperature(MDT),seasonal temperature range(STR),the mid-domain effect(MDE),seasonal precipitation(SP),invertebrate biomass(IB) and enhanced vegetation index(EVI).Climate data were obtained from five local meteorological stations and three temperature/relative humidity smart sensors in 2016.Results:A total of 219 bird species were recorded in the field,of which 204 were recorded during the breeding season(April–August).Species richness curves(calculated separately for total species,large-ranged species,and smallranged species) were all hump-shaped.Large-ranged species contributed more to the total species richness pattern than small-ranged species.EVI and IB were positively correlated with total species richness and small-ranged species richness.LA and MDT were positively correlated with small-ranged species richness,while STR and SP were negatively correlated with small-ranged species richness.MDE was positively correlated with large-ranged species richness.When we considered the combination of candidate factors using multiple regression models and model-averaging,total species richness and large-ranged species richness were correlated with STR(negative) and MDE(positive),while small-ranged species richness was correlated with STR(negative) and IB(positive).Conclusions:Although no single key factor or suite of factors could explain patterns of diversity,we found that MDE,IB and STR play important but varying roles in shaping the elevational richness patterns of different bird species categories.Model-averaging indicates that small-ranged species appear to be mostly influenced by IB,as opposed to large-ranged species,which exhibit patterns more consistent with the MDE model.Our data also indicate that the species richness varied between seasons,offering a promising direction for future work.

Taxonomy of the White-browed Shortwing(Brachypteryx montana)complex on mainland Asia and Taiwan:an integrative approach supports recognition of three instead of one species

Background: The White-browed Shortwing(Brachypteryx montana) is widespread from the central Himalayas to the southeast Chinese mainland and the island of Taiwan, the Philippines and Indonesia. Multiple subspecies are recognised, and several of these have recently been suggested to be treated as separate species based on differences in morphology and songs.Methods: We here analyse plumage, morphometrics, songs, two mitochondrial and two nuclear markers, and geographical distributions of the two mainland Asian taxa B. m. cruralis and B. m. sinensis and the Taiwan Residents B. m. goodfellowi.Results: We conclude that these differ congruently in morphology, songs and DNA. Male B. m. goodfellowi is the most divergent in plumage(sexually monomorphic, unlike the two others; male similar to female), and B. m. cruralis and B. m. sinensis differ in male plumage maturation. The song of B. m. cruralis is strongly divergent from the others, whereas the songs of B. m. sinensis and B. m. goodfellowi are more similar to each other. Brachypteryx m. sinensis and B. m. goodfellowi are sisters, with an estimated divergence time 4.1 million years ago(mya; 95% highest posterior distribution [HPD] 2.8–5.5 mya), and B. m. cruralis separated from these two 5.8 mya(95% HPD 4.1–7.5 mya). We also report notable range extensions of B. m. sinensis as well as sympatry between this taxon and B. m. cruralis in Sichuan Province, China. Brachypteryx m. montana from Java is found to be more closely related to Lesser Shortwing(B. leucophris) and Rusty-bellied Shortwing(B. hyperythra) than to the mainland Asian and Taiwan Residents taxa.Conclusion: Our data support a recent proposal to treat the three mainland Asian and Taiwan Residents taxa as three species, separate from B. montana sensu stricto: B. cruralis(central Himalayas to south central China and south Vietnam), B. sinensis(north central to southeastern part of China's Mainland) and B. goodfellowi(Taiwan Island).

Multispecies hybridization in birds

Hybridization is not always limited to two species;often multiple species are interbreeding. In birds, there are numerous examples of species that hybridize with multiple other species. The advent of genomic data provides the oppotunity to investigate the ecological and evolutionary consequences of multispecies hybridization. The interactions between several hybridizing species can be depicted as a network in which the interacting species are connected by edges. Such hybrid networks can be used to identify ‘hub-species’ that interbreed with multiple other species. Avian examples of such ‘hub-species’ are Common Pheasant (Phasianus colchicus), Mallard (Anas platyrhynchos) and European Herring Gull (Larus argentatus). These networks might lead to the formulation of hypotheses, such as which connections are most likely conducive to interspecific gene flow (i.e. introgression). Hybridization does not necessarily result in introgression. Numerous statistical tests are available to infer interspecific gene flow from genetic data and the majority of these tests can be applied in a multispecies setting. Specifically, model-based approaches and phylogenetic networks are promising in the detection and characterization of multispecies introgression. It remains to be determined how common multispecies introgression in birds is and how often this process fuels adaptive changes. Moreover, the impact of multispecies hybridization on the build-up of reproductive isolation and the architecture of genomic landscapes remains elusive. For example, introgression between certain species might contribute to increased divergence and reproductive isolation between those species and other related species. In the end, a multispecies perspective on hybridization in combination with network approaches will lead to important insights into the history of life on this planet.

Inter-individual variation in provisioning rate,prey size and number,and links to total prey biomass delivered to nestlings in the Collared Flycatcher(Ficedula albicollis)

Background:In bird species where offspring growth and survival rely on parents’food provisioning,parents can maximise their fitness by increasing the quantity and/or the quality of preys delivered to their offspring.Many studies have focused on inter-individual variation in feeding rate,yet this measure may not accurately reflect the total amount of food(i.e.energy)provided by parents if there is large variation in the quantity and quality of preys at each feeding.Here,we explored the relative role of individual(sex,age,body condition),breeding(hatching date,brood size)and environmental(temperature)factors on feeding rate,prey number,size and quality,and their contribution to total prey biomass delivered to the nestlings of 164 Collared Flycatcher(Ficedula albicollis)parents in 98 nests.Results:Preys delivered to the nest were mainly larvae(53.6%)and flying insects(45.6%).Feeding rate increased with brood size and age,and was higher in males than females.Mean prey number decreased,but mean prey size increased,as the season progressed and parents feeding their brood with primary larvae brought more preys per visit.Relationships between feeding rate,mean prey number and size remained when taking into account the provision-ing quality:parents brought either a large number of small prey or a small number of larger items,and the force of the trade-offs between feeding rate and mean prey number and size depended on the quality of the provisioning of the parents.Whatever the percentage of larvae among preys in the provisioning,the variance in total prey biomass was foremost explained by feeding rate(65.1%to 76.6%)compared to mean prey number(16.4%to 26%)and prey size(2.7%to 4%).Conclusions:Our study shows that variation in feeding rate,prey number,size,but not quality(i.e.percentage of lar-vae),were influenced by individual factors(sex and age)and breeding decisions(brood size and timing of breeding)and that,whatever the provisioning strategy adopted,feeding rate was the best proxy of the total biomass delivered to the nestlings.

High-level classification of the Fungi and a tool for evolutionary ecological analyses

High-throughput sequencing studies generate vast amounts of taxonomic data.Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone.We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative.Based on phylogenies and divergence time estimates,we adopt phylum rank to Aphelidiomycota,Basidiobolomycota,Calcarisporiellomycota,Glomeromycota,Entomophthoromycota,Entorrhizomycota,Kickxellomycota,Monoblepharomycota,Mortierellomycota and Olpidiomycota.We accept nine subkingdoms to accommodate these 18 phyla.We consider the kingdom Nucleariae(phyla Nuclearida and Fonticulida)as a sister group to the Fungi.We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework,using this or any other classification system.We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

An updated classification for the hyper-diverse genus Corydalis(Papaveraceae: Fumarioideae)based on phylogenomic and morphological evidence

The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses,based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa,using 65 shared protein-coding plastid genes from313 accessions(including 280 samples of ca. 226species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions(including 271samples of Corydalis) covering all 42 previously recognized sections and five independent “series”.Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include:(i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data;the third,subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus;(ii) among all 42 sections and five“series”, 25 sections and one “series” are resolved as monophyletic in both data sets;(iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes;(iv) we provide a new classification of Corydalis with four subgenera(of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly improved our understanding of the evolution of the genus.

Coprophilous contributions to the phylogeny of Lasiosphaeriaceae and allied taxa within Sordariales(Ascomycota,Fungi)

The phylogenetic relationships of Lasiosphaeriaceae are complicated in that the family is paraphyletic and includes Sordariaceae and Chaetomiaceae,as well as several polyphyletic genera.This study focuses on the phylogenetic relationships of the coprophilous genera,Anopodium,Apodospora,Arnium,Fimetariella and Zygospermella.They are traditionally circumscribed based on ascospore characters,which have proven homoplasious in other genera within the family.Our results based on LSU nrDNA andß–tubulin sequences distinguish four lineages of Lasiosphaeriaceae taxa.Anopodium joins the clade of mor-phologically similar,yellow-pigmented species of Cercophora and Lasiosphaeria.Apodospora is monophyletic and joins a larger group of taxa with unclear affinities to each other,while Arnium is polyphyletic being scattered throughout three of the four major clades of Lasiosphaeriaceae.Fimitariella is represented by a single collection and joins the clade containing Cercophora scortea and Podospora appendiculata.Zygospermella shows affinities to the Lasiosphaeris clade.Based on a combination of morphological and molecular data,Echria stat.nov.is recognized at the genus level for the former Arnium section and two new combinations are proposed:E.gigantospora and E.macrotheca.

Plumage brightness and uropygial gland secretions in barn swallows

The uropygial gland has been hypothesized to play a role in sexual signaling through a "make-up" function derived from the effects of secretions from the gland on the appearanee of the plumage and bare parts of the body. Here we show that plumage brightness of dorsal feathers of individual barn swallows Hirundo rustica was greater in mated than in unmated individuals. In addition, plumage brightness in creased with colony size. Furthermore, plumage bright ness was positively correlated with the amount of wax in the uropygial gland, negatively correlated with time of sampling of uropygial wax (perhaps because more wax is present early in the morning after an entire night of wax production without any preening), and negatively correlated with the number of chewing lice that degrade the plumage. Experimentally preventing barn swallows from access to the uropygial gland reduced plumage brightness, showing a causal link between secretions from the uropygial gland and plumage brightness. These findings provide evidence consistent with a role of uropygial secretions in signaling plumage brightness.

Pefabloc- A sulfonyl fluoride serine protease inhibitor blocks induction of Diotericin in Drosoohila 1（2）mbn cells

Insects protect themselves against microbial infection by an efficient innate immune system that is activated by recognition ofinvariant microbial surface molecules. In the fruit fly Drosophila melanogaster the presence of bacteria is associated with expression of antimicrobial peptides in host immune-competent tissues. Host receptors detect infection and relay the signal to mount the appropriate immune response. In Drosophila hemocyte- like l（2）mbn cells pre-infection treatment with Pefabloc, a commonly used serine protease inhibitor, induced two major effects： it blocked expression of the antibacterial peptide Diptericin in response to live Gram-negative bacteria and bacterial surface molecules （crude lipopolysaccharide contaminated by peptidoglycans） and it induced morphological changes.

Specific detection of the floodwater mosquitoes Aedes sticticus and Aedes vexans DNA in predatory diving beetles

Floodwater mosquitoes （Diptera： Culicidae） are associated with periodically flooded wet meadows, marshes, and swamps in floodplains of major rivers worldwide, and their larvae are abundant in the shallow parts of flooded areas. The nuisance caused by the blood-seeking adult female mosquitoes motivates mosquito control. Larviciding with Bacillus thuringiensis israelensis is considered the most environmentally safe method. However, some concern has been raised whether aquatic predatory insects could be indi- rectly affected by this reduction in a potential vital prey. Top predators in the temporary wetlands in the River Dal/ilven floodplains are diving beetles （Coleoptera： Dytiscidae）, and Aedes sticticus andAe, vexans are the target species for mosquito control. For detailed stud- ies on this aquatic predator-prey system, we developed a polymerase chain reaction （PCR） assay for detection of mosquito DNA in the guts of medinm-sized diving beetles. Primers were designed for amplifying short mitochondrial DNA fragments of the cytochrome C oxidase subunit I （COI） gene in Ae. sticticus and Ae. vexans, respectively. Primer speci- ficity was confirmed and half-life detectability ofAe. sticticus DNA in diving beetle guts was derived from a feeding and digestion experiment. The Ae. sticticus DNA within diving beetle guts was detected up to 12 h postfeeding, and half-life detectability was estimated to 5.6 h. In addition, field caught diving beetles were screened for Ae. sticticus and Ae. vexans DNA and in 14% of the diving beetles one or both mosquito species were detected, showing that these mosquito species are utilized as food by the diving beetles.

No trade-off between trichome production and tolerance to leaf and inflorescence damage in a natural population of Arabidopsis lyrata

Aims Early models of plant defense conceived resistance and tolerance to herbivore damage as mutually exclusive strategies.support for this idea has been equivocal and studies on these two strategies are still needed to understand the evolution of defenses in natural populations.In Arabidopsis lyrata,the production of trichomes,a documented resistance trait,has been associated with a fitness cost in the absence of herbivores.We examined whether trichome production is also associated with reduced tolerance to simulated herbivore damage.Methods We conducted a field experiment in a natural swedish population of A.lyrata where we inflicted leaf(0 vs.50%of the area of each leaf removed)and inflorescence damage(0 vs.50%of inflores-cences removed)to trichome-producing and glabrous plants in a factorial design.We examined the response(survival,growth and reproduction)of the plants to the imposed damage over 2 years.Important Findingstrichome-producing plants were not less tolerant than glabrous plants to simulated herbivore damage(no significant morph×leaf damage or morph×inflorescence damage interactions).Inflorescence and leaf damage had independent negative effects on the performance of damaged plants.leaf damage reduced rosette size the year of damage,but effects on reproductive output in the year of damage,and on survival and reproductive performance the following year were weak and not statistically significant.Inflorescence damage significantly reduced the number of flowers,fruits and seeds the year of damage,but not in the following year.Irrespective of morph,the study population was more tolerant to leaf than to inflorescence damage.the results indicated no trade-off between trichome production and tolerance,suggesting that these two defense mechanisms have the potential to evolve indepen-dently in this A.lyrata population.

Sexual selection and environmental change:what do we know and what comes next?

Anthropogenic environmental change is the most significant threat to biodiversity in the 21st century.Animal populations are experiencing rapid changes in their biotic and abiotic environment,which impose novel selection pressures on organisms and increase the risk of population extinction.There is thus a pressing need to understand what affects the capacity of populations to respond and adapt to environmental change.Because behavioral traits are very labile,they provide a means of rapidly responding to environmental change(Sih et al.2011;Tuomainen and Candolin 2011).