Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. ...Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software Bayesian Phylogenetics and Phylogeography (BPP) explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.
Insects are the focus of many recent studies suggesting population declines, but even invaluable pollination service providers such as bees lack a modern distributional synthesis. Here, we combine a ...uniquely comprehensive checklist of bee species distributions and >5,800,000 public bee occurrence records to describe global patterns of bee biodiversity. Publicly accessible records are sparse, especially from developing countries, and are frequently inaccurate throughout much of the world, consequently suggesting different biodiversity patterns from checklist data. Global analyses reveal hotspots of species richness, together generating a rare bimodal latitudinal richness gradient, and further analyses suggest that xeric areas, solar radiation, and non-forest plant productivity are among the most important global drivers of bee biodiversity. Together, our results provide a new baseline and best practices for studies on bees and other understudied invertebrates.
•Bees show a rare bimodal latitudinal gradient with highest richness at mid-latitudes•Xeric and temperate zones host higher richness than tropical areas•Plant productivity and richness are important drivers when forests are excluded•A global bee species richness reconstruction is presented for the first time
A modern, quantitative synthesis on bee distribution and its drivers at a global scale. Orr et al. show that bees exhibit a rare bimodal pattern of higher species richness at mid-latitudes, based on their great success in xeric and some temperate areas, further supported by a driver analysis. Bee species richness is also reprojected worldwide.
Human-induced biodiversity change impairs ecosystem functions crucial to human well-being. However, the consequences of this change for ecosystem multifunctionality are poorly understood beyond ...effects of plant species loss, particularly in regions with high biodiversity across trophic levels. Here we adopt a multitrophic perspective to analyze how biodiversity affects multifunctionality in biodiverse subtropical forests. We consider 22 independent measurements of nine ecosystem functions central to energy and nutrient flow across trophic levels. We find that individual functions and multifunctionality are more strongly affected by the diversity of heterotrophs promoting decomposition and nutrient cycling, and by plant functional-trait diversity and composition, than by tree species richness. Moreover, cascading effects of higher trophic-level diversity on functions originating from lower trophic-level processes highlight that multitrophic biodiversity is key to understanding drivers of multifunctionality. A broader perspective on biodiversity-multifunctionality relationships is crucial for sustainable ecosystem management in light of non-random species loss and intensified biotic disturbances under future environmental change.
Working landscapes need at least 20% native habitat Garibaldi, Lucas A.; Oddi, Facundo J.; Miguez, Fernando E. ...
Conservation letters,
March/April 2021, 2021-03-00, 20210301, 2021-03-01, Letnik:
14, Številka:
2
Journal Article
Recenzirano
Odprti dostop
International agreements aim to conserve 17% of Earth's land area by 2020 but include no area‐based conservation targets within the working landscapes that support human needs through farming, ...ranching, and forestry. Through a review of country‐level legislation, we found that just 38% of countries have minimum area requirements for conserving native habitats within working landscapes. We argue for increasing native habitats to at least 20% of working landscape area where it is below this minimum. Such target has benefits for food security, nature's contributions to people, and the connectivity and effectiveness of protected area networks in biomes in which protected areas are underrepresented. We also argue for maintaining native habitat at higher levels where it currently exceeds the 20% minimum, and performed a literature review that shows that even more than 50% native habitat restoration is needed in particular landscapes. The post‐2020 Global Biodiversity Framework is an opportune moment to include a minimum habitat restoration target for working landscapes that contributes to, but does not compete with, initiatives for expanding protected areas, the UN Decade on Ecosystem Restoration (2021–2030) and the UN Sustainable Development Goals.
Biodiversity experiments have shown that species loss reduces ecosystem functioning in grassland. To test whether this result can be extrapolated to forests, the main contributors to terrestrial ...primary productivity, requires large-scale experiments. We manipulated tree species richness by planting more than 150,000 trees in plots with 1 to 16 species. Simulating multiple extinction scenarios, we found that richness strongly increased stand-level productivity. After 8 years, 16-species mixtures had accumulated over twice the amount of carbon found in average monocultures and similar amounts as those of two commercial monocultures. Species richness effects were strongly associated with functional and phylogenetic diversity. A shrub addition treatment reduced tree productivity, but this reduction was smaller at high shrub species richness. Our results encourage multispecies afforestation strategies to restore biodiversity and mitigate climate change.
Phylogenetic studies are increasingly reliant on next‐generation sequencing. Transcriptomic and hybrid enrichment sequencing techniques remain the most prevalent methods for phylogenomic data ...collection due to their relatively low demands for computing powers and sequencing prices, compared to whole‐genome sequencing (WGS). However, the transcriptome‐based method is constrained by the availability of fresh materials and hybrid enrichment is limited by genomic resources necessary in probe designs, especially for non‐model organisms.
We present a novel WGS‐based pipeline for extracting essential phylogenomic markers through rapid de novo genome assembling from low‐coverage genome data, employing a series of computationally efficient bioinformatic tools. We tested the pipeline on a Hexapoda dataset and a more focused Phthiraptera dataset (genome sizes 0.1–2 Gbp), and further investigated the effects of sequencing depth on target assembly success rate based on the raw data of six insect genomes (0.1–1 Gbp).
Each genome assembly was completed in 2–24 hr on desktop PCs. We extracted 872–1,615 near‐universal single‐copy orthologs (Benchmarking Universal Single‐Copy Orthologs BUSCOs) per species. This method also enables the development of ultraconserved element (UCE) probe sets; we generated probes for Phthiraptera based on our WGS assemblies, containing 55,030 baits targeting 2,832 loci, from which we extracted 2,125–2,272 UCEs. Resulting phylogenetic trees all agreed with the currently accepted topologies, indicating that markers produced in our methods were valid for phylogenomic studies. We also showed that 10–20× sequencing coverage was sufficient to produce hundreds to thousands of targeted loci from BUSCO sets, and an even lower coverage (5×) was required for UCEs.
Our study demonstrates the feasibility of conducting phylogenomics from low‐coverage WGS for a wide range of organisms without reference genomes. This new approach has major advantages in data collection, particularly in reducing sequencing cost and computing consumption, while expanding loci choices.
Declining plant diversity alters ecological networks, such as plant–herbivore interactions. However, our knowledge of the potential mechanisms underlying effects of plant species loss on ...plant–herbivore network structure is still limited. We used DNA barcoding to identify herbivore–host plant associations along declining levels of tree diversity in a large‐scale, subtropical biodiversity experiment. We tested for effects of tree species richness, host functional and phylogenetic diversity, and host functional (leaf trait) and phylogenetic composition on species, phylogenetic and network composition of herbivore communities. We found that phylogenetic host composition and related palatability/defence traits but not tree species richness significantly affected herbivore communities and interaction network complexity at both the species and community levels. Our study indicates that evolutionary dependencies and functional traits of host plants determine the composition of higher trophic levels and corresponding interaction networks in species‐rich ecosystems. Our findings highlight that characteristics of the species lost have effects on ecosystem structure and functioning across trophic levels that cannot be predicted from mere reductions in species richness.
The Holy Grail of an Insect Tree of Life can only be ‘discovered’ through extensive collaboration among taxon specialists, phylogeneticists and centralized frameworks such as Open Tree of Life, but ...insufficient effort from stakeholders has so far hampered this promising approach. The resultant unavailability of synthesis phylogenies is an unfortunate situation given the numerous practical usages of phylogenies in the near term and against the backdrop of the ongoing biodiversity crisis. To resolve this issue, we establish a new online hub that centralizes the collation of relevant phylogenetic data and provides the resultant synthesis molecular phylogenies. This is achieved through key developments in a proposed pipeline for the construction of a species‐level insect phylogeny. The functionality of the framework is demonstrated through the construction of a highly supported, species‐comprehensive phylogeny of Diptera, built from integrated omics data, COI DNA barcodes, and a compiled database of over 100 standardized, published Diptera phylogenies. Machine‐readable forms of the phylogeny (and subsets thereof) are publicly available at insectphylo.org, a new public repository for species‐comprehensive phylogenies for biological research.
昆虫生命树研究的重大突破只能通过分类学家、系统发育学家和中心化数据库(如Open Tree of Life)之间的广泛合作来达成，但目前各方的努力远远不够，阻碍了这一模式的发展。由此导致的昆虫类群系统发育关系缺失是非常大的缺憾，特别在当前很多研究依赖于这些系统发育框架，同时生物多样性危机愈发严峻。为了解决这个问题，我们建立了一个新的网络中心，集中整理相关的系统发育数据，提供由此产生的综合分子系统发育树。这些是关键通过构建物种级昆虫系统分析流程来实现。分析框架通过构建一个高支持度、物种全面的双翅目系统发育树来展示，该系统发育树是基于100多个标准化的、已发表的双翅目系统发育树，综合组学数据和COI DNA条形码汇编数据库而构建的。该系统发育的机器可读形式(及其子集)可在insectphylo.org公开获得，这是一个新的用于生物研究的物种综合系统发育公共资源库。.
One of the most important non‐Apis groups of bees for agriculture is the mason bee subgenus Osmia Panzer (Osmia), or Osmia s.s. (Hymenoptera: Megachilidae). Out of the 29 known species, four have ...been developed as managed pollinators of orchards. In addition, the group is important as a source of non‐native pollinators, given that several species have been introduced into new areas. Osmia s.s. occurs naturally throughout the northern temperate zone with greatest species richness in Europe and Asia. Here, we integrate phylogenomic data from ultraconserved elements (UCEs), near complete taxon sampling, and a diversity of analytical approaches to infer the phylogeny, divergence times and biogeographic history of Osmia s.s. We also demonstrate how mitochondrial sequence data can be extracted from ultraconserved element data and combined with sequences from public repositories in order to test the phylogeny, examine species boundaries and identify specimen‐associated, non‐bee DNA. We resolve the phylogeny of Osmia s.s. and show strong support that Nearctic Osmia ribifloris is the sister group to the rest of the subgenus. Biogeographic analyses indicate that the group originated during the Late Miocene in the West Nearctic plus East Palearctic region following dispersal from the East Palearctic to the West Nearctic across the Bering land bridge prior to its closure 5.5–4.8 Ma. The mitochondrial DNA results reveal potential taxonomic synonymies involving Osmia yanbianensis and Osmia opima, and Osmia rufina, Osmia rufinoides and Osmia taurus.
Ultraconserved element phylogenomic data resolve the phylogeny of the agriculturally important mason bee subgenus Osmia (Osmia).
Osmia s.s. originated during the Late Miocene in the East Palearctic plus West Nearctic and dispersed several times across Beringia.
Analysis of mitochondrial DNA sequences reveals possible cases of synonymy in several species
•Flame retardant cotton fabrics with fully bio-based coating from chitosan (CS) and phytate (AP) were successfully prepared.•CS/AP/cotton presented lower TSP values, better antibacterial properties ...and tensile strength.•Flame retardant samples can be utilized to decorate walls as well as made theater curtains.
In this study, a fully bio-based coating was constructed by layer-by-layer deposition of chitosan (CS) and ammonium phytate (AP), to obtain fire-safety and antibacterial cotton fabrics. With about 8% weight gains of CS/AP coatings, the treated cotton fabrics self-extinguished in the vertical burning test. The data obtained from cone calorimetry showed CS/AP/cotton had much lower smoke and heat production, which indicated the fire safety of the fabrics was significantly improved for the presence of CS/AP coatings. The flame-retardant mechanism of this system was finally proposed according to the analysis of gaseous products and char residues. What is more, CS/AP coatings had higher antibacterial activity in Gram-negative bacteria and did improve the tensile strength of cotton fabrics compared with AP coating. With its ease of operation and use of non-toxic chemicals, this fully bio-based coating can further offer a feasible flame-retardant and antibacterial solution of the inflammable natural fabrics.
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