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727 results for “phylogenetic diversity”
Fig. 1 in Marked genetic diversity within Blastocystis in Australian wildlife revealed using a next generation sequencing-phylogenetic approach
Fig. 1. Map showing Melbourne's water catchment areas where samples were collected (2009-2022).
Aligned DNA sequence matrix for phylogenetic analyses in the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"</p> <p>The matrix is in NEXUS format. Genes are arranged as follows:</p> <p>16S RNA, tRNA-Leu = 1–1408<br> ND1 codon position 1 = 1409–2369\3;<br> ND1 codon position 2 = 1410–2367\3;<br> ND1 codon position 3 = 1411–2368\3;<br> tRNA-Ile, tRNA-Gln, rRNA-Met = 2370–2544; <br> RAG1 codon position 3 = 2545–3199\3;<br> RAG1 codon position 1 = 2546–3197\3<br> RAG1 codon position 2 = 2547–3198\3;</p>
Figure 1 in Phylogenetic status and genetic diversity of corsac fox (Vulpes corsac) in Golestan Province, Iran
Figure 1. Geographic location of collected samples.
Data from: The spatial structure of phylogenetic and functional diversity in the United States and Canada: an example using the sedge family (Cyperaceae)
Systematically quantifying diversity across landscapes is necessary to understand how clade history and ecological heterogeneity contribute to the origin, distribution, and maintenance of biodiversity. Here, we chart the spatial structure of diversity among all species in the sedge family (Cyperaceae) throughout the USA and Canada. We first identify areas of remarkable species richness, phylogenetic diversity, and functional trait diversity, and highlight regions of conservation priority. We then test predictions about the spatial structure of this diversity based on the historical biogeography of the family. Incorporating a phylogeny, over 400,000 herbarium records, and a database of functional traits mined from online floras, we find that species richness and functional trait diversity peak in the Northeastern USA, while phylogenetic diversity peaks along the Gulf of Mexico. Floristic turnover among assemblages increases significantly with distance, but phylogenetic turnover is twice as rapid along latitudinal gradients as along longitudinal gradients. These patterns reflect the expected distribution of Cyperaceae, which originated in the tropics but radiated in temperate regions. We identify assemblages with an abundance of rare, range-restricted lineages, and assemblages composed of species generally lacking from diverse regions. We argue that both of these metrics are useful for developing targeted conservation strategies. We use the data generated here to establish future research priorities, including the testing of a series of hypotheses regarding the distribution of chromosome numbers, photosynthetic pathways, and resource partitioning in sedges.
Contrasting patterns of phylogenetic diversity and alpine specialization across the alpine flora of the American mountain range system
<p>Although mountainous habitats contribute substantially to global biodiversity, comparatively little is known about biogeographic patterns of distributions of alpine species across multiple mountain ranges. Here, we present a detailed analysis of the distributions and phylogenetic affinities of alpine seed plant lineages across North, Central, and South American mountain systems. Using a comprehensive dataset that characterized the elevational niches of American seed plants in a continuously valued way, we were able to quantitatively investigate how the proportion of alpine habitat occupied by plants related to their biogeographic distributions at a regional scale and place these results in a phylogenetic context. We found alpine species diversity to be greatest in the central Andes and western North America, and that sites with lower phylogenetic diversity contained species with a greater degree of alpine specialization. In particular, near Arctic/ boreal alpine communities were characterized by low phylogenetic diversity and higher degrees of alpine specialization, whereas the opposite was observed for southern Patagonian communities. These results suggest that abiotic filtering alone in these climatically similar regions is unlikely to explain alpine community assembly. Nevertheless, the overall relative rarity of alpine specialists, and the tendency for such specialists to be most closely related to montane lineages, suggested that filtering was still an important factor in shaping alpine community structure. This work corroborates the importance of a nuanced and scale-dependent perspective on the 'history-filtering' debate axis, as both factors have likely contributed to modern biodiversity patterns observed in alpine plant communities across the Americas.</p>
Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
Biodiversity scale-dependence and opposing multi-level correlations underlie differences among taxonomic, phylogenetic, and functional diversity
<p><b>Aim:</b> Biodiversity is a multi-dimensional property of biological communities that represents different information depending on how it is measured, but how dimensions relate to one another and under what conditions is not well understood. We explore how taxonomic, phylogenetic, and functional diversity can differ in scale-of-effect dependence and habitat-biodiversity relationships, and subsequently how spatial differences among biodiversity dimensions may arise.</p> <p><b>Location:</b> Nebraska, United States</p> <p><b>Time period:</b> May-July 2016, 2017</p> <p><b>Major taxa studied:</b> Birds</p> <p><b>Methods:</b> Across 2016 and 2017, we conducted 2,641 point counts at 781 sites. We modeled the occupancy of 141 species using Bayesian Bernoulli-Bernoulli hierarchical logistic regressions. We calculated species richness (SR), phylogenetic diversity (PD), and functional diversity (FD) for each site and year based on predicted occupancy, accounting for imperfect detection. Using Bayesian latent indicator scale selection and multivariate modeling, we quantified the spatial scales-of-effect that best explained the relationships between environmental characteristics and SR, PD, and FD. Additionally, we decomposed the residual between- and within-site biodiversity correlations using our repeated measures design.</p> <p><b>Results:</b> We demonstrate spatial differences among biodiversity predictions, arising from scale-dependence in habitat-biodiversity relationships and variation in correlation structure among biodiversity dimensions. Although relationships between specific land cover types and SR, PD and FD were qualitatively similar, the spatial scales at which these variables were important in explaining biodiversity differed among dimensions. Between-site residual biodiversity correlations were negative, yet within-site biodiversity residual correlations were positive.</p> <p><b>Main conclusions:</b> Our results demonstrate how spatial differences among biodiversity dimensions may arise from biodiversity-specific scale-dependent habitat relationships, low shared environmental correlations and opposing residual correlations between dimensions, which suggest that single-scale and single-dimension analyses are not entirely appropriate for quantifying habitat-biodiversity relationships. After accounting for shared habitat relationships, we found positive within-site residual correlations between taxonomic, phylogenetic, and functional diversity, suggesting that habitat change over time influenced all biodiversity dimensions relatively similarly. However, negative between-site residual correlation among biodiversity dimensions may indicate trade-offs in achieving maximum biodiversity across multiple biodiversity dimensions at any given location. Although habitat management can to a limited degree improve biodiversity relatively across all metrics, other environmental effects may ensure that not all facets of biodiversity can be maximized at once. If maximizing a specific biodiversity dimension is the goal, then care should be taken to consider these within-site residual correlations.</p>
Data from: WHAT DOES FUNCTIONAL DIVERSITY AND PHYLOGENETIC SIGNAL REVEAL ABOUT SOUTHERN BRAZILIAN TERRESTRIAL FERNS' ENVIRONMENTAL PREFERENCES?
<p><span><strong>Questions</strong></span><span>: Our study focuses on the following questions: </span><span>1) Do the climatic and edaphic conditions of the Southern Brazilian Atlantic Forest impact terrestrial ferns' functional diversity</span><span>? 2) Which morphological functional traits are most relevant for terrestrial ferns in response to climatic and edaphic changes? 3) If there are trait-environment relationships, what adaptive </span><span>eco-evolutionary </span><span>mechanisms can be inferred from them?</span></p> <p><span><strong>Study site</strong></span><span>: Subtropical Atlantic Forest, </span><span>encompassing </span><span>Rio Grande do Sul, Santa Catarina, and Paraná States, Brazil.</span></p> <p><span><strong>Method</strong></span><span>: We analyzed </span><span>eleven</span><span> </span><span>morphological traits related to resistance, competitive advantage, and reproductive success. All traits were analyzed with and without phylogenetic correction to compute multi-trait functional diversity using </span><span>the standardized effect size of mean functional distance and functional composition via the community-weighted mean. Both metrics were weighted by the absolute frequency of species within sites. Subsequently, we identified the most influential climatic or </span><span>edaphic</span><span> drivers based on linear models. To assess the significance of trait-environment relationships, we employed </span><span>a </span><span>permutational</span><span> </span><span>approach</span><span>.</span></p> <p><span><strong>Results</strong></span><span>: The functional diversity of terrestrial ferns correlates with rainfall</span><span> and temperature, with subtle changes when</span><span> taking into account the phylogenetic relationship of species</span><span>. Similarly, competitive and reproductive traits were associated with</span><span> annual</span><span> rainfall</span><span> and rainfall seasonality</span><span>. However, most morphological traits vary independently of </span><span>edaphic</span><span> and climatic factors, regardless</span><span> of</span><span> whether phylogenetic relatedness is</span><span> considered or not. Few traits, specifically related to resistance and competition, were dispersed across the phylogeny and were not linked with any factor evaluated, leaving the question of their true determinants unanswered.</span></p> <p><span><strong>Conclusions</strong></span><span>: Combining functional and phylogenetic information on terrestrial ferns indicates that species morphology response highly depends on the scale ob</span><span>served. Our analyses demonstrate that climatic and not edaphic factors are the primary drivers of trait diversity in terrestrial ferns within the Subtropical Atlantic Forest, influencing most evaluated traits.</span><span> These findings may help predict the distribution of terrestrial ferns amidst the increasing trend of land use and cover changes in the Atlantic Forest domain.</span></p>
Unravelling the factors affecting taxonomic, phylogenetic and functional beta diversity of stream macroinvertebrate communities in the World's Third Pole
<p><span><strong>Aim</strong>: </span><span>Disentangling how</span><span> stochastic and deterministic processes contribute to variation in beta diversity is a common goal for ecologists and biogeographers. However, such studies are scarce in alpine streams, especially when different diversity facets are considered. Here, we combined different approaches to examine the drivers of taxonomic, phylogenetic and functional beta diversities and discussed how our results can inform community assembly and biodiversity conservation in Tibetan streams.</span></p> <p><span><strong>Location</strong>: </span><span>Tibet </span><span>Plateau</span></p> <p><span><strong>Taxon</strong>: </span><span>Macroinvertebrates</span></p> <p><span><strong>Methods</strong>: </span><span>We first partitioned multiple facets of beta diversity (B<sub>total</sub>) into species replacement (B<sub>repl</sub>) and richness difference (B<sub>rich</sub>) as well as local (LCBD) or species (SCBD) contributions. Then, we applied ordination methods to examine the relative importance of local, climatic and spatial factors on </span><span>B<sub>total</sub></span><span>, </span><span>B<sub>repl</sub></span><span> and </span><span>B<sub>rich</sub></span><span>, respectively. We explored community assembly rules using null models based on trait and phylogeny structure. </span></p> <p><span><strong>Results</strong>: </span><span>B<sub>total</sub></span><span> displayed high values and was primarily driven by B<sub>repl</sub>. Local, climatic and spatial factors were poor predictors of the different facets of beta diversity. Null models showed that the diversity metrics did not differ from those of null expectations, suggesting that most individual streams might be occupied by species that were merely random draws from the functional or phylogenetic pools available in this region. Partitioning beta diversity into LCBD and SCBD implied that the upper canyon streams were more unique than those at lower elevations and can be valuable for biodiversity conservation.</span></p> <p><span><strong>Main conclusions</strong>: </span><span>Analyzing multiple facets of beta diversity provide important insights into community assembly that cannot be acquired by focusing on taxonomic diversity only. Using a multi-faceted approach involving species, phylogenetic and trait data, our study not only sheds light on the assembly mechanisms of macroinvertebrate communities in alpine streams but also bring inspiration for biodiversity conservation in the 'World's Third Pole' that is highly sensitive to global change. </span></p>
Data from: European bee diversity: Taxonomic and phylogenetic patterns
<p class="MsoNormal"><strong><u><span>Aim </span></u></strong></p> <p class="MsoNormal"><span>Wild bees still face striking shortfalls in knowledge of biodiversity in key regions of the world. This includes Europe, where despite a long tradition of data gathering, the continental scale distribution patterns of wild bees have not been systematically analysed to date. This study aims to characterise large-scale biodiversity patterns to: (i) understand spatial-temporal heterogeneity in large-scale databases, (ii) locate genuine diversity hotspots and their relationship with biogeographical patterns or habitats of interests, and (iii) identify understudied species and areas to further design conservation actions for most at risk species in key regions. </span></p> <p class="MsoNormal"><strong><u><span>Location </span></u></strong></p> <p class="MsoNormal"><span>Europe</span></p> <p class="MsoNormal"><strong><u><span>Taxon</span></u></strong></p> <p class="MsoNormal"><span>Bees </span></p> <p class="MsoNormal"><strong><u><span>Methods</span></u></strong></p> <p class="MsoNormal"><span>We present a continental and standardised study of bee taxonomic and phylogenetic diversity patterns in Europe, using a large compilation of occurrence records of nearly three million validated occurrence records for 1,515 wild bee species.</span></p> <p class="MsoNormal"><strong><u><span>Results</span></u></strong></p> <p class="MsoNormal"><span>Southern and eastern Europe suffer from the largest gaps in data availability while northern and western regions benefit from better historical coverage. Our models show that higher wild bee diversity in Europe is hosted in xeric, warm areas, as highlighted by a clear latitudinal gradient. However, phylogenetic diversity is predicted to be more homogenous across Europe than taxonomic diversity, suggesting that policies and strategies targeted to protect species richness may differ from those targeting greater phylogenetic diversity.</span></p> <p class="MsoNormal"><strong><u><span>Main conclusions</span></u></strong></p> <p class="MsoNormal"><span>This study represents a significant advance in the characterisation of wild bee distribution patterns across Europe and is an important stepping stone towards the design of more targeted survey efforts and conservation actions of this key group of pollinators. This, in turn, will provide the data necessary to improve the spatiotemporal coverage in a context of ongoing and future Europe-wide monitoring schemes, to ultimately develop cost-effective, coordinated and evidence-based conservation actions and tailored habitat management actions that can be implemented on a smaller scale.</span></p>
Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient
<p>Title of dataset</p> <p>Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient</p> <p>Authors of dataset</p> <p>Leon Marshall<sup>1,2</sup>, John S. Ascher<sup>3</sup>, Cristian Villagra<sup>4</sup>, Amaury Beaugendre<sup>1</sup>, Valentina Herrera<sup>4</sup>, Patricia Henríquez-Piskulich<sup>4</sup>, Alejandro Vera<sup>5</sup>, Nicolas J. Vereecken<sup>1</sup></p> <ol> <li>Agroecology Lab, Université libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/2, B 1050 Brussels, Belgium</li> <li>Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands</li> <li>Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore</li> <li>Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> <li>Departamento de Biología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> </ol> <p>Abstract</p> <p>Chile's isolation and varied climates have driven the evolution of a unique biodiversity with a high degree of endemism. As a result, Chile encompasses diverse environments, including the Mediterranean-type ecosystem, a global biodiversity hotspot. These environments are currently threatened by anthropogenic land use change impacting the integrity of local biomes and associated species. This area is the most intensively sampled of the country with high endemicity of native bee species. Characterising habitat requirements of bees is a pressing priority to safeguard these insects and the ecosystem services they provide. We investigated broad-scale patterns of bee (Hymenoptera: Apoidea: Anthophila) diversity using newly accessible expert-validated datasets comprising digitized specimen records from Chilean and US collections, and novel expert-validated type specimen data for the bees of Chile. We used a generalised dissimilarity modelling (GDM) approach to explore both compositional and phylogenetic β-diversity patterns across latitudinal, altitudinal, climate and habitat gradients in well-sampled bee assemblages in Central Chile. Using the GDM measures of increasing compositional and environmental dissimilarity we categorised and compared the most important drivers of these patterns and used them to classify 'wild bee ecoregions' (WBE) representing unique assemblages. Turnover of bee assemblages was explained primarily by latitudinal variation (proxy for climate) from south to north in Chile. However, temperature variations, precipitation and the presence of bare soil also significantly explained turnover in bee assemblages. In comparison, we observed less turnover in phylogenetic biodiversity corresponding to spatial gradients. We identified six de novo ecoregions (WBE), all with distinct taxa, endemic lineages, and representative species. The WBE represent distinct spatial classifications but have similarities to existing biogeographical classifications, ecosystems and bioclimatic zones. This approach establishes the baseline needed to prioritise bee species conservation efforts across this global biodiversity hotspot. We discuss the novelty of this classification considering previous biogeographical characterisations and their relevance in assessing conservation priorities for bee conservation. We argue that Chile's WBE highlight areas in need of funding for bee species surveys and description, distribution mapping and strengthening of conservation policies.</p> <p>Usage notes</p> <p>The dataset contains species occurrence data of chilean bees aggregated to a 5 x 5 km grid shapefile. The shapefile of the grid and the raster mask of the Central Chilean study area are also included. Finally, a database of type specimen data used to supplement the dataset is included here. The code for the analysis can be found at: <a href="https://github.com/lmar116/ChileanBeeDiversity">https://github.com/lmar116/ChileanBeeDiversity</a>.</p> <p>Shapefiles, rasters, CSV files and code were all loaded and analyzed using R statistics software. </p> <p>Four files are included:</p> <ol> <li>Marshall-et-al-2023_Ecosphere_DataTable_bee_grid: contains all species occurrence data used in GDM analysis, Grid column refers to cl.5km.shp.</li> <li>cl.5km.shp (and associated files): 5 x 5 km grid shapefile of the Central Chilean study area</li> <li>chile.mask.tif: raster outline of the Central Chilean study area</li> <li>Marshall-et-al-2023_Ecosphere_CentralChileTypeSpecimens.xlsx: contains type specimen data used to supplement species occurrence dataset.</li> </ol>
Figure 1 in Genetic diversity, phylogenetic and phylogeographic analyses of Oncideres impluviata (Germar, 1823) (Coleoptera: Cerambycidae) in Rio Grande do Sul state, Brazil
Figure 1 Adult specimen of O. impluviata - Dorsal view.
Figure 3 in Genetic diversity, phylogenetic and phylogeographic analyses of Oncideres impluviata (Germar, 1823) (Coleoptera: Cerambycidae) in Rio Grande do Sul state, Brazil
Figure 3 Physiographic regions of Rio Grande do Sul state, Brazil.
Fig. 1 in Genotype diversity, phylogenetic analysis and seasonality of isolates of Acanthamoeba spp. in swimming pools in Kafrelsheikh, Egypt
Fig. 1. Fresh unstained trophozoites (A) and cysts (B–D) of Acanthamoeba spp.
Effects of land use and climate change on functional and phylogenetic diversity of terrestrial vertebrates in a Himalayan biodiversity hotspot
<p>Aim: Land use and climate change interact to impact functional and phylogenetic diversity globally, but this pattern is largely unknown in the eastern Himalayas. We aim to discern the response of community diversity and structure of terrestrial mammals and birds to anthropogenic land use and climate change in this hitherto understudied landscape. Location: Himalayan biodiversity hotspot, Bhutan</p> <p>Methods: We used camera trap and point-count transect data to estimate taxonomic, functional, and phylogenetic diversity while accounting for detectability. We calculated the abundance-weighted standardised effect sizes (ses) of mean pairwise distance and mean nearest taxon distance. The ses metrics were regressed against land use (agriculture and forest) and climate (temperature and precipitation) variables using linear mixed effect models.</p> <p>Results: Community diversity declined with agriculture in both groups. Mammal diversity was higher farther from the settlement but birds remained indifferent. Temperature and precipitation were positively associated with mammal diversity, but birds displayed a mixed response: negative with temperature and positive with precipitation. Agriculture had a strong negative effect on the functional structure of birds but not mammals. The functional and phylogenetic structure declined farther from the settlement for mammals but increased for birds. Except for the functional structure, all other metrics increased with temperature and precipitation for mammals. Except for the positive relationship between functional structure and temperature, other metrics showed a mixed response to climate in birds. </p> <p>Main conclusions: Our findings provide evidence that land use rather than climate has an imminent effect in shaping local and regional patterns of terrestrial vertebrate diversity in a Himalayan biodiversity hotspot. Climate effects, although weak, may reduce functional traits and consequently diminish functional roles. Species that can persist in human-modified environments are clustered within a phylogeny, suggesting possible loss of phylogenetic diversity.</p>
Data from: Global taxonomic, functional, and phylogenetic diversity of bees in apple orchards
<p>An essential prerequisite to safeguard pollinator species is characterisation of the multifaceted diversity of crop pollinators and identification of the drivers of pollinator community changes across biogeographical gradients. The extent to which intensive agriculture is associated with the homogenisation of biological communities at large spatial scales remains poorly understood. In this study, we investigated diversity drivers for 644 bee species/morphospecies in 177 commercial apple orchards across 33 countries and four global biogeographical biomes. Our findings reveal significant taxonomic dissimilarity among biogeographical zones. Interestingly, despite this dissimilarity, species from different zones share similar higher-level phylogenetic groups and similar ecological and behavioural traits (i.e. functional traits), likely due to habitat filtering caused by perennial monoculture systems managed intensively for crop production. Honey bee species dominated orchard communities, while other managed/manageable and wild species were collected in lower numbers. Moreover, the presence of herbaceous, uncultivated open areas and organic management practices were associated with increased wild bee diversity. Overall, our study sheds light on the importance of large-scale analyses contributing to the emerging fields of functional and phylogenetic diversity, which can be related to ecosystem function to promote biodiversity as a key asset in agroecosystems in the face of global change pressures.</p>
Data from: Global variation in the relationship between avian phylogenetic diversity and functional distance is driven by environmental context and constraints
<p>Aim: If evolutionary distance is akin to evolutionary chance, then it follows that species assemblages that are distantly related will also be more disparate in terms of their traits, features and the niches they occupy. Yet, studies have found that the total phylogenetic distance of an assemblages, known as phylogenetic diversity, is an unreliable surrogate for functional diversity. We investigate global variation in the relationship between Faith's Phylogenetic Diversity (PD) and Mean Pairwise Functional Distance (MPFD) across latitude and the influence of migratory species on both these aspects of diversity.</p> <p>Location: Global.</p> <p>Time period: Present day.</p> <p>Major taxa studied: Birds.</p> <p>Methods: We measure PD and MPFD for over 9,000 species of bird across more than 17,000 globally distributed assemblages. We obtain standardised effect sizes for both indices by simulating assemblage composition under an ecologically informed null model. We employ path analysis to characterise variation in the relationship between PD's and MPFD across latitude, elevation and with proportion of migratory species.</p> <p>Results: Globally, assemblages that were phylogenetically diverse tended to be less functionally dispersed than expected; however this relationship showed considerable variation across latitude decreasing with distance from the equator. The proportion of migratory species in an assemblage was found to be an important predictor of functional diversity, with migrant rich assemblages generally showing less functional diversity than expected. We identify the Andes and Hengduan Mountains as regions of exceptional bird functional diversity.</p> <p>Main conclusions: The relationship between phylogenetic diversity and function diversity is context specific, varying across environmental gradients such as latitude, and influenced by ecological phenomena such a migration. Thus, care should be taken using phylogenetic diversity as a proxy for functional diversity, particularly in clades with sparse functional data. Instead we recommend that studies consider how phylogenetic diversity's surrogacy for functional diversity may be impacted by environmental context and evaluate empirical observations against biogeographically constrained and ecological informed null models.</p>
Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest
<p>Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e. β diversity), which can reflect the degree of community-wide biotic homogenization, remains largely unknown, hindering better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0–30 cm soil profiles in a subtropical forest in China. Root segments were identified into 143 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw) and mean nearest neighbor distance (Dnn) to quantify species ecological differences, we tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes, examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Both functional and phylogenetic Dpw (e.g. interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, phylogenetic Dnn (e.g. intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.</p>
Dominant species establishment may influence invasion resistance more than phylogenetic or functional diversity
<ol> <li>Phylogenetic and functional diversity are theorized to increase invasion resistance. Experimentally testing whether plant communities higher in these components of diversity are less invasible is an important step for guiding restoration designs.</li> <li>To investigate how phylogenetic and functional diversity of vegetation affect invasion resistance in a restoration setting, we used experimental prairie restoration plots. The experiment crossed three levels of phylogenetic diversity with two levels of functional diversity while species richness was held constant. We allowed invaders to colonize plots; these included native species from neighboring plots and non-native invasive species from a surrounding old field. We tested if invader biomass was influenced by phylogenetic and functional diversity, and phylogenetic and hierarchical trait distances between invaders and planted species. We binned each invader into three categories: native species from neighboring experimental plots (site-specific invaders); native species not part of the experimental species pool (native invaders); or non-native species (non-native invaders).</li> <li>Counter to expectation, both non-native and native invaders became more abundant in more phylogenetically diverse plots. However, plots with higher abundance of planted Asteraceae, a dominant family of the tallgrass prairie, had lower invader biomass for both native and non-native invaders.</li> <li>We also found that hierarchical trait differences shaped invasion. The species that became most abundant were non-native invaders that were taller, and native invaders with low specific leaf area relative to planted species. Site-specific invaders were not influenced by any plot-level diversity metrics tested.</li> <li> <em>Synthesis and application</em>: Our results suggest greater phylogenetic diversity may lower resistance to invasion. This effect may be due to more even but sparser niche packing in high-diversity plots, associated with greater availability of unsaturated niche space for colonization. However, trait composition fostered invasion resistance in two ways in our study. First, establishment of native species with strongly dominant traits may confer invasion resistance. Second, species mixes that optimize trait differences between planted vegetation and likely invaders may enhance invasion-resistance.</li> </ol>
Spatial patterns of phylogenetic and species diversity of Fennoscandian vascular plants in protected areas
<p>Protected areas are one of the main strategic means for conserving biodiversity. Yet, the design of protected areas usually neglects phylogenetic diversity, an important diversity measure. In this paper, we assess the phylogenetic diversity and species richness of vascular plants in Fennoscandian protected areas. We evaluate how much species richness and phylogenetic diversity is found within and outside protected areas, and the differences in diversity between different categories of protected areas. We also assess the differences in the diversity-area relationship of the different protected area categories in terms of both species richness and phylogenetic diversity. We build a multi-locus phylogeny of 1,519 native vascular plants of Norway, Sweden, and Finland. We estimate the phylogenetic diversity and species richness by combining the phylogeny with publicly available occurrence data and the currently protected area system of Fennoscandia. Our results indicate that protected areas in Fennoscandia hold more diversity when larger, and that phylogenetic diversity increases faster with area than species richness. We found evidence for more diversity outside of protected areas of the different countries of Fennoscandia than inside of protected areas, but no evidence for diversity differences between areas with different protection status. Hence, our results indicate that the current protected area system in Fennoscandia is no more effective in conserving phylogenetic diversity and species richness of vascular plants than a random selection of localities. Our results also indicate that planning conservation strategies around phylogenetic diversity, rather than species richness, might be more effective in protecting vascular plant diversity.</p>
ScienceDex guides
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.