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727 results for “phylogenetic diversity”
Fig. 1 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 1. Map of Peru with the Yanachaga-Chemillén National Park indicated in red.
Phylogenetic and ecological correlates of pollen morphological diversity in a neotropical rainforest
Morphology varies enormously across clades, and the morphology of a trait may reflect ecological function or the retention of ancestral features. We examine the tension between ecological and phylogenetic correlates of morphological diversity through a case study of pollen grains produced by angiosperms in Barro Colorado Island, Panama (BCI). Using a molecular phylogeny of 730 taxa we demonstrate a statistically significant association between morphological and genetic distance for these plants. However, the relationship is non-linear, and while close relatives share more morphological features than distant relatives, above a genetic distance of ~0.7 increasingly distant relatives are not more divergent in phenotype. The pollen grains of biotically pollinated and abiotically pollinated plants overlap in morphological space, but certain pollen morphotypes and individual morphological traits are unique to these pollination ecologies. Our data show that the pollen grains of biotically pollinated plants are significantly more morphologically diverse than those of abiotically pollinated plants.
Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity
<p>Scientific understanding of biodiversity dynamics, resulting from past climate oscillations and projections of future changes in biodiversity, has advanced over the past decade. Little is known about how these responses, past or future, are spatially connected. Analyzing the spatial variability in biodiversity provides insight into how climate change affects the accumulation of diversity across space. Here, we evaluate the spatial variation of phylogenetic diversity of European seed plants among neighboring sites and assess the effects of past rapid climate changes during the Quaternary on these patterns. Our work shows a marked homogenization in phylogenetic diversity across Central and Northern Europe linked to high climate change velocity and large distances to refugia. Our results suggest that the future projected loss in evolutionary heritage may be even more dramatic, as homogenization in response to rapid climate change has occurred among sites across large landscapes, leaving a legacy that has lasted for millennia.</p>
Habitat filtering differentially modulates phylogenetic and functional diversity relationships between predatory arthropods
<p class="MsoNoSpacing">Mechanisms underlying biological diversities at different scales have received significant attention over the last decades. The hypothesis whether local abiotic factors, driving functional and phylogenetic diversities, can differ among taxa of arthropods remains under-investigated. In this study, we compared correlations and drivers of functional (FD) and phylogenetic (PD) diversities between spiders and carabids, two dominant taxa of ground-dwelling arthropods in salt marshes. Both taxa exhibited high correlation between FD and PD; the correlation was even higher in carabids, probably due to their lower species richness. Analyses highlight that FD and PD were positively linked to taxonomic diversity in both taxa; however, abiotic factors driving the FD and PD differed between spiders and carabid. Salinity particularly drove the taxonomic diversity of carabids, but not that of spiders, suggesting that spiders are phenotypically more plastic and less selected by this factor. Conversely, phylogenetic diversity was influenced by salinity in spiders, but not in carabids. This result can be attributed to the different evolutionary history and colonisation process of salt marshes between the two model taxa. Finally, our study highlights that, in taxa occupying the same niche in a constrained habitat, functional and phylogenetic diversities can have different drivers, showing different filtering mechanisms.</p>
Phylogenetic diversity and environment form assembly rules for Arctic diatom genera – a study on recent and ancient sedimentary DNA
<p><span><b>Aim</b></span></p> <p><span>This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian treeline. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover.</span></p> <p><span><b>Location</b></span></p> <p><span>Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7000 years before present, to capture the forest–tundra transition in space and time, respectively. </span></p> <p><span><b>Taxon</b></span></p> <p><span>Arctic freshwater diatoms.</span></p> <p><span><b>Methods</b></span></p> <p><span>We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera).</span></p> <p><span><b>Results</b></span></p> <p><span>Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Further, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time-slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO<sub>3</sub><sup>–</sup> and water depth, largely explain diatom turnover. </span></p> <p><span><b>Main conclusion</b></span></p> <p>Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian treeline ecotone. Using a space–time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.</p>
Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales
<p>Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β-diversity) along ecological gradients. Here, we characterize soil microbial β-diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β-diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β-diversities with respect to plant β-diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β-diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β-diversities were mostly related to plant β-diversity, while bacterial β-diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β-diversities with plant β-diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β-diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early-evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.</p>
Data from: Functional and phylogenetic diversity explain different components of diversity effects on biomass production
<p>The Anthropocene is defined by human-driven environmental change, with one consequence being the modern dramatic decline in biodiversity globally. This is especially worrisome given the long-acknowledged causal linkage between biodiversity and ecosystem functioning and the delivery of ecosystem services. <span class="fontstyle01"><span>However, t</span></span>he exact mechanisms driving biodiversity- ecosystem function (BEF) relationships remain unclear, specifically the linkages between species differences, measured by trait and phylogenetic distances, and how interactions, such as competitive inequality and stable coexistence via niche partitioning, influence these relationships.<span class="fontstyle01"><span> Using complementary plant biodiversity experiments, a </span></span>s<span class="fontstyle01"><span>ynthetic-assembled one that combined species in different phylogenetic distance treatments with a semi- natural functional group removal experiment, we assessed how species differences influence the mechanisms underpinning BEF relationships. We </span></span>calculated the net biodiversity effect (ΔY) of biomass production and partitioned it into two additive parts: the complementarity and <span class="fontstyle01"><span>selection effect</span></span>s at species and functional group level<span class="fontstyle01"><span> to </span></span>test how <span class="fontstyle01"><span>phylogenetic diversity and functional</span></span> diversity capture the influences of the complementarity and <span class="fontstyle01"><span>selection effects.</span></span> For both experiments, we found that phylogenetic and functional diversity explained biodiversity effects through similar mechanisms, with a positive relationship with the complementarity effect, and a negative relationship with the selection effect. However, we found that the <span class="fontstyle01"><span>selection effect was </span></span>best predicted by a negative relationship with functional dispersion (FD<sub>is</sub>) of<sub> </sub>height where the selection effect was strongest in plots with similarly tall species and weakest with a greater diversity of heights, while higher <span class="fontstyle01"><span>complementary </span></span>effects <span class="fontstyle01"><span>were best explained by increasing phylogenetic diversity (i.e., high MPD<sub>a</sub>).</span></span> Our work revealed that the mechanisms underpinning biodiversity-ecosystem function relationships are dependent on species differences and how these differences influence competitive inequalities and niche differences.</p>
Evolutionary history of Neotropical savannas geographically concentrates species, phylogenetic and functional diversity of lizards
<p>Supporting information (scripts) to compute diversity and endemism indices copied and available by Dan Rosauer (https ://github.com/DanRosauer/phylospatial).</p> <p>Aim: Understanding where and why species diversity is geographically concentrated remains a challenge in biogeography and macroevolution. This is true for the Cerrado, the most biodiverse tropical savanna in the world, which has experienced profound biodiversity loss. Previous studies have focused on a single metric (species composition), neglecting the fact that 'species' within the biome are often composed of cryptic species. In order to identify biodiversity hotspots more robustly and across multiple dimensions we integrate functional, spatial and new phylogeographic data for the Cerrado lizard fauna by (a) mapping the spatial patterns of species and phylogenetic diversity; and (b) using endemism measures to identify areas of unique diversity. We then quantify the extent to which existing protected areas represent the diversity.</p> <p>Location: Brazilian savanna (Cerrado).</p> <p>Methods: We generated species distribution models using distribution records for all Cerrado lizard species. These, combined with mitochondrial DNA phylogenies and natural history data, allowed us to map species richness, phylogenetic and functional diversity and phylogenetic and weighted endemism. Phylogenetic endemism maps were then cross-referenced against protected areas to calculate the amount of evolutionary history preserved within these areas.</p> <p>Results: The central region of the Cerrado, a vast and climatically stable plateau, stands out as important under all biodiversity metrics. Including evolutionary relationships in biodiversity assessment, we detected four regional hotspots with high concentration of spatially restricted evolutionary diversity. Protected areas cover only 10% of the Cerrado area and hold 11.64% of the summed phylogenetic endemism of all lizards in the biome.</p> <p>Main Conclusions: We highlighted both stable (Chapada dos Veadeiros and Serra do Espinhaço plateaus) and environmentally heterogenous regions (Araguaia and Tocantins valleys) as hotspots of evolutionary diversity. The creation and/or manipulation of areas for conservation are essential for the conservation and survival of the rich and endemic lizard fauna of the Cerrado.</p>
Data from: Temperature shapes opposing latitudinal gradients of plant taxonomic and phylogenetic β diversity
Latitudinal and elevational richness gradients have received much attention from ecologists but there is little consensus on underlying causes. One possible proximate cause is increased levels of species turnover, or β diversity, in the tropics compared to temperate regions. Here, we leverage a large botanical dataset to map taxonomic and phylogenetic β diversity, as mean turnover between neighboring 100 × 100 km cells, across the Americas and determine key climatic drivers. We find taxonomic and tip‐weighted phylogenetic β diversity is higher in the tropics, but that basal‐weighted phylogenetic β diversity is highest in temperate regions. Supporting Janzen's 'mountain passes' hypothesis, tropical mountainous regions had higher β diversity than temperate regions for taxonomic and tip‐weighted metrics. The strongest climatic predictors of turnover were average temperature and temperature seasonality. Taken together, these results suggest β diversity is coupled to latitudinal richness gradients and that temperature is a major driver of plant community composition and change.
Data from: Cryptic diversity in the Mexican highlands: thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)
With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element (UCE) data set (>3000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum-likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also result in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species-tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species-delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species-tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.
Data for: Phylogenetic structure of body shape in a diverse inland ichthyofauna
<p>Body shape is a fundamental metric of animal diversity affecting critical behavioral and ecological dynamics and conservation status, yet previously available methods <span>capture only a fraction of total body-shape variance</span>. <span>Here we use structure-from-motion (SFM) 3D </span>photogrammetry to generate digital 3D models of adult fishes from the Lower Mississippi Basin, one of the most diverse temperate-zone freshwater faunas on Earth, and 3D geometric morphometrics to capture morphologically distinct shape variables, interpreting <span>principal components as growth fields. The mean body shape in this fauna resembles plesiomorphic teleost fishes, and the major dimensions of body-shape disparity are similar to those of other fish faunas worldwide. Major p</span>atterns of b<span>ody-shape disparity are structured by phylogeny, with nested clades occupying distinct portions of the morphospace, </span>most of the morphospace occupied by multiple distinct clades, and one clade (Acanthomorpha) accounting for over half of the total body shape variance.<span> In contrast to previous studies, variance in </span>body depth (59.4%) structures overall body-shape disparity more than does length (31.1%), while width accounts for a non-trivial (9.5%) amount of the total body-shape disparity.</p>
The interplay between defaunation and phylogenetic diversity affect leaf damage by natural enemies in tropical plants
<ol> <li>Natural enemies play an important role in controlling plant population growth and vegetation dynamics. Tropical rainforests host the greatest diversity of herbivores, from large mammalian ungulates to microscopic pathogens, generating and maintaining plant diversity.</li> <li>By feeding on the same resources, large mammalian herbivores may interfere with plant consumption and leaf damage by important enemy guilds such as invertebrate herbivores and pathogens, triggering indirect trophic cascades. However, the impact of local extinctions of large herbivores on plant-enemy interactions is relatively unknown.</li> <li>We experimentally tested the effects of defaunation of large mammalian herbivores (e.g., peccaries, tapirs, brocket deer; hereafter, large herbivores) on leaf damage of 3,350 understory plants in tropical rainforests of Brazil. We examined leaf damage in 10,050 leaves from 333 morphospecies by assigning the area consumed or damaged by five guilds of insect herbivores and leaf pathogens within 86 paired open-closed plots and investigated the joint effects of defaunation and plant phylogenetic diversity.</li> <li>Plants released from large herbivores had 9% less leaf damage; this difference was due to the lower leaf pathogens incidence (29%) rather than insect herbivory. Evolutionary Distinctness was similarly and positively correlated with leaf damage in all treatments, suggesting additive effects of defaunation and phylogenetic diversity. Total and pathogenic leaf damage (but not insect damage) decreased with plant richness across treatments, and large herbivores' exclusion resulted in increased plant species richness. This suggests that large herbivores' exclusion leads to a dilution of total and pathogens' leaf damage by increasing plant species richness.</li> <li>Our results suggest that large herbivores' indirect effects decrease the dilution potential of plant communities against pathogens and rather reinforce their top-down impact on vegetation, demonstrating a previously overlooked cascading effect of large herbivore extinction on forest ecosystems.</li> <li> <em>Synthesis</em>: The extinction of large mammalian herbivores can lead to a decrease in pathogen-driven leaf damage, a previously unknown indirect effect in forest ecosystems, which might have consequences for plant fitness and ultimately for plant diversity. Large herbivores and plant pathogens might have synergistic effects in regulating the diversity of plant communities in some of the most diverse ecosystems on Earth.</li> </ol>
Habitat simplification affects functional group structure along with taxonomic and phylogenetic diversity of temperate-zone ant assemblages over a ten-year period
<p>Biodiversity is declining at various scales due to habitat simplification. Nevertheless, there is scarce information on how the biotic and abiotic changes linked to simplification affect several diversity dimensions, such as taxonomic, functional, and phylogenetic diversities. This study investigated whether transforming natural oak forests into induced grasslands affected species diversity, functional group structure, and phylogenetic diversity of ant assemblages inhabiting a temperate forest in central Mexico. We placed over 1,000 pitfall traps in five sampling events covering a ten-year period. We used Hill numbers to evaluate species diversity differences between vegetation types and patterns over time. Ant species were classified into stress-related functional groups, which were analyzed for their association with vegetation types and changes to their proportional abundance over time. We calculated the standardized effect size of the mean nearest taxon distance to quantify the evolutionary history and test for non-random patterns within vegetation types and sampling years. Species richness did not differ between vegetation types, yet grasslands showed greater diversity for the q=1 and q=2 orders. Besides, we found three ant species as bioindicators for each vegetation. Regarding functional structure, cold climate specialists were associated with oak forests. In contrast, generalist species were predominant in induced grasslands. Higher phylogenetic diversity with an overdispersed structure was associated with oak forest, whereas lower phylogenetic diversity and a clustered pattern were found in induced grassland. These results indicate that habitat simplification may not affect the number of ant species but rather increases their relative abundance and reorganizes the functional and phylogenetic structure in the ecosystem, particularly shift towards the dominance of evolutionary close-related species and broad-stress tolerant groups. These results highlight the importance of integrating further dimensions of diversity to properly evaluate the reassembly dynamics after habitat simplification and understand the mechanisms driving this biodiversity loss.</p>
Data on arthropod abundance in tropical forest restoration plots with high or low plant phylogenetic diversity
<p>Consideration of plant phylogenetic diversity in ecological restoration carries substantial potential, as communities with a greater diversity of lineages with older evolutionary histories can increase the diversity of niches and thus are likely to recover larger species networks than communities clustered in specific clades with reduced variation in functional traits. In this study, we experimentally assessed how arthropod communities were affected by the phylogenetic diversity of a set of tropical tree species. We established 12 experimental restoration plots with either high or low plant phylogenetic diversity, while maintaining constant the number of plant species. After one and three years, arthropods with different feeding habits (herbivores, predators, pollinators, and detritivores) were collected and identified as morphospecies or operational taxonomic units using metabarcoding techniques. We provide insights on the influence of plant phylogenetic diversity on arthropod abundance and species diversity, particularly among predator, pollinator, and detritivore common and dominant species, which increased with plant phylogenetic diversity. The trend, however, was the opposite for the diversity of herbivore common and dominant species, which decreased as plant phylogenetic diversity increased. These findings highlight the importance of considering plant species richness when designing restoration strategies, but also their evolutionary histories, as the same number of plant species can produce different outcomes for higher trophic levels, as a function of their phylogenetic relationships. </p>
Phylogenetic α- and β-diversities jointly reveal leaf-litter ant community assembly mechanisms along a tropical elevational gradient
<p>This study was conducted along the eastern slope of the Cofre de Perote mountain, in Veracruz, Mexico. This region is located at the junction of the Trans-Mexican volcanic belt and the Sierra Madre Oriental. We selected eight study sites spanning an elevational gradient of 3500 meters of altitude. Regardless of the geographical distance, all sites were systematically separated with an elevational difference of 500 meters on average between each other. We placed our study sites at the following elevations above sea level: 30-50 m, 610-670 m, 900-1010 m, 1470-1650 m, 2020-2230 m, 2470-2600 m, 3070-3160 m and 3480-3540 m, however, for simplicity, we will refer to each site as discrete units (i.e. 0, 600, 1000, 1500, 2100, 2500, 3100, 3500 m).</p> <p>Sampling sites were old-growth forests characterized by no obvious forest use and highly dominance of mature forests, except in the case of the lowest site (i.e., La Mancha), where most of its original vegetation has been transformed. To overcome the effect of perturbation in the studied patterns, we sampled La Mancha in a secondary forest with up to 30 years of regeneration. All sampling sites were closed-canopy forests in which a leaf-litter layer could be guaranteed. During the rainy season (July-September) of 2018 one 300-m transversal transect was located at each one of the eight study locations where we established 10 equidistantly sampling points (i.e., 30 meters between each other). Two independent 1-m2 samples were taken perpendicularly to each sampling point: one 10 meters on the right side and the other 10 meters from the left side. This procedure was repeated in a second transect placed during the dry season (March-May) of 2019 to increase community characterization as well as reduce any seasonality effect on our diversity patterns. Transects within an elevational site were separated at least 1 km away from each other. Thus, we obtained 320 m<sup>2</sup> leaf-litter samples characterized the whole mountain (8 study sites x 20 m<sup>2 </sup>per transect x 2 transects = 320 m<sup>2</sup>). In each 1-m<sup>2</sup> quadrat, we collected the leaf litter inside and sifted it through a coarse mesh screen of 1-cm grid size to remove the largest fragments and concentrate the fine litter. The concentrated fine litter from each sample was suspended in independent mini-Winkler sacks for 3 days in the laboratory. Falling arthropods were collected into a container with 95% ethanol. Ant workers were removed from each container for identification. When possible, specimens were identified at the species level. If not, we assigned a morphospecies number.</p> <p> </p> <p><strong>Phylogenetic tree constructions</strong></p> <p>Ideally, one would use a complete, species-level phylogeny of all ant species present in your study area to calculate phylogenetic diversity, yet our current understanding of ant relationships is still limited. As an alternative, we built a genus-level phylogeny based on the tree by Moreau & Bell, (2013), but using the phylogenetic relationships and divergence times within Myrmicinae from Ward et al. (2015). This phylogeny was then pruned to keep only a single species per genus to generate a genus-level phylogeny. To maximize taxonomic coverage, we replaced genera that were missing from those studies by closely-related lineages that were not present in our dataset using other phylogenetic studies (Borowiec, 2016; Lapolla et al., 2010; Schmidt & Shattuck, 2014). We then used the list of species (Supporting Information Table S1) in our dataset to simulate a species-level phylogeny in which the relationships within genera were obtained from a Yule (pure-birth) process using the <em>genus.to.species.tree</em> function in the “phytools” package (Revell, 2012). A total of 1000 simulated trees were obtained to account for phylogenetic uncertainty [see Arnan et al. (2018) and Divieso et al. (2020) for similar approach]. Additionally, we constructed a maximum clade credibility tree (hereafter MCC tree) which was used to summarize the uncertainty of the 1000 simulated trees. The MCC tree was constructed from the sample of the 1000 trees with the <em>maxCladeCred</em> function incorporated in the “ape” package (Paradis et al., 2019). Both the 1000 hypothetical trees and the MCC tree were used in downstream analyses (Supporting Information Fig. 1).</p>
Phylogenetically diverse diets favor more complex venoms in North American pitvipers
<p>The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are traits composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates considerably over evolutionary timescales, with apparent increases and decreases in complexity, yet the evolutionary causes of this variation is unclear. Here, we tested alternative hypotheses for the link between venom complexity and ecological sources of selection related to diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths <em>Crotalus, Sistrurus </em>and <em>Agkistrodon</em>. We generated independent transcriptomic and proteomic measures of venom complexity and then estimated prey diversity using the past century's extensive natural history studies on these snakes. We then conducted comparative tests relating different measures of predator venom complexity and prey community diversity using the first, genome-scale, dated phylogenies for this clade of snakes. Strikingly, phylogenetic diversity of prey was more strongly correlated to venom diversity than was species diversity, implicating prey species divergence, rather than the number of lineages alone, in the evolution of venom complexity. This positive relationship was observed within three of the four largest toxin gene families in viper venom. Given documented examples of taxonomic specificity of venoms spanning several levels of divergence, we suggest that the phylogenetic diversity of prey measures functionally-relevant divergence in the molecular targets of venom, a claim supported by diversity in the coagulation cascade targets of snake venom serine proteases. Our results support the general concept that the evolved diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.</p>
Phylogenetic data for: High diversity of new and known Phytophthora species from phylogenetic Clade 10 in natural ecosystems of Asia, Europe and the Americas
<p class="MsoNormal"><span>During extensive surveys of <em>Phytophthora</em> diversity, 14 new species were detected in natural ecosystems in Chile, Louisiana, Sweden, Ukraine, Vietnam and Indonesia. Multigene phylogeny based on the nuclear LSU, <em>rpl10</em>, ITS, <em>ßtub</em>, <em>enl</em>, <em>hsp90</em>, <em>tef-1α</em>, </span><em><span>ras-ypt1</span></em><span> and <em>tigA </em>and the mitochondrial <em>cox1</em>, <em>nadh1</em> and <em>rps10</em> gene sequences demonstrated that they belong to phylogenetic Clade 10 which is structured into three subclades. Subclades 10a and 10b comprise soil- and waterborne species with nonpapillate sporangia and variable breeding systems, including the known <em>P. afrocarpa</em>, <em>P. gallica</em> and <em>P. intercalaris</em> and the new </span><em><span>P. ludoviciana, P. procera, P. pseudogallica, P. scandinavica, P. subarctica</span></em><span>, <em>P. tenuimura, P. tonkinensis</em> and<em> P. ukrainensis</em>. In contrast, </span><span>all species in Subclade 10c are airborne with papillate sporangia and homothallic breeding system, including the known <em>P. boehmeriae</em>, <em>P. kernoviae</em> and <em>P. morindae</em> and the new </span><em><span>P. celebensis</span></em><span>, <em>P. chilensis, P. javanensis, P. multiglobulosa, P. pseudochilensis </em>and<em> P. pseudokernoviae</em>.<em> </em></span><span>All new species differed from each other and from related species by a unique combination of morphological characters, the breeding system, cardinal temperatures and growth rates.</span><span> The biogeography and evolutionary history of Clade 10 are discussed and the hypothesis put forward that the extant subclades originate from early divergences of pre-Gondwanan ancestors (>175 Mya) into water-/soilborne and airborne lineages which during their global spread experienced multiple allopatric and sympatric radiations.</span></p>
Taxonomic, functional, and phylogenetic diversity peaks do not coincide along a compositional gradient in forest-grassland mosaics
<p>This is a standard phytocoenological table with trait data for each species. Species are in rows and relevés (plots) are in columns. Habitat codes are according to the caption of Fig. 3 in our paper. Numbers in the relevés are percentage cover values.</p>
The counteracting effects of human-driven speciation and extinction on mammal species richness and phylogenetic diversity
<p><span>Human activities are causing massive increases in extinction rates, but may also lead to drastic increases in speciation rates – for example following the human-mediated spread of species to otherwise unreachable landmasses. The long-term net anthropogenic effects on biodiversity, therefore, remain uncertain. The aim of this paper is to assess the combined anthropogenic effects of extinctions and speciations on biodiversity over geological time scales. </span><span>We estimate known anthropogenic and predicted future extinctions based on Red List categories from the International Union for Conservation of Nature. We infer potential anthropogenic speciations assuming that all introductions to isolated landmasses will over time evolve into distinct species. We then estimate changes in regional and global species richness and phylogenetic diversity due to these extinctions and speciations. </span><span>We show that if all species introduced into new landmasses develop into new species, the number of anthropogenic speciation and extinctions eventually become similar</span><span>. However, even after accounting for an anthropogenic increase in speciation, our estimates suggest recovery times for phylogenetic diversity of several million years</span><span>. </span><span>Our results highlight that while humans are causing drastic biodiversity losses, human-driven speciation could eventually counterbalance these losses in species numbers, while phylogenetic diversity at least within our simulation scenarios would remain permanently reduced. This conclusion, however, requires our pressures on biodiversity to cease soon and requires us to consider geological timescales rather than changes over this century.</span></p>
Supplementary Material 1: Phylogenetic tree from Unraveling an unknown diversity of archaeal and bacterial tetraether membrane lipid producers in a euxinic marine system
<p>Phylogenetic tree (Black Sea MAGs)</p>
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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.