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727 results for “phylogenetic diversity”
FIGURE 3 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 3. Bayesian Inference topology based on Cytb sequence data used to assess the position of Neacomys sp. nov. in relation to other species in the genus (BI and ML analyses resulted in congruent topologies). Support values are indicated for each node (Bayesian posterior probabilities to the left, and percentages of 1,000 bootstrap replicates to the right). Each terminal is identified by country of origin, the next largest political unit, and GenBank accession number (in red). For specimens of N. tenuipes and Neacomys sp. nov. sequenced here, collection numbers are provided, as well as a number referring to localities mapped in FIGURE 2 and listed in Appendix I. Shaded colored boxes enclose the species groups proposed by Hurtado & Pacheco (2017) and Semedo et al. (2020). Abbreviations: BO (Bolivia), BR (Brazil), CO (Colombia), EC (Ecuador), FG (French Guyana), GU (Guyana), PE (Peru), and SU (Suriname).
FIGURE 11 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 11. Selected qualitative morphological traits differentiating Trans-Andean species of Neacomys present in Colombia: A), C), E) Neacomys sp. nov. B), D), F) N. tenuipes. Note the tegmen tympani exposed above the dorsal surface of the ectotympanic, the opened ectotympanic ring, the larger orbicular apophysis of the malleus, the bifurcated paraoccipital process, the deeper folds of the upper molars, and the divided mesoflexus of M1 in the new species. ab: auditory bullae; adeect: anterodorsal edge of the ectotympanic; hyp: hypoflexus; hp: hamular process of the squamosal; M1 prc: procingulum of first upper molar; mes: mesoflexus; met: metaflexus; mt: mastoid tubercle; oa: orbicular apophysis; par: paraflexus; pgf: postglenoid foramen; pp: paraoccipital process; pro: protoflexus; ssf: subsquamosal fenestra; tt: tegmen tympani.
FIGURE 2 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 2. Map showing collection localities of the named and unamed small-bodied species of Neacomys (except N. pictus) along with salient topographic features of northern South America. Localities of N. tenuipes and Neacomys sp. nov are numbered according to Appendix I. Localities of the remaining species are detailed in Voss et al. (2001), Sánchez-Vendizú et al. (2018), and Semedo et al. (2020). Miniature in the right side of the map corresponds to the Bayesian Cytb phylogeny recovered here (FIGURE 3): species in the map and phylogeny are same colored; the numbers in some nodes correspond to the median divergence times estimated by Upham et al. (2019) within Neacomys.
FIGURE 1 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 1. Map of collecting localities of the specimens of Neacomys sp. nov. (stars) 1. Colombia, Department of Santander, Municipality of El Carmen de Chucurí, vereda La Bodega, sector Manchurrias, western slope of the Serranía de los Yariguíes, Finca Buenos Aires, in the basin of the La San Guillerma stream (Type locality); 2. Colombia, Department of Santander, Municipality of Hato, vereda Hoya Negra. Numbers also correspond to the localities listed in Appendix I. Dashed lines represent boundaries of the municipalities encompassing the two localities. Green polygon represents the area comprised by the Serranía de los Yariguíes National Natural Park.
FIGURE 9 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 9. Comparison of the dorsal and ventral views of the skulls of Trans-Andean species of Neacomys present in Colombia: A), C) Neacomys sp. nov. (UIS-MHN-M 1068, holotype). B), D) Neacomys tenuipes (UIS-MHN-M 1723). Note the nasals more expanded anteriorly, the shallower zygomatic notches, the less developed supraorbital ridges, the procingulum of M1 flattened laterally, and the incisive foramina extending almost to anterior alveolus of M1 in Neacomys sp. nov. if: incisive foramen; M1 prc: procingulum of first upper molar; nas: nasal bone; sob: supraorbital beads; zn: zygomatic notch.
Data from: Environmental factors explain the spatial mismatches between species richness and phylogenetic diversity of terrestrial mammals
Aim: Explore the spatial variation of the relationships between species richness (SR), phylogenetic diversity (PD) and environmental factors to infer the possible mechanisms underlying patterns of diversity in different regions of the globe. Location: Global. Time period: Present day. Major taxa studied: Terrestrial mammals. Methods: We used a hexagonal grid to map SR and PD of mammals and four environmental factors (temperature, productivity, elevation and climate-change velocity since the Last Glacial Maximum). We related those variables through direct and indirect pathways using a novel combination of Path Analysis and Geographically Weighted Regression to account for spatial non-stationarity of path coefficients. Results: SR, PD and environmental factors relate differently across the geographic space, with most relationships varying in both, magnitude and direction. Species richness is associated with lower phylogenetic diversity in much of the tropics and in the Americas, which reflects the tropical origin and the recent diversification of some mammalian clades in these regions. Environmental effects on PD are predominantly mediated by their effects on SR. But once richness is controlled for, the relationships between environmental factors and PD (i.e. PDSR) highlight environmentally driven changes in species composition. Environmental-PDSR relationships suggest that the relative importance of different mechanisms driving biodiversity shifts spatially. Across most of the globe, temperature and productivity are the strongest predictors of richness, while PDSR is best predicted by temperature. Main conclusions: Richness explains most spatial variation in PD, but both dimensions of biodiversity respond differently to environmental conditions across the globe, as indicated by the spatial mismatches in the relationships between environmental factors and these two types of diversity. We show that accounting for spatial non-stationarity and environmental effects on PD while controlling for richness uncovers a more complex scenario of drivers of biodiversity than previously observed.
Data from: Contrasting impacts of land use change on phylogenetic and functional diversity of tropical forest birds
1.Biodiversity conservation strategies increasingly target maintaining evolutionary history and the resilience of ecosystem function, not just species richness (SR). This has led to the emergence of two metrics commonly proposed as tools for decision making: phylogenetic diversity (PD) and functional diversity (FD). Yet the extent to which they are interchangeable remains poorly understood. 2.We explore shifts in and relationships between FD and PD of bird communities across a disturbance gradient in Borneo, from old-growth tropical forest to oil palm plantation. 3.We show a marked decline in PD, and an increase in phylogenetic mean nearest taxon distance (MNTD) from forest to oil palm, in line with declining SR across the gradient. However, phylogenetic mean pairwise distance (MPD) is constrained by forest logging more than by conversion to oil palm, taking account of SR. 4.The decline in FD across the gradient is less severe than in PD, with all metrics indicating relatively high trait diversity in oil palm despite low SR, although functional redundancy is much reduced. Accounting for SR, levels of functional over- or under-dispersion of bird communities are strongly coupled to habitat disturbance level rather than to any equivalent phylogenetic metric. 5.Policy Implications. We suggest that while phylogenetic diversity (PD) is an improvement on species richness as a proxy for functional diversity (FD), conservation decisions based on PD alone cannot reliably safeguard maximal FD. Thus, PD and FD are related but still complementary. Priority setting exercises should use these metrics in combination to identify conservation targets.
Data from: Humidity levels drive reproductive modes and phylogenetic diversity of amphibians in the Brazilian Atlantic Forest
AIM: The diversity of reproductive modes among amphibians provides a striking example of how differences in the biology of species furnish can provide important explanations for species distribution patterns on a broad scale. We hypothesized that sites with a higher humidity level will support more different modes of reproduction than drier sites and will consequently exhibit a higher phylogenetic diversity. Furthermore, we predict that if there is a gradient in the tolerance of reproductive modes to desiccation, there will be a nested pattern in the composition of reproductive modes among sites. LOCATION: Twenty-seven forest sites in the Brazilian Atlantic Forest. METHODS: Through a path analysis approach, we evaluated the direct and indirect effects of the humidity level on the number of reproductive modes as well as the relative importance of both variables on amphibian phylogenetic diversity. A nestedness analysis was used to quantify the extent to which the composition of both species and reproductive modes in drier sites correspond to non-random subsets of those in sites with higher annual precipitation. RESULTS: We found that the reproductive modes present in drier sites are non-random subsets of those present in sites with higher humidity levels. Because reproductive modes are phylogenetically conserved among amphibians, sites with a greater number of reproductive modes supported greater phylogenetic diversity. Sites with high precipitation throughout the year provided adequate environmental conditions for a larger number of reproductive modes, whereas sites with low precipitation and typical seasonal climates supported only those reproductive modes specialized to resist desiccation. MAIN CONCLUSIONS: Our results show that humidity-related variables are key environmental factors related to both the richness of reproductive modes and phylogenetic diversity. We hypothesized that the higher phylogenetic diversity found in moister sites reflects differences in the tolerance to desiccation among different reproductive modes. Given that reproductive modes are associated with susceptibility to desiccation, their incorporation into explanatory models may trigger a great advance in the understanding of the mechanisms regulating the species richness and composition of amphibian communities.
Data from: Improving spatial predictions of taxonomic, functional and phylogenetic diversity
1. In this study, we compare two community modelling approaches to determine their ability to predict the taxonomic, functional and phylogenetic properties of plant assemblages along a broad elevation gradient and at a fine resolution. The first method is the standard stacking individual species distribution modelling (SSDM) approach, which applies a simple environmental filter to predict species assemblages. The second method couples the SSDM and macroecological modelling (MEM - SSDM-MEM) approaches to impose a limit on the number of species co-occurring at each site. Because the detection of diversity patterns can be influenced by different levels of phylogenetic or functional trees, we also examine whether performing our analyses from broad to more exact structures in the trees influences the performance of the two modelling approaches when calculating diversity indices. 2. We found that coupling the SSDM with the MEM improves the predictions for the diversity facets compared with those of the SSDM alone. The accuracy of the SSDM predictions for the diversity indices varied greatly along the elevation gradient, and when considering broad to more exact structure in the functional and phylogenetic trees, the SSDM-MEM predictions were more stable. 3. SSDM-MEM moderately but significantly improved the prediction of taxonomic diversity, which was mainly driven by the corrected number of predicted species. The performance of both modelling frameworks increased when predicting the functional and phylogenetic diversity indices. In particular, fair predictions of the taxonomic composition by SSDM-MEM led to increasingly accurate predictions of the functional and phylogenetic indices, suggesting that the compositional errors were associated with species that were functionally or phylogenetically close to the correct ones; this did not always hold for the SSDM predictions. 4. Synthesis. In this study, we tested the use of a recently published approach that couples species distribution and macroecological models to provide the first predictions of the distribution of multiple facets of plant diversity: taxonomic, functional and phylogenetic. Moderate but significant improvements were obtained; thus, our results open promising avenues for improving the predictions of different facets of biodiversityacross broad environmental gradients when functional and phylogenetic information is available.
Data from: Seasonal dynamics of waterbird assembly mechanisms revealed by phylogenetic and functional diversity in a subtropical wetland
Despite growing interest in phylogenetic and functional methods in ecological assembly, less attention has been paid to seasonal variation patterns of migrant species. Migrants can rapidly mediate influences of species interactions and environmental factors through seasonal movement, suggesting dynamical relative importance of different assembly mechanisms among seasons. Here we describe seasonal dynamics in phylogenetic and functional diversity of waterbirds in Mai Po Wetland, in a subtropical region with significant predictable temporal variation. Phylogenetic and functional structure of α diversity varied seasonally. Specifically, phylogenetic structures clustered in summer, while being over-dispersed in winter. However, phylogenetic structure in spring and autumn was intermediate with a transition to random. Functional structure was clustered in spring but showed over-dispersion in the other three seasons. For β diversity, summer and winter assemblages had two distinct groups, while spring and autumn assemblages were mixed. Thus, waterbird assemblages were primarily shaped by interspecific competition in winter. Random processes tended to shape assemblage in spring. Environmental factors played a more important role in summer . In addition, phylogenetic distance of probability of co-occurrence of species pairs was significantly larger in winter than in summer. These results suggest that the relative importance of assemblage mechanisms can vary seasonally in response to changing environmental conditions, suggesting that studies attempting to infer a single dominant assembly mechanism may ignore important assembly processes. Temporal shifts in assembly mechanisms may play an important role in maintaining diversity of subtropical and temperate wetlands and perhaps other dynamic systems.
Data from: Invasive species removal increases species and phylogenetic diversity of wetland plant communities
Plant invasions result in biodiversity losses and altered ecological functions, though quantifying loss of multiple ecosystem functions presents a research challenge. Plant phylogenetic diversity correlates with a range of ecosystem functions, and can be used as a proxy for ecosystem multifunctionality. Laurentian Great Lakes coastal wetlands are ideal systems for testing invasive species management effects because they support diverse biological communities, provide numerous ecosystem services, and are increasingly dominated by invasive macrophytes. Invasive cattails are among the most widespread and abundant of these taxa. We conducted a three-year study in two Great Lakes wetlands, testing the effects of a gradient of cattail removal intensities (mowing, harvest, complete biomass removal) within two vegetation zones (emergent marsh, wet meadow) on plant taxonomic and phylogenetic diversity. To evaluate native plant recovery potential, we paired this with a seed-bank emergence study that quantified diversity metrics in each zone under experimentally manipulated hydroperiods. Pre-treatment, we found that wetland zones had distinct plant community composition. Wet meadow seed banks had greater taxonomic and phylogenetic diversity than emergent marsh seed banks, and high-water treatments tended to inhibit diversity by reducing germination. Aboveground harvesting of cattails and their litter increased phylogenetic diversity and species richness in both zones, more than doubling richness compared to unmanipulated controls. In the wet meadow, harvesting shifted the community toward an early successional state, favoring seed-bank germination from early seral species, whereas emergent marsh complete removal treatments shifted the community toward an aquatic condition, favoring floating-leaved plants. Removing cattails and their litter increased taxonomic and phylogenetic diversity across water levels, a key environmental gradient, thereby potentially increasing the multifunctionality of these ecosystems. Killing invasive wetland macrophytes but leaving their biomass <i>in situ</i> does not address their underlying mechanism of dominance and is less effective than more intensive treatments that also remove their litter.
Data from: Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives
Premise of the study: Species limits of the emerging model organism Setaria viridis (tribe Paniceae, subtribe Cenchrinae) are not well defined. It is thought to be related to S. adhaerens, S. faberi, S. verticillata, and S. verticilliformis and in North America occurs with the morphologically similar S. pumila. An integrated approach was taken to evaluate its variation and relationships with the other taxa. Methods: Statistical morphology, flow cytometry, molecular phylogenetics, and growth experiments were employed to examine the group's physical variation, polyploidy, evolutionary relationships, and drought ecology, respectively. Key results: Setaria viridis contributed one genome to the tetraploids S. faberi, S. verticillata, and S. verticilliformis; the other genome of the latter two was contributed by S. adhaerens. Setaria pumila is unrelated. Morphologically, S. viridis is most similar to S. faberi, but all tested accessions of S. viridis were diploid, whereas those of S. faberi were all tetraploid. Principal component analysis of 70 morphological characters consistently separated S. viridis from S. faberi, largely by spikelet characters. The diagnostic morphological characters are not affected by watering. Setaria faberi is far more sensitive to drought, in terms of mortality and morphological stunting, than S. viridis or S. pumila. Conclusions: Setaria viridis is a diploid species and has contributed to several polyploid derivatives. The most morphologically similar of the polyploids is S. faberi, which differs in spikelet features, phylogenetics, genome size, and ecological response to drought. Researchers using field-collected S. viridis as a model organism will benefit from the clear delimitation provided in this study.
Data from: Managing Neotropical oil palm expansion to retain phylogenetic diversity
The expansion of tropical agriculture is a major driver of the extinction crisis. A key question is whether biodiversity losses can be minimized by restricting future expansion to low-productivity farmland and retaining forest fragments, especially in rapidly changing Neotropical landscapes. We investigated these methods in the context of avian phylogenetic diversity, which summarizes the evolutionary history preserved within communities. Evidence suggests that phylogenetic diversity plays an important role in maintaining key ecosystem functions. We collected data on avian communities in the Colombian Llanos, a region highlighted as being optimal for the expansion of oil palm, at the expense of existing habitats including forest remnants and improved cattle pastures. PD, a measure of phylogenetic richness, and MPD, a measure of the phylogenetic distance between individuals in a community in deep evolutionary time, were significantly higher in forest than in oil palm or pasture, but did not differ significantly between oil palm and pasture. MNTD, a measure of distance between individuals in a community at the intra-familial and intra-generic level, was significantly higher in oil palm and pasture than in forest. However, median evolutionary distinctiveness (ED) was highest in pasture, partly due to the abundance of distinct waterbirds, but did not differ between oil palm and forest. PD in oil palm and pasture increased with the extent of remnant forest cover. Synthesis and applications. The PD (a measure of phylogenetic richness) and MPD (a measure of the phylogenetic distance) of bird communities in this region can best be conserved by ensuring that new oil palm plantations replace pasturelands rather than forest. A secondary benefit of preserving forest would be the enhancement of PD in the surrounding agricultural landscape. This strategy will need to be coupled with measures to either reduce pasture demand or to intensify existing cattle production to ensure that forest is not replaced by pasture elsewhere.
The effects of tropical secondary forest regeneration on avian phylogenetic diversity.
<p>1. The conversion of tropical forests to farmland is a key driver of the current extinction crisis. With the present rate of deforestation unlikely to subside, secondary forests that regenerate on abandoned agricultural land may provide an option for safeguarding biodiversity. While species richness (SR) may recover as secondary forests get older, the extent to which phylogenetic diversity (PD)—the total amount of evolutionary history present in a community—is conserved is less clear. Maximising PD has been argued to be important to conserve both evolutionary heritage and ecosystem function.</p> <p>2. Here, we investigate the effects of secondary forest regeneration on PD in birds. The regeneration of secondary forests could lead to a community of closely related species, despite maintaining comparable SR to primary forests, and thus have diminished biodiversity value with reduced evolutionary heritage.</p> <p>3. We use a meta-dataset of paired primary and secondary forest sites to show that, over time, forest specialist species returned across all sites as secondary forest age increased. Forest specialists colonise secondary tropical forests in both the Old World and the New World, but recovery of PD and community composition with time is only evident in the Old World.</p> <p>4. Synthesis and applications. Whilst preserving primary tropical forests remains a core conservation goal, our results emphasize the important role of secondary forest in maintaining tropical forest biodiversity. Biodiversity recovery differs between Old and New World secondary forests and with proximity to primary forest, highlighting the need to consider local or regional differences in landscape composition and species characteristics, especially resilience to forest degradation and dispersal capability. While farmland abandonment is increasing across marginal areas in the tropics, there remains a critical need to provide long-term management and protection from reconversion to maximize conservation benefits of secondary forests. Our study suggests such investments should be focused on land in close proximity to primary forests. 30-Mar-2020</p>
Data from: Species richness and patterns of overdispersion, clustering and randomness shape phylogenetic and functional diversity-area relationships in habitat islands
<p><b>Aim:</b> To evaluate how the area of habitat island systems influences multiple facets of diversity. </p> <p><b>Location:</b> Southern Brazil. </p> <p><b>Taxon:</b> Birds. </p> <p><b>Methods:</b> Using an Information Theoretic approach, we compared the fit of 20 diversity–area relationship (DARs) models in three habitat island systems. We tested for the best-fit model, model-family, shape, and presence/absence of an asymptote. We used species richness (SR), Faith's phylogenetic diversity (PD) and Faith's functional diversity (FD) to assess species–area (SARs), phylogenetic (PDARs) and functional diversity–area relationships (FDARs). We controlled for the effect of SR in PD and FD via null models to assess PDARs and FDARs independently of SR and to explore the influence of phylogenetic and functional randomness, clustering and overdispersion. </p> <p><b>Results:</b> PDARs and FDARs built with PD and FD resembled SARs and were all best fitted by convex or sigmoidal, upwards oriented, non-asymptotic models. Controlling for SR in diversity indices produced flat or downwards-oriented, weak PDARs and FDARs, which were best fitted by convex, non-asymptotic models or the linear model. Taxonomic diversity accumulated faster with area than functional diversity, which accumulated faster than phylogenetic diversity. Randomness and clustering patterns prevailed in shaping PDARs and FDARs relative to overdispersion. </p> <p><b>Main conclusions: </b>Controlling for SR in PD and FD affects DARs patterns and the strength of the relationships. Irrespective of this influence of SR, a few simple models of the power and exponential model-families best fit DARs. Model parameters reveal differences in the response of each facet of diversity to increases in area, highlighting the complementary nature of DARs. When considered independently of SR, both PDAR and FDAR patterns largely reflect the broad variation of phylogenetic and functional diversity in small islands. It is therefore likely that the ecological processes that promote phylogenetic and functional overdispersion and clustering operate at contrasting spatial scales.</p>
Data from: Non-random loss of phylogenetically distinct rare species degrades phylogenetic diversity in semi-natural grasslands
1. Although biodiversity loss is a critically important topic, our understanding of how both land abandonment and land-use intensification in semi-natural grasslands alters the community diversity and assembly mechanisms is very limited. Large-scale economic drivers of land-use change might inadvertently result in the loss of vulnerable species and reduce ecosystem services provisioning. 2. In this study, we assessed non-random community change by examining patterns of low-abundance species loss, and community assembly in semi-natural grasslands due to land abandonment and intensification in southwest Japan. We analyzed relationships between evolutionary distinctiveness and abundance for each species. In addition, we used metrics of species and phylogenetic diversity and phylogenetic structure to assess patterns of non-random biodiversity loss due to both abandoned and intensified land-use. 3. We demonstrated that low-abundance species were more evolutionarily distinct compared to high-abundance (i.e., dominant) species. Furthermore, land-use intensification resulted in further declines in low-abundance species, whereas land abandonment resulted in declines in all species, regardless of their initial abundance. 4. We found that both forms of land-use change (abandonment and intensification) resulted in non-random patterns of community change, with traditional land-use maintaining the highest biodiversity and land-use change coinciding with decreased species and phylogenetic diversity measures. Intensified land-use caused phylogenetic community structure to be more closely related than expected by chance, whereas the metrics of how distant species are from one another on average based on phylogenetic tree (i.e., mean pairwise phylogenetic distance) did not change from land abandonment. 5. Synthesis and applications. We show that the loss of phylogenetic diversity, and especially of low-abundance species with high value of phylogenetic distinctiveness, resulted in non-random community disassembly. Our results argue that in order to maintain biodiversity in these semi-natural grasslands, traditional management practices should be encouraged over intensification and simple abandonment. Government agencies should adopt policies or provide incentives that encourage the maintenance of traditional practices in rural Japan, and elsewhere where the combination of land consolidation and abandonment are important conservation issues.
Data from: Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands
Global biodiversity is declining rapidly as a consequence of anthropogenic changes to the environment. Traditional diversity indices such as species richness have been used to assess biodiversity, but recent arguments call for a more comprehensive assessment that includes both phylogenetic and functional diversity (PD and FD, respectively). Many PD metrics have been developed, but few empirical studies have compared metrics across sites with the goal of understanding their application to characterizing biodiversity. In this study, 17 PD metrics, four traditional diversity indices, and one measure of FD were calculated and compared between two Nebraska grasslands. PD metrics were calculated from robust phylogenies estimated from next-generation sequencing data of 45 species. Traditional indices were calculated using species abundance data, and FD was quantified by measuring the phylogenetic signal, K, of specific leaf area (SLA). Results showed that PD metrics and traditional indices were not always correlated, and various PD metrics characterized biodiversity differently. In addition, phylogenies estimated from >80 genes were more robust than single- or dual-gene phylogenies resulting in more reliable PD metrics. K of SLA indicated random trait assembly in all sites. Results suggested that metrics that identify phylogenetic structure and relatedness can provide information to conservation planners about the ability of a community to persist in an unpredictable future. A combination of these results with those of future investigations applying PD and FD metrics to varying communities will support concrete recommendations to conservation planners about how to incorporate these metrics into the selection of priority regions.
Data from: The evolution of reproductive diversity in Afrobatrachia: a phylogenetic comparative analysis of an extensive radiation of African frogs
The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co-evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (∼400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift towards using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans.
Data from: Tropical rainforest conversion and land-use intensification reduce understory plant phylogenetic diversity
1. Conversion of rainforest into agricultural land affects multiple facets of tropical plant diversity. While the effects of tropical land use change and intensification on species diversity are comparatively well studied, the effects on phylogenetic diversity and structure of plant communities are largely unknown. Furthermore, it is not clear how the loss of native species and addition of alien species collectively affect phylogenetic diversity and structure. 2. We investigated the phylogenetic diversity and structure of understorey plants; a diverse and ecologically important, yet poorly studied group. We studied four prominent land use systems (tropical lowland rainforest, jungle rubber agroforest, rubber plantations and oil palm plantations) in the lowlands of Sumatra (Indonesia), a region experiencing dramatic land use changes. 3. Across the four systems, we investigated differences in four metrics of phylogenetic community structure (phylogenetic diversity, mean pairwise distance, mean nearest taxon distance and their abundance-weighted variants). Our analyses were based on a comprehensive vegetation survey consisting of 32 plots, 1,197 species of vascular plants, and 146,599 plant individuals. 4. Our results showed that forest conversion into agricultural systems leads to a pronounced loss of phylogenetic diversity. Furthermore, the standard effect size of mean pairwise distance indicated a gradual change from clustered to overdispersed phylogenetic community structure with increasing land use intensity from forest over jungle rubber to the monoculture plantations. In most land use systems, the presence or absence of alien plant species did not affect phylogenetic structure. Only in oil palm plantations, removing alien species from the data led to a more overdispersed structure. In conclusion, conserving the phylogenetic diversity and structure requires efficient protection of the last remaining rainforests. 5. Synthesis and applications. Forest conversion into agricultural areas negatively affects phylogenetic understorey plant diversity and leads to a shift from clustered to overdispersed phylogenetic community structure. These trends are partly driven by alien species particularly in oil palm plantations. Protecting the remaining rainforests, and considering multi-species agroforestry systems in favour of intensive monoculture plantations are thus imperative to conserve phylogenetic plant diversity and community structure.
Data from: The contribution of rare species to community phylogenetic diversity across a global network of forest plots
Niche differentiation has been proposed as an explanation for rarity in species assemblages. Testing this hypothesis requires quantifying the ecological similarity of species. This similarity can potentially be estimated by using phylogenetic relatedness. In this study, we predicted that if niche differentiation does explain the co-occurrence of rare and common species, then rare species should contribute greatly to the overall community phylogenetic diversity (PD), abundance will have phylogenetic signal and that common and rare species will be phylogenetically dissimilar. We tested these predictions by developing a novel method that integrates species rank abundance distributions with phylogenetic trees and trend analyses to examine the relative contribution of individual species to the overall community PD. We then supplement this approach with analyses of phylogenetic signal in abundances and measures of phylogenetic similarity within and between rare and common species groups. We applied this analytical approach to 15 long-term temperate and tropical forest dynamics plots from around the world. We show that the niche differentiation hypothesis is supported in six forests but is rejected in nine forests, and that the three metrics utilized in this study each provide unique but corroborating information regarding the phylogenetic distribution of rarity in communities.
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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.