Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
727
datasets available to search
ShareScore release 0.9.0
Dataset results
727 results for “phylogenetic diversity”
Net N mineralization:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Root biomass:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Soil percent carbon and nitrogen:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Soil pH:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Soil microbial respiration rate:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs
<p>Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA gene only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid <em>Olkasia</em> as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by <em>Ploeotia</em> spp.), <em>Lentomonas</em>, and <em>Keelungia</em> form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes <em>Rapaza</em>, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (<em>Anisonema</em> and <em>Dinema</em> spp.), '<em>Heteronema</em> II' (represented by <em>H. vittatum</em>), and a clade of <em>Neometanema</em> plus Aphagea. Among 'peranemid' phagotrophs, <em>Chasmostoma</em> branches with included <em>Urceolus</em>, and <em>Peranema</em> with the undescribed '<em>Jenningsia</em> II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that <em>Entosiphon</em> is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.</p>
Fig. 22 in Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)
Fig. 22. Image obtained by scanning electron microscope (SEM) of the micropterous wing of a male of Tachydromia apterygon Plant & Deeming, 2006. Scale bar: 10 μm.
Data from: Relationships among taxonomic, functional, and phylogenetic ant diversity across the biogeographic regions of Europe
Understanding how different biodiversity components are related across different environmental conditions is a major goal in macroecology and conservation biogeography. We investigated correlations among alpha and beta taxonomic (TD), phylogenetic (PD), and functional diversity (FD) in ant communities in the five biogeographic regions most representative of western Europe; we also examined the degree of niche conservatism. We combined data from 349 ant communities composed of 154 total species, which were characterized by 10 functional traits and by phylogenetic relatedness. We computed TD, PD, and FD using the Rao quadratic entropy index, which allows each biodiversity component to be partitioned into α and β diversity within the same mathematical framework. We ran generalized least squares and multiple matrix regressions with randomization to investigate relationships among the diversity components. We used Pagel's λ test to explore niche conservatism in each biogeographic region. At the alpha scale, TD was consistently, positively related to PD and FD, although the strength and scatter of this relationship changed among the biogeographic regions. Meanwhile, PD and FD consistently matched up across regions. Accordingly, we found similar degrees of niche conservatism across regions. Nonetheless, these alpha-scale relationships had low coefficients of determination. At the beta scale, the three diversity components were highly correlated across all regions (especially TD and FD, as well as PD and FD). Our results imply that the different diversity components, and especially PD and FD, are consistently related across biogeographic regions and analytical scale. However, the alpha-scale relationships were quite weak, suggesting environmental factors might influence the degree of association among diversity components at the alpha level. In conclusion, conservation programs should seek to preserve functional and phylogenetic diversity in addition to species richness, and this approach should be applied universally, regardless of the biogeographic locations of the sites to be protected.
Data from: Galega orientalis is more diverse than Galega officinalis in Caucasus – whole-genome AFLP analysis and phylogenetics of symbiosis-related genes
Legume plants can obtain combined nitrogen for their growth in an efficient way through symbiosis with specific bacteria. The symbiosis between Rhizobium galegae and its host plant Galega is an interesting case where the plant species G. orientalis and G. officinalis form effective, nitrogen fixing, symbioses only with the appropriate rhizobial counterpart, R. galegae bv. orientalis and R. galegae bv. officinalis respectively. There is plenty of information available on the symbiotic properties of nitrogen fixing rhizobia, while more information is needed on the properties of the host plants. The Caucasus region in Eurasia has been identified as the gene centre (centre of origin) of G. orientalis, although both G. orientalis and G. officinalis can be found in this region. In this study, the diversity of these two Galega species in Caucasus was investigated to test the hypothesis that in this region G. orientalis is more diverse than G. officinalis. The amplified fragment length polymorphism (AFLP) fingerprinting performed here showed that the populations of G. orientalis and R. galegae bv. orientalis are more diverse than those of G. officinalis and R. galegae bv. officinalis respectively. These results are consistent with the centre of origin status of Caucasus for G. orientalis. Phylogenies of the symbiosis-related plant genes NORK and Nfr5 were congruent with the AFLP result from a diversity point of view. Finally, the results of this work indicate that the NORK and Nfr5 genes of Galega follow the same evolutionary pattern as conserved plant genes.
Data from: A new promising phylogenetic marker to study the diversity of fungal communities: the Glycoside Hydrolase 63 gene
In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.
Data from: Conserving phylogenetic diversity can be a poor strategy for conserving functional diversity
For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policy makers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and features (functional diversity [FD]), which may be valuable for a number of reasons. The claim that PD-maximized ("maxPD") sets of taxa will also have high FD is often taken at face value and in cases where researchers have actually tested it, they have done so by measuring the phylogenetic signal in ecologically important functional traits. The rationale is that if traits closely mirror phylogeny, then saving the maxPD set of taxa will tend to maximize FD and if traits do not have phylogenetic structure, then saving the maxPD set of taxa will be no better at capturing FD than criteria that ignore PD. Here, we suggest that measuring the phylogenetic signal in traits is uninformative for evaluating the effectiveness of using PD in conservation. We evolve traits under several different models and, for the first time, directly compare the FD of a set of taxa that maximize PD to the FD of a random set of the same size. Under many common models of trait evolution and tree shapes, conserving the maxPD set of taxa will conserve more FD than conserving a random set of the same size. However, this result cannot be generalized to other classes of models. We find that under biologically plausible scenarios, using PD to select species can actually lead to less FD compared with a random set. Critically, this can occur even when there is phylogenetic signal in the traits. Predicting exactly when we expect using PD to be a good strategy for conserving FD is challenging, as it depends on complex interactions between tree shape and the assumptions of the evolutionary model. Nonetheless, if our goal is to maintain trait diversity, the fact that conserving taxa based on PD will not reliably conserve at least as much FD as choosing randomly raises serious concerns about the general utility of PD in conservation.
Data from: Resilience to fire of phylogenetic diversity across biological domains
Fire alters the structure and composition of above- and belowground communities with concurrent shifts in phylogenetic diversity. The inspection of post-fire trends in the diversity of ecological communities incorporating phylogenetic information allows to better understand the mechanisms driving fire resilience. While fire reduces plant phylogenetic diversity based on the recruitment of evolutionarily-related species with post-fire seed persistence, it increases that of soil microbes by limiting soil resources and changing the dominance of competing microbes. Thus, during post-fire community reassembly, plant and soil microbes might experience opposing temporal trends in their phylogenetic diversity that are linked through changes in the soil conditions. We tested this hypothesis by investigating the post-fire evolution of plant and soil microbial (fungi, bacteria and archaea) communities across three 20-year chronosequences. Plant phylogenetic diversity increased with time since fire as pioneer seeders facilitate the establishment of distantly-related late-successional shrubs. The post-fire increase in plant phylogenetic diversity fostered plant productivity, eventually recovering soil organic matter. These shifts over time in the soil conditions explained the post-fire restoration of fungal and bacterial phylogenetic diversity, which decreased to pre-fire levels, suggesting that evolutionarily-related taxa with high relative fitness recover their competitive superiority during community reassembly. The resilience to fire of phylogenetic diversity across biological domains helps preserve the evolutionary history stored in our ecosystems.
Data from: Taxonomic and phylogenetic diversity of vascular plants at Ma'anling volcano urban park in tropical Haikou, China: Reponses to soil properties
Anthropogenic processes and socio-economic factors play important roles in shaping plant diversity in urban parks. To investigate how plant diversity of Ma' anling urban volcano park in Hainan Province, China respond to these factors, we carried out a field investigation on the taxonomic and phylogenetic diversity of vascular plants and soil properties in this area. We found 284 species of vascular plants belonging to 88 families and 241 genera, which included 194 native species, 23 invasive species, 31 naturalized species, 40 cultivars, and 4 rare / endangered plant species. Tree composition and richness significantly varied between different vegetation formations (plantation, secondary forest, and abandoned land). Plant species richness and community composition were significantly affected by elevation (El), soil water content (WC), total soil nitrogen (TN) and soil organic matter (SOM). There were significant diversity differences between plantations and abandoned lands, but not between the plantations and secondary forests. The flora in the study site was tropical in nature, characterized by pantropic distributions. Compared to adjacent areas, floristic composition in the study site was most similar to that of Guangdong, followed by that of Vietnam. Our study revealed the diversity patterns of volcanic plants and provided the basis for future planning of plant conservation, such as preserving plant species, maintaining plant habitats, and coordinating plant management in this region.
Data from: An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.
In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognised as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study the sequence of eIF4E was analysed in 1090 barley landraces and non-current cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eIF4E haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 out of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest eIF4E may play a role in barley adaptation to local habitats.
Data from: Resident-invader phylogenetic relatedness, not resident phylogenetic diversity, controls community invasibility
A central goal of invasion biology is to elucidate mechanisms regulating community invasibility. Darwin's naturalization hypothesis, one of the oldest hypotheses in invasion biology, emphasizes the importance of phylogenetic relatedness (PR) between resident and invader species for predicting invasibility. Alternatively, a recent extension of the diversity-invasibility hypothesis predicts that phylogenetic diversity (PD) of resident communities influences invasibility. Neither of these hypotheses has undergone rigorous experimental testing, and the relative contributions of PR and PD, whose effects tend to be confounded with each other, to community invasibility are unknown. Here we consider both perspectives together by independently manipulating PR and PD in laboratory bacterial assemblages. We found that while invader abundance declined significantly as PR increased, it was unaffected by PD. Likewise, we found that resident-invader functional similarity, not functional diversity of resident communities, was a significant predictor of invader abundance. Nevertheless, invader abundance was better predicted by PR than functional similarity. These results highlight the importance of considering species evolutionary relationships, especially the phylogenetic relatedness between resident and invader species, for the prediction, prevention and management of biological invasions.
Data from: Ploeotids represent much of the phylogenetic diversity of euglenids
Ploeotids are an assemblage of rigid phagotrophic euglenids that have 10–12 pellicular strips and glide on their posterior flagellum. Molecular phylogenies place them as a poorly resolved, likely paraphyletic assemblage outside the Spirocuta clade of flexible euglenids, which includes the well-known phototrophs and primary osmotrophs. Here, we report SSU rRNA gene sequences from 38 ploeotids, using both single-cell and culture-based methods. Several contain group I or non-canonical introns. Our phylogenetic analyses place ploeotids in 8 distinct clades: Olkasia n. gen, Hemiolia n. gen Liburna n. gen, Lentomonas, Decastava, Keelungia, Ploeotiidae, and Entosiphon. Ploeotia vitrea, the type of Ploeotia, is closely related to P. oblonga and Serpenomonas costata, but not to Lentomonas. Ploeotia cf. vitrea sensu Lax and Simpson 2013 is not related to P. vitrea and has a different pellicle strip architecture (as imaged by scanning electron microscopy): it instead represents a novel genus and species, Olkasia polycarbonata. We also describe new genera, Hemiolia and Liburna, for the morphospecies Anisonema trepidum and A. glaciale. A recent system proposing 13 suprafamilial taxa that include ploeotids is not supported by our phylogenies. The exact relationships between ploeotid groups remain unresolved and multigene phylogenetics or phylogenomics are needed to address this uncertainty.
Data from: Phylogenetic diversity is maintained despite richness losses over time in restored tallgrass prairie plant communities
Ecosystem restoration is an important tool for mitigating biodiversity loss and recovering critical ecosystem services to humanity, but restoration rarely takes into account the evolutionary attributes of the community being restored. Phylogenetic diversity (PD) represents a potentially valuable measure of restoration success because it can correlate with functional trait diversity that drives ecosystem function. However, PD patterns in restored communities are rarely assessed. We surveyed plant communities in restored tallgrass prairies 2–19 years old and calculated two PD measures, SESMNTD and SESMPD, of the communities and seed mixture applied to sites. We also identified high-threat exotic species present in each site to determine whether PD of the seed mixture applied was related to resistance against invasion. We show that PD in North American tallgrass prairie restorations, as measured by both SESMNTD and SESMPD, is maintained over time even as richness declines. Neither the resulting community PD nor invasion by high-threat exotic species was affected by PD of the seed mixture used in site restoration. Thus, simply maximizing PD of seed mixtures without considering the particular component species is unlikely to help achieve restoration goals. Synthesis and applications. These results suggest that species losses over time are not biased towards species with or without close relatives in the community. If phylogenetic diversity (PD) reflects functional trait diversity in communities, then local declines in species richness may not necessarily mean the loss of ecosystem function in restoration projects. However, PD of restored communities may be limited by low establishment rates for most species. Conservation practitioners should consider PD with careful planning to maintain overall community diversity and potentially maximize ecosystem function and services in restorations. This perspective will require a deeper understanding of the relationships between phylogenetic relatedness and traits associated with competition and fitness.
Data from: A phylogenetic perspective on habitat shifts and diversity in the North American Enallagma damselflies
Community ecologists are increasingly aware that the regional history of taxon diversification can have an important influence on community structure. Likewise, systematists recognize that ecological context can have an important influence on the processes of speciation and extinction that create patterns of descent. We present a phylogenetic analysis of 33 species of a North American radiation of damselflies (Zygoptera: Coenagrionidae: Enallagma Selys), which have been well-studied ecologically, in order to elucidate the evolutionary mechanisms that have contributed to differences in diversity between larval habitats (lakes with and without fish predators). Analysis of molecular variation in 842 bp of the mitochondrial cytochrome oxidase I and II subunit and the intervening Leu-tRNA and 37 morphological characters resulted in three well-defined clades that are only partially congruent with previous phylogenetic hypotheses. Molecular and morphological data partitions were significantly incongruent. Lack of haplotype monophyly within species and small levels of sequence divergence (<1%) between related species in 3 of the 4 clades suggests that recent, and parallel, speciation has been an important source of community diversity. Reconstruction of habitat preference over the phylogeny suggests that the greater species diversity in fish-lake habitats is due to the recency of shifts into the fishless-lake habit, although a difference in speciation or extinction rates between the two habitats is difficult to exclude as an additional mechanism.
Data from: Phylogenetic revision of the Strophomenida, a diverse and ecologically important palaeozoic brachiopod order
The order Strophomenida was an ecologically abundant and taxonomically diverse group of Palaeozoic brachiopods that originated in the earliest Ordovician and went extinct in the Carboniferous. During their long geological range, the Strophomenida survived two of the 'Big Five' mass extinction events, the Late Ordovician and the Late Devonian, suggesting that they are potentially informative taxa for studying the evolutionary effects of these two distinct mass extinctions, each with drastically different forcing mechanisms. However, while there have been previous phylogenetic studies on smaller groups within the Strophomenida, the phylogenetic relationships of the whole group are still largely unknown. The group has been divided into two major superfamilies, the Strophomenoidea (strophomenoids) and the Plectambonitoidea (plectambonitoids). Despite being treated as separate clades, the plectambonitoids may form a paraphyletic grade into the strophomenoids. We present a detailed higher-level parsimony-based phylogenetic analysis of the Strophomenida, consisting of 69 characters and 62 exemplar species sampled from the majority of the taxonomically defined families/subfamilies. Several species of basal chonetids (strophochonetids) were also included in this analysis, as they may be closely related to the Strophomenida and share several characters with both the plectambonitoids and strophomenoids. The phylogenetic analysis suggests the plectambonitoids, as originally defined, are paraphyletic to the monophyletic strophomenoids. The basal chonetids are reconstructed as a monophyletic group that is sister to the strophomenoids, suggesting that their proper placement might be within the Strophomenida. The topology also suggests that at least 17 of the taxonomically defined strophomenoid and plectambonitoid families are likely to be monophyletic. The Plectambonitidae and the Taffiidae as defined are paraphyletic, and the Grorudiidae and Leptostrophiidae are polyphyletic. Furthermore, subfamilies Leptodontellinae, Dicoelostrophiinae, Palaeostrophomeninae and Aegiromeninae are raised to the level of family. When analysed within this phylogenetic context, the Late Ordovician mass extinction event had little effect on the large-scale evolution of the group.
Data from: Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies
1.Hundreds of experiments have now manipulated species richness of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than species richness because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis. 2.Here, we re-analyze data from 16 experiments that have manipulated plant species richness in grassland ecosystems and examined the impact on aboveground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the phylogenetic diversity of plants impacts average community biomass production as well as the stability of community biomass production through time. 3.Using four complementary analyses we show that, after statistically controlling for variation in species richness, phylogenetic diversity (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. However, after controlling for species richness, phylogenetic diversity was positively related to variation in community biomass over time due to an increase in the variances of individual species, but this relationship was not strong enough to influence community stability. 4.In contrast to the non-significant relationships between phylogenetic diversity, biomass, and stability, our analyses show that species richness per se tends to increase the mean biomass production of plant communities, after controlling for phylogenetic diversity. The relationship between species richness and temporal variation in community biomass was either positive, non-significant or negative depending on which analysis was used. However, the increases in community biomass with species richness, independently of phylogenetic diversity, always led to increased stability. These results suggest that phylogenetic diversity is no better as a predictor of ecosystem functioning than species richness. 5.Synthesis. Our study on grasslands offers a cautionary tale when trying to relate phylogenetic diversity to ecosystem functioning suggesting that there may be ecologically important trait and functional variation among species that is not explained by phylogenetic relatedness. Our results fail to support the hypothesis that the conservation of evolutionarily distinct species would be more effective than the conservation of species richness as a way to maintain productive and stable communities under changing environmental conditions.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.