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Supplementary material 1 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Appendix 1
Supplementary material 2 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997
Table S1
Divergence time estimation of genus Tribolium by extensive sampling of highly conserved orthologs
<p><i>Tribolium castaneum</i>, the red flour beetle, is among the most well-studied eukaryotic genetic model organisms. <i>Tribolium</i> often serves as a comparative bridge from highly derived <i>Drosophila</i> traits to other organisms. Simultaneously, as a member of the most diverse order of metazoans, Coleoptera, <i>Tribolium</i> informs us about innovations that accompany hyper diversity. However, understanding the tempo and mode of evolutionary innovation requires well-resolved, time-calibrated phylogenies, which are not available for <i>Tribolium</i>. The most recent effort to understand <i>Tribolium</i>phylogenetics used two mitochondrial and three nuclear markers. The study concluded that the genus may be paraphyletic and reported a broad range for divergence time estimates. Here we employ recent advances in Bayesian methods to estimate the relationships and divergence times among <i>Tribolium castaneum</i>, <i>T. brevicornis</i>, <i>T. confusum</i>, <i>T. freemani</i>, and <i>Gnatocerus cornutus </i>using 1368 orthologs conserved across all five species and an independent substitution rate estimate. We find that the most basal split within <i>Tribolium</i> occurred ~86 Mya [95% HPD 85.90–87.04 Mya] and that the most recent split was between <i>T. freemani</i> and <i>T. castaneum</i> at ~14 Mya [95% HPD 13.55-14.00]. Our results are consistent with broader phylogenetic analyses of insects and suggest that Cenozoic climate changes played a role in the <i>Tribolium </i>diversification.</p>
Data from: Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function
Background: Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their "unusual" energy metabolism (where ketone bodies and amino acids are the main oxidative fuel source) and their paradoxical ability to both maintain stable blood glucose levels and tolerate extensive periods of hypoglycemia. In order to shed light on some of these processes, we carried out the first large-scale comparative transcriptomic survey of multiple cartilaginous fish tissues: the pancreas, brain and liver of the lesser spotted catshark, Scyliorhinus canicula. Results: We generated a mutli-tissue assembly comprising 86,006 contigs, of which 44,794 were assigned to a particular tissue or combination of tissues based on mapping of sequencing reads. We have characterised transcripts encoding genes involved in insulin regulation, glucose sensing, transcriptional regulation, signaling and digestion, as well as many peptide hormone precursors and their receptors for the first time. Comparisons to mammalian pancreas transcriptomes reveals that mechanisms of glucose sensing and insulin regulation used to establish and maintain a stable internal environment are conserved across jawed vertebrates and likely pre-date the vertebrate radiation. Conservation of pancreatic hormones and genes encoding digestive proteins support the single, early evolution of a distinct pancreatic gland with endocrine and exocrine functions in jawed vertebrates. In addition, we demonstrate that chondrichthyes lack pancreatic polypeptide (PP) and that reports of PP in the literature are likely due cross-reaction with PYY and/or NPY in the pancreas. A three hormone islet organ is therefore the ancestral jawed vertebrate condition, later elaborated upon only in the tetrapod lineage. Conclusions: The cartilaginous fish are a great untapped resource for the reconstruction of patterns and processes of vertebrate evolution and new approaches such as those described in this paper will greatly facilitate their incorporation into the rank of "model organism".
Data from: Private land conservation has landscape-scale benefits for wildlife in agroecosystems
Private lands contain much of the world's biodiversity. Conservation of private land, especially agricultural land, is urgent yet challenging because of the diverse priorities of landowners. Local effects of farmland conservation programmes have been evaluated thoroughly, but population-level response to these programmes may depend on effects that extend beyond targeted land parcels. We investigated the landscape-scale effects of a grassland conservation initiative, the Conservation Reserve Enhancement Program (CREP), on a socially and economically important gamebird, the Northern Bobwhite (Colinus virginianus). Barriers to assessing population-level response to conservation include determining the spatial scale at which a species responds to environmental change (the scale of effect) and untangling density-dependent processes. We performed point counts over 6 years at 247 sites with similar local CREP density but varying landscape-scale CREP density. We used an open-population distance sampling model to evaluate population response to landscape-level CREP density and to forecast population densities under differing re-enrollment scenarios. Our model included kernel smoothing techniques to estimate scale of effect and an estimator of the strength of density dependence. Density dependence moderated the effectiveness of the CREP, but overall populations responded positively to increasing landscape-scale CREP density. We estimated that at least 5% of the landscape needs to be in CREP to meet population density goals of 0.25 bobwhite/ha. Conservatively, we recommend 10% of the landscape to be in CREP. Our percent cover recommendations are based on a distance-weighted average of CREP around focal sites. Landscape-scale effects diminished with distance. For example, assuming all else is equal, a CREP field 3000 m away had 88% less of an effect on local abundance than a field 1000 m away. Fields farther than 5000 m away had no effect on local abundance. Synthesis and applications. Our study underscores the importance of a landscape-scale approach to farmland conservation. Benefits of these programmes can extend beyond the local scale, but their importance to local populations diminishes with distance. Estimating the relationship between increasing distance and the utility of conservation land to local populations could provide land managers a practical framework in which to target land enrollment to maximize biodiversity outcomes.
Data from: Speed dependency in α-motoneuron activity and locomotor modules in human locomotion: indirect evidence for phylogenetically conserved spinal circuits
Coordinated locomotor muscle activity is generated by the spinal central pattern generators (CPGs). Vertebrate studies have demonstrated the following two characteristics of the speed control mechanisms of the spinal CPGs: (i) rostral segment activation is indispensable for achieving high-speed locomotion; and (ii) specific combinations between spinal interneuronal modules and motoneuron (MN) pools are sequentially activated with increasing speed. Here, to investigate whether similar control mechanisms exist in humans, we examined spinal neural activity during varied-speed locomotion by mapping the distribution of MN activity in the spinal cord and extracting locomotor modules, which generate basic MN activation patterns. The MN activation patterns and the locomotor modules were analysed from multi-muscle electromyographic recordings. The reconstructed MN activity patterns were divided into the following three patterns depending on the speed of locomotion: slow walking, fast walking and running. During these three activation patterns, the proportion of the activity in rostral segments to that in caudal segments increased as locomotion speed increased. Additionally, the different MN activation patterns were generated by distinct combinations of locomotor modules. These results are consistent with the speed control mechanisms observed in vertebrates, suggesting phylogenetically conserved spinal mechanisms of neural control of locomotion.
Data from: Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana
Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the 'edges' of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relationship between dN/dS and other genomic parameters is unclear. We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana. We also obtain lineage-specific dN/dS estimates, making use of the recently sequenced genome of Thellungiella parvula, the second closest sequenced relative after the sister species Arabidopsis lyrata. Overall, we find that the effect of exon edge conservation, as well as the use of lineage-specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level. Furthermore, the removal of exon edges shifts dN/dS estimates upwards, increasing the proportion of genes potentially under adaptive selection. We conclude that lineage-specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters..
Data from: Food web interaction strength distributions are conserved by greater variation between than within predator-prey pairs
Species interactions in food webs are usually recognized as dynamic, varying across species, space and time due to biotic and abiotic drivers. Yet food webs also show emergent properties that appear consistent, such as a skewed frequency distribution of interaction strengths (many weak, few strong). Reconciling these two properties requires an understanding of the variation in pairwise interaction strengths and its underlying mechanisms. We estimated stream sculpin feeding rates in three seasons at nine sites in Oregon to examine variation in trophic interaction strengths both across and within predator-prey pairs. Predator and prey densities, prey body mass, and abiotic factors were considered as putative drivers of within-pair variation over space and time. We hypothesized that consistently skewed interaction strength distributions could result if individual interaction strengths show relatively little variation, or alternatively, if interaction strengths vary but shift in ways that conserve their overall frequency distribution. Feeding rate distributions remained consistently and positively skewed across all sites and seasons. The mean coefficient of variation in feeding rates within each of 25 focal species pairs across surveys was less than half the mean coefficient of variation seen across species pairs within a survey. The rank order of feeding rates also remained conserved across streams, seasons and individual surveys. On average, feeding rates on each prey taxon nonetheless varied by a hundredfold, with some feeding rates showing more variation in space and others in time. In general, feeding rates increased with prey density and decreased with high stream flows and low water temperatures, although for nearly half of all species pairs, factors other than prey density explained the most variation. Our findings show that although individual interaction strengths exhibit considerable variation in space and time, they can nonetheless remain relatively consistent, and thus predictable, compared to the even larger variation that occurs across species pairs. These results highlight how the ecological scale of inference can strongly shape conclusions about interaction strength consistency and collectively help reconcile how the skewed nature of interaction strength distributions can persist in highly dynamic food webs.
Data from: Conserved class of queen pheromones stops social insect workers from reproducing
A major evolutionary transition to eusociality with reproductive division of labor between queens and workers has arisen independently at least 10 times in the ants, bees, and wasps. Pheromones produced by queens are thought to play a key role in regulating this complex social system, but their evolutionary history remains unknown. Here, we identify the first sterility-inducing queen pheromones in a wasp, bumblebee, and desert ant and synthesize existing data on compounds that characterize female fecundity in 64 species of social insects. Our results show that queen pheromones are strikingly conserved across at least three independent origins of eusociality, with wasps, ants, and some bees all appearing to use nonvolatile, saturated hydrocarbons to advertise fecundity and/or suppress worker reproduction. These results suggest that queen pheromones evolved from conserved signals of solitary ancestors.
Data from: Evolutionary conserved neural signature of early life stress affects animal social competence
In vertebrates the early social environment can persistently influence behaviour and social competence later in life. However, the molecular mechanisms underlying variation in animal social competence are largely unknown. In rats, high-quality maternal care causes an upregulation of hippocampal glucocorticoid receptors (gr) and reduces offspring stress responsiveness. This identifies gr regulation as a candidate mechanism for maintaining variation in animal social competence. We tested this hypothesis in a highly-social cichlid fish, Neolamprologus pulcher, reared with or without caring parents. We find that the molecular pathway translating early social experience into later-life alterations of the stress axis is homologous across vertebrates: fish reared with parents expressed the glucocorticoid receptor gr1 more in the telencephalon. Furthermore, expression levels of the transcription factor egr-1 (early growth response 1) were associated with gr1 expression in the telencephalon and hypothalamus. When blocking glucocorticoid receptors (GR) with an antagonist, mifepristone (RU486), parent-reared individuals showed more socially appropriate, submissive behaviour when intruding a larger conspecific's territory. Remarkably, mifepristone-treated fish were less attacked by owners and had a higher likelihood of territory takeover. Our results indicate that early social-environment effects on stress axis programming are mediated by an evolutionary conserved molecular pathway, which is causally involved in environmentally-induced variation of animal social competence.
Data from: Using genomic tools to maintain diversity and fitness in conservation programmes
Conservation programmes aim at maximising the survival probability of populations, by minimising the loss of genetic diversity, which allows populations to adapt to changes, and controlling inbreeding increases. The best known strategy to achieve these goals is optimising the contributions of the parents, to minimise global coancestry in their offspring. Results on neutral scenarios showed that management based on molecular coancestry could maintain more diversity than management based on genealogical coancestry when a large number of markers is available. However, if the population has deleterious mutations, managing using optimal contributions can lead to a decrease in fitness, especially using molecular coancestry, because both beneficial and harmful alleles are maintained, compromising the long-term viability of the population. We introduce here two strategies to avoid this problem: The first one uses molecular coancestry calculated removing markers with low minor allele frequencies, as they could be linked to selected loci. The second one uses a coancestry based on segments of identity by descent, which measures the proportion of genome segments shared by two individuals because of a common ancestor. We compare these strategies under two contrasting mutational models of fitness effects, one assuming many mutations of small effect and another with few mutations of large effect. Using markers at intermediate frequencies maintains a larger fitness than using all markers, but leads to maintaining less diversity. Using the segment-based coancestry provides a compromise solution between maintaining diversity and fitness, especially when the population has some inbreeding load.
New set of microsatellite markers for the great-billed seed-finch (Sporophila maximiliani – Passeriformes: Thraupidae): tools for inspection and conservation
<p>The Thraupidae family is one of the most wanted by bird breeders in Brazil due to its diverse, colorful and melodious singers as representatives. The Great-billed Seed-finch, Sporophila maximiliani, is the only representative of the genus Sporophila considered critically endangered in Brazil. Due to the demands of environmental agencies and of conservation programs, there is a need to increase the number of molecular markers available for the genus and specially for S.maximiliani. Therefore, this work aimed to provide a new set of microsatellite markers for S. maximiliani in order to help bird breeders and environmental agencies on fulfilling its demands as well as contributing with extra genetics tools for conservation programs of the Great-billed Seed-finch. Of the 30 markers developed, 25 successfully amplified and 22 were polymorphic. Annealing temperature varied from 52 to 64°C, number of alleles from two to 13 and the medium allele richness was 7.25 and medium expected and observed heterozygosity was, respectively, 0.812 and 0.661. The identity estimate was 8.54x10 -27 and all the other probabilities of non-exclusion (sib-identity, parent pair and first-parent) were <0.001, indicating that this set of microsatellite markers have high genetic variability and high power of individual genetic differentiation for S.maximiliani. Therefore, this work increases the options of molecular markers to be used on inspection for environmental agencies and for conservation programs on analyzing genetic variability and population studies for the Great-billed Seed-finch.</p>
Data from: Fine-scale genetic structure and conservation status of American badgers at their northwestern range periphery
Peripheral populations are often characterized by small population size and low genetic diversity, with many at risk of extirpation. These characteristics may be even more pronounced in human-modified landscapes that further reduce the resiliency of populations to environmental change. Situated at the northwestern edge of the species' range, the western American badger (Taxidea taxus jeffersonii) is an endangered mammal in Canada, where it inhabits the interior grassland and open forest ecosystems of British Columbia (BC) and continues to be threatened by severe vehicle-induced mortality rates and other anthropogenic factors. Here, we collected mitochondrial DNA haplotypic and microsatellite genotypic data to investigate the extent and distribution of American badger genetic variation within and among sites in British Columbia, and relative to adjacent populations in the USA, including in Washington state. From these data, we reconstructed population structure and connectivity, and examined current designatable unit status. Patterns of genetic variation for American badgers in British Columbia were as expected for peripheral populations, including reduced genetic diversity, increased population differentiation, and evidence of demographic contraction. Furthermore, we found limited connectivity between regional populations in our study area and identified significant substructure isolating the most northwestern sampling unit (Cariboo), findings that starkly contrast with the high levels of gene flow observed between populations across the species' range core. These results have important implications for current designatable unit status for western American badgers in British Columbia and emphasize the need for further population monitoring and mitigation of potential barriers to gene flow.
Allocating resources for land protection using continuous optimization: an application to US biodiversity conservation
Spatial optimization approaches that were originally developed to help conservation organizations determine protection decisions over small spatial scales are now used to inform global or continental scale priority setting. However, the different decision contexts involved in large-scale resource allocation need to be considered. We present a continuous optimization approach in which a decision-maker allocates funding to regional offices. Local decision-makers then use these funds to implement habitat protection efforts with varying effectiveness when evaluated in terms of the funder's goals. We illustrate this continuous formulation by examining the relative priority that should be given to different counties in the coterminous United States (US) when acquiring land to establish new protected areas. If weighting all species equally, counties in the southwest US, where large areas can be bought cheaply, are priorities for protection. If focusing only on species of conservation concern, priorities shift to locations rich in such species, particularly near expanding exurban areas facing high rates of future habitat conversion (e.g., south-central Texas). Priorities for protection are sensitive to what is assumed about local ecological and decision-making processes. For example, decision-makers who doubt the efficacy of local land protection efforts should focus on a few key areas, while optimistic decision-makers should disperse funding more widely. Efforts to inform large-scale conservation priorities should reflect better the types of choice that decision-makers actually face when working over these scales. They also need to report the sensitivity of recommended priorities to what are often unstated assumptions about local processes affecting conservation outcomes.
Data from: Development of conserved microsatellite markers of high cross-species utility in bat species (Vespertilionidae, Chiroptera, Mammalia)
Comparative ecological and behavioural studies of the widespread and diverse Vespertilionidae, which comprise almost 400 of the 1,100 bat species, have been limited by the availability of markers. The potential of new methods for developing conserved microsatellite markers which possess enhanced cross-species utility has recently been illustrated in studies of birds. We have applied these methods to develop enhanced microsatellite markers for vespertilionid bats, in particular for the genus Myotis (103 species). We compared published bat microsatellites with their homologs in the genome sequence of the little brown bat, Myotis lucifugus to create consensus sequences which were used to design candidate primer sets. Primer sets were then tested for amplification and polymorphism in 22 species of bat from nine of the largest families (including 11 Vespertilionidae). Of 46 loci tested, 33 were polymorphic, on average, for each of seven Myotis species tested, 20 in each of four non-Myotis vespertilionid species, and two in 11 non-vespertilionid species.
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: Can physiographic regions substitute for genetically-determined conservation units? A case study with the threatened plant, Silene spaldingii
Protecting genetic diversity throughout the range of a species is important for conservation, as doing so provides for long-term evolutionary potential and persistence under a changing environment. Conservation of diversity at the intraspecific level requires identification of all genetically distinct population segments within species; i.e., conservation units (CUs). Silene spaldingii occurs in grasslands of the Columbia Plateau region of western North America and is listed as threatened under the Federal Endangered Species Act. The recovery plan identified five physiographic regions across the range of the species to use as surrogates for genetic CUs. We collected leaf samples from an average of 26 plants from each of 19 of the largest populations across all five physiographic regions and used variable microsatellite and chloroplast DNA markers to determine how genetic variation is distributed across the range of the species and how well physiographic regions reflect population structure within this species. Results of several multivariate analyses clustered our samples into four genetic groups which did not correspond well with the physiographic regions. We observed little genetic differentiation among populations in the main range of the species which encompasses nearly all of four contiguous physiographic regions. However, three other distinct genetic groups were identified: two in the disjunct northeast corner and one at the southeast edge of the main range. Modification of the CUs to reflect the genetic groups rather than the physiographic regions would result in CUs which better reflect historical patterns of population structure. Moreover, use of the genetic units to inform translocation and genetic rescue efforts could improve our ability to mimic natural patterns of gene flow. Our results suggest that physiographic regions may not always be an accurate reflection of population structure for threatened or endangered species.
Data from: Whole-genome sequencing approaches for conservation biology: advantages, limitations, and practical recommendations
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved (huWGR) or resolved haplotypes (hrWGR), the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq), and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in non-model species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons, and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g. structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently though, no single WGR approach fulfills all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many non-model species and fields including conservation biology.
Data from: Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability
Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have little understanding of its genetic basis, nor its temporal dynamics over generations. To address these open questions we compared patterns of craniofacial modularity among laboratory strains, defined mutant lines and a wild population of zebrafish (Danio rerio). Our findings suggest that relatively simple genetic changes can have profound effects on covariance, without greatly affecting craniofacial shape. Moreover, we show that instead of completely deconstructing the covariance structure among sets of traits, mutations cause shifts among seemingly latent patterns of modularity suggesting that the skull may be predisposed toward a limited number of phenotypes. This new insight may serve to greatly increase the evolvability of a population by providing a range of 'preset' patterns of modularity that can appear readily and allow for rapid evolution.
Data from: Conserved gene expression programs in developing roots from diverse plants
The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants.
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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.