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Data from: Widespread and persistent invasions of terrestrial habitats coincident with larval feeding behavior transitions during snail-killing fly evolution (Diptera: Sciomyzidae)
Background: Transitions in habitats and feeding behaviors were fundamental to the diversification of life on Earth. There is ongoing debate regarding the typical directionality of transitions between aquatic and terrestrial habitats and the mechanisms responsible for the preponderance of terrestrial to aquatic transitions. Snail-killing flies (Diptera: Sciomyzidae) represent an excellent model system to study such transitions because their larvae display a range of feeding behaviors, being predators, parasitoids or saprophages of a variety of mollusks in freshwater, shoreline and dry terrestrial habitats. The remarkable genus Tetanocera (Tetanocerini) occupies five larval feeding groups and all of the habitat types mentioned above. This study has four principal objectives: (i) construct a robust estimate of phylogeny for Tetanocera and Tetanocerini, (ii) estimate the evolutionary transitions in larval feeding behaviors and habitats, (iii) test the monophyly of feeding groups and (iv) identify mechanisms underlying sciomyzid habitat and feeding behavior evolution. Results: Bayesian inference and maximum likelihood analyses of molecular data provided strong support that the Sciomyzini, Tetanocerini and Tetanocera are monophyletic. However, the monophyly of many behavioral groupings was rejected via phylogenetic constraint analyses. We determined that (i) the ancestral sciomyzid lineage was terrestrial, (ii) there was a single terrestrial to aquatic habitat transition early in the evolution of the Tetanocerini and (iii) there were at least 10 independent aquatic to terrestrial habitat transitions and at least 15 feeding behavior transitions during tetanocerine phylogenesis. The ancestor of Tetanocera was aquatic with five lineages making independent transitions to terrestrial habitats and seven making independent transitions in feeding behaviors. Conclusions: The preponderance of aquatic to terrestrial transitions in sciomyzids goes against the trend generally observed across eukaryotes. Damp shoreline habitats are likely transitional where larvae can change habitat but still have similar prey available. Transitioning from aquatic to terrestrial habitats is likely easier than the reverse for sciomyzids because morphological characters associated with air-breathing while under the water's surface are lost rather than gained, and sciomyzids originated and diversified during a general drying period in Earth's history. Our results imply that any animal lineage having aquatic and terrestrial members, respiring the same way in both habitats and having the same type of food available in both habitats could show a similar pattern of multiple independent habitat transitions coincident with changes in behavioral and morphological traits.
Data from: Comparison of population genetic patterns in two widespread freshwater mussels with contrasting life histories in western North America
We investigate population genetic structuring in Margaritifera falcata, a freshwater mussel native to western North America, across the majority of its geographical range. We find shallow rangewide genetic structure, strong population-level structuring and very low population diversity in this species, using both mitochondrial sequence and nuclear microsatellite data. We contrast these patterns with previous findings in another freshwater mussel species group (Anodonta californiensis/A. nuttalliana) occupying the same continental region and many of the same watersheds. We conclude that differences are likely caused by contrasting life history attributes between genera, particularly host fish requirements and hermaphroditism. Further, we demonstrate the occurrence of a 'hotspot' for genetic diversity in both groups of mussels, occurring in the vicinity of the lower Columbia River drainage. We suggest that stream hierarchy may be responsible for this pattern and may produce similar patterns in other widespread freshwater species.
Data from: Evidence for local adaptation to extreme heat across populations of a widespread tree from quantitative proteomics
1. Heat waves are increasing in frequency and intensity globally with negative consequences for biological function. Assessing the effect of extreme heat on species requires an understanding of their adaptive capacity for mitigating physiological damage. Where long-term exposure to hot conditions in natural populations provides sufficient selection pressure, populations should exhibit signals of adaptive thermotolerance to temperature extremes. 2. Using quantitative proteomics, we tested this idea in the widespread and commercially-important tree species Eucalyptus grandis (Flooded Gum). Seedlings from six natural populations of E. grandis spanning a 2000 km gradient were exposed to a four-day extreme heat treatment (42-24°C day-night cycle) in experimental growth chambers. Populations differed in their long-term exposure to extreme heat conditions, defined both as the number of days annually ≥15°C above mean annual temperature (MAT), and average number of days annually with temperature maxima ≥ 35°C between 1960-1990. 3. Long-term exposure to extreme heat conditions in the field predicted the protein-level response of E. grandis to experimental heat waves. Relationships between long-term extreme heat exposure and protein increases were positive and linear for all combinations of extreme heat (days ≥15°C above MAT, mean days with temperature maxima ≥35°C annually) and expression (all differentially expressed proteins, isolated heat shock proteins, proteins involved in molecular stress responses). 4. Although extreme climate events are typically rare (e.g. 1 day 15° ≥ MAT per 5 years in some populations in our study), E. grandis populations sampled from across a 2000km range exhibit a clear capacity to increase expression of proteins involved in heat stress in response to simulated heat wave exposure. Presumably they respond similarly under natural heat wave conditions. 5. We show that a long-lived species with a broad environmental niche exhibits adaptive variation in protein response to temperature extremes at the population level. This implies that restoration, translocation and silvicultural programs should consider the molecular response of source populations to climatic extremes to maximise success under future climates. 6. Tree populations with low exposure to extreme heat conditions may be limited in their ability to respond to heat wave events, potentially limiting their adaptive capacity to withstand novel climate conditions.
Data from: Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales
PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare West African liana family Dioncophyllaceae. We used a variety of methods to infer the species tree, examine gene tree conflict, and infer paleopolyploidy events. KEY RESULTS: Phylogenomic analyses supported the monophyly of the carnivorous Caryophyllales, with a crown age of 68–83 million years. In contrast to previous analyses, we recovered the remaining noncore Caryophyllales as nonmonophyletic, although the node supporting this relationship contained a significant amount of gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously unresolved nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set, regardless of the use of coalescent or supermatrix methods. CONCLUSIONS: Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.
Data from: Widespread forest vertebrate extinctions induced by a mega hydroelectric dam in lowland Amazonia
Mega hydropower projects in tropical forests pose a major emergent threat to terrestrial and freshwater biodiversity worldwide. Despite the unprecedented number of existing, under-construction and planned hydroelectric dams in lowland tropical forests, long-term effects on biodiversity have yet to be evaluated. We examine how medium and large-bodied assemblages of terrestrial and arboreal vertebrates (including 35 mammal, bird and tortoise species) responded to the drastic 26-year post-isolation history of archipelagic alteration in landscape structure and habitat quality in a major hydroelectric reservoir of Central Amazonia. The Balbina Hydroelectric Dam inundated 3,129 km2 of primary forests, simultaneously isolating 3,546 land-bridge islands. We conducted intensive biodiversity surveys at 37 of those islands and three adjacent continuous forests using a combination of four survey techniques, and detected strong forest habitat area effects in explaining patterns of vertebrate extinction. Beyond clear area effects, edge-mediated surface fire disturbance was the most important additional driver of species loss, particularly in islands smaller than 10 ha. Based on species-area models, we predict that only 0.7% of all islands now harbor a species-rich vertebrate assemblage consisting of ≥80% of all species. We highlight the colossal erosion in vertebrate diversity driven by a man-made dam and show that the biodiversity impacts of mega dams in lowland tropical forest regions have been severely overlooked. The geopolitical strategy to deploy many more large hydropower infrastructure projects in regions like lowland Amazonia should be urgently reassessed, and we strongly advise that long-term biodiversity impacts should be explicitly included in pre-approval environmental impact assessments.
Data from: Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi's gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates
Aim: To highlight the significant conservation challenge of evaluating peripheral endemic vertebrates in island archipelago systems and to assess empirically the complexities of approaches to conservation genetic studies across political and biogeographic boundaries. To demonstrate the poignant need for international collaboration and coordination when species delimitation problems with high conservation concern involve island endemics with biogeographically peripheral ranges. Location: Southeast Asia, Lanyu Island, Taiwan, and the Philippines. Methods: Genetic samples were collected and sequenced for one mitochondrial gene and five nuclear loci for species of the Gekko mindorensis-G. kikuchii species complex in Southeast Asia. We used maximum likelihood and Bayesian phylogenetic methods and coalescent-based species delimitation analyses to estimate phylogeographic relationships, construct multilocus haplotype networks and test putative species boundaries. Results: Phylogenetic and population genetic analyses suggest that Kikuchi's Gecko may represent a peripheral population of a widespread species distributed from the northern Philippines to Taiwan. However, we identify a discrepancy between inferences of species boundaries resulting from methods based on allele frequencies versus coalescent-based methods that incorporate evolutionary history. Coalescent-based analyses suggest that G. kikuchii may be a distinct evolutionary lineage. Our study underscores the need for coalescent-based methods in conjunction with population genetic approaches for conservation genetic assessments of widespread species. Main conclusions: This study joins a few recent works suggesting that Philippine-derived anomalies in the fauna of Lanyu (and possibly greater Taiwan) are worthy of careful reconsideration. Determining whether each is the result of recent human-mediated introduction or (possibly more ancient) natural dispersal should be the goal of future studies on this seldom-conceived biogeographic relationship. Isolated species endemic to islands on the outer periphery of biogeographic and political regions represent particular conservation challenges. This is especially true if a species occurs on an isolated island that is allied biogeographically with one nation, but politically administered by another.
Data from: Predicting the impacts of climate change on Papio baboon biogeography: are widespread, generalist primates 'safe'?
Aims: To explore whether wide-ranging, generalist primates like baboons can be presumed 'resilient' in the face of climate change. We identify environmental variables influencing baboons' current distributions and predict their future potential distributions under different climate change scenarios. Location: Africa and Arabia. Taxon: Baboons, Papio spp. Methods: We used localities for olive, yellow, Guinea, hamadryas, chacma and Kinda baboons together with high-resolution data on bioclimatic variables, altitude and vegetation to construct species distribution models (SDMs). These SDMs were run under current and future conditions, with future models based on three General Circulation Models (MIROC-ESM, CCSM4 and HadGEM2-ES) under two Representative Concentration Pathways (RCP2.5 and 6.0) for 2050 and 2070 to explore a range of different possible futures. Results: All SDMs produced AUC values >0.916 suggesting excellent overall performance. Altitude was the most important variable influencing Guinea baboon distributions (contributing 41.6%), temperature seasonality for olive and yellow baboons (47.5% and 35.4% respectively), precipitation of the driest month for hamadryas baboons (24.4%), annual mean precipitation for the Kinda baboon (45.1%) and mean temperature of the driest quarter for chacma baboons (41.4%). Chacma and Kinda baboons are predicted to suffer substantial habitat loss, and Guinea baboons may do the same if conditions aridify as climates warm. In contrast, all models for the olive and hamadryas baboons predicted an increase in suitable habitat and only smaller changes were predicted for the yellow baboon. Main conclusions: Two or three of six baboon taxa are at risk of significant habitat loss as climates warm despite their apparent ecological flexibility. The chacma and Kinda baboons (both IUCN listed as Least Concern) will be worst affected, followed by the Guinea baboon (Near Threatened) if warming brings aridification. We recommend more focus on biogeographic tools as a means of exploring vulnerabilities in seemingly resilient species.
Data from: Herteliana schuyleriana (Squamarinaceae), a new crustose lichen widespread in the Appalachian Mountains of eastern North America
Herteliana schuyleriana is described as new to science based on collections from throughout the Appalachian Mountains of eastern North America. Taxonomic placement is inferred from molecular phylogenic analysis of mtSSU sequence data that recovered the taxon as sister to the type species of Herteliana, H. gagei, and strongly supported these taxa as embedded within the Squamarinaceae. The new species is characterized by its occurrence on non-calcareous shaded rocks in inland forested habitats (vs. exposed maritime oceanic habitats), its greenish-blue crustose thallus, presence of abundant blastidia on the thallus surface, frequent sterility, and by the production of roccellic/angardianic acid together with occasional trace amounts of psoromic acid as accessories to atranorin.
Data from: Drivers of phylogenetic assemblage structure of the Furnariides, a widespread clade of lowland Neotropical birds
Species co-occurrence in local assemblages is shaped by different processes at different spatial and temporal scales. Here we focus on historical explanations and examine the phylogenetic structure of local assemblages of the Furnariides clade (Aves: Passeriformes), assessing the influence of diversification rates on the assembly and species co-occurrence within those assemblages. Using 120 local assemblages across Bolivia and Argentina and a nearly complete phylogeny for the clade, we analyzed assemblage phylogenetic structure applying a recently developed model (DAMOCLES) accounting for the historical processes of speciation, colonization and local extinction. We also evaluated how diversification rates determine species co-occurrence. We found that the assembly of Furnariides assemblages can largely be explained by speciation, colonization and local extinction without invoking current local species interactions. Phylogenetic structure of open habitat assemblages mainly showed clustering, characterized by faster rates of colonization and local extinction than in forest habitats, whereas forest habitat assemblages were congruent with the model's equal rates expectation, thus highlighting the influence of habitat preferences on assembly and co-occurrence patterns. Our results suggest that historical processes are sufficient to explain local assemblage phylogenetic structure, while there is little evidence for species ecological interactions in avian assemblage diversity and composition.
Data from: Population structure of a widespread bat (Tadarida brasiliensis) in an island system
Dispersal is a driving factor in the creation and maintenance of biodiversity, yet little is known about the effects of habitat variation and geography on dispersal and population connectivity in most mammalian groups. Bats of the family Molossidae are fast-flying mammals thought to have potentially high dispersal ability, and recent studies have indicated gene flow across hundreds of kilometers in continental North American populations of the Brazilian free-tailed bat, Tadarida brasiliensis. We examined the population genetics, phylogeography, and morphology of this species in Florida and across islands of The Bahamas, which are part of an island archipelago in the West Indies. Previous studies indicate that bats in the family Phyllostomidae, which are possibly less mobile than members of the family Molossidae, exhibit population structuring across The Bahamas. We hypothesized that T. brasiliensis would show high population connectivity throughout the islands and that T. brasiliensis would show higher connectivity than two species of phyllostomid bats that have been previously examined in The Bahamas. Contrary to our predictions, T. brasiliensis shows high population structure between two groups of islands in The Bahamas, similar to the structure exhibited by one species of phyllostomid bat. Phylogenetic and morphological analyses suggest that this structure may be the result of ancient divergence between two populations of T. brasiliensis that subsequently came into contact in The Bahamas. Our findings additionally suggest that there may be cryptic species within T. brasiliensis in The Bahamas and the West Indies more broadly.
Data from: The faces of Bacidia schweinitzii: molecular and morphological data reveal three new species including a widespread sorediate morph
Bacidia schweinitzii is a common crustose lichen that is widespread in eastern North America. It is comprised of three distinct morphotypes differing in apothecial pigmentation. Here we show that molecular data from the mtSSU region affirms the distinctiveness of these morphotypes, prompting the recognition of three species: B. schweinitzii s.str., B. ekmaniana sp. nov. and B. purpurans sp. nov. We also show that a common sorediate crustose lichen, sympatric with B. schweinitzii, represents a monophyletic lineage whose relationship with B. schweinitzii s.str. could not be resolved with certainty using analyses of ITS and mtSSU sequence data. We recognize this sorediate lineage as a distinct species, B. sorediata sp. nov. All four taxa are described, illustrated and mapped.
Data from: Multilocus phylogeography of a widespread savanna-woodland adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa's Zambezi region
Understanding historical influences of climate and physiographic barriers in shaping patterns of biodiversity remains limited for many regions of the world. For mammals of continental Africa, phylogeographic studies, particularly for West African lineages, implicate both geographic barriers and climate oscillations in shaping small mammal diversity. In contrast, studies for southern African species have revealed conflicting phylogenetic patterns for how mammalian lineages respond to both climate change and geologic events such as river formation, especially during the Pleistocene. However, these studies were often biased by limited geographic sampling or exclusively focused on large-bodied taxa. We exploited the broad southern African distribution of a savanna–woodland-adapted African rodent, Gerbilliscus leucogaster (bushveld gerbil) and generated mitochondrial, autosomal and sex chromosome data to quantify regional signatures of climatic and vicariant biogeographic phenomena. Results indicate the most recent common ancestor for all G. leucogaster lineages occurred during the early Pleistocene. We documented six divergent mitochondrial lineages that diverged ~0.270–0.100 mya, each of which was geographically isolated during periods characterized by alterations to the course of the Zambezi River and its tributaries as well as regional 'megadroughts'. Results demonstrate the presence of a widespread lineage exhibiting demographic expansion ~0.065–0.035 mya, a time that coincides with savanna–woodland expansion across southern Africa. A multilocus autosomal perspective revealed the influence of the Kafue River as a current barrier to gene flow and regions of secondary contact among divergent mitochondrial lineages. Our results demonstrate the importance of both climatic fluctuations and physiographic vicariance in shaping the distribution of southern African biodiversity.
Data from: Sequential horizontal gene transfers from different hosts in a widespread Eurasian parasitic plant, Cynomorium coccineum
Premise of the study: Parasites with large geographic ranges, and different hosts in parts of their range, might acquire horizontally-transferred genes (HGTs), which might sometimes leave a footprint of gradual host and range expansion. Cynomorium coccineum, the only member of the Saxifragales family Cynomoriaceae, is a root holoparasite that occurs in water-stressed habitats from western China to the Canary Islands. It parasitizes at least ten angiosperm families from different orders, some of them only in parts of its range. This parasite therefore offers an opportunity to trace HGTs as long as parasite/host pairs can be obtained and sequenced. Methods: By sequencing mitochondrial, plastid, and nuclear loci from parasite/host pairs from throughout the parasite's range and with prior information from completely assembled mitochondrial and plastid genomes, we detected ten HGTs of five mitochondrial genes. Key Results: The ten HGTs appear to have occurred sequentially as C. coccineum expanded from East to West. Molecular-clock models yield Cynomorium stem ages between 66 and 156 Myr, with relaxed clocks converging on 66–67 Myr. Chinese Sapindales, probably Nitraria, were the first source of transferred genes, followed by Iranian and Mediterranean Caryophyllales. The most recently acquired gene appears to come from a Tamarix host in the Iberian Peninsula. Conclusion: Data on HGTs that have accumulated over the past 15 years, along with this discovery of multiple HGTs within a single widespread species, underline the need for more whole-genome data from parasite/host pairs to investigate if and how transferred copies coexist with, or replace, native functional genes. In compliance with data protection regulations, you may request that we remove your personal registration details at any time. (Use the following URL: https://www.editorialmanager.com/ajb/login.asp?a=r) Please contact the publication office if you have any questions.
Data from: Plasticity of thermoregulatory behaviour in response to the thermal environment by widespread and alpine reptile species
Phenotypic plasticity plays a central role in determining how organisms respond to environmental change over short timescales. Despite this, we know little about how phenotypic plasticity varies between populations or species. We tested the extent of plasticity in basking behaviour in low- and high-altitude populations of two widespread lowland and two highland species of a cool-climate lizard genus: Niveoscincus. We found evidence of divergence in basking behaviour between populations and species, with highland species and high-altitude populations of all species basking more than the widespread lowland species and low-altitude populations. Furthermore, we found differences in the extent of behavioural plasticity between species. Widespread lowland species altered their basking behaviour depending on basking opportunity whereas the highland species maintained high levels of basking independent of basking opportunity. These differences in basking behaviour were concordant with the differences in body temperature across all populations, species and treatments. Combined, this suggests that divergence in thermoregulatory behaviour and thermophysiology between populations and species may have been facilitated by adaptive behavioural plasticity within populations. We discuss this and the implications of our findings for the ability of these animals to cope with ongoing climate change.
Data from: How diverse is Mitopus morio? Integrative taxonomy detects cryptic species in a small-scale sample of a widespread harvestman
Mitopus morio is a widespread harvestman species occurring in most of Europe and in moderate and cold-moderate zones of Asia and North America. The species is characterized by extreme variability in body size and leg length. As leg length is correlated with habitat temperature, M. morio has been considered as an example of Allen's rule. Recently, observations for a single location in Tyrol, Austria, indicated the absence of mating between short- and long-legged individuals. This study examines for signs of putative cryptic species in M. morio using an integrative approach that combines mating trials, amplified fragment length polymorphism whole-genome scans, mitochondrial sequences and morphometrics. The mating trials did not corroborate the initial hypothesis of a reproductive barrier associated with leg size. Both types of genetic data revealed the existence of three distinct groups, in line with the mating results but largely unrelated to leg morphology and geographical origin of specimens. Morphometric characters supporting the findings of the other disciplines were identified using a supervised approach. We infer from all data together the existence of strongly diverged cryptic lineages among the analysed individuals, cautiously interpret them as three sympatric species and conclude that in these harvestmen Allen's rule applies at different levels. Due to the unexpected amount of differentiation found within a geographical scale very small compared with the distribution of M. morio, we suggest a thorough revision of the genus prior to formal taxonomic changes. Our case study underlines the general applicability of the integrative taxonomic protocol used and highlights the relevance of several rationales implemented in the protocol.
Data from: DNA metabarcoding unveils multi‐scale trophic variation in a widespread coastal opportunist
A thorough understanding of ecological networks relies on comprehensive information on trophic relationships among species. Since unpicking the diet of many organisms is unattainable using traditional morphology‐based approaches, the application of high‐throughput sequencing methods represents a rapid and powerful way forward. Here, we assessed the application of DNA‐metabarcoding with nearly universal primers for the mitochondrial marker cytochrome c oxidase I (COI) in defining the trophic ecology of adult brown shrimp, Crangon crangon, in six European estuaries. The exact trophic role of this abundant and widespread coastal benthic species is somewhat controversial, while information on geographical variation remains scant. Results revealed a highly opportunistic behaviour. Shrimp stomach contents contained hundreds of taxa (>1000 molecular operational taxonomic units), of which 291 were identified as distinct species, belonging to 35 phyla. Only twenty ascertained species had a mean relative abundance of more than 0.5%. Predominant species included other abundant coastal and estuarine taxa, including the shore crab Carcinus maenas and the amphipod Corophium volutator. Jacobs' selectivity index estimates based on DNA extracted from both shrimp stomachs and sediment samples were used to assess the shrimp's trophic niche indicating a generalist diet, dominated by crustaceans, polychaetes and fish. Spatial variation in diet composition, at regional and local scales, confirmed the highly flexible nature of this trophic opportunist. Furthermore, the detection of a prevalent, possibly endoparasitic fungus (Purpureocillium lilacinum) in the shrimp's stomach demonstrates the wide range of questions that can be addressed using metabarcoding, towards a more robust reconstruction of ecological networks.
Data from: Revisiting the provenance delineation of a widespread shrub, Frangula alnus—the role of spatial, temporal and environmental patterns
Including population genetic aspects into the selection of planting material within the framework of conservation and restoration measures is of vital importance for the long-term persistence of populations. This is especially true facing climate change since genetic diversity and the spread of potentially beneficial alleles are important for the adaptability of populations. Therefore, knowledge about genetic variability within and between populations is a critical aspect when determining provenance regions. In our study, we investigated the population genetic structure of a widespread, insect-pollinated and mainly bird-dispersed shrub species, Frangula alnus, on the basis of seven microsatellites and two chloroplast DNA markers throughout Germany. The aim was to determine the spatial, temporal and ecological processes genetically structuring populations to critically revise existing provenance regions. Therefore, we conducted analyses on different spatial scales (country-wide, regional and local) using the two different marker sets in addition to environmental variables. We detected distinct patterns on all spatial scales which indicated influences of historic recolonization processes, regional differences of seed dispersal across the landscape, as well as small-scale spatial genetic structures attributable to local dispersal processes. No relation of underlying environmental gradients such as temperature or precipitation and genetic patterns was found. We conclude that different aspects of historic and more recent gene flow shape population genetic structures and that a thorough analysis on a variety of spatial, temporal and environmental scales is necessary to appropriately select planting material for conservation and restoration measures. Correspondingly, management advice regarding provenance delineations will be provided.
Data from: The polyphyly of Plasmodium: comprehensive phylogenetic analyses of the malaria parasites (order Haemosporida) reveal widespread taxonomic conflict
The evolutionary relationships among the apicomplexan blood pathogens known as the malaria parasites (order Haemosporida), some of which infect nearly 200 million humans each year, has remained a vexing phylogenetic problem due to limitations in taxon sampling, character sampling, and the extreme nucleotide base composition biases that are characteristic of this clade. Previous phylogenetic work on the malaria parasites has often lacked sufficient representation of the broad taxonomic diversity within the Haemosporida or the multi-locus sequence data needed to resolve deep evolutionary relationships, rendering our understanding of haemosporidian life history evolution and the origin of the human malaria parasites incomplete. Here we present the most comprehensive phylogenetic analysis of the malaria parasites conducted to date, using samples from a broad diversity of vertebrate hosts that includes numerous enigmatic and poorly known haemosporidian lineages in addition to genome-wide multi-locus sequence data. We find that if base composition differences were corrected for during phylogenetic analysis, we recovered a well-supported topology indicating that the evolutionary history of the malaria parasites was characterized by a complex series of transitions in life history strategies and host usage. Notably we find that Plasmodium, the malaria parasite genus that includes the species of human medical concern, is polyphyletic with the life history traits characteristic of this genus having evolved in a dynamic manner across the phylogeny. We find support for multiple instances of gain and loss of asexual proliferation in host blood cells and production of hemozoin pigment, two traits that have been used for taxonomic classification as well as considered to be important factors for parasite virulence and used as drug targets. Lastly, our analysis illustrates the need for a widespread reassessment of malaria parasite taxonomy.
Data from: A single interacting species leads to widespread parallel evolution of the stickleback genome
Biotic interactions are potent, widespread causes of natural selection and divergent phenotypic evolution, and can lead to genetic differentiation with gene flow among wild populations ("isolation by ecology") [1-4]. Biotic selection has been predicted to act on more genes than abiotic selection thereby driving greater adaptation [5]. However, difficulties in isolating the genome-wide effect of single biotic agents of selection have limited our ability to identify and quantify the number and type of specific genetic regions responding to biotic selection [6-9]. We identified geographically interspersed lakes in which threespine stickleback fish (Gasterosteus aculeatus) have repeatedly adapted to the presence/absence of a single member of the ecological community, prickly sculpin (Cottus asper), a fish species that is both competitor and predator of stickleback [10]. Whole genome sequencing revealed that sculpin presence/absence accounted for the majority of genetic divergence among populations, more so than geography. The major axis of stickleback genomic variation within and between the two lake types was correlated with multiple traits, indicating parallel natural selection across a gradient of biotic environments. A large proportion of the genome - about 1.8%, encompassing more than 600 genes – differentiated stickleback from the two biotic environments. Divergence occurred in 141 discrete genomic clumps located mainly in regions of low recombination within the stickleback genome, suggesting that genes brought to lakes by the colonizing ancestral population often evolved together in linked blocks. Strong selection and a wealth of standing genetic variation explain how a single member of the biotic community can have such a rapid and profound evolutionary impact.
Phylogeography of the widespread Caribbean spiny orb weaver Gasteracantha cancriformis
<p class="Normal1"><b>Background. </b>Modern molecular analyses are often inconsistent with pre-cladistic taxonomic hypotheses, frequently indicating higher richness than morphological taxonomy estimates. Among Caribbean spiders, widespread species are relatively few compared to the prevalence of single island endemics. The taxonomic hypothesis <i>Gasteracantha</i> <i>cancriformis</i> circumscribes a species with profuse variation in size, color, and body form. Distributed throughout the Neotropics, <i>G. cancriformis </i>is the only morphological species of <i>Gasteracantha</i> in the New World in this globally distributed genus.</p> <p class="Normal1"><b>Methods. </b>We inferred phylogenetic relationships across Neotropical populations of <i>Gasteracantha </i>using three target genes. Within the Caribbean, we estimated genetic diversity, population structure, and gene flow among island populations.</p> <p class="Normal1"><b>Results. </b>Our findings revealed a single widespread species of <i>Gasteracantha </i>throughout the Caribbean, <i>G. cancriformis,</i> while suggesting two recently divergent mainland populations that may represent separate species, diverging linages, or geographically isolated demes. The concatenated and <i>COI</i> (Cytochrome c oxidase subunit 1) phylogeny supported a Caribbean clade nested within the New World<i>.</i> Genetic variability was high between island populations for our <i>COI </i>dataset; however, gene flow was also high, especially between large, adjacent islands. We found structured genetic and morphological variation within <i>G. cancriformis</i> island populations; however, this variation does not reflect genealogical relationships. Rather, isolation by distance and local morphological adaptation may explain the observed variation.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.