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3,655 results for “Structural data”
Data from: Canopy leaf area index at its higher end: dissection of structural controls from leaf to canopy scales in bryophytes
There is evidence that mosses with miniature foliage elements have extremely large leaf area indices (LAI), but it is unclear what canopy traits are responsible for these high LAI values in architecturally divergent mosses, and how the inherent tradeoffs limiting maximum LAI in vascular plants can be overcome in mosses. To determine the quantitative significance of different traits in determining LAI, we developed a method to dissect LAI into underlying functionally dependent constituent traits at leaf, shoot and canopy scales. The suites of structural traits were studied altogether for 43 moss canopies from 11 species with contrasting light and water requirements along gap-understory gradients to obtain as large a range of variation in moss architecture as possible and evaluate the differentiation in moss LAI in relation to species ecology. Extensive variation in moss structural traits, 11- (shoot length) to 77-fold (shoot number per area, NS), was observed at all structural scales from leaf to canopy. However, LAI only varied 9-fold, as the result of two key tradeoffs, leaf size vs. number tradeoff and shoot leaf area vs. shoot density tradeoff. Due to these negative relationships, and greater variability in NS, LAI primarily scaled with NS. and LAI increased with site light availability, and LAI was greater in open and dry habitat species. The current study highlights a huge structural diversity among moss canopies, but indicates that canopies converge to a much narrower range of LAI due to trait tradeoffs such that, counterintuitively, minute leaf size and densely leafed stems are not necessarily responsible for high LAI in mosses.
Data from: Subarctic singers: Humpback whale (Megaptera novaeangliae) song structure and progression from an Icelandic feeding ground during winter
Humpback whale songs associated with breeding behaviors are increasingly reported outside of traditional low latitude breeding grounds. Songs from a subarctic feeding ground during the winter were quantitatively characterized to investigate the structure and temporal changes of the songs at such an atypical location. Recordings were collected from 26. January to 12. March, 2011, using bottom mounted recorders. Humpback songs were detected on 91% of the recording days with peak singing activities during 9.–26. February. The majority of the recordings included multiple chorusing singers. The songs were characterized by a) common static themes which transitioned consistently to predictable themes, b) shifting themes which occurred less predictably and c) rare themes. A set median sequence was found for four different periods (sets) of recordings (approximately 1 week each). The set medians were highly similar and formed a single cluster indicating that the sequences of themes sung in this area belonged to a single cluster of songs despite of the variation caused by the shifting themes. These subarctic winter songs could, thus, represent a characteristic song type for this area which is comparable to extensively studied songs from traditional low latitude breeding grounds. An increase in the number of themes per sequence was observed throughout the recording period including minor changes in the application of themes in the songs; indicating a gradual song progression. The results confirm that continual singing of sophisticated songs occur during the breeding season in the subarctic. In addition to being a well-established summer feeding ground the study area appears to be an important overwintering site for humpback whales delaying or canceling their migration where males engage in active sexual displays, i.e. singing. Importantly, such singing activity on a shared feeding ground likely aids the cultural transmission of songs in the North Atlantic.
Data from: The 'filtering' metaphor revisited: competition and environment jointly structure invasibility and coexistence
'Filtering', or the reduction in species diversity that occurs because not all species can persist in all locations, is thought to unfold hierarchically, controlled by the environment at large scales and competition at small scales. However, the ecological effects of competition and the environment are not independent, and observational approaches preclude investigation into their interplay. We use a demographic approach with 30 plant species to experimentally test (i) the effect of competition on species persistence in two soil moisture environments, and (ii) the effect of environmental conditions on mechanisms underlying competitive coexistence. We find that competitors cause differential species persistence across environments even when effects are lacking in the absence of competition, and that the traits that determine persistence depend on the competitive environment. If our study had been observational and trait-based, we would have erroneously concluded that the environment filters species with low biomass, shallow roots, and small seeds. Changing environmental conditions generated idiosyncratic effects on coexistence outcomes, increasing competitive exclusion of some species while promoting coexistence of others. Our results highlight the importance of considering environmental filtering in light of, rather than in isolation from, competition, and challenge community assembly models and approaches to projecting future species distributions.
Data from: Stay at home aphids: comparative spatial and seasonal metapopulation structure and dynamics of two specialist tansy aphid species studied using microsatellite markers
Two tansy-feeding aphids – Macrosiphoniella tanacetaria (MA) and Metopeurum fuscoviride (ME) – were studied at a small spatial scale in and around Jena (< 80 km2) using polymorphic microsatellite markers. Both species were found in ~ 60% of sites formerly known to harbour the aphids, although generally when they did occur, they occurred singly (MA ~ 50%; ME ~60%) and rarely together on the same plant at the same time (~10%) and then usually only in the early part of the growing season. This difference may be due to quasi-apparent competition effects elicited to ants farming ME aphids, and preferentially actively eliminating or disturbing MA aphids. In terms of population genetics, both aphids showed extreme genetic heterogeneity within a metapopulation structure, ME more than MA, i.e. higher FST values, ~ 0.4 vs. 0.15, respectively, and limited levels of interpopulation gene flow. Subpopulations often deviated from Hardy-Weinberg equilibrium and showed linkage disequilibria, as expected in animals with extended parthenogenetic reproduction, and had positive FIS values for most large samples, suggesting inbreeding, and possibly philopatry, certainly in ME. Hierarchical analysis (allele range and number per locus, analysis of molecular variance and FST) strongly suggested that the plant rather than site governs the level of genetic variation. Bayesian clustering analysis revealed that both species had heterogeneous historical genetic patterning, with K (number of subgroups) ranging from 3-7. Evidence is also provided from isolation by distance (IBD) and private allele analyses, that in MA, the presence of winged autumn males, absent in ME where males are wingless, influences comparative population genetic structuring, such that ME subpopulations are comparatively more inbred and genetically differentiated than MA subpopulations. Lastly, additional spatial arrangement (ALLELES-IN-SPACE) analysis showed that in both species, certain subpopulations were genetically isolated from the remainder, probably due to geographical barriers, including intervening buildings and woods. As such, the biology of these tansy aphids living in semi-natural habitats is very different from many pest aphid species examined within agro-ecosystems and infesting ephemeral crops, since the former seem much more reluctant to fly and hence show contrastingly much higher levels of interpopulation divergence, even at small spatial scales as here investigated. Indeed, the number of genotypic clusters found for tansy aphids found using Bayesian approaches is similar to that for the major pest the peach-potato aphid, Myzus persicae, globally.
Data from: Comparative genetic structure and demographic history in endemic Galápagos weevils
The challenge of maintaining genetic diversity within populations can be exacerbated for island endemics if they display population dynamics and behavioral attributes that expose them to genetic drift without the benefits of gene-flow. We assess patterns of genetic structure and demographic history in twenty seven populations of nine species of flightless endemic Galápagos weevils from nine of the islands and one winged introduced close relative. Analysis of mitochondrial DNA reveals significant population structure and moderately variable, though demographically stable, populations for lowland endemics (Fst= 0.094 to 0.541; π: 0.014 to 0.042; Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203), in contrast to signals of past contractions and expansions in highland specialists on two islands (Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203). We interpret this series of variable and highly structured population groups as a system of long-established independently founded island units, where structuring could be a signal of micro-allopatric differentiation due to patchy host plant distribution and poor dispersal abilities. We suggest that the severe reduction and subsequent increase of suitably moist habitat that accompanied past climatic variation could have contributed to the observed population fluctuations in highland specialists. We propose the future exploration of hybridization between the introduced and highland endemic species on Santa Cruz, especially given the expansion of the introduced species into the highlands, the sensitivity to past climatic variation detected in highland populations and the potentially threatened state of single-island endemics.
Data from: Subsampling reveals that unbalanced sampling affects STRUCTURE results in a multi-species dataset
Studying the genetic population structure of species can reveal important insights into several key evolutionary, historical, demographic, and anthropogenic processes. One of the most important statistical tools for inferring genetic clusters is the program STRUCTURE. Recently, several papers have pointed out that STRUCTURE may show a bias when the sampling design is unbalanced, resulting in spurious joining of underrepresented populations and spurious separation of overrepresented populations. Suggestions to overcome this bias include subsampling and changing the ancestry model, but the performance of these two methods has not yet been tested on actual data. Here, I use a dataset of twelve high-alpine plant species to test whether unbalanced sampling affects the STRUCTURE inference of population differentiation between the European Alps and the Carpathians. For four of the twelve species, subsampling of the Alpine populations –to match the sample size between the Alps and the Carpathians– resulted in a drastically different clustering than the full dataset. On the other hand, STRUCTURE results with the alternative ancestry model were indistinguishable from the results with the default model. Based on these results, the subsampling strategy seems a more viable approach to overcome the bias than the alternative ancestry model. However, subsampling is only possible when there is an a priori expectation of what constitute the main clusters. Though these results do not mean that the use of STRUCTURE should be discarded, it does indicate that users of the software should be cautious about the interpretation of the results when sampling is unbalanced.
Data from: Genetic diversity, population structure and migration scenarios of the marsupial "Monito del Monte" in south-central Chile.
In this study, we quantified the three pivotal genetic processes (i.e., genetic diversity, spatial genetic structuring and migration) necessary for a better biological understanding and management of the singular "living-fossil" and near-threatened mouse opossum marsupial Dromiciops gliroides, the "Monito del Monte", in south-central Chile. We used 11 microsatellite loci to genotype 47 individuals distributed on the mainland and northern Chiloé Island. Allelic richness, observed and expected heterozygosity, inbreeding coefficient and levels of genetic differentiation were estimated. The genetic structure was assessed based on Bayesian clustering methods. In addition, potential migration scenarios were evaluated based on a coalescent theory framework and Bayesian approach to parameter estimations. Microsatellites revealed moderate to high levels of genetic diversity across sampled localities. Moreover, such molecular markers suggested that at least two consistent genetic clusters could be identified along the D. gliroides distribution ("Northern" and "Southern" cluster). However, general levels of genetic differentiation observed among localities and between the two genetic clusters were relatively low. Migration analyses showed that the most likely routes of migration of D. gliroides occurred a) from the Southern cluster to the Northern cluster and b) from the Mainland to Chiloé Island. Our results could represent critical information for future conservation programs and for a recent proposal about the taxonomic status of this unique mouse opossum marsupial.
Data from: Landscape and oceanic barriers shape dispersal and population structure in the island nematode, Pristionchus pacificus
Despite the biological importance and diversity of nematodes, little is known of the factors influencing their dispersal and shaping their evolutionary history. Populations of the cosmopolitan species Pristionchus pacificus are characterized by high genetic diversity and strong spatial structure, which contrasts with patterns detected in nematode species such as Caenorhabditis elegans. The environmentally heterogeneous volcanic Mascarene Islands provide an ideal setting for investigating fine-scale patterns of nematode migration and gene flow. Based on the analysis of data from 19 nuclear microsatellites and one mitochondrial marker, we infer support for the colonization of both La Réunion Island and Mauritius from similar multiple geographical sources. Although the long-term persistence of populations on both islands is well supported, the historical colonization of one island from the other cannot be discounted. In fact, periodic, bi-directional migration between the islands following their initial colonization is strongly supported in isolation with migration analyses, supporting the occurrence of rare trans-oceanic dispersal events in P. pacificus. Through a combination of population and landscape genetic analyses we also infer non-uniform dispersal across the landscape on the island of La Réunion, probably mediated by the movements of beetle hosts. Collectively, we show that gene flow in P. pacificus is limited by environmental and oceanic barriers, and shaped by the intricacies of the nematode–beetle host interaction
Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome
Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e., green algal vs. cyanobacterial), mycobiont-types, and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae, and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type, and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.
Data from: Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents
This study is the first large-scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups; (1) samples from the Zanzibar channel, (2) Mozambique, (3) Madagascar, and (4) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (DEST), but the three predominant ocean current systems (i.e. East African Coastal Current, North East Madagascar Current and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e. East African Coastal Current, North East Madagascar Current and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale – across national boarders.
Data from: Palaeobiogeographical structuration of Smithian (Early Triassic) ammonoid faunas within the western USA basin and its controlling parameters
We present the first quantitative palaeobiogeographical analysis in terms of distribution and abundance of Early Triassic ammonoids from the western USA basin during the Smithian, c. 1 myr after the Permian–Triassic boundary mass extinction. The faunal dataset consists of a taxonomically homogenized compilation of spatial and temporal occurrences and abundances from 27 sections distributed within the western USA basin. Two complementary multivariate techniques were applied to identify the main biogeographical structuring recorded in the analysed presence/absence data: additive cluster analysis using the neighbor‐joining algorithm (NJ) and non‐metric multidimensional scaling (NMDS). Regarding abundance data, a taxonomic diversity (sensu evenness) analysis was coupled with graphical comparisons of relative abundances of selected taxa. The identified relationships indicate that middle Smithian ammonoids of the western USA basin were geographically organized in terms of both distribution and abundance, with the biogeographical distinction of a southern and a northern cluster. This N–S structuring in the distribution and abundance of middle Smithian ammonoids is notably paralleled by the relative amount of siliciclastics, which suggests that clastic load of the water column was a major controlling factor. In marked contrast with the middle Smithian, the studied late Smithian ammonoid assemblages do not show any significant differences, whatever the depositional environment. This abrupt biogeographical homogenization, independent from intrabasinal facies heterogeneity, indicates a switch from regional to global drivers, associated with the well‐known late Smithian global extinction and remarkable cosmopolitan ammonoid distributions during that time.
Data from: Community structure of a Neotropical bat fauna as revealed by stable isotope analysis: Not all species fit neatly into predicted guilds
Neotropical bat communities are among the most diverse mammal communities in the world, and a better understanding of these assemblages may permit inferences about how so many species coexist. While broad trophic guilds (e.g., frugivore, insectivore) of bats are recognized, details of diet and similarities among species remain largely unknown. We used stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) to characterize the community structure of a diverse Neotropical bat fauna from Belize to test predictions of niche theory and the competitive exclusion principle. We predicted that (1) interspecific variation in isotopic overlap would be greater within guilds than between guilds, and (2) no two sympatric populations would have isotopic niches that overlap completely, unless there is variation along some other axis (e.g., temporal, spatial). We additionally tested body size as an explanatory metric of potential overlap, and predicted that larger-bodied animals would have greater niche breadths. Results suggest that while guild-level characterizations of communities is at least somewhat informative, there are multiple examples of intra- and inter-guild species pairs with significantly overlapping isotopic niches, suggesting that, counter to predictions, they may compete for resources. Understanding the trophic structure of animal communities is fundamental to conservation and management of endangered species and ecosystems and important for evolutionary studies, and stable isotope analyses can provide key insights as well as informing hypotheses of the diet of species that are not well known.
Data from: Across-year social stability shapes network structure in wintering migrant sparrows
Migratory birds often form flocks on their wintering grounds, but important details of social structure such as the patterns of association between individuals are virtually unknown. We analysed networks of co-membership in short-term flocks for wintering golden-crowned sparrows (Zonotrichia atricapilla) across three years and discovered social complexity unsuspected for migratory songbirds. The population was consistently clustered into distinct social communities within a relatively small area (~ 7 ha). Birds returned to the same community across years, with mortality and recruitment leading to some degree of turnover in membership. These spatiotemporal patterns were explained by the combination of space use and social preference – birds that flocked together in one year flocked together again in the subsequent year more often than were expected based on degrees of home range overlap. Our results suggest that a surprising level of social fidelity across years leads to repeatable patterns of social network structure in migratory populations.
Data from: Predation risk, resource quality, and reef structural complexity shape territoriality in a coral reef herbivore
For many species securing territories is important for feeding and reproduction. Factors such as competition, habitat availability, and male characteristics can influence an individual's ability to establish and maintain a territory. The risk of predation can have an important influence on feeding and reproduction; however, few have studied its effect on territoriality. We investigated territoriality in a haremic, polygynous species of coral reef herbivore, Sparisoma aurofrenatum (redband parrotfish), across eight reefs in the Florida Keys National Marine Sanctuary that were either protected or unprotected from fishing of piscivorous fishes. We examined how territory size and quality varied with reef protection status, competition, predation risk, and male size. We then determined how territory size and quality influenced harem size and female size to understand the effect of territoriality on reproductive potential. We found that protected reefs trended towards having more large predatory fishes and that territories there were smaller but had greater algal nutritional quality relative to unprotected reefs. Our data suggest that even though males in protected sites have smaller territories, which support fewer females, they may improve their reproductive potential by choosing nutritionally rich areas, which support larger females. Thus, reef protection appears to shape the trade-off that herbivorous fishes make between territory size and quality. Furthermore, we provide evidence that males in unprotected sites, which are generally less complex than protected sites, choose territories with higher structural complexity, suggesting the importance of this type of habitat for feeding and reproduction in S. aurofrenatum. Our work argues that the loss of corals and the resulting decline in structural complexity, as well as management efforts to protect reefs, could alter the territory dynamics and reproductive potential of important herbivorous fish species.
Data from: Genomic conflict drives patterns of X-linked population structure in Drosophila neotestacea
Intra-genomic conflict has the potential to cause widespread changes in patterns of genetic diversity and genome evolution. In this study, we investigate the consequences of sex-ratio (SR) drive on the population genetic patterns of the X-chromosome in Drosophila neotestacea. An SR X-chromosome prevents the maturation of Y-bearing sperm during male spermatogenesis, and thus is transmitted to ~100% of the offspring, nearly all of which are daughters. Selection on the rest of the genome to suppress sex-ratio can be strong, and the resulting conflict over the offspring sex ratio can result in the accumulation of multiple loci on the X-chromosome that are necessary for expression of drive. We surveyed variation at 12 random X-linked microsatellites across 16 populations of D. neotestacea that range in SR frequency from 0-30%. First, every locus was differentiated between SR and wild-type chromosomes, and this drives genetic structure at the X-chromosome. Once the association with sex-ratio is accounted for, the patterns of differentiation among populations are similar to the autosomes. Second, within wild-type chromosomes the relative heterozygosity is reduced in populations with an increased prevalence of drive, and the heterozygosity of SR chromosomes is higher than expected based on its prevalence. The combination of the relatively high prevalence of SR drive and the structuring of polymorphism between the SR and wild-type chromosomes suggests that genetic conflict due to SR drive has had significant consequences on the patterns of X-linked polymorphism and thus also likely affects the tempo of X-chromosome evolution in D. neotestacea.
Data from: Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique
Background: Intraspecific genetic variation of African fauna has been signific antly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range. Results: Genetic structure and historical demography of N. furzeri were analysed using a combination of mitochondrial (partial cytochrome b sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish from 36 populations. Genetic markers consistently demonstrated strong population structuring and suggested two main genetic groups associated with river basins. The split was dated to the Pliocene (>2 Mya). The northern group inhabits savannah pools across the basin of the intermittent river Chefu in south-western Mozambique and eastern Zimbabwe. The southern group (from southernmost Mozambique) is subdivided, with the River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong habitat fragmentation (isolated temporary pools) is reflected in significant genetic structuring even between adjacent pools, with a major influence of genetic drift and significant isolation-by-distance. Analysis of historical demography revealed that the expansion of both groups is ongoing, supported by frequent founder effects in marginal parts of the range and evidence of secondary contact between Chefu and Limpopo populations. Conclusions: We demonstrated: (1) ancient (pre-Pleistocene) divergence between the two main N. furzeri lineages, their recent secondary contact and lack of reproductive isolation; (2) important genetic structuring attributed to the fragmented nature of their environment and isolation-by-distance, suggesting that dispersal is limited, occurs over short distances and is not directly associated with river routes; (3) an apparent role of the River Limpopo as a barrier to dispersal and gene flow.
Data from: Population structure of the Chagas disease vector Triatoma infestans in an urban environment
Chagas disease is a vector-borne disease endemic in Latin America. Triatoma infestans, a common vector of this disease, has recently expanded its range into rapidly developing cities of Latin America. We aim to identify the environmental features that affect the colonization and dispersal of T. infestans in an urban environment. We amplified 13 commonly used microsatellites from 180 T. infestans samples collected from a sampled transect in the city of Arequipa, Peru, in 2007 and 2011. We assessed the clustering of subpopulations and the effect of distance, sampling year, and city block location on genetic distance among pairs of insects. Despite evidence of genetic similarity, the majority of city blocks are characterized by one dominant insect genotype, suggesting the existence of barriers to dispersal. Our analyses show that streets represent an important barrier to the colonization and dispersion of T. infestans in Arequipa. The genetic data describe a T. infestans infestation history characterized by persistent local dispersal and occasional long-distance migration events that partially parallels the history of urban development.
Data from: Genetic structure of Pacific trout at the extreme southern end of their native range
Salmonid fishes are cold water piscivores with a native distribution spanning nearly the entire temperate and subarctic northern hemisphere. Trout in the genus Oncorhynchus are the most widespread salmonid fishes and are among the most important fish species in the world, due to their extensive use in aquaculture and valuable fisheries. Trout that inhabit northwestern Mexico are the southernmost native salmonid populations in the world, and the least studied in North America. They are unfortunately also facing threats to their continued existence. Previous work has described one endemic species, the Mexican golden trout (O. chrysogaster), and one endemic subspecies, Nelson's trout (O. mykiss nelsoni), in Mexico, but previous work indicated that there is vastly more biodiversity in this group than formally described. Here we conducted a comprehensive genetic analysis of this important group of fishes using novel genetic markers and techniques to elucidate the biodiversity of trout inhabiting northwestern Mexico, examine genetic population structure of Mexican trout and their relationships to other species of Pacific trout, and measure introgression from non-native hatchery rainbow trout. We confirmed substantial genetic diversity and extremely strong genetic differentiation present in the Mexican trout complex, not only between basins but also between some locations within basins, with at least four species-level taxa present. We also revealed significant divergence between Mexican trout and other trout species and found that introgression from non-native rainbow trout is present but limited, and that the genetic integrity of native trout is still maintained in most locations. This information will help to guide effective conservation strategies for this important group of fishes.
Data from: Investigating sensitivity of phylogenetic community structure metrics using North American desert bats
A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of bats from the 4 great desert regions of North America. We inferred a phylogeny of the regional species pool to calculate PCS metrics using community membership data delimited using 3 different methods. We also randomized our phylogeny to determine how reasonable changes to the tree affect PCS metrics. Overall, PCS metrics are quite robust to moderate changes in the phylogeny from which they are calculated. These metrics also are fairly insensitive to our 3 methods of delimiting communities. Additionally, we found that in general, communities are significantly phylogenetically clustered, suggesting habitat filtering has been important in community assembly.
Data from: The bacterial community structure and functional profile in the heavy metal contaminated paddy soils,surrounding a nonferrous smelter in South Korea
The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. The present study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes, involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.
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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.