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opencc-zeroJun 2020View details →

Data from: The ecology of the collapse of Rapa Nui society

Collapses of food producer societies are recurrent events in prehistory and have triggered a growing concern for identifying the underlying causes of convergences/divergences across cultures around the world. One of the most studied and used as a paradigmatic case is the population collapse of the Rapa Nui society. Here, we test different hypotheses about by developing explicit population dynamic models that integrate feedbacks between climatic, demographic and ecological factors that underpinned the socio-cultural trajectory of these people. We evaluate our model outputs against a reconstruction of past population size based on archaeological radiocarbon dates from the island. The resulting estimated demographic declines of the Rapa Nui people are linked to the long-term effects of climate change on the island's carrying capacity, and in turn on the "per capita food supply".

Data from: Ecological speciation in sympatric palms: 3. genetic map reveals genomic islands underlying species divergence in Howea

Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction-site associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, some of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.

Data from: Evolutionary constraint on low elevation range expansion: defense-abiotic stress tolerance tradeoff in crosses of the ecological model Boechera stricta

Most transplant experiments across species geographic range boundaries indicate that adaptation to stressful environments outside the range is often constrained. However, the mechanisms of these constraints remain poorly understood. We used extended generation crosses from diverged high and low elevation populations. In experiments across low elevation range boundaries, there was selection on the parental lines for abiotic stress tolerance and resistance to herbivores. However, in support of a defense-tolerance tradeoff, extended generation crosses showed non-independent segregation of these traits in the lab across a drought-stress gradient and in the field across the low elevation range boundary. Genotypic variation in a marker from a region of the genome containing a candidate gene (MYC2) was associated with change in the genetic tradeoff. Thus, using crosses and forward genetics, we found experimental genetic and molecular evidence for a pleiotropic tradeoff that could constrain the evolution of range expansion.

Data from: Last Glacial Maximum environmental conditions at Andøya, northern Norway; evidence for a northern ice-edge ecological "hotspot"

Andøya on the NW coast of Norway is a key site for understanding the Last Glacial Maximum (LGM) in northern Europe. Controversy has arisen concerning the local conditions, especially about the timing and extent of local glacial cover, maximum July temperatures and whether pine and/or spruce could have grown there. We reviewed all existing data and add newly analysed ancient sedimentary DNA, pollen, macrofossils, geochemistry and stable isotopes from three lake sediment cores from Øvre Æråsvatnet. A total of 23 new dates and age-depth modelling suggests the lake has been ice-free since GI2 (<22.8 k cal. BP) and possibly GS3 (<27.4 k cal. BP). Pinus and Picea sedimentary ancient DNA (sedaDNA) was found in all three cores but at such low frequencies that it could not be distinguished from background contamination. LGM samples have an exceptionally high organic matter content, with isotopic values indicating that carbon and nitrogen derives from a marine source. Along with finds of bones of the little auk (Alle alle), this indicates that the lake received guano from an adjacent bird colony. DNA, pollen and macrofossil assemblages were dominated by Poaceae, Brassicaceae and Papaver, but scattered occurrence of species currently restricted to the Low Arctic Tundra Zone (July temperature of 8-9°C) such as Apiaceae (DNA, 8-9°C), and Alchemilla alpina (macrofossil, 8-9°C) were also recorded. The review showed 94 recorded vascular plant taxa, of which 38% have a northern limit in Shrub Tundra or more southern vegetation zones. This unusual assemblage likely stems from a combination of proximity to ice-free water in summer, geographical isolation linked with stochastic long- distance dispersal events, and the presence of bird-fertilized habitats. The environmental reconstruction based on all records from the area does not preclude local growth of tree species, as the local climate combined with high nutrient input may have led to periodically suitable environmental 'hotspot' conditions.

Data from: Comparing traditional and Bayesian approaches to ecological meta-analysis

1. Despite the wide application of meta-analysis in ecology, some of the traditional methods used for meta-analysis may not perform well given the type of data characteristic of ecological meta-analyses. 2. We reviewed published meta-analyses on the ecological impacts of global climate change, evaluating the number of replicates used in the primary studies (ni) and the number of studies or records (k) that were aggregated to calculate a mean effect size. We used the results of the review in a simulation experiment to assess the performance of conventional frequentist and Bayesian meta-analysis methods for estimating a mean effect size and its uncertainty interval. 3. Our literature review showed that ni and k were highly variable, distributions were right-skewed, and were generally small (median ni =5, median k=44). Our simulations show that the choice of method for calculating uncertainty intervals was critical for obtaining appropriate coverage (close to the nominal value of 0.95). When k was low (<40), 95% coverage was achieved by a confidence interval based on the t-distribution that uses an adjusted standard error (the Hartung-Knapp-Sidik-Jonkman, HKSJ), or by a Bayesian credible interval, whereas bootstrap or z-distribution confidence intervals had lower coverage. Despite the importance of the method to calculate the uncertainty interval, 39% of the meta-analyses reviewed did not report the method used, and of the 61% that did, 94% used a potentially problematic method, which may be a consequence of software defaults. 4. In general, for a simple random-effects meta-analysis, the performance of the best frequentist and Bayesian methods were similar for the same combinations of factors (k and mean replication), though the Bayesian approaches had higher than nominal (>95%) coverage for the mean effect when k was very low (k<15). Our literature review suggests that many meta-analyses that used z-distribution or bootstrapping confidence intervals may have over-estimated the statistical significance of their results when the number of studies was low; more appropriate methods need to be adopted in ecological meta-analyses.

Data from: Specialization and niche overlap across spatial scales: revealing ecological factors shaping species richness and coexistence in Australian songbirds

1. Ecological specialization enables the partitioning of resources and thus can facilitate the coexistence of species and promote higher species richness. Specialization and niche partitioning are expected to exert a decisive influence on local spatial scales, while species richness at regional scales should be shaped mostly by historical factors and abiotic conditions. Moreover, specialization is expected to be particularly important in communities that are exceptionally species rich for their environmental conditions. Concurrently, niche overlap in these communities should be minimized to enable species coexistence. 2. We tested these hypotheses by studying specialization-richness relationship and niche overlap in assemblages of 298 species of songbirds (Passeriformes) across Australia. We used local (2-6 ha) to regional (bioregions) spatial scales, and detailed data on habitat, diet, and foraging behaviour (method, substrate, and stratum). 3. We expected the richness-specialization relationship to be particularly strong i) on local spatial scales and ii) in communities exceptionally species rich for given environmental conditions (approximated by moisture and vegetation complexity). We also expected iii) low niche overlap in assemblages with specialized species. 4. Only the third prediction was partly supported. First, while the specialization and species richness were often positively related, the strength and the direction of the relationship changed between traits and across spatial scales. The strength of the specialization-richness relationship was consistently positive only in foraging stratum, and it increased towards smaller spatial scales only in case of habitat and diet. Simultaneously, species in local communities demonstrated high overlap in habitat and diet. Second, we did not find particularly strong specialization-richness relationships in exceptionally species rich communities. Third, we found the expected negative relationship between specialization and overlap in foraging stratum and substrate (in local communities), suggesting that species partition ecological space locally in terms of where they find food. 5. Our expectations were only weakly supported. Specialization on foraging stratum was probably important in facilitating species co-existence. Conversely, although species were often specialized on habitat and diet, high overlap in these traits did not preclude their local coexistence. Overall, specialization and overlap in foraging traits were more important for species coexistence than habitat or diet.

opencc-zeroJun 2020View details →

Data from: Phenotypic, ecological and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand's Southern Great Lakes

Depth gradients in lakes are often key drivers of population divergence and speciation in fishes. New Zealand has many deep lakes but no known profundal specialist fishes or cases of intralacustrine speciation. We sampled a native benthic fish, the common bully, from 5–90 m depth in four South Island lakes, to test for morphological, ecological, or genetic differentiation associated with depth. Deeper fish consistently had narrower bodies, while other morphological traits showed variable relationships with depth. Carbon and nitrogen stable isotope values of fish increased with depth, largely tracking isotopic trends with depth of benthic invertebrate prey. Genotyping-by-sequencing showed some genome-wide differentiation between two of the lakes, but no evidence for within-lake genetic structuring along depth gradients. These results indicate that individual bullies associate with shallower or deeper habitats within their lifetimes, but we found no evidence of progress toward genetic divergence within lakes. The apparent lack of intralacustrine genetic divergence in New Zealand's fishes may be explained by a combination of environmental factors and constraints intrinsic to its marine-derived freshwater fish fauna.

Data from: Body temperature, heart rate, and activity patterns of two boreal homeotherms in winter: homeostasis, allostasis, and ecological coexistence

<ol> <li>Organisms survive environmental variation by combining homeostatic regulation of critical states with allostatic variation of other traits, and species differences in these responses can contribute to coexistence in temporally-variable environments.</li> <li>In this paper, we simultaneously record variation in three functional traits – body temperature (Tb), heart rate, and activity - in relation to three forms of environmental variation – air temperature (Ta), photoperiod, and experimentally-manipulated resource levels – in free-ranging snowshoe hares and North American red squirrels to characterize distinctions in homeotherm responses to the extreme conditions of northern boreal winters.</li> <li>Hares and squirrels differed in the level and precision of Tb regulation, but also in the allostatic pathways necessary to maintain thermal homeostasis. Hares demonstrated a stronger metabolic pathway (through heart rate variation reflective of the thermogenesis), while squirrels demonstrated a stronger behavioral pathway (through activity variation that minimizes cold exposure).</li> <li>As intermediate-sized, winter-active homeotherms, hares and squirrels share many functional attributes, yet, through the integrated monitoring of multiple functional traits in response to shared environmental variation, our study reveals many pairwise species differences in homeostatic and allostatic traits, that both define and are defined by the natural history, functional niches, and coexistence of sympatric species.</li> </ol>

Data from: Extending the climatological concept of 'Detection and Attribution' to global change ecology in the Anthropocene

<ol> <li>Research into global change ecology is motivated by the need to understand the role of humans in changing biotic systems. Mechanistic understanding of ecological responses requires the separation of different climatic parameters and processes that often operate on diverse spatiotemporal scales. Yet most environmental studies do not distinguish the effects of internal climate variability from those caused by external, natural (e.g. volcanic, solar, orbital) or anthropogenic (e.g. greenhouse gases, ozone, aerosols, land-use) forcing factors.</li> <li>We suggest extending the climatological concept of 'Detection and Attribution' (DA) to unravel abiotic drivers of ecological dynamics in the Anthropocene. We therefore apply DA to quantify the relative roles of natural versus industrial temperature change on elevational shifts in the outbreak epicentres of the larch budmoth (LBM; Zeiraphera diniana or griseana Gn.); the classic example of a cyclic forest defoliating insect.</li> <li>Our case study shows that anthropogenic warming shifts the epicentre of travelling LBM waves upward, which disrupts the intensity of population outbreaks that occurred regularly over the past millennium in the European Alps. Our findings demonstrate the ability of DA to detect ecological responses beyond internal system variability, to attribute them to specific external climate forcing factors, and to identify climate-induced ecological tipping points.</li> <li>In order to implement the climatological concept of 'Detection and Attribution' successfully into modern global change ecology, future studies should combine high-resolution paleoenvironmental reconstructions and state-of-the-art climate model simulations to inform inference-based ecosystem models.</li> </ol>

Data from: Islands in the desert for cavity-nesting bees and wasps: ecology, patterns of diversity, and conservation at oases of Baja California peninsula

Aims: The oases of Baja California peninsula (BCP) have been proposed as important hotspots of biodiversity that hold an exceptional richness in the middle of desert conditions. We provide the effect of habitat, climatic, biogeographic and anthropogenic disturbance on communities of cavity nesting taxa, emphasizing on bees, wasps and their natural enemies. Location: Baja California Peninsula, Northwest Mexico. Methods: In oases of BCP and desert neighbor environments, trap-nesting taxa were evaluated in response to factors affecting the nest abundance, richness, and community structure. We used statistical models to find the variables controlling the nest abundance and ecological analyses to determine the habitat effect on diversity under different scenarios of disturbance and latitude. Results: The nest abundance varied between bees and wasps, but solar irradiation and relative humidity influenced the abundance of both groups. In general, abundance and richness were higher in oases. Bees did not discriminate between oasis and desert habitats to nest and mud-daubing wasps were highly dependent of oases. However, there were exceptions in both groups. The degree of anthropogenic disturbance affected the species composition, richness, and natural enemies. Main conclusions: The oases of Baja California seem to be functioning as mesic islands into the desert, each oasis hosting a great and unique richness of cavity-nesting taxa. About 65% of nest abundance and 50% of species occurred exclusively in the oasis. Thus, at least 21 species could be threatened if the oases of BCP disappear in the future. Local conditions are shaping the community structure of species, but also large-scale factors, e.g. climate and biogeographic patterns seem to be influencing the community structure. Since habitat loss and fragmentation can be a major problem in most oases, strategies to maintain the ecosystem services of pollinators and predators should be included in the conservation programs of these fragile habitats.

Data from: Rapid generation of ecologically relevant behavioural novelty in experimental cichlid hybrids

The East African cichlid radiations are characterised by repeated and rapid diversification into many distinct species with different ecological specialisations and by a history of hybridization events between non-sister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second-generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialised on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialised on sand sifting. We combined experimental behavioural and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behaviour related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioural traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behaviour in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behaviour, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.

opencc-zeroDec 2019View details →

Data from Beyond MAP: A guide to dimensions of rainfall variability for tropical ecology

Tropical ecologists have long recognized rainfall as the key climate filter shaping tropical ecosystem structure and function across space and time. Still, tropical ecologists have historically had a limited toolkit for characterizing rainfall, largely relying on simple metrics like mean annual precipitation (MAP) and dry season length to characterize rainfall regimes that vary along many more dimensions. Here, we review methods for quantifying dimensions of rainfall variability on multiple time scales, with a focus on ecological applications of these methods. We also discuss key considerations for tropical ecologists looking to use rainfall metrics that better align with hypothesized biological or ecological mechanisms or that more effectively describe rainfall variability in the systems we study, and provide a toolkit (R scripts and gridded datasets) to do so. We argue that incorporating more sophisticated approaches to quantify rainfall variability into study design and statistical analyses will enhance our understanding of past, ongoing, and future changes in tropical ecosystems.

Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers

Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.

Data from: Incorporating alternative interaction modes, forbidden links and trait-based mechanisms increases the minimum trait dimensionality of ecological networks

<ol> <li>Individual-level traits mediate interaction outcomes and community structure. It is important, therefore, to identify the minimum number of traits that characterise ecological networks, i.e. their 'minimum dimensionality'. Existing methods for estimating minimum dimensionality often lack three features associated with increased trait numbers: alternative interaction modes (e.g. feeding strategies such as active vs. sit-and-wait feeding), trait-mediated 'forbidden links' and a mechanistic description of interactions. Omitting these features can underestimate the trait numbers involved, and therefore, minimum dimensionality. We develop a 'minimum mechanistic dimensionality' measure, accounting for these three features.</li> <li>The only input our method requires is the network of interaction outcomes. We assume how traits are mechanistically involved in alternative interaction modes. These unidentified traits are contrasted using pairwise performance inequalities between interacting species. For example, if a predator feeds upon a prey species via a typical predation mode, in each step of the predation sequence the predator's performance must be greater than the prey's. We construct a system of inequalities from all observed outcomes, which we attempt to solve with mixed integer linear programming. The number of traits required for a feasible system of inequalities provides our minimum dimensionality estimate.</li> <li>We applied our method to 658 published empirical ecological networks including primary consumption, predator–prey, parasitism, pollination, seed dispersal and animal dominance networks, to compare with minimum dimensionality estimates when the three focal features are missing. Minimum dimensionality was typically higher when including alternative interaction modes (54% of empirical networks), 'forbidden interactions' as trait-mediated interaction outcomes (92%), or a mechanistic perspective (81%), compared to estimates missing these features. Additionally, we tested minimum dimensionality estimates on simulated networks with known dimensionality. Our method typically estimated a higher minimum dimensionality, closer to the actual dimensionality, while avoiding the overestimation associated with a previous method.</li> <li>Our method can reduce the risk of omitting traits involved in different interaction modes, in failure outcomes, or mechanistically. More accurate estimates will allow us to parameterise models of theoretical networks with more realistic structure at the interaction outcome level. Thus, we hope our method can improve predictions of community structure and structure-dependent dynamics.</li> </ol>

opencc-zeroApr 2020View details →

Data from: The ecological and genomic basis of explosive adaptive radiation

Rates of speciation vary tremendously among evolutionary lineages, with our understanding of what fuels the rapid succession of speciation events within young adaptive radiations remaining particularly incomplete. The cichlid fish family provides the most notable example of such variation among extant metazoans. It includes many slowly speciating lineages as well as the several exceptionally large and rapid adaptive radiations. By reconstructing a large phylogeny of all described cichlid species, we show that explosive speciation is solely concentrated in several large yet young lake species flocks. Across the family, speciation rate increases are associated with absence of top predators, and speciation rate decreases are associated with arid climate, but these factors are not nearly sufficient to explain explosive speciation in lake radiations, in particular the Lake Victoria adaptive radiation. Across lake radiations we observe a positive relationship between speciation rate and enrichment with large indel polymorphisms. Assembly of one hundred Victorian cichlid genomes comprising all extant ecological guilds and taxonomic genera reveals this radiation contains exceptional 'genomic potential' - hundreds of ancient haplotypes bearing indel polymorphisms, many of which are strongly associated with specific ecologies and are shared with ecologically similar species from other older lake radiations elsewhere in Africa. Network analysis reveals fundamentally non-treelike evolution through recombining old haplotypes, with origins of ecological guilds concentrated early in the Victoria radiation. Our results suggest that the combination of ecological opportunity, sexual selection and exceptional genomic potential is the key to understanding explosive adaptive radiation.

Data from: Long-term ecological legacies in western Amazonia

1. Modifications of Amazonian forests by pre-Columbian peoples are thought to have left ecological legacies that have persisted to the modern day. Most Amazonian palaeoecological records do not, however, provide the required temporal resolution to document the nuanced changes of pre-Columbian disturbance or post-disturbance succession and recovery, making it difficult to detect any direct, or indirect, ecological legacies on tree species. 2. Here, we investigate the fossil pollen, phytolith, and charcoal history of Lake Kumpaka, Ecuador, during the last 2415 years in c. 3-50 year time intervals to assess ecological legacies resulting from pre-Columbian forest modification, disturbance, cultivation, and fire usage. 3. Two cycles of pre-Columbian cultivation (one including slash-and burn cultivation, the other including slash-and-mulch cultivation) were documented in the record around 2150-1430 cal. yr BP and 1250-680 cal. yr BP, with following post-disturbance succession dynamics. Modern disturbance was documented after c. 10 cal. yr BP. The modern disturbance produced a plant composition unlike those of the two past disturbances, as fire frequencies reached their peak in the 2415-year record. The disturbance periods varied in intensity and duration, while the overturn of taxa following a disturbance lasted for hundreds of years. The recovery periods following pre-Columbian disturbance shared some similar patterns of early succession, but the longer-term recovery patterns differed. 4. Synthesis. The trajectories of change after a cessation of cultivation can be anticipated to differ depending on the intensity, scale, duration, and manner of the past disturbance. In the Kumpaka record, no evidence of persistent enrichment or depletion of intentionally altered taxa (i.e. direct legacy effects) was found but indirect legacy effects, however, were documented and have persisted to the modern day. These findings highlight the strengths of using empirical data to reconstruct past change rather than relying solely on modern plant populations to infer past human management and ecological legacies, and challenge some of the current hypotheses involving the persistence of pre-Columbian legacies on modern plant populations.

opencc-zeroSep 2020View details →

Data from: Lessons from movement ecology for the return to work: modeling contacts and the spread of COVID-19

Human behavior (movement, social contacts) plays a central role in the spread of pathogens like SARS-CoV-2. The rapid spread of SARS-CoV-2 was driven by global human movement, and initial lockdown measures aimed to localize movement and contact in order to slow spread. Thus, movement and contact patterns need to be explicitly considered when making reopening decisions, especially regarding return to work. Here, as a case study, we consider the initial stages of resuming research at a large research university, using approaches from movement ecology and contact network epidemiology. First, we develop a dynamical pathogen model describing movement between home and work; we show that limiting social contact, via reduced people or reduced time in the workplace are fairly equivalent strategies to slow pathogen spread. Second, we develop a model based on spatial contact patterns within a specific office and lab building on campus; we show that restricting on-campus activities to labs (rather than labs and offices) could dramatically alter (modularize) contact network structure and thus, potentially reduce pathogen spread by providing a workplace mechanism to reduce contact. Here we argue that explicitly accounting for human movement and contact behavior in the workplace can provide additional strategies to slow pathogen spread that can be used in conjunction with ongoing public health efforts.

zenodo32/100

Data collection for Tsuji et al., 2020, Microbial ecology of phototrophs in Boreal Shield lakes, Chapter 3: Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes (PhD thesis)

This data collection includes supplementary or raw data files related to Chapter 3 of the PhD thesis of Jackson M. Tsuji, "Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes" (in "Microbial ecology of phototrophs in Boreal Shield lakes"). Specifically, the following files are included: <ul> <li>ASV_table_non_rarefied_counts.tsv.gz -- non-rarefied ASV table containing 16S rRNA gene amplicon data presented in this study as raw counts. Beyond the index column and sample columns, two additional columns, "Consensus.Lineage" and "Sequence" are included in the table. These columns include the taxonomic classification of the ASV (according to Silva) and the ASV sequence, respectively.</li> <li>ASV_table_non_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>ASV_table_rarefied_counts.tsv.gz -- same as "ASV_table_non_rarefied_counts.tsv.gz", except that data is rarefied to 12,000 sequences per sample. Five samples were dropped due to having <12,000 sequences.</li> <li>ASV_table_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>MAG_abundances_to_unassembled_reads.tsv.gz -- table like an ASV table showing the relative abundances (expressed as percentages) of metagenome-assembled genomes within metagenomes. Aside from the index column and sample columns, additional columns are included to provide the taxonomic classification of the MAGs (based on the Genome Taxonomy Database) and the CheckM statistics of the MAGs. Relative abundances of MAGs in a metagenome are calculated as the number of mapped reads to the MAGs from the given metagenome divided by the total number of unassembled metagenome reads for that metagenome (times 100%).</li> <li>MAG_abundances_to_assembled_reads.tsv.gz -- same as above, except that relative abundances are divided by the total number of unassembled metagenome reads for that metagenome that mapped to that metagenome's assembled contigs.</li> <li>core_sample_metadata.tsv -- table of core physico-chemical and geographic metadata for the samples in this study (used to build biplots presented in the chapter). Note that "nd" means "no data available", and any measurements below detection limits have been set to 0. A limited number of values were inferred from other sampling time points -- these are noted in the table for TDFe measurements, and in addition, the light attenuation coefficient for Lake 373 in Sept. 2017 was inferred from the Sept. 2016 coefficient due to no light data being available for Sept. 2017 samples.</li> <li>metadata_descriptions.tsv -- descriptions of all metadata columns in the above file.</li> </ul>

opencc-by-4.0Sep 2020View details →

opencc-zeroSep 2020View details →

Data from: Strangers in a strange land: Ecological dissimilarity to metatherian carnivores may partly explain early colonization of South America by Cyonasua-group procyonids

It was once thought that the endemic carnivorous mammals of South America, the metatherian sparassodonts, were driven extinct by North American carnivores through competitive exclusion. However, sparassodonts went extinct before most groups of carnivorans entered South America; only the endemic Cyonasua-group procyonids (Cyonasua and Chapalmalania), which immigrated to South America nearly four million years earlier than other carnivorans, significantly overlapped with sparassodonts in time. In this study, we examine the functional morphology of the dentition of Cyonasua and Chapalmalania through quantitative analysis to determine the dietary habits of these taxa and the degree to which they may have ecologically overlapped sparassodonts and large predatory Neogene didelphimorphians. We find Cyonasua and Chapalmalania to be more carnivorous than extant procyonids other than Bassariscus, in agreement with previous studies, but more omnivorous than most other carnivorans and all meat-eating South American metatherians, including sparassodonts. The extreme ecological dissimilarity between Cyonasua-group procyonids and members of the endemic South American predator guild may explain why procyonids were able to successfully establish themselves in South America several million years earlier than most other northern mammals (including all other carnivorans): they moved into a previously unoccupied ecological niche (large omnivore) and avoided direct competition with incumbent native species, a situation similar to that documented in historical cases of biological invasion. The omnivorous diets and climbing/swimming abilities of procyonids may have increased their chances for a successful over-water dispersal relative to other carnivorans, further favoring their successful establishment in South America.