Find research datasets worth reusing

opencc-zeroAug 2020View details →

Data from: Multi-species restoration accelerates recovery of extinguished oyster reefs

1. A multi-species approach to habitat restoration may boost the key processes (e.g. recruitment) that enable foundation species to overcome barriers to recovery. Natural systems tend to be formed by co-occurring foundation species whose synergy drives ecological productivity and resilience beyond that of single foundation species. Yet, restoration remains primarily a single-species focus enterprise where positive interactions are seldom incorporated into planning. A multi-species approach that prioritises species combinations to create emergent properties for their persistence may accelerate habitat recovery and the success of restoration programs. 2. On the largest oyster reef restoration project in the Southern Hemisphere, we experimentally established canopy-forming kelp to test whether they could accelerate the natural recruitment of oysters to substrata monopolised by turf-forming algae. To understand whether facilitation of oysters was a function of the kelp themselves (biological facilitation) or the physical environment they create (physical facilitation), we compared recruitment to the understorey of living kelp and synthetic kelp mimics. 3. Despite observing high density oyster recruitment to the turf-free underside of reef boulders (8,300 oysters/m2), turf algae appeared to inhibit oyster recruitment to the exposed surfaces of the reef, limiting their capacity to grow and form complex, three-dimensional habitat. 4. Transplanted kelp, whether living or synthetic kelp mimics, effectively reduced the biomass of turf and enhanced oyster recruitment, creating turf-free substrata on the upper reef surfaces with up to 26 times the oyster recruitment than turf-covered substrata. 5. Synthesis and applications. Our results provide proof-of-concept that incorporating the transplant of canopy-forming kelp to reefs constructed to restore oysters is not only achievable, but may be imperative to successfully restore oyster reefs in turf-dominated systems. Kelp transplants supressed the turf algae that otherwise excluded oysters from the reef surface, effectively shifting the competitive advantage toward oyster recovery by maintaining bare substrata for oyster recruitment. In demonstrating that co-restoring foundation species facilitates interactions that overcome barriers to recovery, we emphasise the need for restoration programs to incorporate the functional synergy of overlapping foundation species into planning, so to establish emergent properties that can accelerate the recovery of restored habitat.

opencc-zeroAug 2020View details →

Data from msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities

Plant interactions are as important belowground as aboveground. Belowground plant interactions are however inherently difficult to quantify, as roots of different species are difficult to disentangle. Although for a couple of decades molecular techniques have been successfully applied to quantify root abundance, root identification and quantification in multi-species plant communities remains particularly challenging. Here we present a novel methodology, multi-species Genotyping By Sequencing (msGBS), as a next step to tackle this challenge. First, a multi-species meta-reference database containing thousands of gDNA clusters per species is created from GBS derived High Throughput Sequencing (HTS) reads. Second, GBS derived HTS reads from multi-species root samples are mapped to this meta-reference which, after a filter procedure to increase the taxonomic resolution, allows the parallel quantification of multiple species. The msGBS signal of 111 mock-mixture root samples, with up to 8 plant species per sample, was used to calculate the within-species abundance. Optional subsequent calibration yielded the across-species abundance. The within- and across-species abundances highly correlated (R2 range 0.72-0.94 and 0.85-0.98, respectively) to the biomass-based species abundance. Compared to a qPCR based method which was previously used to analyze the same set of samples, msGBS provided similar results. Additional data on 11 congener species groups within 105 natural field root samples showed high taxonomic resolution of the method. <a>msGBS is highly scalable in terms of sensitivity and species numbers within samples, which is a major advantage compared to the qPCR method and advances our tools to reveal hidden belowground interactions.</a> This dataset belongs to the article "msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities". msGBS is a technique that uses Genotyping By Sequencing on mixed plant species root samples which, after a filtering step to increase the taxonomic resolution and calibration, is able to estimate plant species abundances. The article uses data of two different experiment: <ol> <li>the Jena field survay (13 plant species) and</li> <li>the Dutch field survay (120 plant species).</li> </ol>

opencc-by-4.0Dec 2020View details →

Dataset used for the submitted manuscript "The hump-shaped effect of plant functional diversity on the biological control of a multi-species pest community"

Dataset

opencc-zeroDec 2017View details →

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.

opencc-zeroOct 2019View details →

Data from: Modelling misclassification in multi-species acoustic data when estimating occupancy and relative activity

1. Surveying wildlife communities provides data for informing conservation and management decisions that affect multiple species. Autonomous recording units (ARUs) can efficiently gather community data for a variety of taxa, but generally require software algorithms to classify each recorded call to a species. Species classification errors are possible during this process and result in both false negative and false positive detections. Available approaches for analysing ARU data do not model the species classification probabilities, meaning erroneous detections are attributed to an omnibus source instead of the presence of another species. Additionally, counts of call recordings for each species are often summarized to binary detection data for analyses. Expanding statistical models to capture these nuances of ARU data would allow for improved inferences about occupancy and relative activity. 2. Motivated by bat acoustic surveys, we developed a model to analyse counts of call recordings from multiple species simultaneously while accounting for species classification errors. Our model expands on previously developed false positive occupancy models to better describe acoustic data. We used simulations to compare our model to other false positive occupancy models for an example scenario with ARU data from two species. We also analyse acoustic data for eight bat species in Montana using our model. 3. In simulations, single-species models resulted in biased estimates of occupancy and relative activity because they failed to associate false positives with the presence of the second species. Models analysing binary observations ignored available information on relative activity and led to less precise estimates. Applying our model to bat acoustic data from Montana allowed for species-specific estimates of occupancy and relative activity. This analysis illustrates the flexibility in our model framework while also highlighting the assumptions and data requirements for implementation. Specifically, additional information on the species classification probabilities is needed and we discuss considerations for reliably estimating these parameters. 4. Directly modelling the species classification probabilities allows for improved ecological inferences for both occupancy and relative activity using community ARU data. Our statistical framework helps address the challenges posed by acoustic data, allowing ecologists to better utilize this technology to monitor wildlife communities.

opencc-zeroDec 2013View details →

Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing

The development and screening of microsatellite markers have been accelerated by next-generation sequencing (NGS) technology and in particular GS-FLX pyro-sequencing (454). More recent platforms such as the PGM semiconductor sequencer (Ion Torrent) offer potential benefits such as dramatic reductions in cost, but to date have not been well utilized. Here, we critically compare the advantages and disadvantages of microsatellite development using PGM semiconductor sequencing and GS-FLX pyro-sequencing for two gymnosperm (a conifer and a cycad) and one angiosperm species. We show that these NGS platforms differ in the quantity of returned sequence data, unique microsatellite data and primer design opportunities, mostly consistent with the differences in read length. The strength of the PGM lies in the large amount of data generated at a comparatively lower cost and time. The strength of GS-FLX lies in the return of longer average length sequences and therefore greater flexibility in producing markers with variable product length, due to longer flanking regions, which is ideal for capillary multiplexing. These differences need to be considered when choosing a NGS method for microsatellite discovery. However, the ongoing improvement in read lengths of the NGS platforms will reduce the disadvantage of the current short read lengths, particularly for the PGM platform, allowing greater flexibility in primer design coupled with the power of a larger number of sequences.

opencc-zeroDec 2016View details →

Data from: Nest survival modeling using a multi-species approach in forests managed for timber and biofuel feedstock

1. Switchgrass (Panicum virgatum) intercropping is a novel forest management practice for biomass production intended to generate cellulosic feedstocks within intensively managed loblolly pine-dominated landscapes. These pine plantations are important for early-successional bird species, as short rotation times continually maintain early successional habitat. We tested the efficacy of using community models compared to individual surrogate species models in understanding influences on nest survival. We analysed nest data to test for differences in habitat use for 14 bird species in plots managed for switchgrass intercropping and controls within loblolly pine (Pinus taeda) plantations in Mississippi, USA. 2. We adapted hierarchical models using hyper-parameters to incorporate information from both common and rare species to understand community-level nest survival. This approach incorporates rare species that are often discarded due to low sample sizes, but can inform community-level demographic parameter estimates. We illustrate use of this approach in generating both species-level and community-wide estimates of daily survival rates for songbird nests. We were able to include rare species with low sample size (minimum n = 5) to inform a hyper-prior, allowing us to estimate effects of covariates on daily survival at the community level, then compare this with a single-species approach using surrogate species. Using single species models, we were unable to generate estimates below a sample size of 21 nests per species. 3. Community model species-level survival and parameter estimates were similar to those generated by five single species models, with improved precision in community model parameters. 4. Covariates of nest placement indicated that switchgrass at the nest site (< 4 m) reduced daily nest survival, although intercropping at the forest stand level increased daily nest survival. 5. Synthesis and applications. Community models represent a viable method for estimating community nest survival rates and effects of covariates while incorporating limited data for rarely detected species. Intercropping switchgrass in loblolly pine plantations slightly increased daily nest survival at the research plot scale (0.1 km2), although at a local scale (50 m2) switchgrass negatively influenced nest survival. A likely explanation supported by previous research is intercropping shifted community composition, favouring species with greater disturbance tolerance.

opencc-zeroDec 2013View details →

Data from: Landscape connectivity for wildlife: development and validation of multi-species linkage maps

The ability to identify regions of high functional connectivity for multiple wildlife species is of conservation interest with respect to forest management and corridor planning. We present a method that does not require independent, field-collected data, is insensitive to the placement of source and destination sites (nodes) for modeling connectivity, and does not require the selection of a focal species. In the first step of our approach, we created a cost surface that represented permeability of the landscape to movement for a suite of species. We randomly selected nodes around the perimeter of the buffered study area and used circuit theory to connect pairs of nodes. When the buffer was removed, the resulting current density map represented, for each grid cell, the probability of use by moving animals. We found that using nodes that were randomly located around the perimeter of the buffered study area was less biased by node placement than randomly selecting nodes within the study area. We also found that a buffer of ≥ 20% of the study area width was sufficient to remove the effects of node placement on current density. We tested our method by creating a map of connectivity in the Algonquin to Adirondack region in eastern North America, and we validated the map with independently collected data. We found that amphibians and reptiles were more likely to cross roads in areas of high current density, and fishers (Pekania [Martes] pennanti) used areas with high current density within their home ranges. Our approach provides an efficient and cost-effective method of predicting areas with relatively high functional connectivity.

opencc-zeroDec 2017View details →

Data from: What have been and what can be delimited as species using molecular data under the multi-species coalescent model? A case study using Hercules beetles (Dynastes; Dynastidae)

Molecular species delimitation using the multi-species coalescent model has become common for statistically and objectively determining species limits. Empirical examples of how consistently different molecular data sets delimit the same level of divergence as species using coalescent-based methods are still lacking. I applied the method of molecular species delimitation in the Bayesian Phylogenetics and Phylogeography (BPP) program to study species delimitation in the divergence between populations and between putative species across four species of Hercules beetles. The quantity and variability of the molecular data affected species delimitation. A divergence that represented a late stage along the speciation continuum, e.g. between sympatric biological species, could be delimited by BPP by fewer and less variable loci than a recent divergence, e.g. between geographic populations. My results further indicated that the use of genomic data could even over-split geographically continuously distributed populations into species. I compared my results with those from other empirical studies and argue for the need of a thorough review of the kind of evolutionary entities, e.g. geographic populations versus morphologically distinct taxa, that have been designated as species and whether such designations are consistent among studies.

opencc-zeroDec 2017View details →

Data from: Discovery of a multi-species shark aggregation and parturition area in the Ba Estuary, Fiji Islands

Population declines in shark species have been reported on local and global scales, with overfishing, habitat destruction and climate change posing severe threats. The lack of species-specific baseline data on ecology and distribution of many sharks, however, makes conservation measures challenging. Here we present a fisheries-independent shark survey from the Fiji Islands, where scientific knowledge on locally occurring elasmobranchs is largely still lacking despite the location's role as a shark hotspot in the Pacific. Juvenile shark abundance in the fishing grounds of the Ba Estuary (north-western Viti Levu) was assessed with a gillnet- and longline-based survey from December 2015 to April 2016. A total of 103 juvenile sharks identified as blacktip Carcharhinus limbatus (n = 57), scalloped hammerhead Sphyrna lewini (n = 35), and great hammerhead Sphyrna mokarran (n = 11) sharks were captured, tagged, and released. The condition of umbilical scars (68 % open or semi-healed), mean sizes of individuals (± SD) (C. limbatus: 66.5 ± 3.8 cm, S. lewini: 51.8 ± 4.8 cm, S. mokarran 77.4 ± 2.8 cm), and the presence of these species over recent years (based on fishermen interviews), suggest that the Ba Estuary area is a critical habitat for multiple species that are classified as "Near Threatened" or "Endangered". Specifically, the area likely acts as a parturition ground over the studied period, and potentially as a subsequent nursery area. We identified subareas of high abundance and found that temperature, salinity and depth acted as small-scale environmental drivers of shark abundance. The data suggests a tendency for species-specific spatial use, both horizontally (i.e. between sampling areas) and vertically (i.e. across the water column). These results enhance the understanding of shark ecology in Fiji and provide a scientific basis for the implementation of local conservation strategies that contribute to the protection of these threatened species.

opencc-zeroMar 2022View details →

Data from: Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography

This dataset contains GPS coordinates of occurrences from 22 species from Sulawesi, Indonesia. It was used in the manuscript "Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography" to demonstrate the utility of the fauxcurrence R package (<a href="https://github.com/ogosborne/fauxcurrence">https://github.com/ogosborne/fauxcurrence)</a>.

opencc-by-4.0Jul 2024View details →

A multi-species benchmark for training and validating large scale mass spectrometry proteomics machine learning models

This is a de novo sequencing benchmark dataset derived from nine publicly available mass spectrometry datasets. There are two versions of the benchmark: main and balanced. The balanced version randomly eliminates some spectra associated with some species in order to create a smaller, more evenly balanced dataset. Also provided are two zip files containing the raw data as well as intermediate results. Details about how the benchmark was created are provided in an <a href="../records/13653420">associated zenodo release</a>, which contains the source code as well as a manuscript describing the benchmark. This release fixes a bug that incorrectly detected shared peptides between different species. It also includes the annotated spectra in mzSpecLib format.

opencc-zeroOct 2021View details →

Reproductive effort and terminal investment in a multi-species assemblage of Amazon electric fish

The terminal investment hypothesis (TIH) predicts that individuals with favorable prospects for future reproduction (i.e., high residual reproductive value, RRV) should moderate current reproductive investment in favor of growth, survival, and future reproduction, whereas those with low RRV should 'terminally invest' by diverting somatic resources towards current reproduction at the expense of future reproduction. However, support for the TIH in wild animal populations is fragmentary, and the ecological contexts of terminal investment remain poorly known. We report a remarkable case of simultaneous terminal investment involving five sympatric species of the electric knifefish genus Brachyhypopomus, from Amazonian floodplain and terra firme stream habitats. We found that terminal investment is synchronized by seasonal breeding, in response to circannual environmental variation in mortality risk. Four species exhibit a uniseasonal iteroparous (annual) life history with complete post-reproductive mortality after a single breeding season. One species (B. beebei) exhibits a two-year multiseasonal iteroparous life history with breeding in two seasons and post-reproductive mortality after the second. In mature females and (most) males of the annual species, as well as in both mature female and male second-year (but not first-year) B. beebei, we documented an increase in two metrics of reproductive effort (size-adjusted gonad mass and electric signal amplitude) and a concomitant reduction in somatic condition (size-adjusted somatic mass) – all in response to proximity to the end of the common breeding season, when RRV approximates zero. In mature first-year B. beebei, we documented neither an increase in reproductive effort nor a decline in somatic condition, implying an alternative strategy of reproductive restraint. Our findings support Kirkwood's disposable soma theory, which posits that death by reproductive exhaustion can be delayed if terminal investment is replaced by reproductive restraint, allowing individuals to survive and breed in a subsequent season. Deferral of the terminal investment response in annual species, and the origin of a gonadal regression-regeneration sequence, may open pathways for rapid evolutionary transitions to multiseasonal iteroparity. Excepting the age (year-group) dependency of terminal investment in B. beebei, we were unable to identify intrinsic cues or extrinsic environmental cues for the terminal investment response in Brachyhypopomus.

FIGURE 5 in A revision of Gerrhopilus inornatus (Squamata: Gerrhopilidae) reveals a multi-species complex

FIGURE 5. Dorsal and lateral views of heads for members of the Gerrhopilus inornatus Group having 22 midbody scale rows and venters marked with yellow. A, B holotype of Gerrhopilus wallachi (MCZ 140724); C, D holotype of Gerrhopilus flavinotatus (MCZ 175100); E, F holotype of Gerrhopilus lorealis (BPBM 2272).

FIGURE 4 in A revision of Gerrhopilus inornatus (Squamata: Gerrhopilidae) reveals a multi-species complex

FIGURE 4. Dorsal and lateral views of heads for members of the Gerrhopilus inornatus Group having 22 midbody scale rows and uniformly dark venters. A, B holotype of Gerrhopilus papuanorum (BPBM 17236); C, D holotype of Gerrhopilus polyadenus (BMNH 1901.11.27.10).

FIGURE 3 in A revision of Gerrhopilus inornatus (Squamata: Gerrhopilidae) reveals a multi-species complex

FIGURE 3. Habitats for members of the Gerrhopilus inornatus Group. A Forest at Varirata National Park, very near the type locality of G. inornatus (photo M. O'Shea); B the hills around Bunisi and Siyomu from which G. papuanorum was collected (photo F. Kraus).

FIGURE 2 in A revision of Gerrhopilus inornatus (Squamata: Gerrhopilidae) reveals a multi-species complex

FIGURE 2. Map of southern Papua New Guinea showing collecting localities for Gerrhopilus inornatus (star), G. flavinotatus (diamond), G. lorealis (hexagon), G. papuanorum (square), G. polyadenus (open circles), G. slapcinskyi (filled circle), and G. wallachi (triangle).