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opencc-zeroMay 2022View details →

Asymmetric density-dependent competition does not contribute to the maintenance of sex in a mixed population of sexual and asexual Potamopyrgus antipodarum

Asexual reproduction is expected to have a two-fold reproductive advantage over sexual reproduction, owing to the cost of producing males in sexual subpopulations. The persistence of sexual females thus requires an advantage to sexual reproduction, at least periodically. Here we tested the hypothesis that asexual females are more sensitive to limited resources. Under this idea, fluctuations in the availability of resources (per capita) could periodically favor sexual females when resources become limited. We combined sexual and asexual freshwater snails (Potamopyrgus antipodarum) together in nylon mesh enclosures at three different densities in an outdoor mesocosm. After one month, we counted the brood size of fertile female snails. We found that fecundity declined significantly with increasing density. However, sexual females did not produce more offspring than asexual females at any of the experimental densities. Our results thus suggest that the cost of sexual reproduction in P. antipodarum is not ameliorated by periods of intense resource competition.

opencc-zeroMay 2022View details →

Effects of insularity on genetic diversity within and among natural populations

We conducted a review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together "insularity"). Using populations from within the same studies, we were able to control for between-study variation in methodology, as well as demographic and life histories. Contradictory to typical expectations, insularity had relatively minor effects on GD within and among population, which points to the more important roles of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen – particularly in systems (i.e. studies) where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non-insular populations of the same system – suggesting an important role for the "scope" of influences on GD. These conclusions were more robust for within - population GD than among - population GD, although a number of biases might underlie this difference. Overall, our findings indicate that population-level genetic assumptions need to be tested rather than assumed in nature, particularly for topics highly relevant to current conservation management practices.

opencc-by-4.0Mar 2022View details →

POPP Datasets : Datasets for handwriting recognition from French population census

POPP datasets This repository contains 3 datasets created within the POPP project (<a href="https://popp.hypotheses.org/#ancre2">Project for the Oceration of the Paris Population Census</a>) for the task of handwriting text recognition. These datasets have been published in <a href="https://hal.science/hal-03675614/">Recognition and information extraction in historical handwritten tables: toward understanding early 20th century Paris census at DAS 2022.</a> The 3 datasets are called “Generic dataset”, “Belleville”, and “Chaussée d’Antin” and contains lines made from the extracted rows of census tables from 1926. Each table in the Paris census contains 30 rows, thus each page in these datasets corresponds to 30 lines. The structure of each dataset is the following: <ul> <li>double-pages : images of the double pages</li> <li>pages: <ul> <li>images: images of the pages</li> <li>xml: METS and ALTO files of each page containing the coordinates of the bounding boxes of each line</li> </ul> </li> <li>lines: contains the labels in the file <code>labels.json</code> and the line images splitted into the folders train, valid and test. The double pages were scanned at a resolution of 200dpi and saved as PNG images with 256 gray levels. The line and page images are shared in the TIFF format, also with 256 gray levels.</li> </ul> Since the lines are extracted from table rows, we defined 4 special characters to describe the structure of the text: <ul> <li>¤ : indicates an empty cell</li> <li>/ : indicates the separation into columns</li> <li>? : indicates that the content of the cell following this symbol is written above the regular baseline</li> <li>! : indicates that the content of the cell following this symbol is written below the regular baseline</li> </ul> We provide a script <code>format_dataset.py</code> to define which special character you want to use in the ground-truth. The split for the Generic Dataset and Belleville have been made at the double-page level so that each writer only appears in one subset among train, evaluation and test. The following table summarizes the splits and the number of writers for each dataset: <table> <thead> <tr> <th>Dataset</th> <th>train - # of lines</th> <th>validation - # of lines</th> <th>test - # of lines</th> <th># of writers</th> </tr> </thead> <tbody> <tr> <td>Generic</td> <td>3840 (128 pages)</td> <td>480 (16 pages)</td> <td>480 (16 pages)</td> <td>80</td> </tr> <tr> <td>Belleville</td> <td>1140 (38 pages)</td> <td>150 (5 pages)</td> <td>180 (6 pages)</td> <td>1</td> </tr> <tr> <td>Chaussée d’Antin</td> <td>625</td> <td>78</td> <td>77</td> <td>10</td> </tr> </tbody> </table>   Generic dataset (or POPP dataset) <ul> <li>This dataset is made 4800 annotated lines extracted from 80 double pages of the 1926 Paris census.</li> <li>There is one double page for each of the 80 districts of Paris</li> <li>There is one writer per double page so the dataset contains 80 different writers.</li> </ul>   Belleville dataset This dataset is a mono-writer dataset made of 1470 lines (49 pages) from the Belleville district census of 1926.   Chaussée d’Antin dataset This dataset is a multi-writer dataset made of 780 lines (26 pages) from the Chaussée d’Antin district census of 1926 and written by 10 different writers.   Error reporting It is possible that errors persist in the ground truth, so any suggestions for correction are welcome. To do so, please make a merge request on the <a href="https://github.com/Shulk97/POPP-datasets">Github repository</a> and include the correction in both the labels.json file and in the XML file concerned.   Citation Request If you publish material based on this database, we request you to include a reference to paper <a href="http://link.springer.com/chapter/10.1007/978-3-031-06555-2_10"><code>T. Constum, N. Kempf, T. Paquet, P. Tranouez, C. Chatelain, S. Brée, and F. Merveille,Recognition and information extraction in historical handwritten tables: toward understanding early 20th century Paris census ,Document Analysis Systems (DAS), pp. 143- 157, La Rochelle, 2022.</code></a>

opencc-zeroMay 2022View details →

Introduced populations of ragweed show as much evolutionary potential as native populations

Invasive species are a global economic and ecological problem. They also offer an opportunity to understand evolutionary processes in a colonizing context. The impacts of evolutionary factors, such as genetic variation, on the invasion process are increasingly appreciated, but there remain gaps in the empirical literature. The adaptive potential of populations can be quantified using genetic variance–covariance matrices (G), which encapsulate the heritable genetic variance in a population. Here, we use a multivariate Bayesian approach to assess the adaptive potential of invasive populations of ragweed (Ambrosia artemisiifolia), a serious allergen and agricultural weed. We compared several aspects of genetic architecture and the structure of G matrices between three native and three introduced populations, based on phenotypic data collected in a field common garden experiment. We found moderate differences in the quantitative genetic architecture among populations, but we did not find that introduced populations suffer from a limited adaptive potential or increased genetic constraint compared with native populations. Ragweed has an annual life history, is an obligate outcrosser, and produces very large numbers of seeds and pollen grains. These characteristics, combined with the significant additive genetic variance documented here, suggest ragweed will be able to respond quickly to selection pressures in both its native and introduced ranges.

Population connectivity and genetic offset in the spawning coral Acropora digitifera in Western Australia

Anthropogenic climate change has caused widespread loss of species biodiversity and ecosystem productivity across the globe, particularly on tropical coral reefs. Predicting the future vulnerability of reef-building corals, the foundation species of coral reef ecosystems, is crucial for cost-effective conservation planning in the Anthropocene. In this study, we combine regional population genetic connectivity and seascape analyses to explore patterns of genetic offset (the mismatch of gene-environmental associations under future climate conditions) in Acropora digitifera across 12 degrees of latitude in Western Australia. Our data revealed a pattern of restricted gene flow and limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified a suite of loci strongly associated with the regional temperature variation. These loci helped forecasting future genetic offset in random forest and generalised dissimilarity models. These analyses predicted pronounced differences in the response of different reef systems in Western Australia to rising temperatures. Under the most optimistic future warming predictions (RCP 2.6), we observed a general pattern of increasing genetic offset with latitude. Under the most extreme climate scenario (RCP 8.5 in 2090-2100), coral populations at the Ningaloo World Heritage Area were predicted to experience a higher mismatch in genetic composition, compared to populations in the inshore Kimberley region. The study suggest complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing coral reef resilience into the future.

Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations

Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven Quercus canariensis and four Q. faginea rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.

Population genomics and sexual signals identify reproductive interference in Uperoleia

When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favor traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographic history of species interactions is often unknown. Landscape genomic data allows tests of geographic hypotheses about species origins and secondary contact through range expansion. We used landscape genomic data from single nucleotide polymorphisms (SNPs), mitochondrial sequence data, advertisement call data, and morphological data to investigate a species complex of toadlets (Uperoleia borealis, U. crassa, U. inundata) from northern Australia. Although the three species of frogs were morphologically indistinguishable in our analysis, we determined that U. crassa and U. inundata form a single species (synonymized here) based on an absence of genomic divergence. SNP data identified the phylogeographic origin of U. crassa as the Top End, with subsequent westward invasion into the range of U. borealis in the Kimberley. We identified six F1 hybrids, all of which had the U. borealis mitochondrial haplotype, suggesting unidirectional hybridization. Consistent with the RCD hypothesis, U. borealis and U. crassa sexual signals differ more in sympatry than in allopatry. Hybrid males have intermediate calls, which likely reduces attractiveness to females. Integrating landscape genomic data, mitochondrial sequencing, morphology, and behavioral approaches supplies us an unusually detailed collection of evidence for reproductive character displacement following range expansion and secondary contact.

Estimating the abundance of the critically endangered Baltic Proper harbour porpoise (Phocoena phocoena) population using passive acoustic monitoring

Knowing the abundance of a population is a crucial component to assess its conservation status and develop effective conservation plans. For most cetaceans, abundance estimation is difficult given their cryptic and mobile nature, especially when the population is small and has a transnational distribution. In the Baltic Sea, the number of harbour porpoises (Phocoena phocoena) has collapsed since the mid-20th century and the Baltic Proper harbour porpoise is listed as Critically Endangered by the IUCN and HELCOM; however, its abundance remains unknown. Here, one of the largest ever passive acoustic monitoring studies was carried out by eight Baltic Sea nations to estimate the abundance of the Baltic Proper harbour porpoise for the first time. By logging porpoise echolocation signals at 298 stations during May 2011-April 2013, calibrating the loggers' spatial detection performance at sea, and measuring the click rate of tagged individuals, we estimated an abundance of 71-1,105 individuals (95% CI, point estimate 491) during May-October within the population's proposed management border. The small abundance estimate strongly supports that the Baltic Proper harbour porpoise is facing an extremely high risk of extinction, and highlights the need for immediate and efficient conservation actions through international cooperation. It also provides a starting point in monitoring the trend of the population abundance to evaluate the effectiveness of management measures and determine its interactions with the larger neighbouring Belt Sea population. Further, we offer evidence that design-based passive acoustic monitoring can generate reliable estimates of the abundance of rare and cryptic animal populations across large spatial scales.

opencc-by-4.0May 2022View details →

Crater Populations on the Walls of Complex Craters found near the Lunar Southern Pole

Date: June 23, 2022 Authors: C. L. Talkington and P. E. Montalvo Notes: Data sets contain crater counts on floors of 16 lunar south polar complex craters and surface slopes at all counted craters.  Data sets in crater_data.xlsx are updated from the previous version to improve the model age calculation. The current version uses an approach using Poisson’s statistics (Michael and Neukum, 2010; Michael et al., 2016). ArcMap 10.7.1 was used in addition to the CraterTools Add in toolset (Kniessl et al., 2011) and DEM data from the PDS Geosciences Node (https://pds-geosciences.wustl.edu/lro/lro-l-lola-3-rdr-v1/lrolol_1xxx/data/lola_gdr/polar/jp2/) to visualize the craters.Complex craters were selected from previous studies (Cannon et al., 2020; Deutsch et al., 2020; Tye et al., 2015) as regions of interest. The counts from this work span the walls of 16 complex craters found near the lunar southern pole, while those cited refer to the floor regions (Cannon et al., 2020; Deutsch et al., 2020), or the entire crater (Tye et al., 2015). Craters were included within the analysis from definitions described by Deutsch et al., (2020) as circular features with central depressions. We considered primary craters only, and those with morphologies reflecting secondary crater populations (crater chains or clusters) were omitted. Crater sizes range from sub km range to 35 km in diameter. Their slope conditions range from very shallow to very steep.  PDS Geoscience Node DEM used ldem_80s_20m. This DEM has a resolution of 20 m/pixel and was updated 6/2/2017. Data format, .csv files: -    Column A: Diameter. Crater diameter [km] -    Column B: Slope angle of crater [deg] determined by the 500 m buffer size from the determined crater radius.

opencc-by-4.0Sep 2021View details →

Data associated with the manuscript "Simple statistical models can be sufficient for testing hypotheses with population time series data"

This is a revised version of the archive of R code and data used in the manuscript, Simple statistical models can be sufficient for testing hypotheses with population time series data. The data are in three files. etodata1.csv and etodata2.csv contain two versions of the same data for shoal-dwelling fishes in the Etowah River and associated environmental covariates. knz_dat contains data for small mammals collected in the Konza Prairie Biological Station and associated environmental covariates. The R code consists of four primary files that call nine auxiliary files. CaseStudy1-main_code and CaseStudy2-main_code are the primary files for running the two case studies. Simulations1 and Simulations2 are the files for running the two batteries of simulations. We thank the Konza Prairie Biological Station and Konza Prairie Long-Term Ecological Research Program supported by the National Science Foundation (DEB-1440484) for collecting and providing access to mammal community data. More details are in the manuscript and supporting information.

opencc-by-4.0Jun 2022View details →

Population of European Countries

Population of European Countries on the first day of the year. This indicator is a reduced and interpreted verison of the Eurostat [<a href="https://appsso.eurostat.ec.europa.eu/nui/show.do?dataset=demo_pjan&lang=en">demo_pjan</a>] data asset.  It contains the total population for both sexes. Missing values, for example, in Kosovo, are estimated with linear interpolation.  Not yet know values are forecasted.

opencc-zeroDec 2016View details →

Data from: Homogenization of populations in the wildflower Texas bluebonnet (Lupinus texensis)

Wildflowers seeds are routinely spread along highways and thoroughfares throughout North America as part of federal beautification policy, but the genetic effect of the introduction of these cultivated populations on wild populations of the same species is unknown. Interbreeding may occur between these seeded and wild populations, resulting in several possible outcomes. Here we sample 187 individuals in 12 matched pairs of neighboring wild and seeded populations of the Texas bluebonnet (Lupinus texensis), a species popular in commercially available wildflower seed mixes used by both the Texas Department of Transportation and the public. We use genotyping by sequencing to identify 11,741 genome-wide single nucleotide polymorphisms, as well as a smaller number of SNPs from the chloroplast genome, to analyze population structure and genetic diversity within and between the populations. We find a striking lack of population structure both between wild and seeded populations and amongst wild populations. STRUCTURE analyses indicate that all populations are apparently panmictic. This pattern may be explained by extensive swamping of wild populations by seeded germplasm and increased dispersal of semi-domesticated seed across this species' core native range by humans. We discuss the possible negative and positive ramifications of homogenization on the evolutionary future of this popular wildflower species.

Code: A model of wild bee populations accounting for spatial heterogeneity and climate induced temporal variability of food resources at the landscape level

The viability of wild bee populations and the pollination services that they provide are driven by the availability of food resources during their activity period and within the surroundings of their nesting sites. Changes in climate and land use influence the availability of these resources and are major threats to declining bee populations. Because wild bees may be vulnerable to interactions between these threats, spatially explicit models of population dynamics that capture how bee populations jointly respond to land use at a landscape scale and weather are needed. Here, we developed a spatially and temporally explicit theoretical model of wild bee populations aiming for a middle ground between the existing mapping of visitation rates using foraging equations and more refined agent-based modelling. The model is developed for Bombus sp. and captures within-season colony dynamics. The model describes mechanistically foraging at the colony level and temporal population dynamics for an average colony at the landscape level. Stages in population dynamics are temperature-dependent triggered with a theoretical generalized seasonal progression, which can be informed by growing degree days (GDD). The purpose of the LandscapePhenoBee model is to evaluate the impact of systematic changes and within-season variability in resources on bee population sizes and crop visitation rates. In a simulation study, we used the model to evaluate the impact of the shortage of food resources in the landscape arising from extreme drought events in different types of landscapes (ranging from different proportions of semi-natural habitats and early and late flowering crops) on bumblebee populations.

Otolith annual growth increments for cod populations in the Northeast Atlantic

Large-scale, climate-induced synchrony in the productivity of fish populations is becoming more pronounced in the world's oceans. As synchrony increases, a population's 'portfolio' of responses can be diminished, in turn reducing its resilience to strong perturbation. Here we argue that the costs and benefits of trait synchronization, such as the expression of growth rate are context dependent. Synchrony among individuals could actually be beneficial for populations if growth is optimized during favourable conditions and then declines under poor conditions when a broader portfolio of responses is needed. Importantly, growth synchrony among individuals within populations has seldom been measured, despite well-documented evidence of synchrony across populations. Here, we used century-scale time series of annual otolith growth to test for changes in growth synchronization among individuals within multiple populations of a marine keystone species (Atlantic cod, Gadus morhua). On the basis of 74,662 annual growth increments recorded in 13,749 otoliths, we detected a rising conformity in long-term growth rates within northeast Atlantic cod populations in response to both favorable growth conditions and a large-scale, multidecadal mode of climate variability similar to the East Atlantic Pattern. The within-population synchrony was distinct from the across-population synchrony commonly reported for large-scale environmental drivers. Climate-linked, among-individual growth synchrony was also identified in other Northeast Atlantic pelagic, deep-sea and bivalve species. We hypothesize that growth synchrony buffers marine populations to changing climate and growth conditions through its effect on the phenotypic expression of growth diversity, and thus provides an unexpected, but pervasive and stabilizing impact on marine population productivity.

opencc-by-4.0Jan 2022View details →

Data from: A new population record of Critically Endangered Dipterocarpus bourdillonii Brandis from the Anamalai Tiger Reserve, Tamil Nadu

This dataset is based on the following manuscript/publication: Page, N., S. Kasinathan, K. Bhat, G. Moorthi, T. Sundarraj, Divya Mudappa, and T. R. S. Raman (2022). A new population record of Critically Endangered Dipterocarpus bourdillonii Brandis from the Anamalai Tiger Reserve, Tamil Nadu. Journal of Threatened Taxa 14(8): 21651–21659. https://doi.org/10.11609/jott.7860.14.8.21651-21659 Please refer to the README.txt file included with the dataset for complete details and usage notes. Geographic Coverage: Location/Study Area: Valparai Plateau, Tamil Nadu, India; Anamalai Tiger Reserve, Tamil Nadu, India GPS coordinates: Valparai Plateau (0°15'- 10°22'N, 76°52'-76°59'E); Anamalai Tiger Reserve (10°12'-10°35'N, 76°49'-77°24'E) Temporal Coverage: Begins: 2020-10-01 (Year, Month, Day) Ends: 2022-05-31 (Year, Month, Day) Funding: Fondation Franklinia AMM Murugappa Chettiar Research Centre Rohini Nilekani Philanthropies Dataset: The dataset includes 7 files: 1 text file (README.txt), 5 data files in comma-delimited format (CSV), and 1 KML file of seven survey routes. Details of content of each CSV data file are provided below. The following files are included: README.txt: Usage notes and metadata related to the dataset 1_Surveys_ver2.csv: Details of trails covered where Dipterocarpus bourdillonii was recorded during the survey 2_Focal_tree_data_ver2.csv: Details of focal trees of Dipterocarpus bourdillonii 3_Tree_centred_PCQ_ver2.csv: Data from point-centred quarter (PCQ) plots sampled with focal trees at the centre 4_Plant_checklist_ver2.csv: Checklist of plants (mainly trees) recorded on survey trails 5_Seed_fruit_ver2.csv: Measurements of fruits and seeds of Dipterocarpus bourdillonii 06_Dipterocarpus_bourdillonii_survey_trails.kml: This file includes the GPS tracks of the seven survey trails in KML format. Details and data available in the columns in each of the above CSV files and the KML file are explained below. 1_Surveys_ver2.csv Column: Description Date: Date on which the survey was done Place: Name of the place where the focal tree is located. e.g., Candura, Manamboli, Iyerpadi etc Route_description:Description of place or route covered Trail: Name of the tree survey trail Trail_distance: Distance covered on the trail in kilometres (km) Track_filename_kml: Name of the file with GPS track of survey trail/route, where available, in KML format Observers: Names of observers who took measurements and filled datasheet during survey Remarks: Notes and additional information 2_Focal_tree_data_ver2.csv Column: Description FT_ID: Unique numeric linking ID of each focal tree (NA for 3 individuals found in plots around other focal trees) Species: Focal tree species Date: Date on which the survey was done Place: Name of forest range (Manamboli) Waypoint: Unique location waypoint number for the focal tree and GPS instrument used Time: Time when the focal tree's data was collected Location: Landmark where the focal tree is located (NA, if not available) Latitude: Latitude of the focal tree (decimal degrees N) Longitude: Longitude of the focal tree (decimal degrees E) Elevation: Elevation of the focal tree from sea-level in metres Slope: Slope at focal tree location assessed with Clinometer, categorised as Flat, Gentle, Moderate, or Steep (NA, if not available) ID_Notes: Any obvious signs with which to identify focal tree (NA, if not available) Phenophase: Phenophase of the focal tree viz. leaf flush, buds/flowers, fruits (NA, if not available) GBH: Girth of the focal tree in cm, at 1.3m from ground; measured from the higher side if tree is on slope Tree_ht: Focal tree's height in m (NA, if not available) Canopy_ht: Height of canopy in m where the focal tree is located (NA, if not available) Substrate: Substrate where focal tree is standing viz. Earth, Rock, Streamside, Other (NA, if not available) Invasives: List of invasive plant species present within 5 m radius around the focal tree (NA, if not available) Stature: Stature of the focal tree relative to its surroundings (NOT of the species in general) categorised as Understorey, Mid, Canopy, Emergent (NA, if not available) Relatively: Relative height of focal tree in relation to other trees within 10 m radius categorised as Shorter than most, Taller than most, Same height as most (NA, if not available) Deadwood: Estimated percentage of deadwood present on the tree in 4 classes of <25%, 26-50%, 51-75%, 76-100% (NA, if not available) Damage: Observed damages such as Main trunk broken, Branches broken, Hollow at base, Gaping cavity, Infected, Dried leaves (as on a dead branch) (NA, if not available) Shape: Canopy shape of the focal tree (not species in general) categorised as Spreading, Oval, Fan, Column, Cone (NA, if not available) Closure: Canopy closure due to foliage visually estimated standing next to trunk of focal tree and looking up, categorised as 0% (only sky and leafless branches visible), 1-25%, 26-50%, 51-75%, 76-100% (NA, if not available) Seedlings: Count of conspecific seedlings (stems of girth at breast height <10 cm) around the focal tree in a 5 m radius (NA, if not available) Saplings: Count of conspecific saplings (stems of girth at breast height 10-30 cm) around the focal tree in a 5 m radius (NA, if not available) Trees: Count of conspecific trees (stems of girth at breast height >30 cm) around the focal tree in a 5 m radius (NA, if not available) Remarks: Notes and additional information (NA, if not available) 3_Tree_centred_PCQ_ver2.csv Column: Description FT_ID: Unique numeric linking ID of each focal tree in point-centred quarter (PCQ) plot Focal_tree: Scientific name of focal tree species at the centre of the PCQ plot Species: Scientific name of tree species recorded in PCQ plot around focal tree GBH (cm): Girth of PCQ tree in cm, at 1.3 m from ground; measured from the higher side if tree is on a slope. Main stem only. Distance: Distance from focal tree, in m; measured from the approximate centre of bole to centre of bole and not bark to bark Multistem: NA if single-stemmed; if multi-stemmed, then GBH of additional stems given as notes. 4_Plant_checklist_ver2.csv Column: Description Date: Date on which the survey was done Place: Name of the place where the focal tree is located. e.g., Candura, Manamboli, Iyerpadi etc Route: Route of the tree survey trail Checklist_species: Scientific name of tree species observed as present along trail and within 10 m on either side Remarks: Notes and additional information 5_Seed_Fruit_ver2.csv Column: Description Sample: Serial number of sample of single winged fruit measured Species: Scientific name of tree species No_Seeds: Unit number of seed measured Fresh_fruit_weight_g: Weight of each fruit measured on an Ohaus scale in grams Nut_length_cm: Length of nut along the longitudinal axis in cm Nut_width_1_cm: Width of nut in cm measured along axis perpendicular to nut length Nut_width_2_cm: Width of nut in cm measured along axis perpendicular to nut length and nut width 1 Wing1_length_cm: Length of longer wing (sepal) in cm Wing1_width_cm: Width of longer wing (sepal) in cm Wing2_length_cm: Length of shorter wing (sepal) in cm Wing2_width_cm: Width of shorter wing (sepal) in cm 06_Dipterocarpus_bourdillonii_survey_trails.kml This file includes the GPS tracks of the following seven trails in KML format:    2021-01-30_Anali-Ayyankulam-Manamboli (Trail-2)    2021-03-26_Ayyankulam (Trail-4)    2021-04-10_Ayyankulam Parai (Trail-5)    2022-03-07_Ayyankulam Parai to Ayyankulam_leftbank (Trail-8)    2022-03-07_Ayyankulam Parai to Ayyankulam_rightbank (Trail-9)    2022-03-09_Manamboli PH_leftbank (Trail-10)    2022-03-09_Manamboli PH_rightbank (Trail-11)

Multi-surveyor capture-mark-recapture as a powerful tool for butterfly population monitoring in the pre-imaginal stage

For many elusive insect species, which are difficult to cover by standard monitoring schemes, innovative survey methods are needed to gain robust data on abundance and population trends. The recording of pre-imaginal butterfly life stages provides great potential for ecological studies and conservation monitoring. However, using counts of pre-imaginal stages for quantitative research requires detection probability to be determined. We tested different removal and capture-mark-recapture (CMR) approaches to determine the detection probability for overwintering larvae of the endangered nymphalid butterfly Limenitis reducta. Classical removal and CMR studies require movement of the organisms under study but in our approach, we replaced movement of the study organisms by random movement of multiple different surveyors. The study was conducted in three plots within a spruce clear-cut in the 'Alb-Donau' region, Germany. Our dataset provides detection data of nine/ten different surveyors per study plot. The surveyors differed in their experience ('experts' vs. 'novices'). In the R-scripts we present the analysis of the data using i) the removal method, ii) CMR approaches with varying personnel expenditure. In addition, we test the validity of our method by comparing observed and simulated detection frequencies. The results of our study indicate that multi-surveyor removal/CMR techniques are highly suitable for estimating abundance of overwintering L. reducta larvae and that the proposed methodology has several strengths: long survey period, estimates of the absolute population size accompanied by uncertainty measures, estimates of overwinter mortality. The methods from our study can be adapted and used for several different butterfly species, other insect taxa with specific immobile life-stages, and some sessile organisms, e.g. elusive plants, fungi, or corals.

opencc-by-4.0Jul 2022View details →

Code and Data associated with "Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations"

Code and data sufficient to reproduce analyses in "Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations".

opencc-by-4.0Jul 2022View details →

DATASET: Environmental analysis of servicing centralised and decentralised wastewater treatment for population living in neighbourhoods

DATASET: Article: Environmental analysis of servicing centralised and decentralised wastewater treatment for population living in neighbourhoods Journal of Water Process Engineering, Volume 37, October 2020, 101469 https://doi.org/10.1016/j.jwpe.2020.101469

Potential local adaptation in populations of invasive reed canary grass (Phalaris arundinacea) across an urbanization gradient

Urban stressors represent strong selective gradients that can elicit evolutionary change, especially in non-native species that may harbor substantial within-population variability. To test whether urban stressors drive phenotypic differentiation and influence local adaptation, we compared stress responses of populations of a ubiquitous invader, reed canary grass (Phalaris arundinacea). Specifically, we quantified responses to salt, copper, and zinc additions by reed canary grass collected from four populations spanning an urbanization gradient (natural, rural, moderate urban and intense urban). We measured ten phenotypic traits and trait plasticities, because reed canary grass is known to be highly plastic and because plasticity may enhance invasion success. We tested the following hypotheses: 1) source populations vary systematically in their stress response, with the intense urban population least sensitive and the natural population most sensitive, and 2) plastic responses are adaptive under stressful conditions. We found clear trait variation among populations, with the greatest divergence in traits and trait plasticities between the natural and intense urban populations. The intense urban population showed stress tolerator characteristics for resource acquisition traits including leaf dry matter content and specific root length. Trait plasticity varied among populations for over half the traits measured, highlighting that plasticity differences were as common as trait differences. Plasticity in root mass ratio and specific root length were adaptive in some contexts, suggesting that natural selection by anthropogenic stressors may have contributed to root trait differences. Reed canary grass populations in highly urbanized wetlands may therefore be evolving enhanced tolerance to urban stressors, suggesting a mechanism by which invasive species may proliferate across urban wetland systems generally.

Two-sex integrated population model reveals intersexual differences in life history strategies in Cooper's Hawks

This site contains data files and model code for a dynamic nesting territory occupance model and 2-sex integrated population model for Cooper's hawks in Albuquerque, New Mexico, USA, 2011 - 2020.