Find research datasets worth reusing

opencc-by-4.0Apr 2022View details →

Fish habitat associations in shoal habitats and implications for climate change effects on species conservation

The dataset and examples of R script used in our analysis.

opencc-by-4.0May 2022View details →

Aphid conservation biological control in arable crops via flower strips: the predominant role of plant resources over diversity effects

Dataset and R code

opencc-by-4.0Nov 2016View details →

Supplementary material 1 from: Hermes C, Döpper A, Schaefer MH, Segelbacher G (2016) Effects of forest fragmentation on the morphological and genetic structure of a dispersal-limited, endangered bird species. Nature Conservation 16: 39-58. https://doi.org/10.3897/natureconservation.16.10905

Development of species-specific microsatellite primers : Explanation note: The supplementary material contains a detailed description of the development of a set of 10 microsatellite primers for the Ecuadorian Tapaculo, including primer sequences and gene bank accession numbers.

opengpl-2.0Aug 2017View details →

Environmental and geographic variables are effective surrogates for genetic variation in conservation planning

Environmental and geographic variables are effective surrogates for genetic variation in conservation planning Jeffrey O. Hanson, Jonathan R. Rhodes, Cynthia Riginos, Richard A. Fuller. Correspondence should be addressed to jeffrey.hanson@uqconnect.edu.au. Research summary Protected areas buffer species from anthropogenic threats and provide places for the processes that generate and maintain biodiversity to continue. However, genetic variation, the raw material for evolution, is difficult to capture in conservation planning, not least because genetic data require considerable resources to obtain and analyze. Here we show that freely available environmental and geographic distance variables can be highly effective surrogates in conservation planning for representing adaptive and neutral intra-specific genetic variation. We obtained occurrence and genetic data from the IntraBioDiv project for 27 plant species collected over the European Alps using a gridded sampling scheme. For each species, we identified loci that were potentially under selection using outlier loci methods, and mapped their main gradients of adaptive and neutral genetic variation across the grid cells. We then used the cells as planning units to prioritize protected area acquisitions. First, we verified that the spatial patterns of environmental and geographic variation were correlated, respectively, with adaptive and neutral genetic variation. Second, we showed that these surrogates can predict the proportion of genetic variation secured in randomly generated solutions. Finally, we discovered that solutions based only on surrogate information secured substantial amounts of adaptive and neutral genetic variation. Our work paves the way for widespread integration of surrogates for genetic variation into conservation Overview This repository contains the data and source code that underpins the findings in our manuscript "Environmental and geographic variables are effective surrogates for genetic variation in conservation planning". To rerun all computational analyses, run `make clean && make all`. <ul> <li>article <ul> <li>manuscript main text, figures, and supporting information</li> </ul> </li> <li>code <ul> <li>R: scripts used to run the analysis</li> <li>parameters: files used to run analysis in TOML format</li> <li>rmarkdown: files used to compile them manuscript</li> </ul> </li> <li>data <ul> <li>raw: raw data used to run the analysis</li> <li>intermediate_ results generated during processing</li> <li>final: results used in the paper</li> </ul> </li> </ul> Software required <ul> <li>Operating system <ul> <li>Ubuntu (Trusty 14.04 LTS)</li> </ul> </li> <li>Programs <ul> <li>[R (version 3.3.2)](https://www.r-project.org)</li> <li>GNU make</li> <li>pandoc (version 1.16.0.2+)</li> <li>Gurobi (version 7.0.2; academic licenses are available for no cost)</li> <li>LaTeX</li> </ul> </li> </ul>

Supplementary material 4 from: Jones GM, Gutiérrez RJ, Kramer HA, Tempel DJ, Berigan William J, Whitmore Sheila A, Peery MZ (2019) Megafire effects on spotted owls: elucidation of a growing threat and a response to Hanson et al. (2018). Nature Conservation 37: 31-51. https://doi.org/10.3897/natureconservation.37.32741

: Data type: Representative photographs of two spotted owl nest areas burned at high fire severity during the King Fire (2014) and three general areas within the Eldorado Study Area in the central Sierra Nevada, California, USA that depict three general fire severity classes of this fire.

Supplementary material 2 from: Jones GM, Gutiérrez RJ, Kramer HA, Tempel DJ, Berigan William J, Whitmore Sheila A, Peery MZ (2019) Megafire effects on spotted owls: elucidation of a growing threat and a response to Hanson et al. (2018). Nature Conservation 37: 31-51. https://doi.org/10.3897/natureconservation.37.32741

Supplementary material 6 from: Jones GM, Gutiérrez RJ, Kramer HA, Tempel DJ, Berigan William J, Whitmore Sheila A, Peery MZ (2019) Megafire effects on spotted owls: elucidation of a growing threat and a response to Hanson et al. (2018). Nature Conservation 37: 31-51. https://doi.org/10.3897/natureconservation.37.32741

Supplementary material 3 from: Jones GM, Gutiérrez RJ, Kramer HA, Tempel DJ, Berigan William J, Whitmore Sheila A, Peery MZ (2019) Megafire effects on spotted owls: elucidation of a growing threat and a response to Hanson et al. (2018). Nature Conservation 37: 31-51. https://doi.org/10.3897/natureconservation.37.32741

Supplementary material 1 from: Jones GM, Gutiérrez RJ, Kramer HA, Tempel DJ, Berigan William J, Whitmore Sheila A, Peery MZ (2019) Megafire effects on spotted owls: elucidation of a growing threat and a response to Hanson et al. (2018). Nature Conservation 37: 31-51. https://doi.org/10.3897/natureconservation.37.32741

Supplementary material 5 from: Jones GM, Gutiérrez RJ, Kramer HA, Tempel DJ, Berigan William J, Whitmore Sheila A, Peery MZ (2019) Megafire effects on spotted owls: elucidation of a growing threat and a response to Hanson et al. (2018). Nature Conservation 37: 31-51. https://doi.org/10.3897/natureconservation.37.32741

opennotspecifiedJul 2020View details →

FIG. 2 in Density-Dependent Fitness Attributes and Carry-Over Effects in Crawfish Frogs (Rana areolata), a Species of Conservation Concern

FIG. 2. Field data showing effects of juvenile density on juvenile body size (A, C) and time to metamorphosis (E), and breeding adult size (B, D) and survivorship (F). Lines reflect regression calculations. While suggestive, none of these trends is significant except for the adult SVL data shown in B.

dryad32/100

Data from: Consequences for conservation: population density and genetic effects on reproduction of an endangered lagomorph

Understanding reproduction and mating systems is important for managers tasked with conserving vulnerable species. Genetic tools allow biologists to investigate reproduction and mating systems with high resolution and are particularly useful for species that are otherwise difficult to study in their natural environments. We conducted parentage analyses using 19 nuclear DNA microsatellite loci to assess the influence of population density, genetic diversity, and ancestry on reproduction, and to examine the mating system of pygmy rabbits (Brachylagus idahoensis) bred in large naturalized enclosures for the reintroduction and recovery of the endangered distinct population in central Washington, USA. Reproductive output for females and males decreased as population density and individual homozygosity increased. We identified an interaction indicating that male reproductive output decreased as genetic diversity declined at high population densities, but there was no effect at low densities. Males with high amounts (>50%) of Washington ancestry had higher reproductive output than the other ancestry groups, while reproductive output was decreased for males with high northern Utah/Wyoming ancestry and females with high Oregon/Nevada ancestry. Females and males bred with an average of 3.8 and 3.6 mates per year, respectively, and we found no evidence of positive or negative assortative mating with regards to ancestry. Multiple paternity was confirmed in 81% of litters, and we report the first documented cases of juvenile breeding by pygmy rabbits. This study demonstrates how variation in population density, genetic diversity, and ancestry impact fitness for an endangered species being bred for conservation. Our results advance understanding of basic life history characteristics for a cryptic species that is difficult to study in the wild, and provide lessons for managing populations of vulnerable species in captive and free-ranging populations.

opencc-zeroDec 2014View details →

FIGURES 37–39 in Three new species of Collembola (Arthropoda: Hexapoda) from Central Brazilian shallow caves: side effects of long term application of environmental law on conservation

FIGURES 37–39. Pseudosinella guanhaensis sp.nov.; 37, Abd IV chaetotaxy, left side; 38, tibiotarsi I; 39 empodial complex leg III.

FIGURES 30–34 in Three new species of Collembola (Arthropoda: Hexapoda) from Central Brazilian shallow caves: side effects of long term application of environmental law on conservation

FIGURES 30–34. Pseudosinella guanhaensis sp.nov.; 30, Details of sense organ of Ant. III with two type c, three type e and one type h sensilla, and surrounded by macrochaetae; 31, Details of sensilla at the ventro-lateral distal half Ant. II; 32, details of Ant. I dorso-laterally with 3 type h, 1 type i and 1 type a sensilla, and 2 h and 3 l; 33, ventro-lateral sensilla; 34, dorsal cephalic chaetotaxy.

FIGURES 35–36 in Three new species of Collembola (Arthropoda: Hexapoda) from Central Brazilian shallow caves: side effects of long term application of environmental law on conservation

FIGURES 35–36. Pseudosinella guanhaensis sp.nov.; 35, labial triangle chaetotaxy, left side; 36, trunk chaetotaxy, left side.

FIGURES 26–29 in Three new species of Collembola (Arthropoda: Hexapoda) from Central Brazilian shallow caves: side effects of long term application of environmental law on conservation

FIGURES 26–29. Pseudosinella guanhaensis sp.nov.; 26, antennal segment IV dorsal view, letters as in Fig. 17; 27, antennal segment III dorsal view, letter as in Fig. 17; 28, antennal segments I and II dorsal view, letters as in Fig. 17; 29, antennal segments I and II ventral view, letters as in Fig. 17.

FIGURES 21–25 in Three new species of Collembola (Arthropoda: Hexapoda) from Central Brazilian shallow caves: side effects of long term application of environmental law on conservation

FIGURES 21–25. Pseudosinella ambigua sp. nov.: 21, Abd IV dorsal chaetotaxy; 22, empodial complex leg III; 23, ventral tube anterior side (left); 24, Ventral tube posterior side (rigth); 25, mucro.

FIGURES 19–20 in Three new species of Collembola (Arthropoda: Hexapoda) from Central Brazilian shallow caves: side effects of long term application of environmental law on conservation

FIGURES 19–20. Pseudosinella ambigua sp. nov.: 19, labial triangle chaetotaxy, right side; 20, trunk chaetotaxy, right side.

FIGURES 11–12 in Three new species of Collembola (Arthropoda: Hexapoda) from Central Brazilian shallow caves: side effects of long term application of environmental law on conservation

FIGURES 11–12. Arrhopalites glabrofasciatus sp. nov.: 11, chaetotaxy of manubrium and dens; 12, mucro.

FIGURES 17–18 in Three new species of Collembola (Arthropoda: Hexapoda) from Central Brazilian shallow caves: side effects of long term application of environmental law on conservation

FIGURES 17–18. Pseudosinella ambigua sp. nov.: 17, antennal and body chaetae: a) subapical micro sense rod. b) sense type I. c) sense type II. d) sense type III. e) sense type IV. f) bristle-like. g) ciliated chaeta. h) microsensillum. i) micro sense organ. j) sense type V. l) sense type VI. m) fan-shaped chaeta type I. n) fan-shaped chaeta type II. o) micro or mesochaeta symbol. p) macrochaeta symbols. q) pseudopore symbols. r) bothriotrix. s) stout ciliated macrochaetae; 18, dorsal cephalic chaetotaxy.