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opencc-zeroDec 2018View details →

Data from: Population genetics reveals high connectivity of giant panda populations across human disturbance features in key nature reserve

The giant panda is an example of a species that has faced extensive historical habitat fragmentation and anthropogenic disturbance, and is assumed to be isolated in numerous subpopulations with limited gene flow between them. To investigate the population size, health and connectivity of pandas in a key habitat area, we noninvasively collected a total of 539 fresh wild giant panda fecal samples for DNA extraction within Wolong Nature Reserve, Sichuan, China. Seven validated tetra-microsatellite markers were used to analyze each sample, and a total of 142 unique genotypes were identified. Non-spatial and spatial capture-recapture models estimated the population size of the reserve at 164 and 137 individuals (95% confidence intervals 153-175 and 115-163), respectively. Relatively high levels of genetic variation and low levels of inbreeding were estimated, indicating adequate genetic diversity. Surprisingly, no significant genetic boundaries were found within the population despite the national road G350 that bisects the reserve, which is also bordered with patches of development and agricultural land. We attribute this to high rates of migration, with 4 giant panda road-crossing events confirmed within a year based on repeated captures of individuals. This likely means that giant panda populations within mountain ranges are better connected than previously thought. Increased development and tourism traffic in the area and throughout the current panda distribution poses a threat of increasing population isolation, however. Maintaining and restoring adequate habitat corridors for dispersal is thus a vital step for preserving the levels of gene flow seen in our analysis and the continued conservation of the giant panda meta-population in both Wolong and throughout their current range.

opencc-zeroJun 2019View details →

Data from: Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (Striga hermonthica)

Host-specific interactions can maintain genetic and phenotypic diversity in parasites that attack multiple host species. Host diversity, in turn, may promote parasite diversity by selection for genetic divergence or plastic responses to host type. The parasitic weed purple witchweed [Striga hermonthica (Delile) Benth.] causes devastating crop losses in sub-Saharan Africa and is capable of infesting a wide range of grass hosts. Despite some evidence for host adaptation and host-by-Striga genotype interactions, little is known about intraspecific Striga genomic diversity. Here we present a study of transcriptomic diversity in populations of S. hermonthica growing on different hosts (maize [Zea mays L.] vs. grain sorghum [Sorghum bicolor (L.) Moench]). We examined gene expression variation and differences in allelic frequency in expressed genes of aboveground tissues from populations in western Nigeria parasitizing each host. Despite low levels of host-based genome-wide differentiation, we identified a set of parasite transcripts specifically associated with each host. Parasite genes in several different functional categories implicated as important in host–parasite interactions differed in expression level and allele on different hosts, including genes involved in nutrient transport, defense and pathogenesis, and plant hormone response. Overall, we provide a set of candidate transcripts that demonstrate host-specific interactions in vegetative tissues of the emerged parasite S. hermonthica. Our study shows how signals of host-specific processes can be detected aboveground, expanding the focus of host–parasite interactions beyond the haustorial connection.

Figure 4 in Natural history and population dynamics of the subsocial tortoise beetle Omaspides (Paromaspides) brunneosignata Boheman 1854 (Coleoptera: Chrysomelidae: Cassidinae)

Figure 4. Omaspides (Paromaspides) brunneosignata Boheman (A) Predation of female guardian by Hemiptera; (B) adult predation of Omaspides brunneosignata by unidentified Araneae species; (C) larva predation by Polybia minarum Ducke 1906 (Hymenoptera: Vespidae); (D) union of two Omaspides brunneosignata offspring; one of them in the pupae stage (bottom of the photo) and the other in the pre-pupae stage, with an individual passing the pupa (indicated by the red arrow); (E) predation of pupae by Pseudomyrmex phyllophilus Smith 1858 (Hymenoptera: Formicidae); (F) pupae being attacked by Brachymeria sp. (Hymenoptera: Chalcididae).

Figure 6 in Natural history and population dynamics of the subsocial tortoise beetle Omaspides (Paromaspides) brunneosignata Boheman 1854 (Coleoptera: Chrysomelidae: Cassidinae)

Figure 6. (A) Density of Omaspides (Paromaspides) brunneosignata Boheman (adults, egg masses, larval and pupal aggregations) found in the Floresta Nacional de Passa Quatro during its reproductive period from October 2010 to May 2011. (B) Density of Omaspides brunneosignata Boheman (adults, egg masses, larval and pupal aggregations) and leaves of its host plant Ipomoea syringifolia Meisn (Convolvulaceae) found in the Floresta Nacional de Passa Quatro from October 2016 to January 2018. Temperature (° C) and precipitation (mm) date are data are given for the same period of study and were provided by the Instituto Nacional de Meteorologia.

Figure 5 in Natural history and population dynamics of the subsocial tortoise beetle Omaspides (Paromaspides) brunneosignata Boheman 1854 (Coleoptera: Chrysomelidae: Cassidinae)

Figure 5. Omaspides (Paromaspides) brunneosignata Boheman (A) Sign of herbivory by early-stage larvae (second – third instar); (B)female next to larvae in cycloalexic defence formation; (C) female next to leaf migrating larvae; (D) final stage larvae scraping the stem of the host plant; (E) marked female with newly emerged; (F) sign of herbivory by newly emerged.

Figure 2 in Natural history and population dynamics of the subsocial tortoise beetle Omaspides (Paromaspides) brunneosignata Boheman 1854 (Coleoptera: Chrysomelidae: Cassidinae)

Figure 2. Part of native forest of study area with understory constituted mainly by Pinus elliottii Engel. 1880 forests.

Figure 3 in Natural history and population dynamics of the subsocial tortoise beetle Omaspides (Paromaspides) brunneosignata Boheman 1854 (Coleoptera: Chrysomelidae: Cassidinae)

Figure 3. Omaspides (Paromaspides) brunneosignata Boheman 1854 (A) Female on newly oviposited egg mass; (B) pedunculated egg mass on the abaxial surface of the Ipomoea syringifolia Meisn (Convolvulaceae); (C) female defensive behaviour against Crematogaster sp. Natural enemies at the egg stage. The hymenopterans (D) Emersonella pubipennis Hansson 2002 (Eulophidae: Entedoninae); (E) predation by Crematogaster sp. (Formicidae); and by (F) Pseudomyrmex phyllophylus (Smith, 1858) (Formicidae).

Figure 1 in Natural history and population dynamics of the subsocial tortoise beetle Omaspides (Paromaspides) brunneosignata Boheman 1854 (Coleoptera: Chrysomelidae: Cassidinae)

Figure 1. Geographic location of Floresta Nacional de Passa Quatro, Passa Quatro, Minas Gerais/Brazil. Source: ICMBio 2009.

opencc-by-4.0Jun 2021View details →

Leaf traits Plantago major, urban sidewalk, city park and nature reserve populations

These measurements include the raw data on the petiole and lamina length and width of Plantago major populations growing within city parks, urban sidewalks or nature reserves in the Netherlands. The data was collected between 12-04-2021 and 07-05-2021 by Roman Beukema. The dataset includes both GPS longitude and latitude locations from each sample, as well as the lamina and petiole length and width in millimeters precise.

opencc-zeroJul 2021View details →

Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the Chocolate Tree

Genomic structural variants (SVs) can play important roles in adaptation and speciation. Yet, the overall fitness effects of SVs are poorly understood, partly because accurate population-level identification of SVs requires multiple high-quality genome assemblies. Here, we use 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao – an outcrossing, long-lived tree species that is the source of chocolate – to investigate the fitness consequences of SVs in natural populations. Among the 31 accessions, we find over 160 thousand SVs, which together cover eight times more of the genome than SNPs and short indels (125 Mb vs. 15 Mb). Our results indicate that a vast majority of these SVs are deleterious: they segregate at low frequencies and are depleted from functional regions of the genome. We show that SVs influence gene expression, which likely impairs gene function and contributes to the detrimental effects of SVs. We also provide empirical support for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleterious nucleotide variants as a result of suppressed recombination. Despite the overall detrimental effects, we identify individual SVs bearing signatures of local adaptation, several of which are associated with genes differentially expressed between populations. Genes involved in pathogen resistance are strongly enriched among these candidates, highlighting the contribution of SVs on this important local adaptation trait. Beyond revealing new empirical evidence for the evolutionary importance of SVs, these 31 de novo assemblies provide a valuable resource for genetic and breeding studies in T. cacao.

opencc-zeroJul 2021View details →

Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads

Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.

opencc-zeroJul 2021View details →

Proximity to natural habitat and flower plantings increases insect populations and pollination services in South African apple orchards

Introducing areas of wildflower vegetation within crop fields has been shown to enhance pollinator activity and pollination services to crops, and findings in Europe showed an interaction effect between floral treatments and landscape context. Natural fynbos patches in the South African Cape Floristic Region (CFR) are potential reservoirs for beneficial insects that could enhance pollinator populations and crop pollination in commercial apple orchards. However, the effect of proximity to natural habitat and floral enhancement treatments on crop pollinators and yield are yet to be fully tested in southern temperate regions. To elucidate the impact of enhanced floral resources to apple flower visitors and crop yield, we established small experimental patches of flowers in non-productive areas of commercial apple (Malus domestica) orchards in the CFR. Experimental orchards were embedded in landscapes with varying proportions of natural habitat within 1 km. We used pollinator exclusion experiments to determine the benefits of insect pollination on apple yield, quality and economic value. We found that the primary pollinators of apple flowers in the region is the endemic Cape honey bee, Apis mellifera capensis. Floral plantings enhanced overall pollinator abundance and honey bee flower visitation within the orchards, and positively affected apple size and economic value. Increased landscape complexity had a significantly positive effect on wild bees but not on honey bees. Synthesis and applications. We demonstrate that presence of floral plantings within orchards enhances pollinator activity within apple orchards and apple quality. This sustainable management practice may represent a profitable choice for growers, which could increase pollination services while reducing reliance on renting hives. These practices can indirectly contribute to increased landscape-scale resilience and connectivity, while also benefiting pollinators within the remaining natural habitat.

opencc-zeroDec 2022View details →

Dataset: Effect of flower identity and diversity on reducing aphid populations via natural enemy communities

This dataset contains data from the paper: Zytynska SE, Eicher M, Fahle R, Weisser W. Effect of flower identity and diversity on reducing aphid populations via natural enemy communities. Ecology and Evolution. Floral plantings are often used in agriculture to attract pollinator communities but they also play an important role in recruiting and establishing natural communities for natural pest control. Inconsistent effects of floral plantings for pest control may be a result of an absence of mechanistic insights and a reliance on the idea that simply increasing flower diversity will benefit these services. A more tailored set of flower species may be needed to benefit the natural enemies through provision of nectar and alternative prey. We used an outside pot experiment to investigate the effect of three flower plants (Fagopyrum esculentum, Vicia faba, Trifolium pratense) on reducing aphid pests on four different plant cultivars of barley (Hordeum vulgare), over two years. We grew the four cultivars of barley alone, next to a single flower or next to a mixture of flowers and observed aphid and natural enemy colonisation across the growing season. Aphid populations sizes were reduced on all barley cultivars grown next to a flower with stronger pest suppression when all flowers were present. Each flower species recruited a different community of non-barley aphids that, in turn, varied in their ability to establish the natural enemy populations, and subsequently the ability to reduce barley aphid populations. Overall increased pest suppression in the mixed treatments was a result of numerous weaker interactions between different flower, pest, and natural enemy species, rather than a few dominant interactions. Natural enemy communities could be enhanced by incorporating flower species that vary in their ability to attract and host alternative prey (i.e. non-pest) as well as suitable nectar provisioning. We can use our knowledge of ecological interactions to tailor floral plantings to increase the effectiveness of pest control services.

opencc-zeroApr 2023View details →

Phenotypic selection in natural populations: what have we learned in 40 years?

In 1983, Russell Lande and Stevan Arnold published "The measurement of selection on correlated characters," which became a highly influential citation classic in evolutionary biology. This paper stimulated a cottage industry of field studies of natural and sexual selection in nature and resulted in several large-scale meta-analyses, statistical developments and methods papers. The statistical tools in their paper contributed to a breakdown of the traditional dichotomy between ecological and evolutionary time scales and stimulated later developments such as "eco-evolutionary dynamics". However, regression-based selection analyses also became criticized from philosophical, methodological and statistical viewpoints and stimulated some still ongoing debates about causality in evolutionary biology. Here I return to this landmark paper by Lande and Arnold, analyse the controversies and debates it gave rise to and discuss the past, present and future of selection analyses in natural populations. A remaining legacy of Lande and Arnold (1983) is that studies of selection and inheritance can fruitfully be decoupled and be studied separately, since selection acts on phenotypes regardless of their genetic basis, and hence selection and evolutionary responses to selection are distinct processes.

opencc-by-4.0Apr 2023View details →

Auditory cortex single unit population activity during natural sound presentation -- dataset

Overview High-density multi-channel neurophysiology data were collected from primary (A1) and secondary (PEG) fields of auditory cortex of passively listening ferrets during presentation of a large natural sound library. Single unit spikes were sorted using Kilosort. This dataset includes spike times for 849 A1 units and 398 PEG units. Stimulus waveforms were transformed to log-spaced spectrograms for analysis (18 channels, 10 ms time bins). Data set includes raw sound waveforms as well and high resolution (1000 samples/sec) single-trial spike data. The authors request that any publication using this data cite the following work: https://www.biorxiv.org/content/10.1101/2022.06.10.495698v2 Version 1.1 is updated with more examples and documentation. It also includes a less-processed version of the spike data that permits reconstruction of the experimental sequence used at each recording site and single-trial responses to the repeated validation stimuli. Data format/description Preprocessed neural data are aggregated in two main files. All recordings were performed during presentation of the same natural sound library to passively listening  animals. During each experiments, stimuli were presented in a random order, and repeated validation stimuli were interleaved throughout the experiment. In the main files, data have been aligned to the same order by stimulus and averaged across repeated presentations (for the validation stimuli, which were presented 20 times during each experiment). The averaged validation data make up the first 27 seconds of each recoding block. <ul> <li>A1_NAT4_ozgf.fs100.ch18.tgz - data from 849 A1 single units and log spectrogram of stimuli aligned with spike times.  Data are aggregated across 64- or 128-channel recordings from 22 sites in 4 animals.</li> <li>PEG_NAT4_ozgf.fs100.ch18.tgz - data from 398 PEG single units and log spectrogram of stimuli aligned with spike times. Data are aggregated across 64-channel recordings from 12 sites in 2 animals.</li> </ul> Raw sound files (44100/s sampling, wav format) and spike times (1K/s sampling, in the original experimental order) are also provided in separate files. Summary data of model performance from the paper are also included. <ul> <li>wav.zip - raw wav files. As of version 2 of this repository, the wav files have been truncated to the 1-sec duration that was used in the experiments</li> <li>A1_single_sites.zip, PEG_single_sites.zip - collections of files, one per recording site, with spike times stored in the actual order of data collection (including interleaved repeated validation stimuli). These spikes have been binned at 100 Hz and sorted to have matched order across all sites in the processed files (A1_NAT4_ozgf.fs100.ch18.tgz, PEG_NAT4_ozgf.fs100.ch18.tgz, respectively).</li> <li>A1_pred_correlation.csv, PEG_pred_correation.csv - Comma-separated value file containing cross-validated prediction accuracy for each A1, PEG unit for each of the five exemplar models. The "sig_auditory" column is true for all units classified as having significant auditory responses, as classified in the publication.</li> </ul> Example scripts Python scripts included with this dataset demonstrate how to load the neural data and perform a CNN model fit. Running the scripts requires the NEMS0 python library, which is available open source at <a href="http://github.com/lbhb/NEMS0">https://github.com/lbhb/NEMS0</a>. Quick install Create and activate a new conda environment: <blockquote> conda create -n NEMS0 python=3.7 conda activate NEMS0 </blockquote> Download NEMS0: <blockquote> git clone https://github.com/lbhb/NEMS0 </blockquote> Install NEMS0: <blockquote> pip install -e NEMS0 </blockquote> Detailed instructions for installing NEMS0 are available in the Github repository (https://github.com/lbhb/NEMS0). Demo scripts Once NEMS0 is installed and the data are downloaded, move to the directory where the data and demo scripts are stored and run them in a NEMS0 environment. <ul> <li>pop_cnn_load.py - Load the A1 data and compare predictions for two neurons (Fig 3) by two population models (stage 1 fit complete). Illustrates how to load the data using Python.</li> <li>pop_cnn_fit.py - Load  a pre-fit A1 population model (stage 1) and complete stage 2 fit (refinement) for a single neuron. Illustrates use of NEMS0 for CNN model fitting.</li> <li>single_trial_demo.py - Script demonstrating how to load the single trial data for a repeated validation stimulus from one A1 neuron. Also how to compute the average population PSTH for a single validation stimulus at 1000 sec-1 sampling. Unzip A1_single_sites.zip in the director containing this script first in order for it to run correctly.</li> </ul> Funding Data collection, software development and processing were supported by funding from the NIH (R01DC014950, R01EB028155).