Data from: Ultra-long telomeres shorten with age in nestling great tits but are static in adults and mask attrition of short telomeres

Telomere length (TL) is increasingly used as a biomarker of senescence, but measuring telomeres remains a challenge. Within tissue samples, TL varies between cells and chromosomes. Class I telomeres are (presumably static) interstitial telomeric sequences, and terminal telomeres have been divided in shorter (Class II) telomeres and ultra-long (Class III) telomeres, and the presence of the latter varies strongly between species. Class II telomeres typically shorten with age, but little is known of Class III telomere dynamics. Using multiple experimental approaches, we show great tits to have ultra-long telomeres, and we investigated age effects on Class II and III telomeres using a longitudinal approach (our method excludes Class I telomeres). In adults, TL averaged over the whole distribution did not significantly change with age. The data package contains three datasets: - The file TLadults.xlsx contains the information on the telomere measurements (TRF in bp) in adults with age in years. The file contains three sheets: (1) measurements of the complete telomere range, (2) measurements of the ‘smear’ at the lower end of the distribution only, (3) measurements of the telomere range above the ‘smear’. - The file “qPCRdata.xlsx” contains telomere length data measured using two different techniques, TRF (in bp) and qPCR, for great tits and blue tits (i.e. the data used for figure 4 and associated analyses). - The file TLchicks contains the information on the telomere measurements (TRF in bp) in nestlings with age in days. The file contains three sheets: (1) measurements of the complete telomere range, (2) measurements of the ‘smear’ at the lower end of the distribution only, (3) measurements of the telomere range above the ‘smear’

Manipulation of photoperiod perception advances gonadal growth but not laying date in the great tit

In seasonal environments, organisms use biotic and abiotic cues to time various biological processes that are crucial for growth, survival and reproductive success. Photoperiod is the best-known cue used to regulate gonadal development, migration and moult of many animal species. In birds, the relationship between photoperiod and gonadal development is clearly established, but we have little understanding on whether photoperiod also regulates actual timing of egg laying under natural conditions. Elucidating the link between photoperiod and timing of breeding is however key to understand whether an evolutionary change in sensitivity to photoperiod is a possible mechanism through which organisms could adjust their seasonal timing in response to climate warming. Here, we investigated the causal relationship between photoperiod, gonadal growth and laying date in wild female great tits. We experimentally increased the photoperiod perceived by the birds in spring by clipping head feathers, and we subsequently monitored gonadal development in the lab and egg laying dates in the wild. We show that our manipulation increased the photoperiod perceived by the birds to a level that approximately corresponds to an advancement of ten calendar days. This increase in perceived photoperiod led to an acceleration of gonadal development, but not to an advancement of egg laying dates. Our results indicate that photoperiod sensitivity is not constraining the advancement of laying date under current environmental conditions and suggest that evolution of sensitivity to other supplementary cues is necessary to advance reproduction under global warming.,Data collection and analysis is decribed in the materials and methods section of the corresponding paper. Light trasmission data were collected in 3 individuals and then averaged. The average was used for plotting in figure 2.

Dataset: The preference and costs of sleeping under light at night in forest and urban great tits

We studied 35 (17 forest and 18 urban) male great tits. The birds were caught in the wild (see electronic supplementary material, figure S1, for a map of catching locations) and transported to the Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands. Birds were housed in individual cages (90 × 50 × 40 m), initially spread over three adjacent rooms. Each cage had two light sources, one for day and one for night. The front of each cage was covered with a wooden board to exclude any external light from the outside and neighbouring cages. Birds were provided with food and water ad libitum. Over the course of the first experiment (experiment 1), which was from 9 October until 28 October (21 days), birds had a constant photoperiod of 10.15 h light : 13.45 h dark, and for the second experiment (experiment 2), which was from 6 November until 17 December (42 days) birds had a constant photoperiod of 8.15 h light : 15.45 h dark. This was the average of natural daytime and night-time hours throughout the dates that the experiments were carried out

Data underlying the publication: “Spatial and seasonal variation in the phytoplankton community of Lake Victoria’s Mwanza Gulf, compared to northern parts of the lake”

The dataset contains the raw data of chlorophyll content, and of taxonomy, numbers, and sizes of phytoplankton samples collected in Mwanza Gulf of Lake Victoria (Africa) in 2011-2011. The R-script used for data analysis is also included.</p

Data underlying the publication: “Spatial and seasonal variation in the phytoplankton community of Lake Victoria’s Mwanza Gulf, compared to northern parts of the lake”

The dataset contains the raw data of chlorophyll content, and of taxonomy, numbers, and sizes of phytoplankton samples collected in Mwanza Gulf of Lake Victoria (Africa) in 2011-2011. The R-script used for data analysis is also included.</p

Transcriptional regulation underlying the temperature response of embryonic development rate in the winter moth

Climate change will strongly affect the developmental timing of insects, as their development rate largely depends on ambient temperature. However, we know little about the genetic mechanisms underlying the temperature sensitivity of embryonic development in insects. We investigated embryonic development rate in the winter moth (Operophtera brumata), a species with egg dormancy that has been under selection due to climate change. We used RNAseq to investigate which genes are involved in the regulation of winter moth embryonic development rate in response to temperature. Over the course of development, we sampled eggs before and after an experimental change in ambient temperature, including two early development weeks when the temperature sensitivity of eggs is low and two late development weeks when temperature sensitivity is high. We found temperature-responsive genes that responded in a similar way across development, as well as genes with a temperature response specific to a particular development week. Moreover, we identified genes whose temperature effect size changed around the switch in temperature sensitivity of development rate. Interesting candidate genes for regulating the temperature sensitivity of egg development rate included genes involved in histone modification, hormonal signalling, nervous system development, and circadian clock genes. In conclusion, the diverse sets of temperature-responsive genes we found here indicate that there are many potential targets of selection to change the temperature sensitivity of embryonic development rate. Identifying for which of these genes there is genetic variation in wild insect populations will give insight into their adaptive potential in the face of climate change.,This dataset consists of all processed data and phenotypic data needed to reproduce the analysis of RNAseq data from winter moth embryos, published in Molecular Ecology under the same title. Data included here: the final transcriptome incl. functional annotation, GO annotation table, final gene counts matrix, and phenotypic data. The raw RNAseq reads can be found on the European Nucleotide Archive (ENA) under accession no. PRJEB55675. All the scripts needed to process the data and reproduce the analysis can be found on GitHub at https://github.com/NEvanDis/WM_RNAseq. Briefly: raw RNAseq reads were quality screened and processed according to the 'new Tuxedo' pipeline (see Pertea et al. 2016 Nature Protocols 11(9). This pipeline includes transcript assembly and quantification with StringTie, guided by the winter moth reference genome v1 with annotation v2. StringTie produces a transcriptome including only transcripts in the dataset with each transcript coordinated to the winter moth reference genome. We functionally annotated this transcriptome e.g. with BLAST, which included producing a GO annotation table. StringTie then uses this transcriptome to do transcript quantification at the gene level, of which the product is the final gene counts matrix deposited here. This final gene counts matric and the phenotypic data were used for statistical analysis and the production of the final figures in the Mol Ecol publication. Please see the scripts on GitHub for pipeline and analysis details.,File extensions of the deposited data files include .gff, .txt, and .csv. These are all text-based file formats that can be opened with any text processor

R Markdown scripts for Additional file 2 and 3

R Markdown scripts for data analyses and to produce supplementary material (Additional filen 2 and 3). Files and functions therein for RStudio https://www.rstudio.com/ and R https://www.r-project.org/

Additional information: ambient temperature and sex info

Ambient temperature data from temperature logger (stensoffa.temp): timestamp, temperature (temp) and data. Information about individuals i.e. sex (sexinfo): frequency of attached transmitter and sex