Contains supplementary text describing statistical methods, supplementary figures S1-S8, and supp... more Contains supplementary text describing statistical methods, supplementary figures S1-S8, and supplementary tables S1 and S2;Contains the SCOR and DOT records used in our analyses.
The occupancy and relative abundance of species are temporally varying. Estimating these, given i... more The occupancy and relative abundance of species are temporally varying. Estimating these, given incomplete and biased sampling is challenging, not least for fossilized organisms, where preservation is an additional issue. Here, we describe a relative abundance-focused multi-species occupancy model (TRAMPOline) in a hierarchical Bayesian framework. We designed our model on the basis of the need to understand the dynamics of several focal species over 2.3 million years, by drawing on additional information provided by non-focal species observed in the same fossilized community. We expanded our model by adding random effects of species and time intervals (geological formations) and explored potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled geological time intervals. Our new model, set in an occupancy modeling framework widely used in ecology but little applied in paleoecology, is applicable across a...
The number of individuals of species within communities varies, but estimating abundance, given i... more The number of individuals of species within communities varies, but estimating abundance, given incomplete and biased sampling, is challenging. Here, we describe a new occupancy model in a hierarchical Bayesian framework with random effects, where multi-species occupancy and detection are modeled as a means to estimate relative species abundance and relative population densities. The modelling framework is suited for occupancy data for temporal samples of fossil communities with repeated sampling including multiple species with similar preservation potential. We demonstrate our modelling framework using a fossil community of benthic organisms to estimate changing relative species abundance dynamics and relative population densities of focal species in 9 (geological) time-intervals over 2.3 million years. We also explored potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled time-intervals. The modell...
The genetic basis for the fine-tuned regulation of gene expression is complex and ultimately infl... more The genetic basis for the fine-tuned regulation of gene expression is complex and ultimately influences the phenotype and thus the local adaptation of natural populations. Short tandem repeats (STRs) consisting of repetitive DNA motifs have been shown to regulate gene expression. STRs are variable in length within a population and serve as a heritable, but semi-reversible, reservoir of standing genetic variation. For sessile organisms, such as plants, STRs could be of major importance in fine-tuning gene expression as a response to a shifting local environment. Here, we used a transcriptome dataset from natural accessions of Arabidopsis thaliana to investigate population-wide gene expression patterns in light of genome-wide STR variation. We empirically modeled gene expression as a response to the STR length within and around the gene and demonstrated that an association between gene expression and STR length variation is unequivocally present in the sampled population. To support o...
Background Earlier breeding is one of the strongest responses to global change in birds and is a ... more Background Earlier breeding is one of the strongest responses to global change in birds and is a key factor determining reproductive success. In most studies of climate effects, the focus has been on large-scale environmental indices or temperature averaged over large geographical areas, neglecting that animals are affected by the local conditions in their home ranges. In riverine ecosystems, climate change is altering the flow regime, in addition to changes resulting from the increasing demand for renewable and clean hydropower. Together with increasing temperatures, this can lead to shifts in the time window available for successful breeding of birds associated with the riverine habitat. Here, we investigated specifically how the environmental conditions at the territory level influence timing of breeding in a passerine bird with an aquatic lifestyle, the white-throated dipper Cinclus cinclus. We relate daily river discharge and other important hydrological parameters, to a long-t...
Recent climate change has led to advanced spring phenology in many temperate regions. The phenolo... more Recent climate change has led to advanced spring phenology in many temperate regions. The phenological response to variation in the local environment, such as the habitat characteristics of the territories birds occupy, is less clear. The aim of this study is to understand how ecological conditions affect breeding time, and its consequences for reproduction, in a white-throated dipper Cinclus cinclus population in a river system in Norway during 34 years (1978–2011). Hatching date advanced almost nine days, indicating a response to higher temperatures and the advanced phenology in the area. Earlier breeding was found in warm springs and at lower altitudes. High population density facilitated earlier breeding close to the coast. Furthermore, when population density was low, breeding was early at territories that were rarely occupied, while in years with high density, breeding was early at territories that were frequently occupied. Also, when population density was low, earlier breedi...
Distinguishing correlative and causal connections among time series is an important challenge in ... more Distinguishing correlative and causal connections among time series is an important challenge in evolutionary biology, ecology, macroevolution and palaeobiology. Here, we present layeranalyzer, an r package that uses linear stochastic differential equations as a tool for parametrically describing evolutionary and ecological processes and for modelling temporal correlation and Granger causality between two or more time series. We describe the basic functions in layeranalyzer and briefly discuss modelling strategies by demonstrating our tool with three disparate case studies. First, we model a single time series of phenotypic evolution in a bird species; second, we extract cyclical connections in the well‐known hare‐lynx dataset; third, we infer the correlative and causal connections among the genus origination and extinction rates of brachiopods and bivalves. We summarize the advantages and limitations of using linear stochastic differential equations and layeranalyzer for studying c...
Contains supplementary text describing statistical methods, supplementary figures S1-S8, and supp... more Contains supplementary text describing statistical methods, supplementary figures S1-S8, and supplementary tables S1 and S2;Contains the SCOR and DOT records used in our analyses.
The occupancy and relative abundance of species are temporally varying. Estimating these, given i... more The occupancy and relative abundance of species are temporally varying. Estimating these, given incomplete and biased sampling is challenging, not least for fossilized organisms, where preservation is an additional issue. Here, we describe a relative abundance-focused multi-species occupancy model (TRAMPOline) in a hierarchical Bayesian framework. We designed our model on the basis of the need to understand the dynamics of several focal species over 2.3 million years, by drawing on additional information provided by non-focal species observed in the same fossilized community. We expanded our model by adding random effects of species and time intervals (geological formations) and explored potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled geological time intervals. Our new model, set in an occupancy modeling framework widely used in ecology but little applied in paleoecology, is applicable across a...
The number of individuals of species within communities varies, but estimating abundance, given i... more The number of individuals of species within communities varies, but estimating abundance, given incomplete and biased sampling, is challenging. Here, we describe a new occupancy model in a hierarchical Bayesian framework with random effects, where multi-species occupancy and detection are modeled as a means to estimate relative species abundance and relative population densities. The modelling framework is suited for occupancy data for temporal samples of fossil communities with repeated sampling including multiple species with similar preservation potential. We demonstrate our modelling framework using a fossil community of benthic organisms to estimate changing relative species abundance dynamics and relative population densities of focal species in 9 (geological) time-intervals over 2.3 million years. We also explored potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled time-intervals. The modell...
The genetic basis for the fine-tuned regulation of gene expression is complex and ultimately infl... more The genetic basis for the fine-tuned regulation of gene expression is complex and ultimately influences the phenotype and thus the local adaptation of natural populations. Short tandem repeats (STRs) consisting of repetitive DNA motifs have been shown to regulate gene expression. STRs are variable in length within a population and serve as a heritable, but semi-reversible, reservoir of standing genetic variation. For sessile organisms, such as plants, STRs could be of major importance in fine-tuning gene expression as a response to a shifting local environment. Here, we used a transcriptome dataset from natural accessions of Arabidopsis thaliana to investigate population-wide gene expression patterns in light of genome-wide STR variation. We empirically modeled gene expression as a response to the STR length within and around the gene and demonstrated that an association between gene expression and STR length variation is unequivocally present in the sampled population. To support o...
Background Earlier breeding is one of the strongest responses to global change in birds and is a ... more Background Earlier breeding is one of the strongest responses to global change in birds and is a key factor determining reproductive success. In most studies of climate effects, the focus has been on large-scale environmental indices or temperature averaged over large geographical areas, neglecting that animals are affected by the local conditions in their home ranges. In riverine ecosystems, climate change is altering the flow regime, in addition to changes resulting from the increasing demand for renewable and clean hydropower. Together with increasing temperatures, this can lead to shifts in the time window available for successful breeding of birds associated with the riverine habitat. Here, we investigated specifically how the environmental conditions at the territory level influence timing of breeding in a passerine bird with an aquatic lifestyle, the white-throated dipper Cinclus cinclus. We relate daily river discharge and other important hydrological parameters, to a long-t...
Recent climate change has led to advanced spring phenology in many temperate regions. The phenolo... more Recent climate change has led to advanced spring phenology in many temperate regions. The phenological response to variation in the local environment, such as the habitat characteristics of the territories birds occupy, is less clear. The aim of this study is to understand how ecological conditions affect breeding time, and its consequences for reproduction, in a white-throated dipper Cinclus cinclus population in a river system in Norway during 34 years (1978–2011). Hatching date advanced almost nine days, indicating a response to higher temperatures and the advanced phenology in the area. Earlier breeding was found in warm springs and at lower altitudes. High population density facilitated earlier breeding close to the coast. Furthermore, when population density was low, breeding was early at territories that were rarely occupied, while in years with high density, breeding was early at territories that were frequently occupied. Also, when population density was low, earlier breedi...
Distinguishing correlative and causal connections among time series is an important challenge in ... more Distinguishing correlative and causal connections among time series is an important challenge in evolutionary biology, ecology, macroevolution and palaeobiology. Here, we present layeranalyzer, an r package that uses linear stochastic differential equations as a tool for parametrically describing evolutionary and ecological processes and for modelling temporal correlation and Granger causality between two or more time series. We describe the basic functions in layeranalyzer and briefly discuss modelling strategies by demonstrating our tool with three disparate case studies. First, we model a single time series of phenotypic evolution in a bird species; second, we extract cyclical connections in the well‐known hare‐lynx dataset; third, we infer the correlative and causal connections among the genus origination and extinction rates of brachiopods and bivalves. We summarize the advantages and limitations of using linear stochastic differential equations and layeranalyzer for studying c...
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