This dataset includes data on 25 transitions of a matrix demographic model of the invasive species Vincetoxicum nigrum (L.) Moench (black swallow-wort or black dog-strangling vine) and Vincetoxicum rossicum (Kleopow) Barb. (pale swallow-wort or dog-strangling vine) (Apocynaceae, subfamily Asclepiadoideae), two invasive perennial vines in the northeastern U.S.A. and southeastern Canada. The matrix model was developed for projecting population growth rates as a result of changes to lower-level vital rates from biological control although the model is generalizable to any control tactic. Transitions occurred among the five life stages of seeds, seedlings, vegetative juveniles (defined as being in at least their second season of growth), small flowering plants (having 1–2 stems), and large flowering plants (having 3 or more stems). Transition values were calculated using deterministic equations and data from 20 lower-level vital rates collected from 2009-2012 from two open field and two forest understory populations of V. rossicum (43°51’N, 76°17’W; 42°48'N, 76°40'W) and two open field populations of V. nigrum (41°46’N, 73°44’W; 41°18’N, 73°58’W) in New York State. Sites varied in plant densities, soil depth, and light levels (forest populations). Detailed descriptions of vital rate data collection may be found in: Milbrath et al. 2017. Northeastern Naturalist 24(1):37-53. Five replicate sets of transition data obtained from five separate spatial regions of a particular infestation were produced for each of the six populations. Note: Added new excel file of vital rate data on 12/7/2018. Resources in this dataset:Resource Title: Matrix model transition data for Vincetoxicum species. File Name: Matrix_model_transition_data.csvResource Description: This data set includes data on 25 transitions of a matrix demographic model of two invasive Vincetoxicum species from six field and forest populations in New York State.Resource Title: Variable definitions. File Name: Matrix_model_metadata.csvResource Description: Definitions of variables including equations for each transition and definitions of the lower-level vital rates in the equationsResource Title: Vital Rate definitions. File Name: Vital_Rate.csvResource Description: Vital Rate definitions of lower-level vital rates used in transition equations - to be substituted into the Data Dictionary for full definition of each transition equation.Resource Title: Data Dictionary. File Name: Matrix_Model_transition_data_DD.csvResource Description: See Vital Rate resource for definitions of lower-level vital rates used in transition equations where noted.Resource Title: Matrix model vital rate data for Vincetoxicum species. File Name: Matrix_model_vital rate_data.csvResource Description: This data set includes data on 20 lower-level vital rates used in the calculation of transitions of a matrix demographic model of two invasive Vincetoxicum species in New York State as well as definitions of the vital rates. (File added on 12/7/2018)Resource Software Recommended: Microsoft Excel,url: https://office.microsoft.com/excel/

Grandmothers provide key care to their grandchildren in both contemporary and historic human populations. The length of the grandmother-grandchild relationship provides a basis for such interactions, but its variation and determinants have rarely been studied in different contexts, despite changes in age-specific mortality and fertility rates likely having affected grandmotherhood patterns across the demographic transition. Understanding how often and long grandmothers have been available for their grandchildren in different conditions may help explain the large differences between grandmaternal effects found in different societies, and is vital for developing theories concerning the evolution of menopause, post-reproductive longevity, and family living. Using an extensive genealogical dataset from Finland spanning the demographic transition, we quantify the length of grandmotherhood and its determinants from 1790–1959. We found that shared time between grandmothers and grandchildren was consistently low before the demographic transition, only increasing greatly during the 20th century. Whilst reduced childhood mortality and increasing adult longevity had a role in this change, grandmaternal age at birth remained consistent across the study period. Our findings further understanding of the temporal context of grandmother-grandchild relationships, and emphasise the need to consider the demography of grandmotherhood in a number of disciplines, including biology (e.g. evolution of the family), sociology (e.g. changing family structures), population health (e.g. changing age structures), and economics (e.g. workforce retention).

Bolund et al. DATAExcel file containing data used for "Effects of the demographic transition on the genetic variances and covariances of human life history traits". Full data is given for individuals born more than 100 years prior to the end of data collection. Summary data only is provided for individuals born in the last 100 years. Summaries of G and P matrices are provided for all time periods. For further information, see the ReadMe file.BolundetalDATAandTABLES.xlsx

ResourcesMapTeacher guide Student worksheetGet startedOpen the map.Use the teacher guide to explore the map with your class or have students work through it on their own with the worksheet.New to GeoInquiriesTM? See Getting to Know GeoInquiries.Science standardsAPES: III. B. – Population biology concepts.APES: II.B.1. – Human population dynamics - historical population sizes; distribution; fertility rates; growth rates and doubling times; demographic transition; age-structure diagrams.Learning outcomesStudents will predict total historical population trends from age-structure information.Students will relate population growth to k (carrying capacity) or r (reproductive factor) selective environmental conditions.

This folder contains the data file and R scripts necessary to model population growth rates (lambda) of a natural population, based on data from five transects from 2010-2012. Please contact Jill Anderson (jta24@uga.edu) with questions.

The molecular clock hypothesis is fundamental in evolutionary biology as by assuming constancy of the molecular rate it provides a time frame for evolution. However, increasing evidence shows time dependence of inferred molecular rates with inflated values obtained using recent calibrations. As recent demographic calibrations are virtually non-existent in most species, older phylogenetic calibration points (>1 Ma) are commonly used, which overestimate demographic parameters. To obtain more reliable rates of molecular evolution for population studies, I propose the Calibration of Demographic Transition (CDT) method, which uses the timing of climatic changes over the late glacial warming period to calibrate expansions in various species. Simulation approaches and empirical datasets from a diversity of species (from mollusk to humans) confirm that, when compared to other genealogy-based calibration methods, the CDT provides a robust and broadly applicable clock for population genetics. ...

This collection contains the subsets of FIA (https://apps.fs.usda.gov/fia/datamart/datamart.html) and PRISM (http://prism.oregonstate.edu/) data used in "Climate-driven, but dynamic and complex? A reconciliation of competing hypotheses for species' distributions".The two datasets contain demographic data (survival and growth in SurvivalData.csv and recruitment in RecruitData.csv) and climate data used to fit vital rate models estimating the effects of climate and competition on Pinus edulis in the southwestern US.

Testing Inferential FrameworksScript, parameter, result, and POD files for testing inferential frameworks simulation experiment.1 Testing Inferential Frameworks.zip2 Pulse Buffer on Prior Space and Truncating Hyperprior RangeScript and result files for pulse buffer on prior space and truncating hyperprior range simulation experiments.

File Name: Matrix_model_transition_data.csvResource Description: This data set includes data on 25 transitions of a matrix demographic model of two invasive Vincetoxicum species from six field and forest populations in New York State.Resource Title: Variable definitions. File Name: Matrix_model_metadata.csvResource Description: Definitions of variables including equations for each transition and definitions of the lower-level vital rates in the equationsResource Title: Vital Rate definitions. File Name: Vital_Rate.csvResource Description: Vital Rate definitions of lower-level vital rates used in transition equations - to be substituted into the Data Dictionary for full definition of each transition equation.Resource Title: Data Dictionary. File Name: Matrix_Model_transition_data_DD.csvResource Description: See Vital Rate resource for definitions of lower-level vital rates used in transition equations where noted.Resource Title: Matrix model vital rate data for Vincetoxicum species. File Name: Matrix_model_vital rate_data.csvResource Description: This data set includes data on 20 lower-level vital rates used in the calculation of transitions of a matrix demographic model of two invasive Vincetoxicum species in New York State as well as definitions of the vital rates. (File added on 12/7/2018)Resource Software Recommended: Microsoft Excel,url: https://office.microsoft.com/excel/

CSV files of the simulation data plotted in Figures 2-4 of Levine et al. 2024 in Global Change Biology, "Demographic but not competitive time lags can transiently amplify climate-induced changes in vegetation carbon storage," by Jonathan M. Levine, Janneke HilleRisLambers, William K. Petry, Jacob Usinowicz, and Thomas W. Crowther.The units of the values in the files are numbers of individuals, except for the dead individuals, which are in units of large adults, and carbon which is in units of tonnes.

The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence, and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek to fill this gap by using simulation to characterize the sensitivity of inference under the multispecies coalescent to several violations of model assumptions thought to be common in empirical data. We also assess the fit of the multispecies coalescent model to empirical data in the context of species delimitation. Our results show substantial variation in model fit across d...

Population structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M-ratio and msvar), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size and migration rate. It is noteworthy that the spurious signals of demographic changes also depended on the statistical approach underlying each of the three methods. For one of the three methods, biases induced by asymmetric gene flow were confirmed in an empirical multispecific data set involving four freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio gobio and Phoxinus phoxinus). However, for the two other methods, strong signals of bottlenecks were detected for all species and across two rivers. This suggests that, although potentially biased by asymmetric gene flow, some of these methods were able to bypass this bias when a bottleneck actually occurred. Our results show that population structure and dispersal patterns have to be considered for proper inference of demographic changes from genetic data.

The Central Balkans region is of great importance for understanding the spread of the Neolithic in Europe but the Early Neolithic population dynamics of the region is unknown. In this study we apply the method of summed calibrated probability distributions to a set of published radiocarbon dates from the Republic of Serbia in order to reconstruct population dynamics in the Early Neolithic in this part of the Central Balkans. The results indicate that there was a significant population growth after ~6200 calBC, when the Neolithic was introduced into the region, followed by a bust at the end of the Early Neolithic phase (~5400 calBC). These results are broadly consistent with the predictions of the Neolithic Demographic Transition theory and the patterns of population booms and busts detected in other regions of Europe. These results suggest that the cultural process that underlies the patterns observed in Central and Western Europe was also in operation in the Central Balkan Neolithic and that the population increase component of this process can be considered as an important factor for the spread of the Neolithic as envisioned in the demic diffusion hypothesis.

Since the rediscovery of Mendelian genetics over a century ago, there has been much debate about the evolutionary importance of mutations with large phenotypic effects. While population genetic models predict that large-effect mutations will typically contribute to adaptation following an abrupt change in environment, the prediction applies to populations of stable size and overlooks effects of population size change on adaptation (e.g., population decline following habitat loss; growth during range expansion). We evaluate the phenotypic and fitness effects of mutations contributing to adaptation immediately following an abrupt environmental shift that alters both selection and population size dynamics. We show that large-effect mutations are likely to contribute to adaptation in populations declining to a new carrying capacity, somewhat smaller-effect mutations contribute to evolutionary rescue, and small-effect mutations predominate in growing populations. We also show that the relative contributions of positively selected and overdominant mutations to adaptation depend on interactions between the phenotypic effect size distribution for new mutations and the specific form of population size change during adaptation (i.e., growth, decline, or evolutionary rescue). Our results illustrate how population size dynamics can shape the genetic basis of adaptation, which should motivate empirical comparisons of populations adapting in different demographic contexts. This is R simulation code used in the paper. The code will run in R/Rstudio.

How to optimally allocate time, energy and investment in an effort to maximize one's reproductive success is a fundamental problem faced by all organisms. This effort is complicated when the production of each additional offspring dilutes the total resources available for parental investment. Although a quantity–quality trade-off between producing and investing in offspring has long been assumed in evolutionary biology, testing it directly in humans is difficult, partly owing to the long generation time of our species. Using data from an Icelandic genealogy (Íslendingabók) over two centuries, I address this issue and analyse the quantity–quality trade-off in humans. I demonstrate that the primary impact of parents on the fitness of their children is the result of resources and or investment, but not genes. This effect changes significantly across time, in response to environmental conditions. Overall, increasing reproduction has negative fitness consequences on offspring, such that each additional sibling reduces an individual's average lifespan and lifetime reproductive success. This analysis provides insights into the evolutionary conflict between producing and investing in children while also shedding light on some of the causes of the demographic transition.

Drosophila melanogaster is a fruit fly pest found around the world. This insect responds plastically to variation in temperature and has been known to be locally adapted to different locations across the globe, with varying maximum and minimum thermal limits. Artificial selection can be used to create adaptive responses in a laboratory setting, which can be used to mimic a range of thermal responses. Previous research has shown that within 30 generations of selection, naturally caught D. melanogaster from North Carolina, USA, can produce populations with both increased and decreased responses to cold stress as demonstrated by the chill-coma recovery trait (Gerken et al. 2016). This dataset expands on cross-tolerances to reproductive capacity and includes data from the four artificially selected D. melanogaster populations and two control populations. Egg production and total lifespan were measured in a laboratory setting at five different temperatures. Two data resources are included: full egg production and longevity for each fly assayed. This study was used to establish how selection for cold tolerance can affect reproductive capacity and longevity. Resources in this dataset: Resource Title: Oviposition (egg laying) data for entire lifespan File Name: Full_egg_data.csv Resource Description: Egg laying (oviposition) data for entire lifespan for 6 populations of Drosophila melanogaster. Fly_ID is a unique identifier for each female fly assayed. SelectionLine is the specific replicate line and SelectionRegime is the overall increased (Resistant) or decreased (Susceptible) cold tolerance parameter (or Control, no selection). Treatment is in degrees Celsius and is the temperature at which the female was put to lay eggs. The remaining columns represent each day of egg counting. The first count was on day 6 after introduction to the temperature assigned, and counts were conducted every 6 days until the female died or until day 210. Resource Title: Longevity (in days) for Drosophila melanogaster populations File Name: Full_longevity_data.csv Resource Description: Longevity data (survival) for 6 populations of Drosophila melanogaster. Fly_ID is a unique identifier for each female fly assayed. SelectionLine is the specific replicate line which includes the overall selection regime of increased (Resistant) or decreased (Susceptible) cold tolerance parameter (or Control, no selection) and the specific replicate for each selection regime (1 or 2). Treatment is in degrees Celsius and is the temperature at which the female was put to lay eggs. Longevity_days is the total lifespan of the individual female fly. If the Longevity_days is set at -9, the fly outlived the maximum days of 210 and was not counted in overall survival parameters.

The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather than within the same statistical framework. Here, we applied an integrative approach, using different model-based inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the demic diffusion model. They also show that population structure and differential growth between farmers and hunter-gatherers are necessary to explain both types of data. However, we also found some differences between male and female markers, suggesting that the female effective population size was larger than that of the males, probably due to different demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the increase of patrilocality.

Environmental change has been observed to generate simultaneous responses in population dynamics, life history, gene frequencies, and morphology in a number of species. But how common are such eco-evolutionary responses to environmental change likely to be? Are they inevitable, or do they require a specific type of change? Can we accurately predict eco-evolutionary responses? We address these questions using theory and data from the study of Yellowstone wolves. We show that environmental change is expected to generate eco-evolutionary change, that changes in the average environment will affect wolves to a greater extent than changes in how variable it is, and that accurate prediction of the consequences of environmental change will probably prove elusive.

Changes in climate can alter individual body size, and the resulting shifts in reproduction and survival are expected to impact population dynamics and viability. However, appropriate methods to account for size-dependent demographic changes are needed, especially in understudied yet threatened groups such as amphibians. We investigated individual and population-level demographic effects of changes in body size for a terrestrial salamander using capture-mark-recapture data. For our analysis, we implemented an integral projection model parameterized with capture-recapture likelihood estimates from a Bayesian framework. Our study combines survival and growth data from a single dataset to quantify the influence of size on survival while including different sources of uncertainty around these parameters, demonstrating how selective forces can be studied in populations with limited data and incomplete recaptures. We found a strong dependency of the population growth rate on changes in indivi..., ,

Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analyzed across 150 species (16,992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predi...