scholarly journals Rcompadre and Rage ‐ two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life history traits from matrix population models

Author(s):  
Owen R. Jones ◽  
Patrick Barks ◽  
Iain Stott ◽  
Tamora D. James ◽  
Sam Levin ◽  
...  
2021 ◽  
Author(s):  
Owen R Jones ◽  
Patrick Barks ◽  
Iain M Stott ◽  
Tamora D James ◽  
Sam C. Levin ◽  
...  

Matrix population models (MPMs) are an important tool in the arsenal of biologists seeking to understand the causes and consequences of variation in vital rates (e.g. survival, reproduction) across life cycles. MPMs describe the age- or stage-structured demography of organisms and represent the life history of a population during a particular time frame at a specific geographic location. The COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database are the most extensive resources for MPM data, collectively containing >12,000 MPMs for >1,100 species globally. Although these databases represent an unparalleled resource for researchers, land managers, and educators, the current computational tools available to answer questions with MPMs impose significant barriers to potential users by requiring advanced knowledge to handle diverse data structures and program custom analysis functions. To close this knowledge gap, we present two R packages designed to (i) facilitate the use of these databases by providing functions to acquire, check, and manage the MPM data contained in COMPADRE and COMADRE (Rcompadre), and (ii) expand the range of life history traits that can be calculated from MPMs in support of ecological and evolutionary analyses (Rage). We provide vignettes to illustrate the use of both Rcompadre and Rage. Rcompadre and Rage will facilitate demographic analyses using MPM data and contribute to the improved replicability of studies using these data. We hope that this new functionality will allow researchers, land managers, and educators to unlock the potential behind the thousands of MPMs and ancillary metadata stored in the COMPADRE and COMADRE matrix databases.


2005 ◽  
Vol 62 (4) ◽  
pp. 886-902 ◽  
Author(s):  
Kenneth A Rose

Relationships between fish population responses to changes in their vital rates and commonly available life history traits would be a powerful screening tool to guide management about species vulnerability, to focus future data collection on species and life stages of concern, and to aid in designing effective habitat enhancements. As an extension of previous analyses by others, I analyzed the responses to changes in fecundity and yearling survival of age-structured matrix and individual-based population models of 17 populations comprising 10 species. Simulations of the matrix models showed that the magnitude of population responses, but not the relative order of species sensitivity, depended on the state (sustainable or undergoing excessive removals) of the population. Matrix and individual-based models predicted population responses that appeared to be unrelated to their species-level life history traits when responses were plotted on a three-end-point life history surface. Density-dependent adult growth was added to the lake trout (Salvelinus namaycush) matrix model, and simulations demonstrated the potential importance to predicted responses of density-dependent processes outside the usual spawner–recruit relationship. Four reasons for the lack of relationship between population responses and life history traits related to inadequate population models, incorrect analysis, inappropriate life history model, and important site-specific factors are discussed.


2020 ◽  
Vol 650 ◽  
pp. 7-18 ◽  
Author(s):  
HW Fennie ◽  
S Sponaugle ◽  
EA Daly ◽  
RD Brodeur

Predation is a major source of mortality in the early life stages of fishes and a driving force in shaping fish populations. Theoretical, modeling, and laboratory studies have generated hypotheses that larval fish size, age, growth rate, and development rate affect their susceptibility to predation. Empirical data on predator selection in the wild are challenging to obtain, and most selective mortality studies must repeatedly sample populations of survivors to indirectly examine survivorship. While valuable on a population scale, these approaches can obscure selection by particular predators. In May 2018, along the coast of Washington, USA, we simultaneously collected juvenile quillback rockfish Sebastes maliger from both the environment and the stomachs of juvenile coho salmon Oncorhynchus kisutch. We used otolith microstructure analysis to examine whether juvenile coho salmon were age-, size-, and/or growth-selective predators of juvenile quillback rockfish. Our results indicate that juvenile rockfish consumed by salmon were significantly smaller, slower growing at capture, and younger than surviving (unconsumed) juvenile rockfish, providing direct evidence that juvenile coho salmon are selective predators on juvenile quillback rockfish. These differences in early life history traits between consumed and surviving rockfish are related to timing of parturition and the environmental conditions larval rockfish experienced, suggesting that maternal effects may substantially influence survival at this stage. Our results demonstrate that variability in timing of parturition and sea surface temperature leads to tradeoffs in early life history traits between growth in the larval stage and survival when encountering predators in the pelagic juvenile stage.


2020 ◽  
Vol 27 (4) ◽  
pp. 195-200
Author(s):  
Ufuk Bülbül ◽  
Halime Koç ◽  
Yasemin Odabaş ◽  
Ali İhsan Eroğlu ◽  
Muammer Kurnaz ◽  
...  

Age structure of the eastern spadefoot toad, Pelobates syriacus from the Kızılırmak Delta (Turkey) were assessed using phalangeal skeletochronology. Snout-vent length (SVL) ranged from 42.05 to 86.63 mm in males and 34.03 to 53.27 mm in females. Age of adults ranged from 2 to 8 years in males and 3 to 5 years in females. For both sexes, SVL was significantly correlated with age. Males and females of the toads reached maturity at 2 years of age.


Author(s):  
Maren N. Vitousek ◽  
Laura A. Schoenle

Hormones mediate the expression of life history traits—phenotypic traits that contribute to lifetime fitness (i.e., reproductive timing, growth rate, number and size of offspring). The endocrine system shapes phenotype by organizing tissues during developmental periods and by activating changes in behavior, physiology, and morphology in response to varying physical and social environments. Because hormones can simultaneously regulate many traits (hormonal pleiotropy), they are important mediators of life history trade-offs among growth, reproduction, and survival. This chapter reviews the role of hormones in shaping life histories with an emphasis on developmental plasticity and reversible flexibility in endocrine and life history traits. It also discusses the advantages of studying hormone–behavior interactions from an evolutionary perspective. Recent research in evolutionary endocrinology has provided insight into the heritability of endocrine traits, how selection on hormone systems may influence the evolution of life histories, and the role of hormonal pleiotropy in driving or constraining evolution.


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