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

2021 ◽  
Author(s):  
Owen R Jones ◽  
Patrick Barks ◽  
Iain M Stott ◽  
Tamora D James ◽  
Sam C. Levin ◽  
...  
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Geographic Location ◽  
Time Frame ◽  
Life Cycles ◽  
Population Models ◽  
Vital Rates ◽  
Matrix Population Models ◽  
History Of ◽  
R Packages

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.

Coevolutionary interactions between host life histories and parasite life cycles

Parasitology ◽  
1998 ◽  
Vol 116 (S1) ◽  
pp. S47-S55 ◽  
Author(s):  
J. C. Koella ◽  
P. Agnew ◽  
Y. Michalakis
Keyword(s):  
Life History ◽  
Life Cycle ◽  
Life Histories ◽  
Life History Traits ◽  
Evolutionary Ecology ◽  
Life Cycles ◽  
Microsporidian Parasite ◽  
History Of ◽  
Host Life ◽  
Host Parasite

SummarySeveral recent studies have discussed the interaction of host life-history traits and parasite life cycles. It has been observed that the life-history of a host often changes after infection by a parasite. In some cases, changes of host life-history traits reduce the costs of parasitism and can be interpreted as a form of resistance against the parasite. In other cases, changes of host life-history traits increase the parasite's transmission and can be interpreted as manipulation by the parasite. Alternatively, changes of host's life-history traits can also induce responses in the parasite's life cycle traits. After a brief review of recent studies, we treat in more detail the interaction between the microsporidian parasite Edhazardia aedis and its host, the mosquito Aedes aegypti. We consider the interactions between the host's life-history and parasite's life cycle that help shape the evolutionary ecology of their relationship. In particular, these interactions determine whether the parasite is benign and transmits vertically or is virulent and transmits horizontally.Key words: host-parasite interaction, life-history, life cycle, coevolution.

Lack of relationship between simulated fish population responses and their life history traits: inadequate models, incorrect analysis, or site-specific factors?

2005 ◽  
Vol 62 (4) ◽  
pp. 886-902 ◽  
Author(s):  
Kenneth A Rose
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Lake Trout ◽  
Fish Population ◽  
Population Models ◽  
Site Specific ◽  
Density Dependent ◽  
Population Responses ◽  
Adult Growth ◽  
Specific Factors

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.

scholarly journals Life history of a secondary bark beetle, Pseudips mexicanus (Coleoptera: Curculionidae: Scolytinae), in lodgepole pine in British Columbia

2009 ◽  
Vol 141 (1) ◽  
pp. 56-69 ◽  
Author(s):  
G.D. Smith ◽  
A.L. Carroll ◽  
B.S. Lindgren
Keyword(s):  
Life History ◽  
Bark Beetle ◽  
Pinus Contorta ◽  
Life History Traits ◽  
Lodgepole Pine ◽  
Degree Days ◽  
Northern Portion ◽  
History Of ◽  
Bark Beetle Associates

AbstractPseudips mexicanus (Hopkins) is a secondary bark beetle native to western North and Central America that attacks most species of pine (Pinus L. (Pinaceae)) within its range. A pair of life-history studies examined P. mexicanus in other host species, but until now, no work has been conducted on lodgepole pine (Pinus contorta Douglas ex Louden var. latifolia Engelm. ex S. Watson). Pseudips mexicanus in lodgepole pine was found to be polygynous. Galleries were shorter, offspring smaller, and the eggs laid per niche and the potential progeny fewer than in populations from California and Guatemala. Development from the time of female attack to emergence of adult offspring took less than 50 days at 26.5 °C, and the accumulated heat required to complete the life cycle was determined to be 889.2 degree days above 8.5 °C, indicating that in the northern portion of its range P. mexicanus is univoltine. Determination of these life-history traits will facilitate study of interactions between P. mexicanus and other bark beetle associates in lodgepole pine.

Life history variation in plants: an exploration of the fast-slow continuum hypothesis

1996 ◽  
Vol 351 (1345) ◽  
pp. 1341-1348 ◽  
Keyword(s):  
Life History ◽  
Life Histories ◽  
Sexual Maturity ◽  
Life History Traits ◽  
Continuum Hypothesis ◽  
Adult Mortality ◽  
Life Cycles ◽  
Differential Mortality ◽  
Life History Variation ◽  
Net Reproductive Rate

Several empirical models have attempted to account for the covariation among life history traits observed in a variety of organisms. One of these models, the fast-slow continuum hypothesis, emphasizes the role played by mortality at different stages of the life cycle in shaping the large array of life history variation. Under this scheme, species can be arranged from those suffering high adult mortality levels to those undergoing relatively low adult mortality. This differential mortality is responsible for the evolution of contrasting life histories on either end of the continuum. Species undergoing high adult mortality are expected to have shorter life cycles, faster development rates and higher fecundity than those experiencing lower adult mortality. The theory has proved accurate in describing the evolution of life histories in several animal groups but has previously not been tested in plants. Here we test this theory using demographic information for 83 species of perennial plants. In accordance with the fast-slow continuum, plants undergoing high adult mortality have shorter lifespans and reach sexual maturity at an earlier age. However, demographic traits related to reproduction (the intrinsic rate of natural increase, the net reproductive rate and the average rate of decrease in the intensity of natural selection on fecundity) do not show the covariation expected with longevity, age at first reproducion and life expectancy at sexual maturity. Contrary to the situation in animals, plants with multiple meristems continuously increase their size and, consequently, their fecundity and reproductive value. This may balance the negative effect of mortality on fitness, thus having no apparent effect in the sign of the covariation between these two goups of life history traits.

Life-history traits of a small-bodied coastal shark

2013 ◽  
Vol 64 (1) ◽  
pp. 54 ◽  
Author(s):  
Adrian N. Gutteridge ◽  
Charlie Huveneers ◽  
Lindsay J. Marshall ◽  
Ian R. Tibbetts ◽  
Mike B. Bennett
Keyword(s):  
Life History ◽  
Life Histories ◽  
Life History Traits ◽  
Logistic Function ◽  
Early Maturation ◽  
Large Size ◽  
History Of ◽  
Age Model ◽  
Best Fit ◽  
Combined Data

The life histories of small-bodied coastal sharks, particularly carcharhinids, are generally less conservative than those of large-bodied species. The present study investigated the life history of the small-bodied slit-eye shark, Loxodon macrorhinus, from subtropical Hervey Bay, Queensland, and compared this species' biology to that of other coastal carcharhinids. The best-fit age model provided parameters of L∞ = 895 mm total length (TL), k = 0.18 and t0 = –6.3 for females, and L∞ = 832 mm TL, k = 0.44 and t0 = –2.6 for males. For sex-combined data, a logistic function provided the best fit, with L∞ = 842 mm TL, k = 0.41 and α = –2.2. Length and age at which 50% of the population was mature was 680 mm TL and 1.4 years for females, and 733 mm TL and 1.9 years for males. Within Hervey Bay, L. macrorhinus exhibited an annual seasonal reproductive cycle, producing an average litter of 1.9 ± 0.3 s.d. With the exception of the low fecundity and large size at birth relative to maximum maternal TL, the life-history traits of L. macrorhinus are comparable to other small-bodied coastal carcharhinids, and its apparent fast growth and early maturation contrasts that of large-bodied carcharhinids.

scholarly journals Transgenerational effects on development following microplastic exposure in Drosophila melanogaster

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11369
Author(s):  
Eva Jimenez-Guri ◽  
Katherine E. Roberts ◽  
Francisca C. García ◽  
Maximiliano Tourmente ◽  
Ben Longdon ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Life History ◽  
Polyvinyl Chloride ◽  
Life History Traits ◽  
Pupal Stage ◽  
Life Cycles ◽  
Adult Size ◽  
Chemical Additives ◽  
Plastic Pollution ◽  
Marine Realm

Background Plastic pollution affects all ecosystems, and detrimental effects to animals have been reported in a growing number of studies. However, there is a paucity of evidence for effects on terrestrial animals in comparison to those in the marine realm. Methods We used the fly Drosophila melanogaster to study the effects that exposure to plastics may have on life history traits and immune response. We reared flies in four conditions: In media containing 1% virgin polyethylene, with no chemical additives; in media supplemented with 1% or 4% polyvinyl chloride, known to have a high content of added chemicals; and control flies in non-supplemented media. Plastic particle size ranged from 23–500 µm. We studied fly survival to viral infection, the length of the larval and pupal stage, sex ratios, fertility and the size of the resultant adult flies. We then performed crossings of F1 flies in non-supplemented media and looked at the life history traits of the F2. Results Flies treated with plastics in the food media showed changes in fertility and sex ratio, but showed no differences in developmental times, adult size or the capacity to fight infections in comparison with controls. However, the offspring of treated flies reared in non-supplemented food had shorter life cycles, and those coming from both polyvinyl chloride treatments were smaller than those offspring of controls.

Abundance and Life History of Mysis relicta in the St. Lawrence Great Lakes

1974 ◽  
Vol 31 (3) ◽  
pp. 319-325 ◽  
Author(s):  
G. F. Carpenter ◽  
E. L. Mansey ◽  
N. H. F. Watson
Keyword(s):  
Life History ◽  
Generation Time ◽  
Lake Superior ◽  
Life Cycles ◽  
Lake Huron ◽  
Summer Period ◽  
Mysis Relicta ◽  
Frequency Distributions ◽  
History Of ◽  
Major Period

In sampling on lakes Ontario, Erie, and Superior during three cruises from spring to fall, and on Lake Huron during eight cruises, Mysis relicta was generally not taken or not abundant in waters less than 25 m in depth. Its abundance appeared to increase with depth at least up to 200 m. Populations appeared to be concentrated in waters 125–200 m deep during summer and more dispersed during spring and fall. Highest numbers were found in Lake Superior, followed by lakes Ontario and Huron. A small localized population was found in the deep eastern part of Lake Erie.Size-frequency distributions from the various cruises on lakes Superior, Huron, and Ontario indicated differences in life cycles of the mysid in the three lakes. In Lake Superior there was one major period of recruitment, from February to July, and the generation time appeared to be 2 yr. In lakes Huron and Ontario recruitment appeared to occur from February to August and to be separated into a winter and a summer period; each of the generations appeared to mature in 18 mo.

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