Applying comparative methods to different databases: lessons from demographic analyses across mammal species

2021 ◽  
pp. 299-312
Author(s):  
Jean-Michel Gaillard ◽  
Victor Ronget ◽  
Jean-François Lemaître ◽  
Christophe Bonenfant ◽  
Guillaume Péron ◽  
...  

Comparative demographic analyses aim to identify axes of variation in vital rates and the factors that determine the position of species along these axes. These analyses can be performed using different primary data sets, with marked heterogeneity in data quality and structure. Whether the outcome of demographic comparative analyses depends on the database used because theoretical predictions of evolutionary ecology are not that robust and depend on the set of species analysed or because data limitation prevents the identification of the expected patterns has never been investigated. This chapter fills this knowledge gap by performing a comparative demographic analysis across mammalian species from two distinct databases (Comadre and Malddaba) that were built for different purposes. The chapter first estimates some demographic metrics for each database, analyses their allometric relationships, and compares the estimates with theoretical expectations by performing phylogenetic regressions. Using Malddaba led to stronger allometric relationships closer to the expectation than Comadre. Moreover, the contribution of dimensionless demographic metrics to axes of variation in the shape of demographic trajectories was different between databases. The findings in the chapter demonstrate the key role of age dependence in vital rates for shaping demographic tactics across mammalian species and highlight the need for carefully choosing the database and the metrics to use depending on the question asked. Instead of opposing databases, the authors’ analysis nicely illustrates that different databases could be used to address different questions about life history variation.

2021 ◽  
Vol 2021 (2) ◽  
Author(s):  
DianYu Liu ◽  
ChuanLe Sun ◽  
Jun Gao

Abstract The possible non-standard interactions (NSIs) of neutrinos with matter plays important role in the global determination of neutrino properties. In our study we select various data sets from LHC measurements at 13 TeV with integrated luminosities of 35 ∼ 139 fb−1, including production of a single jet, photon, W/Z boson, or charged lepton accompanied with large missing transverse momentum. We derive constraints on neutral-current NSIs with quarks imposed by different data sets in a framework of either effective operators or simplified Z′ models. We use theoretical predictions of productions induced by NSIs at next-to-leading order in QCD matched with parton showering which stabilize the theory predictions and result in more robust constraints. In a simplified Z′ model we obtain a 95% CLs upper limit on the conventional NSI strength ϵ of 0.042 and 0.0028 for a Z′ mass of 0.2 and 2 TeV respectively. We also discuss possible improvements from future runs of LHC with higher luminosities.


Author(s):  
M P Roriz ◽  
M Lugaro ◽  
C B Pereira ◽  
N A Drake ◽  
S Junqueira ◽  
...  

Abstract Barium (Ba) stars are chemically peculiar stars that display in their atmospheres the signature of the slow neutron-capture (the s-process) mechanism that occurs in asymptotic giant branch (AGB) stars, a main contributor to the cosmic abundances. The observed chemical peculiarity in these objects is not due to self-enrichment, but to mass transfer between the components of a binary system. The atmospheres of Ba stars are therefore excellent astrophysical laboratories providing strong constraints for the nucleosynthesis of the s-process in AGB stars. In particular, rubidium (Rb) is a key element for the s-process diagnostic because it is sensitive to the neutron density and therefore its abundance can reveal the main neutron source for the s-process in AGB stars. We present Rb abundances for a large sample of 180 Ba stars from high resolution spectra (R = 48000), and we compare the observed [Rb/Zr] ratios with theoretical predictions from AGB s-process nucleosynthesis models. The target Ba stars in this study display [Rb/Zr] <0, showing that Rb was not efficiently produced by the activation of branching points. Model predictions from the Monash and FRUITY data sets of low-mass (≲ 4 M⊙) AGB stars are able to cover the Rb abundances observed in the target Ba stars. These observations indicate that the 13C(α,n)16O reaction is the main neutron source of the s-process in the low-mass AGB companions of the observed Ba stars. We have not found in the present study candidate companion for IR/OH massive AGB stars.


1990 ◽  
Vol 68 (12) ◽  
pp. 2457-2464 ◽  
Author(s):  
Susan M. Glenn

An unresolved question in conservation biology is whether a single large reserve will support more or fewer species than several smaller reserves adding up to the same total area, and how this affects species composition. Within 'mammal provinces' of Canada, several parks supported the same number of mammalian species, or more, than a single large park with the same area. The proportion of species that require undisturbed habitats increased with total area conserved. Human disturbances should be reduced in parks because these undisturbed-site species are unable to survive in disturbed environments not protected by a park system. An analysis of species distributions across parks indicated that not all small parks had the same composition. I therefore recommend establishing many parks in a biologically defined region and incorporating as much total area as possible. To aid in developing a strategy for placing parks across Canada, areas with high total mammalian richness and high richness of mammal species intolerant of disturbances are highlighted. Maps showing these areas are particularly useful because it is unlikely that several large parks will be established in every region and it is therefore important to identify the most diverse sites.


2021 ◽  
Author(s):  
Andrew J Kavran ◽  
Aaron Clauset

Abstract Background: Large-scale biological data sets are often contaminated by noise, which can impede accurate inferences about underlying processes. Such measurement noise can arise from endogenous biological factors like cell cycle and life history variation, and from exogenous technical factors like sample preparation and instrument variation.Results: We describe a general method for automatically reducing noise in large-scale biological data sets. This method uses an interaction network to identify groups of correlated or anti-correlated measurements that can be combined or “filtered” to better recover an underlying biological signal. Similar to the process of denoising an image, a single network filter may be applied to an entire system, or the system may be first decomposed into distinct modules and a different filter applied to each. Applied to synthetic data with known network structure and signal, network filters accurately reduce noise across a wide range of noise levels and structures. Applied to a machine learning task of predicting changes in human protein expression in healthy and cancerous tissues, network filtering prior to training increases accuracy up to 43% compared to using unfiltered data.Conclusions: Network filters are a general way to denoise biological data and can account for both correlation and anti-correlation between different measurements. Furthermore, we find that partitioning a network prior to filtering can significantly reduce errors in networks with heterogenous data and correlation patterns, and this approach outperforms existing diffusion based methods. Our results on proteomics data indicate the broad potential utility of network filters to applications in systems biology.


Rangifer ◽  
2019 ◽  
Vol 39 (1) ◽  
pp. 43-58
Author(s):  
Alexander K. Prichard ◽  
Ryan L. Klimstra ◽  
Brian T. Person ◽  
Lincoln S. Parrett

With industrial development expanding in the Arctic, there is increasing interest in quantifying the impacts of development projects on barren ground caribou (Rangifer tarandus granti). The primary data source to assess caribou distribution and predict impacts in remote areas of Alaska has shifted in recent decades from aerial survey data to telemetry data, but these techniques have different strengths and weaknesses. The ranges of two caribou herds, the Western Arctic Herd and the Teshekpuk Herd, overlap in northwest Alaska between Wainwright and Atqasuk, Alaska. Based on long-term telemetry data sets, this region was thought to be outside of the core calving ranges of both herds. Calving has long been reported to occur in this general area, but early reports assumed caribou were from the Western Arctic Herd and only one systematic aerial survey of caribou density and distribution during calving has been conducted in this area in recent decades. Following interest in industrial development in this area, we conducted aerial strip-transect surveys during early to mid-June 2013–2015 to directly assess the density and distribution of caribou in the area and we used existing telemetry data to compare our results to the seasonal distribution of both herds. Total caribou densities varied between 0.36 and 1.06 caribou/km² among years, and calf densities varied 0.04 and 0.25 calves/km² among years. Contrary to assumptions by early researchers in the area, telemetry data indicated that caribou in this area during early to mid-June were from the Teshekpuk Herd. The use of telemetry data alone underestimated the importance of this area for calving, but the combination of aerial surveys and telemetry data provided complementary information on caribou use of this area showing the importance of collecting the appropriate types of data for assessing potential impacts of development on caribou.


Paleobiology ◽  
1996 ◽  
Vol 22 (2) ◽  
pp. 121-140 ◽  
Author(s):  
Mike Foote ◽  
David M. Raup

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy.Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased. (3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.


Author(s):  
T. S. Kemp

From the very start of the spread of humans, the world’s mammals have been irreversibly, and mostly detrimentally, affected through direct exploitation for food and for skins to make clothes and shelter. Our domestication of certain mammal species has also had a huge impact on the rest of the world’s mammalian fauna, and indeed on its whole biota. ‘Humans and mammals: the past and the future’ considers how human activity has caused the latest megafaunal extinction and looks at the future crisis facing many mammalian species. A quarter of mammalian species are, today, faced with severe population decreases that may result in extinction. What can be done to conserve them?


The Condor ◽  
2000 ◽  
Vol 102 (1) ◽  
pp. 9-22 ◽  
Author(s):  
Robert E. Ricklefs

Abstract Although we have learned much about avian life histories during the 50 years since the seminal publications of David Lack, Alexander Skutch, and Reginald Moreau, we still do not have adequate explanations for some of the basic patterns of variation in life-history traits among birds. In part, this reflects two consequences of the predominance of evolutionary ecology thinking during the past three decades. First, by blurring the distinction between life-history traits and life-table variables, we have tended to divorce life histories from their environmental context, which forms the link between the life history and the life table. Second, by emphasizing constrained evolutionary responses to selective factors, we have set aside alternative explanations for observed correlations among life-history traits and life-table variables. Density-dependent feedback and independent evolutionary response to correlated aspects of the environment also may link traits through different mechanisms. Additionally, in some cases we have failed to evaluate quantitatively ideas that are compelling qualitatively, ignored or explained away relevant empirical data, and neglected logical implications of certain compelling ideas. Comparative analysis of avian life histories shows that species are distributed along a dominant slow-fast axis. Furthermore, among birds, annual reproductive rate and adult mortality are directly proportional to each other, requiring that pre-reproductive survival is approximately constant. This further implies that age at maturity increases dramatically with increasing adult survival rate. The significance of these correlations is obscure, particularly because survival and reproductive rates at each age include the effects of many life-history traits. For example, reproductive rate is determined by clutch size, nesting success, season length, and nest-cycle length, each of which represents the outcome of many different interactions of an individual's life-history traits with its environment. Resolution of the most basic issues raised by patterns of life histories clearly will require innovative empirical, modeling, and experimental approaches. However, the most fundamental change required at this time is a broadening of the evolutionary ecology paradigm to include a variety of alternative mechanisms for generating patterns of life-history variation.


2019 ◽  
Vol 59 ◽  
pp. e20195942 ◽  
Author(s):  
Átilla Colombo Ferreguetti ◽  
Isadora Cristina Motta Lessa ◽  
Emerson Monteiro Vieira ◽  
André Almeida Cunha ◽  
Helena Godoy Bergallo

The Cerrado is the second largest Brazilian biome and only 2.8% is represented by protected areas. Considering the relevance of the Cerrado and Conservation Units in preserving the mammalian diversity, we provided the first assessment of the diversity of medium- and large-sized mammal species in the Chapada dos Veadeiros National Park (CVNP) and surroundings. We tested the effectiveness of the CVNP by assessing the difference in species composition within the park and its surroundings. We sampled CVNP in the rainy (October-December 2013) and dry seasons (March-June 2014) in order to characterize the seasonality within the community. We selected 36 sampling sites to evaluate the composition of the medium and large mammals in the CVNP and its surroundings, 18 in the CVNP and 18 in the park surroundings. We ordered mammalian composition and frequency of individuals data by using a Non-metric Multidimensional Scaling analysis (NMDS). We assessed the effect of season (dry and rainy seasons) and locality (within the CVNP and surroundings) on mammalian species richness with a two-way analysis of variance (Two-way ANOVA). We recorded 23 species, 13 within the CVNP and 17 species in its surroundings. Composition and frequency of records differed between dry and rainy seasons, with higher richness in the rainy season. Species’ composition and the frequency of records were also different between within the CVNP and its surroundings, with higher richness in the surroundings. These results provide information for the increase of the knowledge of mammalian ecology but also is useful as a tool for future strategies to the conservation of these species. More attention should be given to the monitoring of these species in the long term because this area still harbor some viable populations.


Ecology ◽  
2009 ◽  
Vol 90 (3) ◽  
pp. 720-728 ◽  
Author(s):  
Amanda M. Sparkman ◽  
Carol M. Vleck ◽  
Anne M. Bronikowski

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