Structure from motion photogrammetry in ecology: Does the choice of software matter?

Image‐based modeling, and more precisely, Structure from Motion (SfM) and Multi‐View Stereo (MVS), is emerging as a flexible, self‐service, remote sensing tool for generating fine‐grained digital surface models (DSMs) in the Earth sciences and ecology. However, drone‐based SfM + MVS applications have developed at a rapid pace over the past decade and there are now many software options available for data processing. Consequently, understanding of reproducibility issues caused by variations in software choice and their influence on data quality is relatively poorly understood. This understanding is crucial for the development of SfM + MVS if it is to fulfill a role as a new quantitative remote sensing tool to inform management frameworks and species conservation schemes. To address this knowledge gap, a lightweight multirotor drone carrying a Ricoh GR II consumer‐grade camera was used to capture replicate, centimeter‐resolution image datasets of a temperate, intensively managed grassland ecosystem. These data allowed the exploration of method reproducibility and the impact of SfM + MVS software choice on derived vegetation canopy height measurement accuracy. The quality of DSM height measurements derived from four different, yet widely used SfM‐MVS software—Photoscan, Pix4D, 3DFlow Zephyr, and MICMAC, was compared with in situ data captured on the same day as image capture. We used both traditional agronomic techniques for measuring sward height, and a high accuracy and precision differential GPS survey to generate independent measurements of the underlying ground surface elevation. Using the same replicate image dataset (n = 3) as input, we demonstrate that there are 1.7, 2.0, and 2.5 cm differences in RMSE (excluding one outlier) between the outputs from different SfM + MVS software using High, Medium, and Low quality settings, respectively. Furthermore, we show that there can be a significant difference, although of small overall magnitude between replicate image datasets (n = 3) processed using the same SfM + MVS software, following the same workflow, with a variance in RMSE of up to 1.3, 1.5, and 2.7 cm (excluding one outlier) for “High,” “Medium,” and “Low” quality settings, respectively. We conclude that SfM + MVS software choice does matter, although the differences between products processed using “High” and “Medium” quality settings are of small overall magnitude.     

Does rapid evolution matter? Measuring the rate of contemporary evolution and its impacts on ecological dynamics

Rapid contemporary evolution due to natural selection is common in the wild, but it remains uncertain whether its effects are an essential component of community and ecosystem structure and function. Previously we showed how to partition change in a population, community or ecosystem property into contributions from environmental and trait change, when trait change is entirely caused by evolution (Hairston et al. 2005). However, when substantial non-heritable trait change occurs (e.g. due to phenotypic plasticity or change in population structure) that approach can mis-estimate both contributions. Here, we demonstrate how to disentangle ecological impacts of evolution vs. non-heritable trait change by combining our previous approach with the Price Equation. This yields a three-way partitioning into effects of evolution, non-heritable phenotypic change and environment. We extend the approach to cases where ecological consequences of trait change are mediated through interspecific interactions. We analyse empirical examples involving fish, birds and zooplankton, finding that the proportional contribution of rapid evolution varies widely (even among different ecological properties affected by the same trait), and that rapid evolution can be important when it acts to oppose and mitigate phenotypic effects of environmental change. Paradoxically, rapid evolution may be most important when it is least evident.     

Drugs and parasites: global experiments in life history evolution?

Recent work has shown that the evolution of Drosophila melanogaster resistance to attack by the parasitoid Asobara tabida is constrained by a trade-off with larval competitive ability. However, there are two very important questions that need to be answered. First, is this a general cost, or is it parasitoid specific? Second, does a selected increase in immune response against one parasitoid species result in a correlated change in resistance to other parasitoid species? The answers to both questions will influence the coevolutionary dynamics of these species, and also may have a previously unconsidered, yet important, influence on community structure.     

Cadherins and the cortex: A matter of time?

Cell adhesion systems commonly operate in close partnership with the cytoskeleton. Adhesion receptors bind to the cortex and regulate its dynamics, organization and mechanics; conversely, the cytoskeleton influences aspects of adhesion, including strength, stability and ductility. In this review we consider recent advances in elucidating such cooperation, focusing on interactions between classical cadherins and actomyosin. The evidence presents an apparent paradox. Molecular mechanisms of mechanosensation by the cadherin-actin apparatus imply that adhesion strengthens under tension. However, this does not always translate to the broader setting of confluent tissues, where increases in fluctuations of tension can promote intercalation due to the shrinkage of adherens junctions. Emerging evidence suggests that understanding of timescales may be important in resolving this issue, but that further work is needed to understand the role of adhesive strengthening across scales.     

Are mimics monophyletic? The necessity of phylogenetic hypothesis tests in character evolution

Background  

The processes governing the origin and maintenance of mimetic phenotypes can only be understood in a phylogenetic framework. Phylogenetic estimates of evolutionary relationships can provide a context for analyses of character evolution; however, when phylogenetic estimates conflict, rigorous analyses of alternative evolutionary histories are necessary to determine the likelihood of a specific history giving rise to the observed pattern of diversity. The polyphenic butterfly Limenitis arthemis provides a case in point. This species is comprised of three lineages, two of which are mimetic and one of which is non-mimetic. Conflicting estimates of the relationships among these three lineages requires direct evaluation of the alternative hypotheses of mimicry evolution.     

Does centrifugation matter? Centrifugal force and spinning time alter the plasma metabolome

Background

Centrifugation is an indispensable procedure for plasma sample preparation, but applied conditions can vary between labs.

Aim

Determine whether routinely used plasma centrifugation protocols (1500×g 10 min; 3000×g 5 min) influence non-targeted metabolomic analyses.

Methods

Nuclear magnetic resonance spectroscopy (NMR) and High Resolution Mass Spectrometry (HRMS) data were evaluated with sparse partial least squares discriminant analyses and compared with cell count measurements.

Results

Besides significant differences in platelet count, we identified substantial alterations in NMR and HRMS data related to the different centrifugation protocols.

Conclusion

Already minor differences in plasma centrifugation can significantly influence metabolomic patterns and potentially bias metabolomics studies.

     

Does biogeographical history matter? Diversity and distribution of lotic midges (Diptera: Chironomidae) in the Australian Wet Tropics

Abstract We examined broad scale patterns of diversity and distribution of lotic Chironomidae (Diptera) within the Wet Tropics bioregion of northern Queensland, Australia. Field surveys across broad latitudinal and altitudinal gradients within the Wet Tropics revealed a fauna of 87 species‐level taxa in 49 genera comprising three main elements: a small genuinely tropical fraction, and larger cosmopolitan and Gondwanan components. The latter group originated when Australia, as part of the ancient Gondwana supercontinent, was situated over Antarctic latitudes with a cooler, wetter climate than today. In the Wet Tropics, cool Gondwanan taxa occurred predominantly in upland and shaded lowland sites, but no species appeared narrowly temperature restricted, and there was no faunal zonation with altitude. Most chironomid species occurred at all latitudes within the Wet Tropics, with no evidence for an enduring effect of the historical rainforest contractions on current‐day distribution patterns. These findings contrast with those for aquatic faunas elsewhere in the world and for the terrestrial Wet Tropics fauna. We relate this to the generally broad environmental tolerances of Australian chironomids, and comment on why the latitudinal diversity gradient does not apply to the Australian chironomid fauna.     

What can population genetics tell us about dispersal and biogeographic history of coral-reef fishes?

Abstract Coral-reef fishes, like many other marine organisms, generally possess a benthic adult stage and pelagic larval stage. What can population genetics studies tell us about the demographic, evolutionary and biogeographic consequences of this life cycle? Ten studies of geographical patterns of intraspecific genetic differentiation in reef fishes have been published. These studies have included 2t > species/species complexes (14 in the family Pomacentridae, the remaining 12 in 9 different families) and have been about equally divided between the tropical Pacific and the tropical western Atlantic. A survey of these studies shows the following: (i) the existence of the pelagic larval stage appears to have led to high levels of gene flow even among populations separated by thousands of kilometres of open ocean; (ii) an apparent pattern of increased gene flow among populations connected by intermediate 'stepping stones’; (iii) very tentative evidence for a relationship between length of pelagic larval life and gene flow; (iv) no clear relationship between egg type (pelagic rs non-pelagic) and gene flow; and (v) suggestive evidence that damselfishes (family Pomacentridae) may have more restricted dispersal (less gene flow) than other reef fishes. The application of current and future molecular tools has the strong potential to clarify some of these relationships, particularly by using relatively neutral genetic markers. Additionally, discoveries of DNA markers having very high rates of mutation may allow tracking of demographically relevant levels of larval dispersal. Molecular tools are becoming especially valuable in uncovering the biogeographic and phylogenetic history of reef fishes. The one molecular study to date has suggested that at least some speciation events may have occurred during the climate changes and sea-level regressions associated with Pleistocene glacial episodes. Molecular tools need to be used to further explore the means by which high species diversity can be generated in the face of the apparently high gene flow observed in most coral-reef fishes.     

Condensed tannins in the diets of primates: a matter of methods?

To understand the ways in which condensed tannins (CT) affect primate diet selection and nutritional status, correct measurements are essential. In the majority of studies of the CT contents of primate foods, a tannin source such as "quebracho" is used to standardize CT assays, but the CT in quebracho tannin may not be similar to those in the plants of interest. We investigated how the choice of standard to calibrate CT assays affects the estimation of CT in the diets of mountain gorillas (Gorilla beringei). We purified the CT from gorilla foods and compared the actual amounts of CT in the foods with estimates produced by using the quebracho tannin. When quebracho was used, the estimates of CT contents of gorilla foods were, on average, 3.6 times the actual content of CT so that the amounts in frequently eaten gorilla foods were substantially overestimated. The overestimation for a given plant could not be predicted reliably and the ranking of plants by tannin content differed according to the standard used. Our results demonstrate that accurate measurements of CT necessitate the use of tannins purified from the plant species of interest. A reevaluation of primatology studies using interspecific comparisons of tannin content will provide new insights into primate food selection and nutritional ecology.     

Does intrauterine site of insemination in cattle really matter?

Two trials were conducted to determine the influence of semen placement on pregnancy rate in dairy heifers and cows. Seventy-two dairy heifers were artificially inseminated (AI) 10 to 12 h after the first detection of estrus. Control heifers (n = 25) were inseminated at the junction of the uterine body and internal cervical os. The remaining heifers were inseminated deep in one uterine horn, 3 to 5 cm anterior to the external bifurcation. Twenty-three heifers were inseminated in the horn ipsilateral to the ovary bearing the ovulatory follicle, and 24 heifers were inseminated in the contralateral horn. Pregnancy rates did not differ for the three groups of heifers. In a second trial, 64 inseminations were performed in 38 nonlactating, adult dairy cattle. Thirty-one inseminations were made deep in the uterine horn ipsilateral to the ovary bearing the ovulatory follicle and 33 in the contralateral horn. Pregnancy rates were similar for both groups. Combining both trials, pregnancy rates for ipsilateral and contralateral inseminations were equal (32 54 = 59% and 34 57 = 60% , respectively). Therefore, placement of semen in one horn of the uterus does not appear to be a cause of decreased or increased pregnancy rate with AI.     

Trade-offs and the evolution of virulence of microparasites: do details matter?

Models of the within-host dynamics of parasites have been used to consider the evolution of microparasites causing acute infections in vertebrate hosts. In this paper, we use these models to examine how the level of virulence to which a parasite evolves, depends on factors such as the relationship between parasite density and its rate of transmission from infected hosts, and the mechanism of parasite-induced pathogenesis. We show that changes in the terms describing transmissibility and pathogenesis may lead to dramatic differences in the level of virulence to which a parasite evolves. This suggests that no single factor is likely to be responsible for the differences in virulence of different parasites, and that understanding of the evolution of virulence of parasites will require a detailed quantitative understanding of the interaction between the parasite and its host.     

Does one subgenome become dominant in the formation and evolution of a polyploid?

BackgroundPolyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution.ScopeIn addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered.ConclusionsContrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.     

Do biogeographic parameters matter? Plant species richness and distribution of macrophytes in relation to area and isolation of ponds in NW Polish agricultural landscape

Effects of pond size and isolation on total vascular plant species richness and number of obligate wetland species were compared. Subsequently, the potential for the presence of spatial patterns in wetland species distribution among ponds in an agricultural landscape was explored. Relationships between species richness and two main biogeographic parameters were analysed using simple and multiple linearised regression models. Spatial patterns were looked for by means of analyses carried out with the R CRAN software (join-count statistics). Simple regression analyses performed on the regional scale (n = 50) revealed the significance of the effect of pond size only (r = 0.46 for total plant species richness and r = 0.28 for wetland species richness vs. pond area). Further analyses conducted on the local scale identified the best multiple regression models in the largest pond cluster (n = 20); the models showed statistical significance of relationships between the species richness and both independent variables (r = 0.80 for total plant species richness and r = 0.70 for wetland species richness vs. pond area and isolation, including mean distance to the nearest ten ponds). Spatial analyses were performed for 26 obligate wetland species selected from 149 species recorded in all the 50 ponds. Exploratory spatial data analysis revealed the presence of significant positive spatial autocorrelation in the distribution of 8 species. In such cases, it is possible to reject the random distribution hypothesis, which justifies exploration of spatial regimes. In practice, correct spatial model specifications may have implications for predicting species occurrences under changing environmental conditions, e.g. changes in the number of ponds.     

Nectary structure of Labiatae in relation to their nectar secretion and characteristics in a Mediterranean shrub community — Does flowering time matter?

We studied the interrelation between nectary structure (13 parameters), nectar characteristics (yield, chemical composition), and flower size of 11 Labiatae species in a Mediterranean shrub community near Athens, Greece. We also explored whether the above attributes are affected by the Mediterranean summer drought constraints. Our findings show that among all nectary parameters studied, nectary size and stomatal opening are the most important in (positively) shaping nectar secretion, nectary size being the most meaningful. Nectary structure is correlated to quantity of the nectar secreted, not its quality. Wide flowers bear wide nectaries with large stomatal openings, whereas deep flowers are not related to any nectary size. Corolla size (both length and width) and nectary stomatal opening decrease with flowering time. This applies also to nectary size, nectar volume and sugar content of the perennials (9 species). All above cases of time dependence show that there is a constraint effect of Mediterranean climate on floral and nectary structure, reflected also as a decrease in nectar secretion. Nectary structure in Labiatae is largely shaped by both phylogenetic and climate constraints. On the other hand, although nectar is largely influenced by nectary structure, it is to a large extent ecologically biased, implying that, in addition to phylogeny, there are many other ecological parameters interfering in its secretion such as time within the season, life history, and light requirements.     

Does colonization asymmetry matter in metapopulations?

Despite the considerable evidence showing that dispersal between habitat patches is often asymmetric, most of the metapopulation models assume symmetric dispersal. In this paper, we develop a Monte Carlo simulation model to quantify the effect of asymmetric dispersal on metapopulation persistence. Our results suggest that metapopulation extinctions are more likely when dispersal is asymmetric. Metapopulation viability in systems with symmetric dispersal mirrors results from a mean field approximation, where the system persists if the expected per patch colonization probability exceeds the expected per patch local extinction rate. For asymmetric cases, the mean field approximation underestimates the number of patches necessary for maintaining population persistence. If we use a model assuming symmetric dispersal when dispersal is actually asymmetric, the estimation of metapopulation persistence is wrong in more than 50% of the cases. Metapopulation viability depends on patch connectivity in symmetric systems, whereas in the asymmetric case the number of patches is more important. These results have important implications for managing spatially structured populations, when asymmetric dispersal may occur. Future metapopulation models should account for asymmetric dispersal, while empirical work is needed to quantify the patterns and the consequences of asymmetric dispersal in natural metapopulations.     

Quail and rain in semiarid rangelands: Does management matter?

Rainfall is a strong driver of quail populations on southwestern rangelands and can account for a large portion (~70–95%) of the variability in regional quail production and abundance. Landowners have attempted to moderate these boom-and-bust fluctuations via management; however, presently it is unknown whether management can increase or stabilize quail populations in semiarid environments or whether rainfall remains as influential at small spatial extents. Our objectives were to evaluate the efficacy of management at mitigating the effects of rainfall on northern bobwhite (Colinus virginianus) populations on semiarid rangelands and to quantify the influence of rainfall on bobwhite density at smaller spatial extents. We conducted a study to evaluate these objectives during 2014–2020 in the Rio Grande Plains (n = 11 sites; 1,100‒6,500 ha) and Rolling Plains (n = 4 sites; 1,900‒4,000 ha) of Texas, USA. We estimated bobwhite density during late autumn (Dec‒Jan) on all sites using helicopter surveys within a distance-sampling framework. We also obtained site-level seasonal rainfall (Apr‒Aug) and quantified management intensity via landowner surveys and a scoring rubric to categorize sites into 3 classes (low, medium, and high management intensity). Bobwhite populations during this study experienced a boom-bust cycle in both the Rio Grande Plains and Rolling Plains, with mean bobwhite density fluctuating considerably (0.57‒2.96 bobwhites/ha and 0.02‒2.88 bobwhites/ha, respectively). In the Rio Grande Plains, mean bobwhite density significantly increased from low to high management intensity in 2015 (1.12 ± 0.17 bobwhites/ha vs. 2.87 ± 0.39 bobwhites/ha, respectively), 2016 (1.06 ± 0.20 bobwhites/ha vs. 2.96 ± 0.36 bobwhites/ha, respectively), 2017 (0.73 ± 0.16 bobwhites/ha vs. 1.91 ± 0.32 bobwhites/ha, respectively), and 2019 (0.42 ± 0.14 bobwhites/ha vs. 1.01 ± 0.26 bobwhites/ha, respectively; P < 0.05). In addition, rainfall at the site level accounted for a low amount of the variation in bobwhite density (r² = 0.09; P < 0.01). Similarly, in the Rolling Plains, mean bobwhite density significantly increased from low to high management intensity in 2015 (1.30 ± 0.27 bobwhites/ha vs. 2.20 ± 0.29 bobwhites/ha, respectively) and 2016 (1.26 ± 0.26 bobwhites/ha vs. 2.88 ± 0.34 bobwhites/ha, respectively; P < 0.05). Rainfall at the site level also accounted for a low amount of the variation in bobwhite density (r² < 0.02; P = 0.82). Our findings suggest that management can increase bobwhite density beyond that of less-managed properties but does not completely eliminate inter-annual fluctuations in semiarid environments. In addition, rainfall appears to exert less of an influence on bobwhite density at a site level (e.g., 2,000 ha) than has been documented at a regional level (e.g., ≥8 million ha).     

Does size really matter? Weight and values in public health

The medical community has long regarded obesity and overweight as serious health risks, and popular culture reflects these concerns. A focus on body weight reduction motivates many contemporary exercise and diet practices, especially among women. Yet, there is significant evidence that those risks have been exaggerated, that weight loss regimens may be more detrimental to health than moderate obesity, and that pressure to be thin leads to disordered eating and unhealthy lifestyle choices. This paper examines the problematic manners in which some national health policies regard the problems of overweight and obesity. It contends that concepts of aesthetics, grounded in 19th-century beliefs about the body, guide clinicians to emphasize measurement of the body in health assessment at potential cost to individual wellness.