Coevolution of species colonisation rates controls food-chain length in spatially structured food webs

How the complexity of food webs depends on environmental variables is a long-standing ecological question. It is unclear though how food-chain length should vary with adaptive evolution of the constitutive species. Here we model the evolution of species colonisation rates and its consequences on occupancies and food-chain length in metacommunities. When colonisation rates can evolve, longer food-chains can persist. Extinction, perturbation and habitat loss all affect evolutionarily stable colonisation rates, but the strength of the competition-colonisation trade-off has a major role: weaker trade-offs yield longer chains. Although such eco-evo dynamics partly alleviates the spatial constraint on food-chain length, it is no magic bullet: the highest, most vulnerable, trophic levels are also those that least benefit from evolution. We provide qualitative predictions regarding how trait evolution affects the response of communities to disturbance and habitat loss. This highlights the importance of eco-evolutionary dynamics at metacommunity level in determining food-chain length.     

Economics of membrane occupancy and respiro‐fermentation

The simultaneous utilization of efficient respiration and inefficient fermentation even in the presence of abundant oxygen is a puzzling phenomenon commonly observed in bacteria, yeasts, and cancer cells. Despite extensive research, the biochemical basis for this phenomenon remains obscure. We hypothesize that the outcome of a competition for membrane space between glucose transporters and respiratory chain (which we refer to as economics of membrane occupancy) proteins influences respiration and fermentation. By incorporating a sole constraint based on this concept in the genome‐scale metabolic model of Escherichia coli, we were able to simulate respiro‐fermentation. Further analysis of the impact of this constraint revealed differential utilization of the cytochromes and faster glucose uptake under anaerobic conditions than under aerobic conditions. Based on these simulations, we propose that bacterial cells manage the composition of their cytoplasmic membrane to maintain optimal ATP production by switching between oxidative and substrate‐level phosphorylation. These results suggest that the membrane occupancy constraint may be a fundamental governing constraint of cellular metabolism and physiology, and establishes a direct link between cell morphology and physiology.     

Studying Large Mammals With Imperfect Detection: Status and Habitat Preferences of Wild Cattle and Large Carnivores in Eastern Cambodia

Studying large mammal species in tropical forests is a conservation challenge with species’ behavior and ecology often increasing the probability of non‐detection during surveys. Consequently, knowledge of the distribution, status, and natural history of many large mammal species in Southeast Asia is limited. I developed occupancy models from camera‐trapping data, thereby accounting for imperfect detection at sampling sites, to clarify the status and habitat requirements of four globally threatened or near threatened large mammals (banteng Bos javanicus, gaur Bos gaurus, dhole Cuon alpinus, and leopard Panthera pardus) in Mondulkiri Protected Forest, eastern Cambodia. Camera traps were operational for >3500 trap nights with 202 photographic encounters of the four study species. Model averaged occupancy estimates were between 5 percent (leopard) and 140 percent (gaur) higher than naive estimates (i.e., proportion of camera‐trap sites species recorded from) thus highlighting the importance of accounting for detectability during conservation surveys. I recommend the use of an occupancy framework when using camera‐trap data to study the status, ecology, and habitat preferences of poorly known and elusive species. The results highlight the importance of mixed deciduous and semi‐evergreen forest for wild cattle in eastern Cambodia and I emphasize that these habitats must be considered in conservation planning across the Lower Mekong Dry Forest Ecoregion.     

Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish

The effectiveness and accuracy of detection using environmental DNA (eDNA) is dependent on understanding the influence laboratory methods such as DNA extraction and PCR strategies have on detection probability. Ideally choice of sampling and extraction method will maximize eDNA yield and detection probability. Determining the survey effort required to reach a satisfactory detection probability (via increased PCR replicates or more sampling) could compensate for a lower eDNA yield if the sampling and extraction method has other advantages for a study, species or system. I analysed the effect of three different sampling and extraction methods on eDNA yield, detection probability and PCR replication for detecting the endangered freshwater fish Macquaria australasica from water samples. The impact of eDNA concentration, PCR strategy, target amplicon size and two marker regions: 12S (a mitochondrial gene) and 18S (a nuclear gene) was also assessed. The choice of sampling and extraction method and PCR strategy, rather than amplicon size and marker region, had the biggest effect on detection probability and PCR replication. The PCR replication effort required to achieve a detection probability of 0.95, ranged from 2 to 6 PCR replicates depending on the laboratory method used. As all methods yielded eDNA from which M. australasica was detected using the three target amplicons, differences in eDNA yield and detection probability between the three methods could be mitigated by determining the appropriate PCR replication effort. Evaluating the effect sampling and extraction methods will have on the detection probability and determining the laboratory protocols and PCR replication required to maximize detection and minimize false positives and negatives is a useful first step for eDNA occupancy studies.     

Metapopulation theory for fragmented landscapes

We review recent developments in spatially realistic metapopulation theory, which leads to quantitative models of the dynamics of species inhabiting highly fragmented landscapes. Our emphasis is in stochastic patch occupancy models, which describe the presence or absence of the focal species in habitat patches. We discuss a number of ecologically important quantities that can be derived from the full stochastic models and their deterministic approximations, with a particular aim of characterizing the respective roles of the structure of the landscape and the properties of the species. These quantities include the threshold condition for persistence, the contributions that individual habitat patches make to metapopulation dynamics and persistence, the time to metapopulation extinction, and the effective size of a metapopulation living in a heterogeneous patch network.     

Spatio-temporal variation in post-recovery dynamics in a large Peregrine Falcon (Falco peregrinus) population in the Jura mountains 2000–2020†

After spectacular population crashes in the 1960 and 1970s, Peregrine Falcon Falco peregrinus populations recovered worldwide, and in the 2000s many study populations were back to normal. However, post-recovery trends have been documented less well. We combined three long-term population studies covering the entire Jura mountain range (16 304 km²) to examine spatio-temporal variation in population dynamics during 2000–2020 in 420 known nesting sites in five regions: Ain, Jura and Doubs in France, and Jura Sud and Jura Nord in Switzerland. Every year about 60% of all sites were surveyed at least once, and this proportion increased over time. We used Bayesian occupancy modelling to investigate site persistence and colonization probabilities and correct status and trend estimates for bias due to non-random site coverage. Based on the average of two models correcting for preferential sampling, we estimated that population size peaked in 2002 (Jura), 2005 (Doubs), 2007 (Ain, Jura Nord) and in 2007 for the Jura as a whole. Thereafter, the population declined significantly in four regions and in the Jura as a whole, with the strongest decline found in the Jura Nord ( –38%, 95% credible interval –34%/–41%) during 2007–2020. Thus, we found considerable spatial heterogeneity in post-recovery trends and widespread post-recovery declines. Reasons for the latter may include Eagle Owl Bubo bubo predation, illegal persecution and human disturbance. Our results illustrate how quickly positive population trends may be reversed, such that continuous long-term monitoring even for species seemingly ‘out of danger’ remains invaluable. Our study also emphasizes the importance of correcting for both coverage bias in general and preferential sampling in particular when assessing population trends in studies where not every territory can be surveyed in all years.     

Occupancy of Mountain Plover and Burrowing Owl in Colorado

Abstract: Concern over the decline of grassland birds has spurred efforts to increase understanding of grassland bird-habitat relationships. Previous studies have suggested that black-tailed prairie dogs (Cynomys ludovicianus) provide important habitat for shortgrass prairie avifauna, such as mountain plover (Charadrius montanus) and western burrowing owl (Athene cunicularia hypugaea), although such studies are lacking in Colorado (USA). We used methods to estimate occupancy (ψ) of mountain plover and burrowing owl on prairie dog colonies and other shortgrass prairie habitats in eastern Colorado. Mountain plover occupancy was higher on prairie dog colonies (ψ = 0.50, 95% CI = 0.36–0.64) than on grassland (ψ = 0.07, 95% CI = 0.03–0.15) and dryland agriculture (ψ = 0.13, 95% CI = 0.07–0.23). Burrowing owl occupancy was higher on active prairie dog colonies (ψ = 0.80, 95% CI = 0.66–0.89) compared with inactive colonies (ψ = 0.23, 95% CI = 0.07–0.53), which in turn was much higher than on grassland (ψ = 0.01, 95% CI = 0.00–0.07) and dryland agriculture (ψ = 0.00, 95% CI ψ 0.00–0.00). Mountain plover occupancy also was positively correlated with increasing amounts of prairie dog colony in the landscape. Burrowing owl occupancy was negatively correlated with increasing amounts of prairie dog colony in the surrounding landscape. Our results suggest that actions to conserve mountain plovers and burrowing owls should incorporate land management to benefit prairie dogs. Because managing for specific colony attributes is difficult, alternative management that promotes heterogeneity may ensure that suitable habitat is available for the guild of grassland inhabitants.     

Cattle grazing in CRP grasslands during the nesting season: effects on avian abundance and diversity

The Conservation Reserve Program (CRP) is a primary tool for restoring grassland in the United States, in part as wildlife habitat, which has benefited declining grassland bird populations. Among potential mid-contract management practices used to maintain early-successional CRP grasslands, cattle grazing had been prohibited and is currently disincentivized during the primary nesting season for birds (much of the growing season), despite the important role that large herbivores historically played in structuring grassland ecosystems. Conservative grazing of CRP grasslands could increase spatial heterogeneity in vegetation structure and plant diversity, potentially supporting higher densities of some grassland bird species and higher bird diversity. Our objective was to determine the effect of experimental cattle grazing on species-specific relative abundance and occupancy, species diversity, and community dissimilarity of grassland birds on CRP grasslands across the longitudinal extent of Kansas, USA (a 63.5-cm precipitation gradient) during the 2017–2019 avian breeding seasons. Fifty-three of 108 fields were grazed by cattle during the growing seasons of 2017 and 2018 and all fields were rested from grazing in 2019. For all analyses, we examined separate model sets for semiarid western versus more mesic eastern Kansas. Using data from line transect surveys, we modeled relative abundances of 5 songbird species: grasshopper sparrow (Ammodramus savannarum), dickcissel (Spiza americana), eastern meadowlark (Sturnella magna), western meadowlark (Sturnella neglecta), and brown-headed cowbird (Molothrus ater). Grazing had delayed yet positive effects on abundances of grasshopper sparrow in western Kansas, and eastern meadowlark in eastern Kansas, but negative effects on dickcissel abundance in western Kansas and especially on burned fields in eastern Kansas. Somewhat counterintuitively, brown-headed cowbirds in western Kansas were more abundant on ungrazed versus grazed fields in the years after grazing began. In addition, we modeled multi-season occupancy of 3 gamebird species (ring-necked pheasant [Phasianus colcicus], northern bobwhite [Colinus virginianus], mourning dove [Zenaida macroura]) and Henslow's sparrow (Centronyx henslowii); grazing did not affect occupancy of these species. In eastern Kansas, species diversity was highest in grazed, unburned fields. In western Kansas, bird communities in grazed and ungrazed fields were dissimilar, as determined from multivariate analysis. Though regionally variable, conservative stocking of cattle on CRP grasslands during the nesting season as a mid-contract management tool might increase bird species diversity by restructuring habitat that accommodates a greater variety of species and decreasing abundances of species associated with taller, denser stands of vegetation.