Biology subjects

Ives, A. R.

Publications and source records attributed to Ives, A. R..

10 recordsLinked to original sources

bioRxiv2025

The forecasted mean of 80 percent of wild populations and communities shows no change, and why

Many retrospective analyses of biodiversity trends reveal a complex picture, including significant declines but also increases. However, prospective analyses (i.e. what near-term trends to expect) remain comparatively rare. Here, we generate and assess forecasts for approximately 43,000 population-level and 10,000 community-level time series from localities across the globe and covering taxa across the Tree of Life. Using unobserved components models and model selection, we found that only 23.5% of wild populations exhibit forecasted time trends (with increasing and decreasing trends roughly equal), while 76.5% show a forecasted constant mean. For communities (temporal - and {beta}-diversity), this figure rises to 84.0%. We identified high variation in the rate of change, var(RoC), as the most important predictor of a forecasted constant mean, and it scaled more strongly with intrinsic ecological dynamics than observation noise. Furthermore, biological structure (taxonomy, life-history traits, and locality) contributed to the identification of trends, highlighting that biological factors underlie, in part, predictions of trends. In summary, despite time trends being identifiable in ecological time-series data, parsimonious statistical models will very often forecast no change. Our results suggest that the absence of directional change may be the norm rather than the exception across the Tree of Life.

ecology↗

bioRxiv2024

Enemy release of introduced parasitoids does not affect their establishment or success

The enemy release hypothesis, that the success of invading species is due to release from natural enemies that occur in their home range but not in the new range, can be an important explanation for successful invasions. Testing this hypothesis is difficult, however, because testing requires documented cases of not only successful, but also unsuccessful invasions. Therefore, observational data on after-the-fact establishment following unintentional introductions is insufficient, because they only include successful invasions. Here, we investigate the role of enemy release for parasitoid biological control agents and their hyperparasitoid natural enemies. We created a dataset of all aphid parasitoid wasp species introduced into North America, including data on their hyperparasitoid species in the native and new range. In total, information on 29 species of primary parasitoids and 54 species of hyperparasitoids was obtained, combining to create 259 parasitoid-hyperparasitoid species associations. Results show that introduced parasitoids experience partial enemy release, but the degree of enemy release does not affect the chance of successful establishment or successful control. This lack of effect of enemy release might be due to the broad geographical range of the hyperparasitoids (perhaps from unintentional introductions) which reduces the degree of enemy release. In addition, the life-history traits of the hyperparasitoid communities in the new range were different from the native range, with relatively more generalist hyperparasitoid species in the new range. These results show that introduced natural enemies can experience enemy release, but that this does not necessarily help to predict their successful establishment.

ecology↗

bioRxiv2023

Shared features underlying compact genomes and extreme habitat use in chironomid midges

Non-biting midges (family Chironomidae) are found throughout the world in a diverse array of aquatic and terrestrial habitats, can often tolerate harsh conditions such as hypoxia or desiccation, and have consistently compact genomes. Yet we know little about the shared molecular basis for these attributes and how they have evolved across the family. Here, we address these questions by first creating high-quality, annotated reference assemblies for Tanytarsus gracilentus (subfamily Chironominae, tribe Tanytarsini) and Parochlus steinenii (subfamily Podonominae). Using these and other publicly available assemblies, we created a time-calibrated phylogenomic tree for family Chironomidae with outgroups from order Diptera. We used this phylogeny to test for features associated with compact genomes, as well as examining patterns of gene family evolution and positive selection that may underlie chironomid habitat tolerances. Our results suggest that compact genomes evolved in the most recent common ancestor of Chironomidae and Ceratopogonidae, and that this occurred mainly through reductions in non-coding regions (introns, intergenic sequences, and repeat elements). Gene families that significantly expanded in Chironomidae included biological processes that may relate to tolerance of stressful environments, such as temperature homeostasis, inflammatory response, melanization defense response, and trehalose transport. We identified a number of genes with evidence for positive selection in Chironomidae, notably sulfonylurea receptor, peroxiredoxin-1, and protein kinase D. Our results help to understand the genomic basis for the small genomes and extreme habitat use in this widely distributed group. Significance StatementChironomid midges are known for having small genomes and being able to tolerate many forms of environmental stress, yet little is known of the shared features of their genomes that may underlie these traits. We found that reductions in non-coding regions coincide with small chironomid genomes, and we identified duplicated and/or selected genes that may equip chironomids to tolerate harsh conditions. These results describe the key genomic changes in chironomid midges that may explain their ability to inhabit a range of extreme habitats across the world.

genomics↗

bioRxiv2023

Predictability of ecological and evolutionary dynamics in a changing world

Ecological and evolutionary predictions are being increasingly employed to inform decision-makers confronted with intensifying pressures menacing life on Earth. For these efforts to effectively guide conservation actions, knowing the limit of predictability is pivotal. In this study, we provide realistic expectations about the enterprise of predicting changes in ecological and evolutionary observations through time. We begin with an intuitive explanation of predictability (that is, the extent to which predictions are possible) employing an easy-to-use metric, predictive power PP(t). To illustrate the challenge of forecasting, we then show that among insects, birds, fishes, and mammals (i) 50% of the populations are predictable at most one year in advance, and (ii) the median one-year-ahead predictive power corresponds to a sobering prediction R2 of approximately 20%. Nonetheless, predictability is not an immutable property of ecological systems. For example, different harvesting strategies can impact the predictability of exploited populations to varying degrees. Moreover, considering multivariate time series, incorporating explanatory variables or accounting for time trends (environmental forcing) can enhance predictability. To effectively address the urgent challenge of biodiversity loss, researchers and practitioners must be aware of the predictive information within the available data and explore efficient ways to leverage this information for environmental stewardship.

ecology↗

bioRxiv2022

When should coevolution among competitors promote coexistence versus exclusion?

Coevolution of competitors can lead to niche partitioning promoting coexistence or to heightened conflicts promoting competitive exclusion. If both are possible, when should coevolution favor coexistence versus exclusion? We investigated this question with a general eco-evolutionary model in which species can reduce the interspecific competition they experience through evolutionary investments in two types of competitive traits: partitioning traits that promote coexistence and conflict traits that promote exclusion. We found that communities were generally mixed, consisting of species investing in both trait types or mixtures of species specializing in one type. For each species, its competitors abundances and investments determined its experienced competition, and stronger competition begot greater competitive trait investment. Species investing in conflict traits strengthened competition for other species both directly and indirectly, whereas partitioning traits only weakened competition via direct effects. Conflict traits were therefore the stronger driver of community-wide investments in all traits. However, species investing most in conflict traits experienced less competition, so they ultimately evolved least investment, making them most likely to be excluded by the next invader. Thus, coevolution may provide an open door for species that play nice and a revolving door of exclusion for those that do not.

ecology↗

bioRxiv2022

Resource use differences of two coexisting chironomid species at localized scales

The abundances of competing species may show positive correlations in time and space if they rely on a shared resource. Such positive correlations might obscure resource partitioning that facilitates coexistence of competitors and affects their abundances, spatial distributions, and population dynamics. Here, we examine the potential for resource partitioning between two ecologically similar midge species (Diptera: Chironomidae) in Lake Myvatn, Iceland. Tanytarsus gracilentus and Chironomus islandicus larvae coexist at high abundances in benthic habitats, and they have been previously described as feeding upon diatoms and detritus. Furthermore, both species show large, roughly synchronized population fluctuations, implying potential reliance on a shared fluctuating resource and posing the question of how these species coexist at high abundances. We first considered spatial partitioning of larvae; across multiple sites, abundances of both species were positively correlated. Thus, spatial partitioning across different sites in the lake did not appear to be strong. We then inferred differences in dietary resource use with stable carbon isotopes. T. gracilentus larvae had higher {delta}13C values than C. islandicus (mean difference = 5.39 {+/-} 1.84{per thousand}), suggesting interspecific differences in resource use. Differences in resource selectivity, tube-building behavior, and feeding styles may facilitate resource partitioning between these two species. Relative to surface sediments, T. gracilentus had higher {delta}13C values (1.84 {+/-} 0.96{per thousand}), suggesting that they selectively graze on 13C-enriched resources such as productive algae from the surface of their tubes. In contrast, C. islandicus had lower {delta}13C values than surface sediments (-2.87 {+/-} 1.95{per thousand}), suggesting reliance on isotopically depleted resources, which may include detrital organic matter and associated microbes that larvae selectively consume from the sediment surface or within their tube walls. Overall, our study illustrates that coexisting and ecologically similar species may show positive correlations in space and time while using different resources at fine spatial scales.

ecology↗

bioRxiv2021

Dependence of an aquatic insect population on contemporaneous primary production

O_LICharacterizing the dynamics of energy flow through ecosystems requires quantifying the degree to which primary and secondary production are coupled. This coupling is expected to be tight in ecosystems with high internal production relative to external carbon and energy inputs. C_LIO_LIWe experimentally quantified the dependence of aquatic insect emergence on fresh primary production, specifically for the midge population in Lake Myvatn, Iceland. Using field mesocosms, we manipulated algal primary production by reducing light availability via shading. We then used dissolved oxygen incubations to estimate fluxes of carbon through photosynthesis (i.e., gross primary production or "GPP") over the course of the experiment. C_LIO_LIWe found that elevated GPP was associated with higher emergence rates of adults, as judged both by comparison of emergence across the experimental shading treatments and estimates of in situ GPP within the mesocosms. Furthermore, larger adults emerged earlier than smaller ones, suggesting that asymmetries in resource availability among individuals affected the timing of emergence. Nonetheless, midge emergence was substantial under light-limiting conditions, indicating that while midges benefit from primary production contemporaneous with larval development, they are also capable of completing their life cycles on carbon already existing in the organic matter pool. C_LIO_LIOur results show that even in systems with limited allochthonous inputs, contemporaneous primary production may be not necessary for high secondary production and insect emergence. Instead, consumers can develop from consumption of biomass derived from past autochthonous primary production. This suggests that primary production and consumer dynamics can be partially decoupled in time in systems that depend on internal production. C_LI

ecology↗

bioRxiv2020

phyr: An R package for phylogenetic species-distribution modelling in ecological communities

O_LIModel-based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model-based methods do not include phylogenies despite the well-known importance of phylogenetic relationships in shaping species distributions and community composition. In part, this is due to lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily. C_LIO_LITo fill this gap, the R package phyr (pronounced fire) implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other ecological and evolutionary phenomena. The phyr workhorse functions are implemented in C++ making all calculations and model estimations fast. C_LIO_LIphyr can fit a variety of models such as phylogenetic joint-species distribution models, spatiotemporal-phylogenetic autocorrelation models, and phylogenetic trait-based bipartite network models. phyr also estimates phylogenetically independent trait correlations with measurement error to test for adaptive syndromes and performs fast calculations of common alpha and beta phylogenetic diversity metrics. All phyr methods are united under Brownian motion or Ornstein-Uhlenbeck models of evolution and phylogenetic terms are modelled as phylogenetic covariance matrices. C_LIO_LIThe functions and model formula syntax we propose in phyr serves as a simple and unified framework that ignites the use of phylogenies to address a variety of ecological questions. C_LI

ecology↗

bioRxiv2017

Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment

Although genome sequencing is becoming cheaper and faster, reducing the quantity of data by only sequencing part of the genome lowers both sequencing costs and computational burdens. One popular genome-reduction approach is restriction site associated DNA sequencing, or RADseq. RADseq was initially designed for studying genetic variation across genomes usually at the population level, and it has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data. Alignment-free methods are both efficient and accurate for phylogenetic reconstructions with whole genomes and are especially practical for non-model organisms; nonetheless, alignment-free methods have only been applied with whole genome sequences. Here, we test a full-genome assembly and alignment-free method, AAF, in application to RADseq data and propose two procedures for reads selection to remove missing data. We validate these methods using both simulations and a real dataset. Reads selection improved the accuracy of phylogenetic construction in every simulated scenario and the real dataset, making AAF comparable to or better than alignment-based method with much lower computation burdens. We also investigated the sources of missing data in RADseq and their effects on phylogeny reconstruction using AAF. The AAF pipeline modified for RADseq data, phyloRAD, is available on github (https://github.com/fanhuan/phyloRAD).

bioinformatics↗

bioRxiv2016

The need to include phylogeny in trait-based analyses of community composition

O_LIA growing number of studies incorporate functional trait information to analyse patterns and processes of community assembly. These studies of trait-environment relationships generally ignore phylogenetic relationships among species. When functional traits and the residual variation in species distributions among communities have phylogenetic signal, however, analyses ignoring phylogenetic relationships can decrease estimation accuracy and power, inflate type I error rates, and lead to potentially false conclusions.\nC_LIO_LIUsing simulations, we compared estimation accuracy, statistical power, and type I error rates of linear mixed models (LMM) and phylogenetic linear mixed models (PLMM) designed to test for trait-environment interactions in the distribution of species abundances among sites. We considered the consequences of both phylogenetic signal in traits and phylogenetic signal in the residual variation of species distributions generated by an unmeasured (latent) trait with phylogenetic signal.\nC_LIO_LIWhen there was phylogenetic signal in the residual variation of species among sites, PLMM provided better estimates (closer to the true value) and greater statistical power for testing whether the trait-environment interaction regression coefficient differed from zero. LMM had unacceptably high type I error rates when there was phylogenetic signal in both traits and the residual variation in species distributions. When there was no phylogenetic signal in the residual variation in species distributions, LMM and PLMM had similar performances.\nC_LIO_LILMMs that ignore phylogenetic relationships can lead to poor statistical tests of trait-environment relationships when there is phylogenetic signal in the residual variation of species distributions among sites, such as caused by unmeasured traits. Therefore, phylogenies and PLMMs should be used when studying how functional traits affect species abundances among communities in response to environmental gradients.\nC_LI

ecology↗