Biology subjects

Mooers, A. O.

Publications and source records attributed to Mooers, A. O..

9 recordsLinked to original sources

bioRxiv2025

Tip rate estimates can predict future diversification, but are unreliable and context dependent

Understanding the variability of processes leading to the emergence of new lineages is one of the major tasks of macroevolution as a scientific field. Recent years have seen the rise of rate-variable diversification models and metrics that estimate the rates of species diversification at the tips of phylogenetic trees and are thus potentially useful for predicting future evolutionary success of individual species. These methods use various assumptions about the variability and heritability of diversification rates. However, the general performance of rate-variable diversification methods have never been consistently tested against real world data. Here we explore the capacity of multiple rate-variable diversification methods to predict near-future diversification using temporal slices of empirical fossil and extant phylogenies. We do this using a newly developed approach similar to generalized linear models, allowing us to quantify the relationship between predictor tip rates and subsequent diversification rates derived from a probability distribution of numbers of daughter species. We find that tip rates estimated from current methods have non-zero but limited capacity to predict diversification in both fossil and extant phylogenies. The quality of the predictions depends not only on the methods used but also on the specific phylogeny, suggesting that diversification dynamics in some taxa may be more predictable in principle. Our results suggest that future cladogenesis can be, to a certain extent, predicted using existing tip rate methods, but the quality of such predictions is highly variable and depends on factors that are difficult to evaluate in practical applications.

evolutionary biology↗

bioRxiv2023

75 years of anthropogenic change and its impact on Canadian butterfly taxonomic and phylogenetic diversity

Previous studies have documented very little net change in average quadrat-level species richness and phylogenetic diversity. However, although the average remains centered around 0, there is much variation around this mean and many outliers. The relative contribution of anthropogenic drivers (such as climate change or land use change) to these outliers remains unclear. Traits may dictate species responses to these changes, and if relatedness is correlated with trait similarity, then the impacts of anthropogenic change may be clustered on the phylogeny. We build the first regional phylogeny of all Canadian butterfly species in order to examine change in community phylogenetic structure in response to two main documented drivers of change -- climate change and land use change -- across 265 species, 75 years and 96 well-sampled quadrats. We find no evidence that, on average, communities are becoming more or less clustered than one would expect. However, there is much variation depending on the magnitude and type of anthropogenic change occurring within a quadrat. We find that climate change as well as agricultural development is reducing species richness within a quadrat, and these species that are lost tend to be scattered across the phylogeny. However, agricultural abandonment is having the opposite effect: we find increasing species richness in the years immediately following it and decreasing distance between species in quadrats with the highest rates of abandonment, such that the species that colonize these plots tend to be close relatives of those already present and thus contribute little novel phylogenetic diversity to an assemblage. Consistent with previous work, small changes in local species richness may conceal simultaneous change in other facets of biodiversity.

ecology↗

bioRxiv2022

EDGE2: advancing the prioritisation of threatened evolutionary history for conservation action

The global biodiversity crisis threatens the natural world and its capacity to provide benefits to humans into the future. The conservation of evolutionary history, captured by the measure phylogenetic diversity (PD), is linked to the maintenance of these benefits and future options. The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to identify species for conservation action that embody large amounts of threatened evolutionary history. In 2017, we convened a workshop to update the EDGE metric to incorporate advances in the field of phylogenetically-informed conservation. Building on that workshop, we devised the metric EDGE2, which we present here. EDGE2 uses a modular, tiered approach to provide priority rankings--and associated measures of uncertainty in both phylogenetic and extinction risk data--for all species in a clade. EDGE2 takes into account the extinction risk of closely-related species to better reflect the contribution a species is expected to make to overall PD in the future. We applied EDGE2 to the worlds mammals to identify an updated list of priority EDGE species and compare the results with the original EDGE approach. Despite similarity in the priority lists produced between EDGE and EDGE2, EDGE2 places greater priority on species with fewer close relatives on the Tree of Life. As we approach a crossroads for global biodiversity policy, EDGE2 exemplifies how academic and applied conservation biologists can collaborate to guide effective priority-setting to conserve the most irreplaceable components of biodiversity upon which humanity depends.

zoology↗

bioRxiv2021

Predicting long pendant edges in model phylogenies, with applications to biodiversity and tree inference

AO_SCPLOWBSTRACTC_SCPLOWIn the simplest phylogenetic diversification model (the pure-birth Yule process), lineages split independently at a constant rate {lambda} for time t. The length of a randomly chosen edge (either interior or pendant) in the resulting tree has an expected value that rapidly converges to [Formula] as t grows, and thus is essentially independent of t. However, the behaviour of the length L of the longest pendant edge reveals remarkably different behaviour: L converges to t/2 as the expected number of leaves grows. Extending this model to allow an extinction rate (where < {lambda}), we also establish a similar result for birth-death trees, except that t/2 is replaced by t/2 {middle dot} (1 - /{lambda}). This complete tree may contain subtrees that have died out before time t; for the reduced tree that just involves the leaves present at time t and their direct ancestors, the longest pendant edge length L again converges to t/2. Thus, there is likely to be at least one extant species whose associated pendant branch attaches to the tree approximately half-way back in time to the origin of the entire clade. We also briefly consider the length of the shortest edges. Our results are relevant to phylogenetic diversity indices in biodiversity conservation, and to quantifying the length of aligned sequences required to correctly infer a tree. We compare our theoretical results with simulations, and with the branch lengths from a recent phylogenetic tree of all mammals.

evolutionary biology↗

bioRxiv2021

Predictors of Taxonomic Inflation and its Role in Primate Conservation

Species are the main unit used to measure biodiversity, but different preferred diagnostic criteria can lead to very different delineations. For instance, named primate species have more than doubled in number since 1982. Such increases have been attributed to a shift away from the biological species concept (BSC) in favour of less inclusive species criteria. Critics of recent changes in primate taxonomy have suggested taxonomic splitting may be biased toward certain clades and have unfavourable consequences for conservation. Here, we explore predictors of taxonomic splitting across primate taxa since the initial shift away from the BSC nearly 40 years ago. We do not find evidence that diversification rate, the rate of lineage formation over evolutionary time, is significantly linked to splitting, contrary to expectations if new species concepts and taxonomic methods identify incipient species. We also do not find evidence that research effort in fields where work has been suggested to motivate splitting is associated with increases in species numbers among genera. To test the suggestion that splitting groups is likely to increase their perceived risk of extinction, we test whether genera that have undergone more splitting have also observed a greater increase in their proportion of threatened species since the initial shift away from traditional taxonomic methods. We find no cohesive signal of taxonomic splitting leading to higher threat probabilities across primate genera. Overall, this analysis sends a positive message: threat statuses of primate species are not being overwhelmingly affected by splitting. Regardless, we echo warnings that it is unwise for conservation to be reliant on taxonomic stability. Species (however defined) are not independent from one another, thus, monitoring and managing them as such may not meet the overarching goal of conserving biodiversity.

zoology↗

bioRxiv2020

The role of behavioural flexibility in primate diversification

Identifying the factors that influence species diversification is fundamental to our understanding of the evolutionary processes underlying extant biodiversity. Behavioural innovation, coupled with the social transmission of new behaviours, has been proposed to increase rates of evolutionary diversification, as novel behaviours expose populations to new selective regimes. Thus, it is believed that behavioural flexibility may play an important role in driving evolutionary diversification across animals. We test this hypothesis within the primates, a taxonomic group with considerable among-lineage variation in both species diversity and behavioural flexibility. We employ a time cut-off in our phylogeny to help account for biases associated with recent taxonomic reclassifications and compare three alternative measures of diversification rate that consider different phylogenetic depths. We find that the presence of behavioural innovation and social learning are positively correlated with diversification rates among primate genera, but not at shallower phylogenetic depths. Given that we find stronger associations when examining older rather than more recent diversification events, we suggest that extinction resistance, as opposed to speciation, may be an important mechanism linking behavioural flexibility and primate diversification. Our results contrast with work linking behavioural flexibility with diversification of birds at various phylogenetic depths. We offer a possible dispersal-mediated explanation for these conflicting patterns, such that the influence behavioural flexibility plays in dictating evolutionary trajectories differs across clades. Our results suggest that behavioural flexibility may act through several different pathways to shape the evolutionary trajectories of lineages.

evolutionary biology↗

bioRxiv2020

Formal Links between Feature Diversity and Phylogenetic Diversity

AO_SCPLOWBSTRACTC_SCPLOWThe extent to which phylogenetic diversity (PD) captures feature diversity (FD) is a topical and controversial question in biodiversity conservation. In this short paper, we formalise this question and establish a precise mathematical condition for FD (based on discrete characters) to coincide with PD. In this way, we make explicit the two main reasons why the two diversity measures might disagree for given data; namely, the presence of certain patterns of feature evolution and loss, and using temporal branch lengths for PD in settings that may not be appropriate (e.g. due to rapid evolution of certain features over short periods of time). Our paper also explores the relationship between the Fair Proportion index of PD and a simple index of FD (both of which correspond to Shapley values in cooperative game theory). In a second mathematical result, we show that the two indices can take identical values for any phylogenetic tree, provided the branch lengths in the tree are chosen appropriately.

evolutionary biology↗

bioRxiv2018

The Effect of Phylogenetic Uncertainty and Imputation on EDGE Scores

Faced with the challenge of saving as much diversity as possible given financial and time constraints, conservation biologists are increasingly prioritizing species on the basis of their overall contribution to evolutionary diversity. Metrics such as EDGE (Evolutionary Distinct and Globally Endangered) have been used to set such evolutionarily-based conservation priorities for a number of taxa, such as mammals, birds, corals, amphibians, and sharks. Each application of EDGE has required some form of correction to account for species whose position within the tree of life are unknown. Perhaps the most advanced of these corrections is phylogenetic imputation, but to date there has been no systematic assessment of both the sensitivity of EDGE scores to a phylogeny missing species, and the impact of using imputation to correct for species missing from the tree. Here we perform such an assessment, by simulating phylogenies, removing some species to make the phylogeny incomplete, imputating the position of those species, and measuring (1) how robust ED scores are for the species that are not removed and (2) how accurate the ED scores are for those removed and then imputed. We find that the EDGE ranking for species on a tree is remarkably robust to missing species from that tree, but that phylogenetic imputation for missing species, while unbiased, does not accurately reconstruct species evolutionary distinctiveness. On the basis of these results, we provide clear guidance for EDGE scoring in the face of phylogenetic uncertainty.

zoology↗

bioRxiv2017

Biodiversity loss under future global socio-economic and climate scenarios

Efficient forward-looking mitigation measures are needed to halt the global biodiversity decline. These require spatially explicit scenarios of expected changes in multiple indicators of biodiversity under future socio-economic and environmental conditions. Here we link five future (2050 and 2100) global gridded maps (0.25{degrees} x 0.25{degrees} resolution) available from the land use harmonization (LUH) database that represent alternative representative concentration and shared socio-economic pathways (RCP-SSP) with the countryside species-area relationship model to project the future land use change driven rates of species extinctions and phylogenetic diversity loss (in million years) for mammals, birds and amphibians in each of the 804 terrestrial ecoregions and 176 countries and compare them to the current (1900-2015) and past (850-1900) rates of biodiversity loss. Future land-use changes are projected to commit an additional 209-818 endemic species and 1190-4402 million years of evolutionary history to extinction by 2100 depending upon the scenario, equivalent to 20-80% of the number committed to extinction under current (2015) land use extent. Results show that hotspots of future biodiversity loss differ depending upon the scenario, taxon and metric considered. The most aggressive climate mitigation scenario (RCP2.6 SSP-1), representing a world shifting towards a radically more sustainable path including increasing crop yields, reduced meat production and reduced tropical deforestation coupled with high trade, projects the lowest land use change driven global biodiversity loss followed by RCP8.5 SSP-5, RCP6.0 SSP-4 and RCP7.0 SSP-3. Interestingly, the scenario with the second most aggressive climate target (RCP3.4 SSP-4) projected the highest biodiversity loss among the five scenarios tested. This is because it represents a world with continued high consumption in rich countries and increased land clearing for crop production in species rich, low-income countries such as Indonesia, Madagascar, Tanzania, Philippines and DR Congo. These contrasting results illustrate that the strategies to prevent climate change could simultaneously contribute to reduction in current high rates of biodiversity loss, but only if habitat preservation is incorporated into national and global sustainable development plans.

ecology↗