Biology subjects

Wagner, C. E.

Publications and source records attributed to Wagner, C. E..

8 recordsLinked to original sources

bioRxiv2026

Intermediate abundance promotes speciation when dispersal is limited

Why do some lineages diversify while others do not? This remains a central question in evolutionary ecology. A long-standing assumption, dating to Darwin and embedded in the Unified Neutral Theory of Biodiversity, holds that abundant species should speciate at higher rates. Conversely, theoretical and empirical work highlights the possibility that rare and dispersal-limited clades might be more prone to speciation. Using a birth-death-immigration model with protracted speciation in a multi-population landscape connected by limited dispersal, we show that abundance has a hump-shaped effect on probability of speciation. Our model reveals that intermediate abundance maximizes speciation probability because larger populations disperse more, swamping regional differentiation and inhibiting speciation completion, while smaller populations lack the persistence and incipient speciation needed to diversify. We find empirical support for this prediction with an analysis of data from arthropods endemic to Hawaii, where genus-level species richness shows a significant hump-shaped relationship with mean genus abundance. These findings provide a mechanistic explanation for a nuanced relationship between abundance and diversification.

evolutionary biology↗

bioRxiv2025

Genomes reveal age and demographic consequence of ultrafast adaptive radiation

New species typically evolve over several million years1. However, rates of speciation and ecological diversification vary by orders of magnitude across the tree of life1-3, with the fastest shown by some adaptive radiations. Eight hundred endemic species of cichlid fishes emerged and formed entire food webs in Lake Victoria and nearby lakes in East Africa. According to Victorias paleolimnological history4, five hundred may have arisen within the past 16,700 years, but molecular phylogenies estimated a much older origin5-8. We reconstruct the age and demography of all Lake Victoria region radiations from whole genomes. We show that indeed, in Lake Victoria all trophic guilds diverged <16,700 years ago, corresponding to between 537 and nearly 30000 speciation events per species per million years, the fastest speciation rate in metazoans1,2. Cichlid radiations in lakes Edward, Albert and Kivu too began <20,000 years ago, an order of magnitude faster than previously thought. Evolutionary transitions between trophic levels led to divergence in effective population sizes as predicted by the trophic pyramid of numbers concept9 and replicated across three parallel food web radiations. Our results demonstrate that classical theory of trophic interactions in ecologically assembled food webs applies equally to food webs that assembled through rapid adaptive radiation.

evolutionary biology↗

bioRxiv2025

Admixture and environmental fluctuations shape the evolutionary history of a predator radiation in East Africa's Lake Tanganyika

Top predators have oversized influence on food webs and ecosystem dynamics, and introducing a novel predator to a naive environment can have dramatic consequences for endemic biodiversity. Using genomic data, we find that the colonization of Lake Tanganyika by Lates fishes--the top predators in this ancient lake--occurred more recently than other diverse clades within the lake. Diversification into four endemic Lates species occurred within the lake during a time of dramatic changes in lake levels driven by glacial-interglacial cycles, supporting the hypothesis that these fluctuations were a "species pump" for lacustrine taxa. These lake level fluctuations also likely contributed to multiple admixture events among Lates species during the Pleistocene ([~] 90-500 Kya). Together, our findings suggest a dynamic and environmentally-linked evolutionary history of this predator radiation, and that their colonization of the lake and subsequent diversification likely had dramatic ecosystem consequences for taxa already present in Lake Tanganyika.

evolutionary biology↗

bioRxiv2024

Nonlinear thinking in ecology and evolution: The case for ecological scaling of the Threshold Elemental Ratio

Nonlinear dynamics govern ecological processes, thus understanding thresholds is important for measuring and forecasting effects of climate change and management of natural resources. However, identifying whether and how such thresholds scale across biological levels of organization remains challenging. Ecological stoichiometry, the study of the balance of multiple elements and energy in ecological systems, provides a framework for scaling thresholds. We broaden a key organismal concept from ecological stoichiometry theory, the Threshold Elemental Ratio (TER), to study how nonlinear dynamics operate in evolutionary and ecological processes across the organizational hierarchy. Traditionally, TERs are used to describe the elemental ratio at which the limitation of organismal growth shifts from one element to another. Following this definition, we make a case for broadening the ecological scale of the TER beyond organisms to include populations, clades, communities, and ecosystems. We show how TERs can be detected and translated across different scales of biological and evolutionary organization through simulation modeling, literature review, and synthesis of empirical examples from diverse systems and ecological scales including: cyanotoxin production in lakes, alder-salmon dynamics, and the Cambrian explosion. Collectively, we demonstrate that TERs are widespread and consequential across levels of biological organization and that such thresholds manifest from a diversity of mechanisms. Thus, scaling of the TER concept holds promise for advancing our understanding of nonlinear dynamics from the micro-evolutionary to macro-ecological.

ecology↗

bioRxiv2022

Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

AO_SCPLOWBSTRACTC_SCPLOWMolecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant-calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate to what extent the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find greatest topological accuracy when filtering sites for minor allele count >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with minor allele count >1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short read genomic data for phylogenetic inference.

bioinformatics↗

bioRxiv2021

Isotopic signatures induced by upwelling tag regional fish populations in Lake Tanganyika

Lake Tanganyikas pelagic fish sustain the second largest inland fishery in Africa and are under pressure from heavy fishing and global warming related increases in stratification. Only little is known about whether basin-scale hydrodynamics - including a more stratified north and an upwelling-driven south - induce ecological and genetic differences among populations of highly mobile, pelagic fish inhabiting these different areas. Here, we examine whether the basin-scale dynamics leave distinct isotopic imprints in the pelagic fish of Lake Tanganyika, which may reveal differences in habitat, diet, or lipid content. We conducted two lake-wide campaigns during different seasons and collected physical, nutrient, chlorophyll, phytoplankton and zooplankton data. Additionally, we analyzed the pelagic fish - the clupeids Stolothrissa tanganicae, Limnothrissa miodon and four Lates species - for their isotopic and elemental carbon (C) and nitrogen (N) compositions. The {delta}13C values were significantly higher in the productive south after the upwelling/mixing period across all trophic levels, implying that the fish have regional foraging grounds, and thus record these latitudinal isotope gradients. By combining our isotope data with genetics, we demonstrate that the fish form regional populations on a seasonal to multiannual time scale. Based on {delta}15N and C:N ratios, we found no strong evidence for varying diets or lipid contents between those regional populations. Additional analyses revealed that isotopic variations between specimens from the same location are not linked to genetic differences. We suggest that the development of basinscale ecological differences in response to the prevailing hydrodynamic regimes may be inhibited by lake-wide gene flow on the long term. Our findings show that the pelagic fish species are genetically adapted to the whole lake, but they form regional populations on short time scales. This implies that sustainable management strategies may adopt basin-scale fishing quotas.

ecology↗

bioRxiv2021

The genetic population structure of Lake Tanganyika's Lates species flock, an endemic radiation of pelagic top predators

Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae and L. angustifrons) using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST = 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure within L. mariae, with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis, and L. angustifrons). Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species--particularly that of L. mariae--which may be important for conservation and management of this culturally and economically important clade of fish.

evolutionary biology↗

bioRxiv2019

Sex differentiation and a chromosomal inversion lead to cryptic diversity in Lake Tanganyika sardines

Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyikas two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal unexpected differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large segregating inversion in L. miodon. We found all inversion karyotypes throughout Lake Tanganyika, but the frequencies vary along a north-south gradient, and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation-by-distance, even over the hundreds of kilometers covered by our sampling, but we do find shallow population structure.

evolutionary biology↗