Biology subjects

McGee, M. D.

Publications and source records attributed to McGee, M. D..

7 recordsLinked to original sources

bioRxiv2026

Inference of Cichlid Speciation Patterns is Dependent on Spatial Covariance and Species Delimitation

Macroevolutionary analyses typically treat species as discrete units and account for shared evolutionary history. However, speciation is a continuous process and taxa are often spatially clustered, potentially biasing inferences of diversification. Here, we investigate how species delimitation and spatial non-independence influence speciation dynamics and inferred drivers using cichlid fishes as a model system. Using a phylogeny and trait dataset of 1,712 species, we first generated a reduced dataset of 820 species by removing incipient species based on known breeding compatibilities. We then fit phylogenetic and spatiophylogenetic models using an integrated nested Laplace approximation framework to jointly account for phylogenetic and spatial covariance. We find that the treatment of incipient species and spatial non-independence both alter speciation patterns and inferred drivers. Analyses of the full phylogeny identified strong trait associations and spatial hotspots driven by young adaptive radiations in Lake Victoria and Lake Malawi, whereas removing incipient species and accounting for spatial non-independence reduced extreme speciation rates, weakened or removed trait effects, and largely eliminated spatial hotspots. These results demonstrate that macroevolutionary inference is sensitive to species delimitation and spatial structure, highlighting the need to consider the influence of incipient species and spatial covariance in comparative analyses.

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↗

bioRxiv2023

Replicated Functional Evolution in Cichlid Adaptive Radiations

Adaptive radiations highlight the mechanisms by which species and traits diversify and the extent to which these patterns are predictable. We used 1,110 high-speed videos of suction feeding to study functional and morphological diversification in 300 cichlid species from three African Great Lake radiations of varying ages (Tanganyika, Malawi and Victoria) and an older, spatially dispersed continental radiation in the Neotropics. Among African radiations, standing diversity was reflective of time. Morphological and functional variance in Lake Victoria, the youngest radiation, was a subset of that within Lake Malawi, which itself was nested within the older Tanganyikan radiation. However, functional diversity in Neotropical cichlids was often lower than in Lake Tanganyika, despite being at least 25 My older. These two radiations broadly overlapped, but each diversified into novel trait spaces not found in the youngest lake radiations. Evolutionary rates across radiations were inversely related to age, suggesting, at least for lake radiations, extremely rapid trait evolution at early stages. Despite this support for early bursts, other patterns of trait diversity were inconsistent with expectations of adaptive radiations. This work suggests that cichlid functional evolution has played out in strikingly similar fashion in different radiations, with contingencies eventually resulting in lineage-specific novelties.

evolutionary biology↗

bioRxiv2023

No evidence for song evolution influencing speciation patterns in honeyeaters

Birdsongs are acoustic signals that can play a role in sexual selection. Despite the established role of birdsong in selection and reproductive isolation at microevolutionary scales, the macroevolutionary relationships between song evolution and clade diversification remain largely unexplored. We test the hypothesis that shifts in diversification influence rates of song evolution in honeyeaters, a diverse clade of songbirds restricted to Australasia. Using a song dataset for 163 honeyeater species, we identify lineage-specific shifts in diversification, and test the influence of these shifts on song evolution with state-dependent, relaxed, multivariate Brownian motion models. We also explore the underlying patterns of song evolution and phylogenetic signal of song. Shifts to lower rates of diversification are associated with lower rates of song evolution. This suggests the two factors are correlated, but is contrary to expectations that elevated rates of diversification will be associated with elevated rates of song evolution. We also found that song follows a punctuated mode of evolution, implying that birdsong has an important role in speciation events, although this signal likely erodes over time and is subject to phylogenetic constraints.

evolutionary biology↗

bioRxiv2023

Body size shapes song in honeyeaters

Birdsongs are among the most distinctive animal signals. Their evolution is thought to be shaped simultaneously by habitat structure and by the constraints of morphology. Habitat structure affects song transmission and detectability, thus influencing song (the acoustic adaptation hypothesis), while body size and beak size and shape necessarily constrain song characteristics (the morphological constraint hypothesis). Yet, support for the acoustic adaptation and morphological constraint hypotheses remains equivocal, and their simultaneous examination is infrequent. Using a phenotypically diverse Australasian bird clade, the honeyeaters (Aves: Meliphagidae), we compile a dataset consisting of song, environmental, and morphological variables for 163 species and jointly examine predictions of these two hypotheses. Overall, we find that body size constrains song frequency and pace in honeyeaters. Although habitat type and environmental temperature influence aspects of song, that influence is indirect, likely via effects of environmental variation on body size, with some evidence that elevation constrains the evolution of song peak frequency. Our results demonstrate that morphology has an overwhelming influence on birdsong, in support of the morphological constraint hypothesis, with the environment playing a secondary role generally via body size rather than habitat structure. These results suggest that changing body size, a consequence of both global effects such as climate change, and local effects such as habitat transformation, will substantially influence the nature of birdsong.

evolutionary biology↗

bioRxiv2022

Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal

O_LIThe evolutionary history of Southern Hemisphere graylings (Retropinnidae) in Aotearoa New Zealand--including the number of colonisation events, the directionality and timing of dispersal, and their relationship to the Australian grayling--is poorly understood. The New Zealand grayling (Prototroctes oxyrhynchus) is the only known freshwater fish species to have gone extinct since human arrival in New Zealand. Despite its historical abundance, only 23 formalin-fixed specimens (both wet and dried) exist in museum collections globally, which were previously non-amenable to palaeogenetic analysis. C_LIO_LIHere, we used high-throughput DNA sequencing techniques, specifically designed for formalin-fixed specimens, to generate mitochondrial genomes of P. oxyrhynchus, and analysed these within a temporal phylogenetic framework of retropinnid and osmerid taxa. C_LIO_LIWe recovered strong evidence for a sister relationship between the New Zealand and Australian grayling (P. mareana), with the two having a common ancestor around 13.8 Mya (95% HPD: 6.1-23.2 Mya), after the height of Oligocene marine inundation in New Zealand. C_LIO_LIOur temporal phylogenetic analysis suggests a single marine dispersal event between New Zealand and Australia, though the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance. C_LIO_LIThis study provides further insights into the possible drivers of the extinction of the New Zealand grayling, and highlights how advancements in palaeogenetic techniques can be used to test evolutionary hypotheses in extinct (and living) fish, which have been comparatively neglected in the field of ancient DNA. C_LI

evolutionary biology↗

bioRxiv2021

Genetic evidence for environment-dependent hybrid incompatibilities in threespine stickleback

Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are intrinsic, meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (semi-natural experimental ponds) or the laboratory (aquaria). We tested for differences in excess heterozygosity between these two environments at ancestry informative loci--a genetic signature of selection against incompatibilities. We found that excess ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Previous results from F1 hybrids in the field suggest that pond-specific (single-locus) heterosis is unlikely to explain this finding. Our study suggests that, in stickleback, a coarse signal of environment-dependent hybrid incompatibilities is reliably detectable and that extrinsic incompatibilities have evolved before intrinsic incompatibilities.

evolutionary biology↗