Biology subjects

Lee, M. S. Y.

Publications and source records attributed to Lee, M. S. Y..

6 recordsLinked to original sources

bioRxiv2026

Anthropogenic effects, not climatic, shaped Holocene population expansion of an insular bee fauna

AimRemote island systems with small landmasses and reliable estimates of human occupancy are ideal model systems to disentangle the roles of global climatic changes and local human occupation on biota. Here, we tested this with demographic reconstructions of native, ground-nesting bees with non-specialised floral visitation habits to infer changes in effective population size (Ne). LocationViti Levu, Fiji, southwest Pacific. TaxonLasioglossum (Homalictus) bees (Hymenoptera: Halictidae) MethodsWe applied a combination of both mitochondrial and genomic datasets from five species distributed across the elevational range for our analyses. Both kinds of data were used for validation of population assignments and testing for structure, and to investigate any demographic shifts. ResultsAll lowland species and populations showed strong signals of increasing Ne that correspond to the timing of human occupation of Fiji, but not Holocene climatic changes. Highland populations, with greater isolation and less affected by anthropogenic impacts, did not show evidence of recent rapid increases in Ne. Population expansion rates across the elevational gradient differed between taxa, with earlier and larger increases in predominantly lowland species. This is consistent with the movement of people inland and into montane elevations of the island, and corresponding landscape changes that benefit the ecology of these bees. Main conclusionsSpecific life history traits of these bees, combined with substantive clearing of forest cover and floristic changes at lower elevations, has likely increased nesting opportunities and abundance of invasive floral resources. Our findings contrast with recent evidence that human occupation of Fiji has resulted in decreased ant biodiversity and raise the paradoxical possibility that human-mediated environmental changes may benefit some native montane tropical insect faunas.

evolutionary biology↗

bioRxiv2025

Cryptovaranoides is not a squamate

Accurate reconstruction of the timescale of organismal evolution requires placement of extinct representatives among living branches. In this way, the fossil record has the capacity to revise hypotheses of organismal evolution by producing representatives of clades that far pre-date the age of the clade inferred using phylogenies built from molecular data and previous fossil calibrations. Recently, one fossil with the potential to drastically change current understanding surrounding the timescale of reptile diversification was described from Triassic fissure-fill deposits in the United Kingdom. This taxon, {dagger}Cryptovaranoides microlanius, was originally placed deep within the squamate crown clade, suggesting that many lineages of living lizards and snakes must have appeared by the Triassic and implying long ghost lineages that paleontologists and molecular phylogeneticists have failed to detect using all other available data. Our team challenged this identification and instead suggested {dagger}Cryptovaranoides had unclear affinities to living reptiles, but a crown-squamate interpretation was later re-iterated by the team that originally described this species. Here, we again challenge the morphological character codings used to support a crown squamate affinity for {dagger}Cryptovaranoides microlanius and illustrate several empirical problems with analyses that find this taxon is a crown squamate. Our analyses emphasize the importance of stringency in constructing hypodigms of fossils, particularly when they may be key for proper time calibration of the Tree of Life.

paleontology↗

bioRxiv2025

Where do the Dmanisi hominins fit on the human evolutionary tree?

Archeological excavations at the site of Dmanisi in the Republic of Georgia have yielded a rich assemblage of hominin fossil remains, as well as lithic artefacts and bones of fossil fauna. The site is considered to be between 1.95 Ma and 1.77 Ma (Gabunia et al. 2000b) and presents us with the first skeletal evidence of hominins to emerge from Africa, a key event in human evolution. Their morphology, and the degree of morphological variation observed among the assemblage, has generated considerable controversy about their affinities and heterogeneity. Here we use parsimony analyses to test the competing hypotheses for Dmanisi hominins employing characters from the cranium, mandible, dentition, and postcranium; and we address anomalies in endocranial volume, dentition and mandibular structure among the assemblage. We propose that the Dmanisi hominins are not Homo erectus, and that two species are represented among the assemblage: one comprises Homo georgicus and the other an as yet unnamed species. Our review of the dating of the Dmanisi site leads us to propose that Homo georgicus was probably present by 1.8 Ma and that the other hominins recovered from the Dmanisi excavations accumulated at some time or times during the reverse polarity of 1.07 Ma and 1.77 Ma. The specific, individual, ages of these hominins remain unknown.

evolutionary biology↗

bioRxiv2024

Trait-space disparity in fish communities spanning 380 million years from the Late Devonian to present

The diversity and distribution of species traits in an ecological community determine how it functions. While modern fish communities conse rve trait space across similar habitats, little is known about trait-space variation through deep time or across different habitats. We examined how fish trait diversity varies through space and time by comparing three Late Devonian fish communities -- a tropical reef (Gogo, Australia), a tropical estuary (Miguasha, Canada), and a temperate freshwater system (Canowindra, Australia) -- with six modern communities from diverse habitats. Trait-space metrics reflecting within-community diversity (functional richness) and species similarity (functional nearest-neighbour distance) indicated Late Devonian communities had scores similar to modern communities. However, they were less functionally rich than their closest modern analogues, and their species tended to be more functionally distinct from one another. Metrics describing location in trait space (centroid distances and hypervolume overlap) showed modern communities were similar to each other, Gogo and Miguasha were similar but distinct from modern communities, and Canowindra was distinct from all others. This pattern suggests period-associated differentiation and substantial heterogeneity among some Late Devonian communities. In addition to temporal changes, we found consistent differences associated with habitat type and climate zone. Reef and tropical communities were the most functionally rich, whereas functional nearest-neighbour scores were highest in estuarine and temperate communities. These results indicate fish community trait space varies with time, habitat and climate, suggesting (i) lability in fish trait space and (ii) that evolutionary history, environmental filtering, and stochasticity influence community assembly.

evolutionary biology↗

bioRxiv2022

Predicting predator-prey interactions in terrestrial endotherms using random forest

Species interactions play a fundamental role in ecosystems. However, few ecological communities have complete data describing such interactions, which is an obstacle to understanding how ecosystems function and respond to perturbations. Because it is often impractical to collect empirical data for all interactions in a community, various methods have been developed to infer interactions. Machine learning is increasingly being used for making interaction predictions, with random forest being one of the most frequently used of these methods. However, performance of random forest in inferring predator-prey interactions in terrestrial vertebrates and its sensitivity to training data quality remain untested. We examined predator-prey interactions in two diverse, primarily terrestrial vertebrate classes: birds and mammals. Combining data from a global interaction dataset and a specific community (Simpson Desert, Australia), we tested how well random forest predicted predator-prey interactions for mammals and birds using species ecomorphological and phylogenetic traits. We also tested how variation in training data quality--manipulated by removing records and switching interaction records to non-interactions--affected model performance. We found that random forest could predict predator-prey interactions for birds and mammals using ecomorphological or phylogenetic traits, correctly predicting up to 88% and 67% of interactions and non-interactions in the global and community-specific datasets, respectively. These predictions were accurate even when there were no records in the training data for focal species. In contrast, false non-interactions for focal predators in training data strongly degraded model performance. Our results demonstrate that random forest can identify predator-prey interactions for birds and mammals that have few or no interaction records. Furthermore, our study provides guidance on how to prepare training data to optimise machine-learning classifiers for predicting species interactions, which could help ecologists (i) address knowledge gaps and explore network-related questions in data-poor situations, and (ii) predict interactions for range-expanding species.

ecology↗

bioRxiv2020

Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge

The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far north-east Asia) and Eastern Beringia (north-west North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation, and vegetation, impacting faunal community structure and demography. While these paleoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyze mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underscore the crucial biogeographic role of the Bering Land Bridge in the distribution, turnover, and maintenance of megafaunal populations in North America.

evolutionary biology↗