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  1. Abstract

    Body size is a key morphological attribute, often used to delimit species boundaries among closely related taxa. But body size can evolve in parallel, reaching similar final states despite independent evolutionary and geographic origins, leading to faulty assumptions of evolutionary history. Here, we document parallel evolution in body size in the widely distributed leaf-nosed bat genus Hipposideros, which has misled both taxonomic and evolutionary inference. We sequenced reduced representation genomic loci and measured external morphological characters from three closely related species from the Solomon Islands archipelago, delimited by body size. Species tree reconstruction confirms the paraphyly of two morphologically designated species. The nonsister relationship between large-bodied H. dinops lineages found on different islands indicates that large-bodied ecomorphs have evolved independently at least twice in the history of this radiation. A lack of evidence for gene flow between sympatric, closely related taxa suggests the rapid evolution of strong reproductive isolating barriers between morphologically distinct populations. Our results position Solomon Islands Hipposideros as a novel vertebrate system for studying the repeatability of parallel evolution under natural conditions. We conclude by offering testable hypotheses for how geography and ecology could be mediating the repeated evolution of large-bodied Hipposideros lineages in the Solomon Islands.

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  2. Free, publicly-accessible full text available May 1, 2025
  3. Abstract

    Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately and may have unique and even conflicting evolutionary histories. Phylogenetic reconstructions from these discrete genomes can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance (i.e. discordant evolutionary histories between the nuclear and mitochondrial genomes) has been widely documented, but its causes are often considered idiosyncratic and inscrutable. We show that a case of mitonuclear discordance inTodiramphuskingfishers can be explained by extensive genome‐wide incomplete lineage sorting (ILS), likely a result of the explosive diversification history of this genus. For these kingfishers, quartet frequencies reveal that the nuclear genome is dominated by discordant topologies, with none of the internal branches in our consensus nuclear tree recovered in >50% of genome‐wide gene trees. Meanwhile, a lack of inter‐species shared ancestry, non‐significant pairwise tests for gene flow, and little evidence for meaningful migration edges between species, leads to the conclusion that gene flow cannot explain the mitonuclear discordance we observe. This lack of evidence for gene flow combined with evidence for extensive genome‐wide gene tree discordance, a hallmark of ILS, leads us to conclude that the mitonuclear discordance we observe likely results from ILS, specifically deep coalescence of the mitochondrial genome. Based on this case study, we hypothesize that similar demographic histories in other ‘great speciator’ taxa across the Indo‐Pacific likely predispose these groups to high levels of ILS and high likelihoods of mitonuclear discordance.

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  4. Abstract Aim

    Periodic lowering of sea levels and formation of land bridges can reshape phylogeographic patterns of insular biotas. Using archipelago‐wide sampling, we aimed to test if phylogeography of an old‐endemic bat lineage reflected Pleistocene land bridges.


    Solomon Islands and Papua New Guinea.


    MelonycterisandNesonycterisbats (Pteropodidae).


    We sequenced genome‐wide RADseq data for 49 specimens from 15 islands. We assessed phylogenetic relationships using maximum likelihood inRAxMLand quartet‐based methods inSVDquartets, population structure usingStructure, and admixture using maximum likelihood methods inTreeMix. We tested for genetic and geographic distance correlations using distance‐based redundancy analyses (dbRDA), identifying best‐fit models using stepwise model selection.


    Phylogenetic analyses identified fiveNesonycterisclades corresponding to Greater Bukida, Guadalcanal, Makira, Malaita and New Georgia group. Makira samples were sister to remainingNesonycteris.Structureidentified four populations: New IrelandMelonycteris melanops; andNesonycterisfrom Greater Bukida (including Guadalcanal); Malaita and Makira; and New Georgia group. Genetic backgrounds of Mono, Ngella and Guadalcanal separated from remaining Greater Bukida islands. Makira and Malaita separated into two populations. New Georgia group lacked structure, and genetic and geographic distances were not correlated. The best‐fit geographic distance models forNesonycterisand a Greater Bukida subset were least shore‐to‐shore distance; and Euclidean and least‐cost distances respectively.

    Main Conclusions

    Influences of modern and Pleistocene island isolation and connectivity were evident in the overall Phylogeography ofNesonycteris. The lack of structure or geographic distance correlations within the New Georgia group indicated all islands were interconnected during the Last Glacial Maximum or contemporary oceanic divides are ineffective barriers. Conversely, genetic divergence across Greater Bukida islands reflected land‐bridge constrained dispersal. A Makira clade sister to allNesonycterispossibly indicates an origin on Makira. Alternately it reflects Makira's long‐isolated geographic status, as similar results exist for a range of taxa.

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