Church SH, Donoughe S, de Medeiros BAS, Extavour CG.
A database of egg size and shape from more than 6,700 insect species. bioRxiv. 2018 :471953.
Publisher's VersionAbstractOffspring size is a fundamental trait in disparate biological fields of study. This trait can be measured as the size of plant seeds, animal eggs, or live young, and it influences ecological interactions, organism fitness, maternal investment, and embryonic development. Although multiple evolutionary processes have been predicted to drive the evolution of offspring size, the phylogenetic distribution of this trait remains poorly understood, due to the difficulty of reliably collecting and comparing offspring size data from many species. Here we present a database of 10,449 morphological descriptions of insect eggs, with records for 6,706 unique insect species and representatives from every extant hexapod order. The dataset includes eggs whose volumes span more than eight orders of magnitude. We created this database by partially automating the extraction of egg traits from the primary literature. In the process, we overcame challenges associated with large-scale phenotyping by designing and employing custom bioinformatic solutions to common problems. We matched the taxa in this database to the currently accepted scientific names in taxonomic and genetic databases, which will facilitate the use of this data for testing pressing evolutionary hypotheses in offspring size evolution.
Church SH, Donoughe S, de Medeiros BAS, Extavour CG.
Insect egg size and shape evolve with ecology, not developmental rate. bioRxiv. 2018 :471946.
Publisher's VersionAbstractThe evolution of organism size is hypothesized to be predicted by a combination of development, morphological constraints, and ecological pressures. However, tests of these predictions using phylogenetic methods have been limited by taxon sampling. To overcome this limitation, we generated a database of more than ten thousand observations of insect egg size and shape from the entomological literature and combined them with published genetic and novel life-history datasets. This enabled us to perform phylogenetic tests of long-standing predictions in size evolution across hexapods. Here we show that across eight orders of magnitude in egg volume variation, the relationship between egg shape and size itself evolves, such that predicted universal patterns of scaling do not adequately explain egg shape diversity. We test the hypothesized relationship between size and development, and show that egg size is not correlated with developmental rate across insects, and that for many insects egg size is not correlated with adult body size either. Finally, we show that the evolution of parasitism and aquatic oviposition both help to explain the diversification of egg size and shape across the insect evolutionary tree. Our study challenges assumptions about the evolutionary constraints on egg morphology, suggesting that where eggs are laid, rather than universal mathematical allometric constants, underlies egg size and shape evolution.
Kim S, de Medeiros BAS, Byun BK, Lee S, Kang JH, Lee B, Farrell BD.
West meets East: How do rainforest beetles become circum-Pacific? Evolutionary origin of Callipogon relictus and allied species (Cerambycidae: Prioninae) in the New and Old Worlds. Molecular Phylogenetics and Evolution. 2018;125 :163–176.
Publisher's VersionAbstractThe longhorn beetle genus Callipogon Audinet-Serville represents a small group of large wood-boring beetles whose distribution pattern exhibits a unique trans-Pacific disjunction between the East Asian temperate rainforest and the tropical rainforest of the Neotropics. To understand the biogeographic history underlying this circum-Pacific disjunct distribution, we reconstructed a molecular phylogeny of the subfamily Prioninae with extensive sampling of Callipogon using multilocus sequence data of 99 prionine and four parandrine samples (ingroups), together with two distant outgroup species. Our sampling of Callipogon includes 18 of the 24 currently accepted species, with complete representation of all species in our focal subgenera. Our phylogenetic analyses confirmed the purported affinity between the Palearctic Callipogon relictus and its Neotropical congeners. Furthermore, based on molecular dating under the fossilized birth–death (FBD) model with comprehensive fossil records and probabilistic ancestral range reconstructions, we estimated the crown group Callipogon to have originated in the Paleocene circa 60 million years ago (Ma) across the Neotropics and Eastern Palearctics. The divergence between the Palearctic C. relictus and its Neotropical congeners is explained as the result of a vicariance event following the demise of boreotropical forest across Beringia at the Eocene-Oligocene boundary. As C. relictus represents the unique relictual species that evidentiates the lineage's expansive ancient distribution, we evaluated its conservation importance through species distribution modelling. Though we estimated a range expansion for C. relictus by 2050, we emphasize a careful implementation of conservation programs towards the protection of primary forest across its current habitats, as the species remains highly vulnerable to habitat disturbance.
McKenna DD, Clarke DJ, Anderson R, Astrin JJ, Brown S, Chamorro L, Davis SR, de Medeiros B, del Rio GM, Haran J, et al. Morphological and Molecular Perspectives on the Phylogeny, Evolution, and Classification of Weevils (Coleoptera: Curculionoidea): Proceedings from the 2016 International Weevil Meeting. Diversity. 2018;10 (3) :64.
PDF file de Medeiros BAS, Farrell BD.
Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci. PeerJ. 2018;6 :e5089.
Publisher's VersionAbstractWhole-genome amplification by multiple displacement amplification (MDA) is a promising technique to enable the use of samples with only limited amount of DNA for the construction of RAD-seq libraries. Previous work has shown that, when the amount of DNA used in the MDA reaction is large, double-digest RAD-seq (ddRAD) libraries prepared with amplified genomic DNA result in data that are indistinguishable from libraries prepared directly from genomic DNA. Based on this observation, here we evaluate the quality of ddRAD libraries prepared from MDA-amplified genomic DNA when the amount of input genomic DNA and the coverage obtained for samples is variable. By simultaneously preparing libraries for five species of weevils (Coleoptera, Curculionidae), we also evaluate the likelihood that potential contaminants will be encountered in the assembled dataset. Overall, our results indicate that MDA may not be able to rescue all samples with small amounts of DNA, but it does produce ddRAD libraries adequate for studies of phylogeography and population genetics even when conditions are not optimal. We find that MDA makes it harder to predict the number of loci that will be obtained for a given sequencing effort, with some samples behaving like traditional libraries and others yielding fewer loci than expected. This seems to be caused both by stochastic and deterministic effects during amplification. Further, the reduction in loci is stronger in libraries with lower amounts of template DNA for the MDA reaction. Even though a few samples exhibit substantial levels of contamination in raw reads, the effect is very small in the final dataset, suggesting that filters imposed during dataset assembly are important in removing contamination. Importantly, samples with strong signs of contamination and biases in heterozygosity were also those with fewer loci shared in the final dataset, suggesting that stringent filtering of samples with significant amounts of missing data is important when assembling data derived from MDA-amplified genomic DNA. Overall, we find that the combination of MDA and ddRAD results in high-quality datasets for population genetics as long as the sequence data is properly filtered during assembly.
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