Yu Y-S, Jin S, Cho N, Lim J, Kim C-H, Lee S-G, Kim SI, Park J-S, Kim K, Park C, et al. Genome Size Estimation of Callipogon relictus Semenov (Coleoptera: Cerambycidae), an Endangered Species and a Korea Natural Monument. Insects [Internet]. 2021;12 (2). DOI (full text)Abstract
We estimated the genome size of a relict longhorn beetle, Callipogon relictus Semenov (Cerambycidae: Prioninae)—the Korean natural monument no. 218 and a Class I endangered species—using a combination of flow cytometry and k-mer analysis. The two independent methods enabled accurate estimation of the genome size in Cerambycidae for the first time. The genome size of C. relictus was 1.8 ± 0.2 Gb, representing one of the largest cerambycid genomes studied to date. An accurate estimation of genome size of a critically endangered longhorned beetle is a major milestone in our understanding and characterization of the C. relictus genome. Ultimately, the findings provide useful insight into insect genomics and genome size evolution, particularly among beetles.
Chamorro ML, de Medeiros BAS, Farrell BD. First phylogenetic analysis of Dryophthorinae (Coleoptera, Curculionidae) based on structural alignment of ribosomal DNA reveals Cenozoic diversification. Ecology and Evolution [Internet]. 2021;11 (5). DOI (full text)Abstract
Abstract Dryophthorinae is an economically important, ecologically distinct, and ubiquitous monophyletic group of pantropical weevils with more than 1,200 species in 153 genera. This study provides the first comprehensive phylogeny of the group with the aim to provide insights into the process and timing of diversification of phytophagous insects, inform classification and facilitate predictions. The taxon sampling is the most extensive to date and includes representatives of all five dryophthorine tribes and all but one subtribe. The phylogeny is based on secondary structural alignment of 18S and 28S rRNA totaling 3,764 nucleotides analyzed under Bayesian and maximum likelihood inference. We used a fossil-calibrated relaxed clock model with two approaches, node-dating and fossilized birth-death models, to estimate divergence times for the subfamily. All tribes except the species-rich Rhynchophorini were found to be monophyletic, but higher support is required to ascertain the paraphyly of Rhynchophorini with more confidence. Nephius is closely related to Dryophthorini and Stromboscerini, and there is strong evidence for paraphyly of Sphenophorina. We find a large gap between the divergence of Dryophthorinae from their sister group Platypodinae in the Jurassic-Cretaceous boundary and the diversification of extant species in the Cenozoic, highlighting the role of coevolution with angiosperms in this group.
de Medeiros BAS, Farrell BD. Evaluating insect-host interactions as a driver of species divergence in palm flower weevils. Communications Biology [Internet]. 2020;3 (1) :749. DOI (full text)Abstract
Plants and their specialized flower visitors provide valuable insights into the evolutionary consequences of species interactions. In particular, antagonistic interactions between insects and plants have often been invoked as a major driver of diversification. Here we use a tropical community of palms and their specialized insect flower visitors to test whether antagonisms lead to higher population divergence. Interactions between palms and the insects visiting their flowers range from brood pollination to florivory and commensalism, with the latter being species that feed on decaying–and presumably undefended–plant tissues. We test the role of insect-host interactions in the early stages of diversification of nine species of beetles sharing host plants and geographical ranges by first delimiting cryptic species and then using models of genetic isolation by environment. The degree to which insect populations are structured by the genetic divergence of plant populations varies. A hierarchical model reveals that this variation is largely uncorrelated with the kind of interaction, showing that antagonistic interactions are not associated with higher genetic differentiation. Other aspects of host use that affect plant-associated insects regardless of the outcomes of their interactions, such as sensory biases, are likely more general drivers of insect population divergence.
Fernández E, Ferreras I, Farrell BD, de Medeiros BAS, Romero-González GA. Studies in Aristolochia (Aristolochiaceae) of Hispaniola. Phytotaxa [Internet]. 2019;420 :1-20. DOI (full text)Abstract
A review of the literature at large and the field photographic record of the senior author of this study indicate that there are several undescribed species of Aristolochia in Hispaniola (Dominican Republic and Haiti), related to A. bilobata. Here we show that A. mirandae is a synonym of A. bilobata and that what appears as A. bilobata in Marión H. (2011: 76–77) is a new species here described as Aristolochia adiastola. In addition, two new species, A. bonettiana and A. marioniana, also related to A. bilobata, are described and illustrated herein.
Church SH, Donoughe S, de Medeiros BAS, Extavour CG. A dataset of egg size and shape from more than 6,700 insect species. Sci Data [Internet]. 2019;6 :104. DOI (Full text)Abstract
Offspring 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 dataset 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 dataset 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 dataset to the currently accepted scientific names in taxonomic and genetic databases, which will facilitate the use of these data for testing pressing evolutionary hypotheses in offspring size evolution.
Pérez-de la Fuente R, Gehler A, Farnum CW, Farrell BD. Digitisation as a tool to promote transparency between collections: the case of the Baltic amber from the Königsberg collection at the Museum of Comparative Zoology. Spanish Journal of Palaeontology [Internet]. 2019;34 (1) :145-151. Full textAbstract
A total of 383 Baltic amber samples, including 43 type specimens, held at the Museum of Comparative Zoology (MCZ), Harvard University, for near a century were found to belong to the classic amber collection from the Albertus-Universität of Königsberg. This discovery was greatly facilitated by the public availability online of digital images produced during a four-year project that digitised the over 30,000 samples from the MCZ’s fossil insect collection. The amber samples were hand carried and reincorporated to the portion of the original Königsberg collection that was saved from World War II, held at the Geowissenschaftliches Museum from the Geowissenschaftliches Zentrum of the Georg-August-Universität, Göttingen. This study showcases the importance of sharing collection data through public digitised records, and highlights the understanding of digitisation not only as a tool of education, public engagement, and research, but also of rediscovery, tracking, repatriation, and ultimately safeguard of the movable palaeontological heritage on a global scale.
Church SH, Donoughe S, de Medeiros BAS, Extavour CG. Insect egg size and shape evolve with ecology but not developmental rate. Nature [Internet]. 2019;571 :58-62. DOI (full text)Abstract
Over the course of evolution, organism size has diversified markedly. Changes in size are thought to have occurred because of developmental, morphological and/or ecological pressures. To perform phylogenetic tests of the potential effects of these pressures, here we generated a dataset of more than ten thousand descriptions of insect eggs, and combined these with genetic and life-history datasets. We show that, across eight orders of magnitude of variation in egg volume, the relationship between size and shape itself evolves, such that previously predicted global patterns of scaling do not adequately explain the diversity in egg shapes. We show that egg size is not correlated with developmental rate and that, for many insects, egg size is not correlated with adult body size. Instead, we find that the evolution of parasitoidism and aquatic oviposition help to explain the diversification in the size and shape of insect eggs. Our study suggests that where eggs are laid, rather than universal allometric constants, underlies the evolution of insect egg size and shape.
Valente RM, Da Silva PAL, de Medeiros BAS. The first species of Cotithene Voss (Coleoptera: Curculionidae: Curculioninae) from Amazonian Brazil, with notes on its role as a pollinator of Evodianthus funifer (Poit.) Lindm. (Cyclanthaceae). Zootaxa. 2019;4576 :461.
de Medeiros BAS, Núñez-Avellaneda LA, Hernandez AM, Farrell BD. Flower visitors of the licuri palm (Syagrus coronata): brood pollinators coexist with a diverse community of antagonists and mutualists. Biological Journal of the Linnean Society. 2019.
McKenna DD, Clarke D, Anderson R, Astrin J, Brown S, Chamorro L, Davis S, de Medeiros BAS, del Rio M, 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 :64.
de Medeiros BAS, Farrell BD. Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci. PeerJP [Internet]. 2018;(6) :e5089. DOI (full text)Abstract
Whole-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.
Kim SI, de Medeiros BAS, Byun B-K, Lee S, Kang J-H, 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 [Internet]. 2018;125 :163-176. DOI (full text)Abstract
The 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.
De-la-Mora M, Piñero D, Oyama K, Farrell BD, Magallón S, Núñez-Farfán J. Evolution of Trichobaris (Curculionidae) in relation to host plants: Geometric morphometrics, phylogeny and phylogeography. Molecular Phylogenetics and Evolution [Internet]. 2018;124 (July 2018) :37-49. DOI (full text)Abstract
The family Curculionidae (Coleoptera), the “true” weevils, have diversified tightly linked to the evolution of flowering plants. Here, we aim to assess diversification at a lower taxonomic level. We analyze the evolution of the genus Trichobaris in association with their host plants. Trichobaris comprises eight to thirteen species; their larvae feed inside the fruits of Datura spp. or inside the stem of wild and cultivated species of Solanaceae, such as potato, tobacco and tomato. We ask the following questions: (1) does the rostrum of Trichobaris species evolve according to the plant tissue used to oviposit, i.e., shorter rostrum to dig in stems and longer to dig in fruits? and (2) does Trichobaris diversify mainly in relation to the use of Datura species? For the first question, we estimated the phylogeny of Trichobaris based on four gene sequences (nuclear 18S and 28S rRNA genes and mitochondrial 16S rRNA and COI genes). Then, we carried out morphogeometric analyses of the Trichobaris species using 75 landmarks. For the second question, we calibrated a COI haplotype phylogeny using a constant rate of divergence to infer the diversification time of Trichobaris species, and we traced the host plant species on the haplotype network. We performed an ancestral state reconstruction analysis to infer recent colonization events and conserved associations with host plant species. We found that ancestral species in the Trichobaris phylogeny use the stem of Solanum plants for oviposition and display weak sexual dimorphism of rostrum size, whereas other, more recent species of Trichobaris display sexual dimorphism in rostrum size and use the fruits of Datura species, and a possible reversion to use the stem of Solanaceae was detected in one Trichobaris species. The use of Datura species by Trichobaris species is widely distributed on haplotype networks and restricted to Trichobaris species that originated ca. 5 ± 1.5 Ma. Given that the origin of Trichobaris is estimated to be ca. 6 ± 1.5 Ma, it is likely that Datura has played a role in its diversification.
Shin S, Clarke D, Lemmon AR, Lemmon EM, Aitken AL, Haddad S, Farrell BD, Marvaldi AE, Oberprieler RG, McKenna DD. Phylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils. Molecular Biology and Evolution [Internet]. 2018;35 (4) :823-836. DOI (full text)Abstract
The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in the large family Curculionidae (true weevils; > 50,000 species), remain uncertain. We used phylogenomic methods to obtain DNA sequences from 522 protein-coding genes for representatives of all families of weevils and all subfamilies of Curculionidae. Most of our phylogenomic results had strong statistical support, and the inferred relationships were generally congruent with those reported in previous studies, but with some interesting exceptions. Notably, the backbone relationships of the weevil phylogeny were consistently strongly supported, and the former Nemonychidae (pine flower snout beetles) were polyphyletic, with the subfamily Cimberidinae (here elevated to Cimberididae) placed as sister group of all other weevils. The clade comprising the sister families Brentidae (straight-snouted weevils) and Curculionidae was maximally supported and the composition of both families was firmly established. The contributions of substitution modeling, codon usage and/or mutational bias to differences between trees reconstructed from amino acid and nucleotide sequences were explored. A reconstructed timetree for weevils is consistent with a Mesozoic radiation of gymnosperm-associated taxa to form most extant families and diversification of Curculionidae alongside flowering plants—first monocots, then other groups—beginning in the Cretaceous.
Laurindo da Silva F, Farrell BD. Non-biting midges (Diptera: Chironomidae) research in South America: subsidizing biogeographic hypotheses. Annales de Limnologie - International Journal of Limnology [Internet]. 2017;53 :111-128. DOI (full text)Abstract
We present data on Chironomidae (Insecta: Diptera) collected in South America together with results on the mitochondrial DNA diversity within selected megadiverse genera. This work is part of an on-going project on the ancient origin of South American biodiversity using non-biting midges. Collections were made at 42 localities, in March 2014 and February 2015, in a diverse array of habitats, including small streams, rivers, ponds, lakes and bays. In total, 3196 representatives of six subfamilies were collected. Sixty-one genera were identified, containing at least 211 species. The subfamilies Chironominae and Orthocladiinae predominated in all samples. Tanypodinae were often present, but rarely in large numbers. Except for Podonomus pepinellii, reported from Brazil, Podonominae were collected in a few localities in Argentina (Arroyo Lopez, and Arroyo Gutierrez and Gutierrez Lake) and Chile (Llanquihue Lake). Prodiamesinae were only recorded in Chile. Analysis of DNA barcode sequences using neighbor-joining estimation supported 66 species within the selected genera. The chironomid fauna of South America includes multiple genera with worldwide distributions, with Australian, Nearctic and Neotropical components.
de Medeiros BAS, Barghini A, Vanin SA. Streetlights attract a broad array of beetle species. Revista Brasileira de Entomologia [Internet]. 2017;61 (1) :74 - 79. DOI (full text)Abstract
Light pollution on ecosystems is a growing concern, and knowledge about the effects of outdoor lighting on organisms is crucial to understand and mitigate impacts. Here we build up on a previous study to characterize the diversity of all beetles attracted to different commonly used streetlight set ups. We find that lights attract beetles from a broad taxonomic and ecological spectrum. Lights that attract a large number of insect individuals draw an equally high number of insect species. While there is some evidence for heterogeneity in the preference of beetle species to different kinds of light, all species are more attracted to some light radiating ultraviolet. The functional basis of this heterogeneity, however, is not clear. Our results highlight that control of ultraviolet radiation in public lighting is important to reduce the number and diversity of insects attracted to lights.
Haddad S, Shin S, Lemmon AR, Lemmon EM, Svacha P, Farrell BD, Ślipinski A, Windsor D, McKenna DD. Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae). Systematic Entomology [Internet]. 2017. DOI (full text)Abstract
Cerambycidae is a species-rich family of mostly wood-feeding (xylophagous) beetles containing nearly 35,000 known species. The higher-level phylogeny of Cerambycidae has never been robustly reconstructed using molecular phylogenetic data or a comprehensive sample of higher taxa, and its internal relationships and evolutionary history remain the subjects of ongoing debate. We reconstructed the higher-level phylogeny of Cerambycidae using phylogenomic data from 522 single copy nuclear genes, generated via anchored hybrid enrichment. Our taxon sample included exemplars of all families and 23/30 subfamilies of Chrysomeloidea, with a focus on the large family Cerambycidae. Our results reveal a monophyletic Cerambycidae sensu stricto in all but one analysis, and a polyphyletic Cerambycidae sensu lato. When monophyletic, Cerambycidae sensu stricto was sister to the family Disteniidae. Relationships among the subfamilies of Cerambycidae sensu stricto were also recovered with strong statistical support except for Cerambycinae being made paraphyletic by Dorcasomus (Dorcasominae) in the nucleotide (but not amino acid) trees. Most other chrysomeloid families represented by more than one terminal taxon – Chrysomelidae, Disteniidae, Vesperidae, and Orsodacnidae – were monophyletic, but Megalopodidae was rendered paraphyletic by Cheloderus (Oxypeltidae). Our study corroborates some relationships within Chrysomeloidea that were previously inferred from morphological data, while also reporting several novel relationships. The present work thus provides a robust framework for future, more deeply taxon-sampled, phylogenetic and evolutionary studies of the families and subfamilies of Cerambycidae sensu lato and other Chrysomeloidea.
Peris D, Pérez-de la Fuente R, Peñalver E, Delclòs X, Barrón E, Labandeira CC. False Blister Beetles and the Expansion of Gymnosperm-Insect Pollination Modes before Angiosperm Dominance. Current Biology [Internet]. 2017;27 :897–904. DOI (full text)
Pérez-de la Fuente R, Delclòs X, Peñalver E, Engel MS. A defensive behavior and plant-insect interaction in Early Cretaceous amber - The case of the immature lacewing Hallucinochrysa diogenesi. Arthropod Structure and Development [Internet]. 2016;45 (2) :133–139. DOI (full text)Abstract

Amber holds special paleobiological significance due to its ability to preserve direct evidence of biotic interactions and animal behaviors for millions of years. Here we review the finding of Hallucinochrysa diogenesi Pérez-de la Fuente, Delclòs, Peñalver and Engel, 2012, a morphologically atypical larva related to modern green lacewings (Insecta: Neuroptera) that was described in Early Cretaceous amber from the El Soplao outcrop (northern Spain). The fossil larva is preserved with a dense cloud of fern trichomes that corresponds to the trash packet the insect gathered and carried on its back for camouflaging and shielding, similar to that which is done by its extant relatives. This finding supports the prominent role of wildfires in the paleoecosystem and provides direct evidence of both an ancient planteinsect interaction and an early acquisition of a defensive behavior in an insect lineage. Overall, the fossil of H. diogenesi showcases the potential that the amber record offers to reconstruct not only the morphology of fossil arthropods but, more remarkably, their lifestyles and ecological relationships.

Farrell BD. The Biology of Consciousness. ReVista : Harvard Review of Latin America. [Internet]. 2016;16 (1) :26–29. Web version Biology of Consciousness (PDF)