Publications

2024
Gutiérrez-Trejo N, Van Dam MH, Lam AW, Martínez-Herrera G, Noguera FA, Weissling T, Ware JL, Toledo-Hernández VH, Jr. FWSkillma, Farrell BD, et al. Phylogenomics of Tetraopes longhorn beetles unravels their evolutionary history and biogeographic origins. 2024;14 (1) :7285. DOI (full text)Abstract
Tetraopes longhorn beetles are known for their resistance to milkweed plant toxins and their coevolutionary dynamics with milkweed plants (Asclepias). This association is considered a textbook example of coevolution, in which each species of Tetraopes is specialized to feed on one or a few species of Asclepias. A major challenge to investigating coevolutionary hypotheses and conducting molecular ecology studies lies in the limited understanding of the evolutionary history and biogeographical patterns of Tetraopes. By integrating genomic, morphological, paleontological, and geographical data, we present a robust phylogeny of Tetraopes and their relatives, using three inference methods with varying subsets of data, encompassing 2–12 thousand UCE loci. We elucidate the diversification patterns of Tetraopes species across major biogeographical regions and their colonization of the American continent. Our findings suggest that the genus originated in Central America approximately 21 million years ago during the Miocene and diversified from the Mid-Miocene to the Pleistocene. These events coincided with intense geological activity in Central America. Additionally, independent colonization events in North America occurred from the Late Miocene to the early Pleistocene, potentially contributing to the early diversification of the group. Our data suggest that a common ancestor of Tetraopini migrated into North America, likely facilitated by North Atlantic land bridges, while closely related tribes diverged in Asia and Europe during the Paleocene. Establishing a robust and densely sampled phylogeny of Tetraopes beetles provides a foundation for investigating micro- and macroevolutionary phenomena, including clinal variation, coevolution, and detoxification mechanisms in this ecologically important group.
Laurindo da Silva F, de Medeiros BAS, Farrell BD. Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification. Molecular Phylogenetics and Evolution. 2024;194 :108025.Abstract
Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.
2023
Pereira TPLavinsc, Heller K, Sutou M, Sikes DS. Discovery of snakeworm gnats in Alaska: a new species of Sciara Meigen (Diptera: Sciaridae) based on morphological, molecular, and citizen science data. Integrative Systematics: Stuttgart Contributions to Natural History. 2023;6 (2) :91-111, 21. DOI (full text)Abstract
A new species of Sciara Meigen, 1803, Sciara serpens Pereira, Heller & Sutou, sp. n., is described based on morphological, molecular, and citizen science data. The new species forms larval masses moving in columns, referred to as “snakeworms” or “armyworms” in the literature, and is closely related to Sciara mirabilis (Bechstein, 1794). Sciara minor Strobl, 1898restit. et stat. n. is revalidated based on morphological and molecular data. Sciara mirabilis is used for a European species previously referred to under its junior synonym Sciara militaris Nowicki, 1868. An estimate of the mitochondrial phylogeny of representative Sciara species, a summary of snakeworm sightings in North America, and a brief review of hypotheses for why such larval mass-movement behavior occurs are provided.
Gorring PS, Farrell BD. Evaluating species boundaries using coalescent delimitation in pine-killing Monochamus (Coleoptera: Cerambycidae) sawyer beetles. Molecular Phylogenetics and Evolution. 2023;184 :107777. DOI (full text)Abstract
Plant-feeding beetle species are diverse and often individually highly variable. Accurate classifications can be difficult to establish yet are essential for study of evolutionary patterns and processes. Molecular data are key to further characterizing morphologically difficult groups and defining genus and species boundaries.

Monochamus Dejean species are ecologically and economically significant, and in coniferous forests they vector the nematode that causes Pine Wilt Disease. This study uses nuclear and mitochondrial genes to test the monophyly and relationships of Monochamus and applies coalescent methods to further delimit the conifer-feeding species.

Monochamus has also included approximately 120 Old World species associated with diverse angiosperm tree species. We sample from these additional morphologically diverse species to determine their placement in the Lamiini. Through supermatrix and coalescent methods, the higher-level relationships of Monochamus show that conifer-feeders are a monophyletic group that includes the type species and has split into Nearctic and Palearctic clades. Molecular dating indicates a single dispersal of conifer-feeders to North America over the second Bering Land Bridge circa 5.3 Ma. All other Monochamus sampled fall in different parts of the Lamiini tree. Small-bodied angiosperm-feeding Monochamus group with the monotypic genus Microgoes Casey. The African Monochamus subgenera sampled are distantly related to the conifer-feeding clade.

The multispecies coalescent delimitation methods BPP and STACEY delimit 17 conifer-feeding Monochamus species for a total of 18 species, and supports the retention of all current species. An interrogation with nuclear gene allele phasing reveals that unphased data can be unreliable for accurate delimitations and divergence times. The delimited species are discussed with integrative evidence, highlighting real-world challenges in recognizing the completion of speciation trajectories.
2022
Memet E, Farrell BD, Mahadevan L. An allometric prior enhances acoustic niche partitioning signal. J R Soc Interface. 2022;19 :20220421. Full textAbstract
The acoustic niche hypothesis suggests that vocal signals of sympatric animal species are structured so as to minimize acoustic interference and facilitate communication. Accordingly, each species attempts to establish its own acoustic bandwidth so that intra-species signals are not masked. Detecting a non-random partitioning of the frequency spectrum among sympatric species could constitute evidence for the existence of acoustic avoidance behaviour. However, results from previous studies have been mixed or inconclusive, possibly as a consequence of overlooking the importance of physiological and ecological constraints. Here we introduce an improved test that incorporates prior information on body mass to account for the allometric correlation between mass (size) and vocalization frequency. By correcting for the bias induced by this correlation, the new test uncovers evidence of acoustic niche partitioning as a function of frequency in several tropical bird communities that would not be detected under a more standard test. Separately, we introduce a spatial version of the acoustic partitioning test which, in theory, could prove effective when data are collected from multiple sites located in close spatial proximity.
Kim S, Jung S, Choi J, Tsai C-L, Farrell BD, Shin S. History Does Not Repeat Itself; It Rhymes: Range Expansion and Outbreak of Plecia longiforceps (Diptera: Bibionidae) in East Asia. J Integr Pest Manag. 2022;13 (1) :31. DOI (full text)Abstract
Plecia longiforceps Duda (Diptera: Bibionidae) is reported for the first time from Korea. P. longiforceps has been previously known from the East Asian subtropics, south of the 33rd parallel, including southeastern China, Taiwan, and the Ryukyu Islands of Japan. An integrative taxonomic approach based on morphological examination of male genitalia and molecular analysis of mitochondrial cytochrome c oxidase subunit I gene sequences confirms the species identification. The recent outbreak of P. longiforceps in the Seoul Metropolitan Area, Korea, documented herein represents the northernmost record of this species and suggests its possible range expansion into the temperate zone. Similar to the range expansion and outbreak history of Plecia nearctica Hardy (Diptera: Bibionidae) in North America around the Gulf of Mexico in the 1960–1970s, P. longiforceps may become a new invasive pest in temperate East Asia. Here, we evaluate range expansion and invasion potential of P. longiforceps through Ensemble species distribution modeling and show that a great portion of Northeast Asia and Japan will likely become habitable for P. longiforceps in the next 50 years.
Mitra Das S. ‘Insects outnumber all species on Earth — some beetle groups are as old as dinosaurs’. Times of India. 2022. Read online farrell_220820_timesofindia.pdf
Altman GH, Farrell BD. Sericulture as a sustainable agroindustry. Cleaner and Circular Bioeconomy. 2022;2 :100011. DOI (full text)Abstract
The rich history of silk production (or sericulture) spans over five millennia. The sericulture industry supports jobs, economic development and health and begins with cultivation of mulberry trees with their manifold uses, including production of leaves as food for silkworms. Sericulture culminates in the production of high-quality silk thread as well as high-protein food for humans and animals. It depends, in turn, on one of the most versatile plants known, with additional benefits ranging from enhancing human health to soil conservation. Sericulture represents a rare end-to-end sustainable industry with minimal ecological impact when care is taken with supply chain management. Silk itself is a naturally versatile polymer, known as poly-fibroin, with the versatility of plastic and the advantage of biodegradability. With new developments in (bio)-harvesting technology, markets can now gain access to the single protein monomer, silk fibroin, solubilized in water, at large production scales. We can therefore envision a sustainable silk-derivatives industry that supports the replacement of petrochemicals with compounds derived from fibroin, in applications ranging from common everyday health and wellness products to advanced biopharmaceuticals and implants.
2021
Chen Y-J, Kim SI, Wan X. Mitochondrial genomes of the Dorcus velutinus complex (Coleoptera: Lucanidae) with the large intergenic spacer showing unique short sequence repeats and their implications for systematics. Journal of Asia-Pacific Entomology. 2021;24 :493-501. DOIAbstract
Mitochondrial genomes of the three lucanid species in the Dorcus velutinus complex – Dorcus velutinus Thomson, D. ursulus Arrow and D. tenuihirsutus Kim and Kim – were assembled and analyzed through next generation sequencing. The mitogenome sequences were used to infer phylogenetic relationships among Dorcus species. Our analyses revealed that the newly sequenced mitogenomes are comparable in their size, content, and gene arrangement to other lucanid mitogenomes reported to date. However, we confirmed the presence of a large intergenic spacer (IGS) between trnS(UCN) and ND1 genes, whose length varied from 170 bp (in D. tenuihirsutus) to 193 bp (in D. ursulus and D. velutinus). Within this IGS region, a short sequence fragment (TACTAAATT) was found uniquely across the three species of Dorcus velutinus complex. Our phylogenetic analyses show that the D. velutinus complex constitutes a distinct clade with a significant divergence from other species of the genus Dorcus sensu stricto. Furthermore, we reaffirm the validity of D. tenuihirsutus – a species originally described from Korea – as a distinct species, though the taxonomic status of D. ursulus remains to be studied further. Finally, we find the presence and location of large IGSs to be useful for studying evolutionary history and species delimitation in stag beetles.
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. 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. 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.
2020
de Medeiros BAS, Farrell BD. Evaluating insect-host interactions as a driver of species divergence in palm flower weevils. Communications Biology. 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.
2019
Fernández E, Ferreras I, Farrell BD, de Medeiros BAS, Romero-González GA. Studies in Aristolochia (Aristolochiaceae) of Hispaniola. Phytotaxa. 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. 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. 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. 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.
2018
Rykken JJ, Farrell BD. Exploring the Microwilderness of Boston Harbor Islands National Recreation Area: Terrestrial Invertebrate All Taxa Biodiversity Inventory. Northeastern Naturalist. 2018;25 :23-44.
Rykken JJ, Farrell BD. Six-Legged Colonists: The Establishment and Distribution of Non-Native Beetles in Boston Harbor Islands NRA. Northeastern Naturalist. 2018;25 :1-22.Abstract
Boston Harbor Islands National Recreation Area lies in a busy, urban harbor that has been receiving immigrants, both vertebrate and invertebrate, since the 17th century. As part of an All Taxa Biodiversity Inventory conducted in the park from 2005 to 2011, we documented the abundance and distribution of native and non-native beetles across 15 islands and peninsulas in Boston Harbor. We hypothesized that proportions of non-native species on the islands would be high relative to the nearby mainland (Rhode Island) and other more isolated coastal islands in Massachusetts. We also compared distribution patterns between native and non-native species and tested the predictive value of island size and isolation for determining species richness on individual islands. Focusing on 6 beetle families, we documented 105 non-native beetles out of a total of 442 species. The proportion of non-native species was 2–3 times higher in Boston Harbor Islands than in Rhode Island for all 6 beetle families, as well as for beetles on several Massachusetts islands. We discuss likely routes of immigration for beetles over the past several centuries and why islands in Boston Harbor may be attractive to non-native species. Within the park, non-native species in most focal families were, on average, more abundant and widespread across islands than native beetles, but the number or proportion of non-native species was not strongly related to island size or isolation. The high proportions of non-native species in the park, including some known pests and several new state, US, and North American records, emphasize the need for continued inventory and surveillance.

Pages