Genome Assembly of Pyrocephalus nanus: A Step Toward the Genetic Conservation of the Endangered Little Vermilion Flycatcher of the Galapagos Islands.

Incredibly powerful whole genome studies of conservation genetics, evolution, and biogeography become possible for non-model organisms when reference genomes are available. Here, we report the sequence and assembly of the whole genome of the little vermilion flycatcher (Pyrocephalus nanus; family Tyrannidae), which is an endemic, endangered, and declining species of the Galapagos Islands. Using PacBio HiFi reads to assemble long contigs and Hi-C reads for scaffolding, we assembled a genome of 1.07 Gb comprising 267 contigs in 152 scaffolds, scaffold N50 74 M, contig N50 17.8 M, with 98.9% assigned to candidate chromosomal sequences and 99.72% of the BUSCO passeriformes 10,844 single-copy orthologs present. In addition, we used the novel HiFiMiTie pipeline to fully assemble and verify all portions of the mitochondrial genome from HiFi reads, obtaining a mitogenome of 17,151 bases, containing 13 protein-coding genes, 22 tRNAs, 2 rRNAs, two control regions, and a unique structure of control region duplication and repeats. These genomes will be a critical tool for much-needed studies of phylogenetics, population genetics, biogeography, and conservation genetics of Pyrocephalus and related genera. This genome and other studies that use it will be able to provide recommendations for conservation management, taxonomic improvement, and to understand the evolution and diversification of this genus within the Galapagos Islands.

Phylogenomics of Tetraopes longhorn beetles unravels their evolutionary history and biogeographic origins.

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.

How the Easter Egg Weevils Got Their Spots: Phylogenomics Reveals Müllerian Mimicry in Pachyrhynchus (Coleoptera, Curculionidae).

The evolutionary origins of mimicry in the Easter egg weevil, Pachyrhynchus, have fascinated researchers since first noted more than a century ago by Alfred Russel Wallace. Müllerian mimicry, or mimicry in which 2 or more distasteful species look similar, is widespread throughout the animal kingdom. Given the varied but discrete color patterns in Pachyrhynchus, this genus presents one of the best opportunities to study the evolution of both perfect and imperfect mimicry. We analyzed more than 10,000 UCE loci using a novel partitioning strategy to resolve the relationships of closely related species in the genus. Our results indicate that many of the mimetic color patterns observed in sympatric species are due to convergent evolution. We suggest that this convergence is driven by positive frequency-dependent selection. [Biogeography, discrete traits, frequency-dependent selection, mimicry, partitioning, Philippines, polymorphic, UCE.].

Pachyrhynchus Weevils Use 3D Photonic Crystals with Varying Degrees of Order to Create Diverse and Brilliant Displays.

The brilliant appearance of Easter Egg weevils, genus Pachyrhynchus (Coleoptera, Curculionidae), originates from complex dielectric nanostructures within their elytral scales and elytra. Previous work, investigating singular members of the Pachyrhynchus showed the presence of either quasi-ordered or ordered 3D photonic crystals based on the single diamond ( Fd3¯m ) symmetry in their scales. However, little is known about the diversity of the structural coloration mechanisms within the family. Here, the optical properties within Pachyrhynchus are investigated by systematically identifying their spectral and structural characteristics. Four principal traits that vary their appearance are identified and the evolutionary history of these traits to identify ecological trends are reconstructed. The results indicate that the coloration mechanisms across the Easter Egg weevils are diverse and highly plastic across closely related species with features appearing at multiple independent times across their phylogeny. This work lays a foundation for a better understanding of the various forms of quasi-ordered and ordered diamond photonic crystal within arthropods.

Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens.

Phylogenomics via ultraconserved elements (UCEs) has led to improved phylogenetic reconstructions across the tree of life. However, inadvertently incorporating non-targeted DNA into the UCE marker design will lead to misinformation being incorporated into subsequent analyses. To date, the effectiveness of basic metagenomic filtering strategies has not been assessed in arthropods. Designing markers from museum specimens requires careful consideration of methods due to the high levels of microbial contamination typically found in such specimens. We investigate if contaminant sequences are carried forward into a UCE marker set we developed from insect museum specimens using a standard bioinformatics pipeline. We find that the methods currently employed by most researchers do not exclude contamination from the final set of targets. Lastly, we highlight several paths forward for reducing contamination in UCE marker design.

The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution.

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.

Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction.

Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.].

Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny.

Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. We then test our Acari UCE baits in-silico by constructing a phylogeny using 13 existing Acari genomes, as well as 6 additional taxa from a variety of genomic sources. Our Acari-specific probe kit improves the recovery of loci within mites over an existing general arachnid UCE probe set. Our initial phylogeny recovers the major mite lineages, yet finds mites to be non-monophyletic overall, with Opiliones (harvestmen) and Ricinuleidae (hooded tickspiders) rendering Parasitiformes paraphyletic.

Correction: Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils.

[This corrects the article DOI: 10.1371/journal.pone.0188044.].

Stream flow alone does not predict population structure of diving beetles across complex tropical landscapes.

Recent theoretical advances have hypothesized a central role of habitat persistence on population genetic structure and resulting biodiversity patterns of freshwater organisms. Here, we address the hypothesis that lotic species, or lineages adapted to comparably geologically stable running water habitats (streams and their marginal habitats), have high levels of endemicity and phylogeographic structure due to the persistent nature of their habitat. We use a nextRAD DNA sequencing approach to investigate the population structure and phylogeography of a putatively widespread New Guinean species of diving beetle, Philaccolilus ameliae (Dytiscidae). We find that P. ameliae is a complex of morphologically cryptic, but geographically and genetically well-differentiated clades. The pattern of population connectivity is consistent with theoretical predictions associated with stable lotic habitats. However, in two clades, we find a more complex pattern of low population differentiation, revealing dispersal across rugged mountains and watersheds of New Guinea up to 430 km apart. These results, while surprising, were also consistent with the original formulation of the habitat template concept by Southwood, involving lineage-idiosyncratic evolution in response to abiotic factors. In our system, low population differentiation might reflect a young species in a phase of range expansion utilizing vast available habitat. We suggest that predictions of life history variation resulting from the dichotomy between lotic and lentic organisms require more attention to habitat characterization and microhabitat choice. Our results also underpin the necessity to study fine-scale processes but at a larger geographical scale, as compared to solely documenting macroecological patterns, to understand ecological drivers of regional biodiversity. Comprehensive sampling especially of tropical lineages in complex and threatened environments such as New Guinea remains a critical challenge.

Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils.

Weevils (Curculionoidea) comprise one of the most diverse groups of organisms on earth. There is hardly a vascular plant or plant part without its own species of weevil feeding on it and weevil species diversity is greater than the number of fishes, birds, reptiles, amphibians and mammals combined. Here, we employ ultraconserved elements (UCEs) designed for beetles and a novel partitioning strategy of loci to help resolve phylogenetic relationships within the radiation of Australasian smurf-weevils (Eupholini). Despite being emblematic of the New Guinea fauna, no previous phylogenetic studies have been conducted on the Eupholini. In addition to a comprehensive collection of fresh specimens, we supplement our taxon sampling with museum specimens, and this study is the first target enrichment phylogenomic dataset incorporating beetle specimens from museum collections. We use both concatenated and species tree analyses to examine the relationships and taxonomy of this group. For species tree analyses we present a novel partitioning strategy to better model the molecular evolutionary process in UCEs. We found that the current taxonomy is problematic, largely grouping species on the basis of similar color patterns. Finally, our results show that most loci required multiple partitions for nucleotide rate substitution, suggesting that single partitions may not be the optimal partitioning strategy to accommodate rate heterogeneity for UCE loci.

Phylogenetic niche conservatism explains an inverse latitudinal diversity gradient in freshwater arthropods.

The underlying mechanisms responsible for the general increase in species richness from temperate regions to the tropics remain equivocal. Many hypotheses have been proposed to explain this astonishing pattern but additional empirical studies are needed to shed light on the drivers at work. Here we reconstruct the evolutionary history of the cosmopolitan diving beetle subfamily Colymbetinae, the majority of which are found in the Northern hemisphere, hence exhibiting an inversed latitudinal diversity gradient. We reconstructed a dated phylogeny using 12 genes, to investigate the biogeographical history and diversification dynamics in the Colymbetinae. We aimed to identify the role that phylogenetic niche conservatism plays in the inversed diversification pattern seen in this group. Our results suggest that Colymbetinae originated in temperate climates, which supports the hypothesis that their distribution is the result of an ancestral adaptation to temperate environmental conditions rather than tropical origins, and that temperate niche conservatism can generate and/or maintain inverse latitudinal diversity gradients.

Four new species of Trigonopterus Fauvel from the island of New Britain (Coleoptera, Curculionidae).

The hyperdiverse genus Trigonopterus has its center of diversity in Melanesia, but only a single species is recorded from the Bismarck Archipelago to date. Here we describe four new species from the island of New Britain: Trigonopterus chewbacca sp. n., Trigonopterus obsidianus sp. n., Trigonopterus puncticollis sp. n. and Trigonopterus silaliensis sp. n. We provide cytochrome oxidase subunit I (cox1) sequences of the new species and a key to all five species known from the Bismarck Archipelago.

Macroevolution of hyperdiverse flightless beetles reflects the complex geological history of the Sunda Arc.

The Sunda Arc forms an almost continuous chain of islands and thus a potential dispersal corridor between mainland Southeast Asia and Melanesia. However, the Sunda Islands have rather different geological histories, which might have had an important impact on actual dispersal routes and community assembly. Here, we reveal the biogeographical history of hyperdiverse and flightless Trigonopterus weevils. Different approaches to ancestral area reconstruction suggest a complex east to west range expansion. Out of New Guinea, Trigonopterus repeatedly reached the Moluccas and Sulawesi transgressing Lydekker's Line. Sulawesi repeatedly acted as colonization hub for different segments of the Sunda Arc. West Java, East Java and Bali are recognized as distinct biogeographic areas. The timing and diversification of species largely coincides with the geological chronology of island emergence. Colonization was not inhibited by traditional biogeographical boundaries such as Wallace's Line. Rather, colonization patterns support distance dependent dispersal and island age limiting dispersal.

Review of the genus Miloderes Casey, 1888 (Coleoptera: Curculionidae: Entiminae), with desciptions of three new species.

The genus Miloderes Casey, 1888 is reviewed and three new species are described. The genus now has eight valid species: M. amargosensis sp. nov., M. mercuryensis Tanner, M. nelsoni Kissinger, M. panamintensis sp. nov., M. setosus Casey, M. tingi Tanner, M. ubehebensis sp. nov. and M. viridis Pierce. Miloderes allredi Tanner, 1974 is a new junior synonym of M. viridis Pierce, 1910. The relationships of the species are discussed based on morphological characters from external morphology as well as from the endophallus. A key to species is provided.