Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera

Chromosomal mutations such as fusions and fissions are often thought to be deleterious, especially in heterozygotes (underdominant), and consequently are unlikely to become fixed. Yet, many models of chromosomal speciation ascribe an important role to chromosomal mutations. When the effective population size (Ne) is small, the efficacy of selection is weakened, and the likelihood of fixing underdominant mutations by genetic drift is greater. Thus, it is possible that ecological and phenotypic transitions that modulate Ne facilitate the fixation of chromosome changes, increasing the rate of karyotype evolution. We synthesize all available chromosome number data in Coleoptera and estimate the impact of traits expected to change Ne on the rate of karyotype evolution in the family Carabidae and 12 disparate clades from across Coleoptera. Our analysis indicates that in Carabidae, wingless clades have faster rates of chromosome number increase. Additionally, our analysis indicates clades exhibiting multiple traits expected to reduce Ne, including strict inbreeding, oligophagy, winglessness, and island endemism, have high rates of karyotype evolution. Our results suggest that chromosome number changes are likely fixed by genetic drift despite an initial fitness cost and that chromosomal speciation models may be important to consider in clades with very small Ne.

MicroCT data provide evidence correcting the previous misidentification of an Eocene amber beetle (Coleoptera, Cicindelidae) as an extant species

The fossil record suggests some insect species have a marked longevity. The oldest fossils purported to represent extant insect species are from the Oligocene and Eocene. One of the most cited fossils is the extant tiger beetle Tetracha carolina (Coleoptera: Cicindelidae) that was identified over a century ago by Walther Horn in Eocene Baltic amber. We examined this and compared it to the previously described cincindelid Baltic amber fossil Palaeoiresina cassolai using X-ray microscopy and 3D imaging techniques. We conclude that Horn's fossil tiger beetle specimen is conspecific with the Eocene P. cassolai and is a member of an extinct stem group lineage of Cicindelidae. Based on a review of all the tiger beetle fossils described from Cretaceous and Paleogene deposits, we found that the assignment of these fossil species to extant lineages is not supported. There are currently no synapomorphies known from fossils that can provide evidence for Cretaceous Manticorni or Megacephalini nor is there evidence for Eocene Iresina. We provide evidence that rejects the idea of a recent beetle species persisting since the Eocene period, which is crucial for using the currently known fossil Cicindelidae species to calibrate divergence dating of beetle phylogenies.

Formation of the Holarctic Fauna: Dated molecular phylogenetic and biogeographic insights from the Quedius-lineage of Ground-Dwelling Rove Beetles (Coleoptera, Staphylinidae)

Although the Holarctic fauna has been explored for centuries, many questions on its formation are still unanswered. For example, i) what was the impact of the uplift of the Himalaya and Tibetan Plateau?, ii) what were the timings and climate of the faunal bridges connecting the Nearctic and Palearctic regions?, and iii) how did insect lineages respond to the late Paleogene global cooling and regional aridification? To answer these, we developed a phylogenetic dataset of 1229 nuclear loci for a total of 222 species of rove beetles (Staphylinidae) with emphasis in the tribe Quediini, especially Quedius-lineage and its subclade Quedius sensu stricto. Using eight fossils for calibrating molecular clock, we estimated divergence times and then analysed in BioGeoBEARS paleodistributions of the most recent common ancestor for each target lineage. For each species we generated climatic envelopes of the temperature and precipitation and mapped them across the phylogeny to explore evolutionary shifts. Our results suggest that the warm and humid Himalaya and Tibetan Plateau acted as an evolutionary cradle for the Quedius-lineage originating during the Oligocene from where, in the Early Miocene, the ancestor of the Quedius s. str. dispersed into the West Palearctic. With the climate cooling from the Mid Miocene onwards, new lineages within Quedius s. str. emerged and gradually expanded distributions across the Palearctic. In Late Miocene, a member of the group dispersed to the Nearctic region via Beringia before the closure of this land bridge 5.3 Ma. Paleogene global cooling and regional aridification largely shaped the current biogeographic pattern for Quedius s. str. species, many of them originating during the Pliocene and shifting or contracting their ranges during Pleistocene.

Genomic signatures of recent convergent transitions to social life in spiders

The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.

Anchored Phylogenomics, Evolution and Systematics of Elateridae: Are All Bioluminescent Elateroidea Derived Click Beetles?

Simple Summary

In the era of phylogenomics, new molecular sequencing and computational techniques can aid in resolving phylogenetic relationships that were previously intractable by morphological or limited molecular data. In this study, we used anchored hybrid enrichment—designed to recover DNA sequences from hundreds of single-copy orthologous genes—to resolve the phylogeny of the Elateridae (click-beetles) and establish their placement within superfamily Elateroidea. The resulting data were compatible with published transcriptomes, allowing for integrating our dataset with previously published data. Using a wide range of analyses on these molecular data, we tested hypotheses long-debated in the morphological literature and also the robustness of our phylogenetic inferences. Our results placed the bioluminescent lampyroids (fireflies and relatives) within the click-beetles, challenging the current classification of Elateridae, Lampyridae, Phengodidae, and Rhagophthalmidae. However, despite the large amount of molecular data analyzed, a few nodes with conflicting phylogenetic signals could not be unambiguously resolved. Overall, we recovered well-resolved tree topologies that will serve as a framework for further systematic and evolutionary studies of click-beetles. This work further demonstrates that the click-beetle lineage contains not only pest wireworms, but also many species that benefit agriculture.

Abstract

Click-beetles (Coleoptera: Elateridae) are an abundant, diverse, and economically important beetle family that includes bioluminescent species. To date, molecular phylogenies have sampled relatively few taxa and genes, incompletely resolving subfamily level relationships. We present a novel probe set for anchored hybrid enrichment of 2260 single-copy orthologous genes in Elateroidea. Using these probes, we undertook the largest phylogenomic study of Elateroidea to date (99 Elateroidea, including 86 Elateridae, plus 5 non-elateroid outgroups). We sequenced specimens from 88 taxa to test the monophyly of families, subfamilies and tribes. Maximum likelihood and coalescent phylogenetic analyses produced well-resolved topologies. Notably, the included non-elaterid bioluminescent families (Lampyridae + Phengodidae + Rhagophthalmidae) form a clade within the otherwise monophyletic Elateridae, and Sinopyrophoridae may not warrant recognition as a family. All analyses recovered the elaterid subfamilies Elaterinae, Agrypninae, Cardiophorinae, Negastriinae, Pityobiinae, and Tetralobinae as monophyletic. Our results were conflicting on whether the hypnoidines are sister to Dendrometrinae or Cardiophorinae + Negastriinae. Moreover, we show that fossils with the eucnemid-type frons and elongate cylindrical shape may belong to Eucnemidae, Elateridae: Thylacosterninae, ancestral hard-bodied cantharoids or related extinct groups. Proposed taxonomic changes include recognition of Plastocerini as a tribe in Dendrometrinae and Hypnoidinae stat. nov. as a subfamily within Elateridae.

HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma  burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.