Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

<p>Abstract</p> <p>Background</p> <p>Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.</p> <p>Results</p> <p>We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis.</p> <p>The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites.</p> <p>Conclusion</p> <p>The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.</p

Females are the Brighter Sex: Differences in External Fluorescence across Sexes and Life Stages of a Crab Spider

Fluorescence is increasingly recognized to be widespread in nature. In particular, some arachnids fluoresce externally, and in spiders the hemolymph fluoresces. In this study, we examined the external fluorescence and the fluorophores of different sexes and life stages of the crab spider Misumena vatia (Clerk 1757), a sit-and-wait predator that feeds on insects as they visit flowers. We designed novel instrumentation to measure external fluorescence in whole specimens. We found that although males and females possess internal fluorophores with similar properties, the external expression of fluorescence varies across sexes and life stages. Spiders fluoresce brightly as immatures. Females maintain their brightness to adulthood, whereas males become increasingly dim as they mature. We suggest that external fluorescence likely contributes to visual signaling in these animals, and that it differs between the sexes as a result of differences in foraging ecology and behavior

Spiders fluoresce variably across many taxa

The evolution of fluorescence is largely unexplored, despite the newfound occurrence of this phenomenon in a variety of organisms. We document that spiders fluoresce under ultraviolet illumination, and find that the expression of this trait varies greatly among taxa in this species-rich group. All spiders we examined possess fluorophores in their haemolymph, but bright fluorescence appears to result when a spider sequesters fluorophores in its setae or cuticle. By sampling widely across spider taxa, we determine that fluorescent expression is labile and has evolved multiple times. Moreover, examination of the excitation and emission properties of extracted fluorophores reveals that spiders possess multiple fluorophores and that these differ among some families, indicating that novel fluorophores have evolved during spider diversification. Because many spiders fluoresce in wavelengths visible to their predators and prey (birds and insects), we propose that natural selection imposed by predator–prey interactions may drive the evolution of fluorescence in spiders

Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics?: a case study within spiders (Arthropoda: Araneae)

The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput sequencing. Here we assess the effectiveness of a wide range of targeted long-range PCR strategies, encapsulating single and dual fragment primer design approaches to provide full mitogenomic coverage within the Araneae (Spiders). Despite extensive rounds of optimisation, full mitochondrial genome PCR amplifications were stochastic in most taxa, although 454 Roche sequencing confirmed the successful amplification of 10 mitochondrial genomes out of the 33 trialled species. The low success rates of amplification using long-Range PCR highlights the difficulties in consistently obtaining genomic amplifications using currently available DNA polymerases optimised for large genomic amplifications and suggests that there may be opportunities for the use of alternative amplification methods

Nest Structure of Pseudoanthidium Nanum Mocsary, 1880 (hymenoptera: Megachilidae: Anthidiini), and Additional Records of This Newly Introduced Bee in the Pacific Northwest

Pseudoanthidium nanum Mocsáry, 1880 is a small megachilid bee native to Europe and the Middle East (see range map in Litman et al. 2022). It is part of the Pseudoanthidium scapulare complex, a group of similar-looking and closely related taxa, which was recently revised by Litman et al. (2022). These 6–8-mm-long bees have black bodies with broadly broken yellow bands or spots on the terga, yellow maculations on the head, five teeth on the mandibles, and lamellate pronotal lobes (Michener 2007, Portman et al. 2019). Pseudanthidium nanum can be distinguished from other members of the P. scapulare complex by characters of the male genitalia and by the combs on the fifth sternite of the males, as detailed in Litman et al. (2022)

The complete mitochondrial genome sequence of the spider habronattus oregonensis reveals rearranged and extremely truncated tRNAs

We sequenced the entire mitochondrial genome of the jumping spider Habronattus oregonensis of the arachnid order Araneae (Arthropoda: Chelicerata). A number of unusual features distinguish this genome from other chelicerate and arthropod mitochondrial genomes. Most of the transfer RNA gene sequences are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. At least nine of the tRNA sequences lack the potential to form TYC arm stem pairings, and instead are inferred to have TV-replacement loops. Furthermore, sequences that could encode the 3' aminoacyl acceptor stems in at least 10 tRNAs appear to be lacking, because fully paired acceptor stems are not possible and because the downstream sequences instead encode adjacent genes. Hence, these appear to be among the smallest known tRNA genes. We postulate that an RNA editing mechanism must exist to restore the 3' aminoacyl acceptor stems in order to allow the tRNAs to function. At least seven tRNAs are rearranged with respect to the chelicerate Limulus polyphemus, although the arrangement of the protein-coding genes is identical. Most mitochondrial protein-coding genes of H. oregonensis have ATN as initiation codons, as commonly found in arthropod mtDNAs, but cytochrome oxidase subunit 2 and 3 genes apparently use UUG as an initiation codon. Finally, many of the gene sequences overlap one another and are truncated. This 14,381 bp genome, the first mitochondrial genome of a spider yet sequenced, is one of the smallest arthropod mitochondrial genomes known. We suggest that posttranscriptional RNA editing can likely maintain function of the tRNAs while permitting the accumulation of mutations that would otherwise be deleterious. Such mechanisms may have allowed for the minimization of the spider mitochondrial genome

The complete mitochondrial genome sequence of the spider habronattus oregonensis reveals rearranged and extremely truncated tRNAs

We sequenced the entire mitochondrial genome of the jumping spider Habronattus oregonensis of the arachnid order Araneae (Arthropoda: Chelicerata). A number of unusual features distinguish this genome from other chelicerate and arthropod mitochondrial genomes. Most of the transfer RNA gene sequences are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. At least nine of the tRNA sequences lack the potential to form TYC arm stem pairings, and instead are inferred to have TV-replacement loops. Furthermore, sequences that could encode the 3' aminoacyl acceptor stems in at least 10 tRNAs appear to be lacking, because fully paired acceptor stems are not possible and because the downstream sequences instead encode adjacent genes. Hence, these appear to be among the smallest known tRNA genes. We postulate that an RNA editing mechanism must exist to restore the 3' aminoacyl acceptor stems in order to allow the tRNAs to function. At least seven tRNAs are rearranged with respect to the chelicerate Limulus polyphemus, although the arrangement of the protein-coding genes is identical. Most mitochondrial protein-coding genes of H. oregonensis have ATN as initiation codons, as commonly found in arthropod mtDNAs, but cytochrome oxidase subunit 2 and 3 genes apparently use UUG as an initiation codon. Finally, many of the gene sequences overlap one another and are truncated. This 14,381 bp genome, the first mitochondrial genome of a spider yet sequenced, is one of the smallest arthropod mitochondrial genomes known. We suggest that posttranscriptional RNA editing can likely maintain function of the tRNAs while permitting the accumulation of mutations that would otherwise be deleterious. Such mechanisms may have allowed for the minimization of the spider mitochondrial genome

Preferences of Cavity Nesting Bees in Portland

Little is known about the diverse life histories of our many native bee species, although many are threatened by habitat loss through urbanization. For example, few studies have examined the role of nest height or cavity size in attracting our lesser known native cavity-nesting bees. To remedy this paucity of data, we set up cavity nest boxes across fourteen locations in the greater Portland area and erected wooden posts with nest blocks at 3 different heights (0.5, 1.5, and 2.3 meters). To accommodate a diversity of bee species, cavity diameters ranged in size from 3.0 to 10.0 mm. From these nests, we collected data to determine nest occupancy, nest diameter size preferences, and percent bee and wasp occurrence rates. The overall nest height occupancy rates greatly varied amongst the fourteen locations, but overall the 2.3 m height had the greatest percent occupancy. Although the bees and wasps from the nests collected in 2019 have not yet emerged we estimate that the nests will yield about 68% bees and 32% wasps. Lastly, the greatest occupancy rates were observed in the two smallest cavity diameters, 3.0 and 4.5 mm. Nesting preference data will be used to better inform residents of greater Portland how best to provide nesting habitat for cavity nesting bees, and the solitary wasps that use similar nesting sites