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We use integrative taxonomy to elucidate species boundaries of the plant bug genus Pseudoloxops  (Kirkaldy 1905) in the Austral and Society archipelagos of French Polynesia. We operationalize the unified species concept by treating each individual as a potential species and then establish initial groupings (putative species) following statistically highly-supported reciprocal monophyly of individuals in a phylogenetic analysis of CO1, 16S, and 28S gene fragments. We then test our species hypotheses against additional lines of evidence from geometric morphometrics, genetic distance, discrete genitalic morphology, plant association, and geographic distribution partitions. Twenty species endemic to French Polynesia are recognized as follows: Pseudoloxops aama Balukjian & Van Dam, sp. nov. Pseudoloxops anaana Balukjian & Van Dam, sp. nov. Pseudoloxops baileyi Balukjian & Van Dam, sp. nov. Pseudoloxops chastaoliancai Balukjian & Van Dam, sp. nov. Pseudoloxops harrisonfordi Balukjian & Van Dam, sp. nov. Pseudoloxops kamalaharrisae Balukjian & Van Dam, sp. nov. Pseudoloxops oboyskii Balukjian & Van Dam, sp. nov. Pseudoloxops papepihaa Balukjian & Van Dam, sp. nov. Pseudoloxops puarata Balukjian & Van Dam, sp. nov. Pseudoloxops raimana Balukjian & Van Dam, sp. nov. Pseudoloxops ravataputuarai Balukjian & Van Dam, sp. nov. Pseudoloxops simberloffi Balukjian & Van Dam, sp. nov. Pseudoloxops tairoto Balukjian & Van Dam, sp. nov. Pseudoloxops temehanirahi Balukjian & Van Dam, sp. nov. Pseudoloxops tiapai Balukjian & Van Dam, sp. nov. Pseudoloxops toparaamahana Balukjian & Van Dam, sp. nov. Pseudoloxops tupapaau Balukjian & Van Dam, sp. nov. New synonyms are proposed for Pseudoloxops flavus (Knight, 1937) [= Pseudoloxops rubrocuneatus (Knight, 1937)] and Pseudoloxops adamsoni (Knight, 1937) [=  Pseudoloxops nigribasicornis (Knight, 1937) and =  Pseudoloxops tahiticus (Knight, 1937)]. Pseudoloxops rubroclavus (Knight, 1937) is redescribed. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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.] [ABSTRACT FROM AUTHOR]

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.] [ABSTRACT FROM AUTHOR]

Despite the dominance of terrestriality in spiders, species across a diverse array of families are associated with aquatic habitats. Many species in the spider family Dictynidae are associated with water, either living near it or, in the case of Argyroneta aquatica , in it. Previous studies have indicated that this association arose once within the family. Here we test the hypothesis of a single origin via the broadest phylogeny of dictynids and related 'marronoids' to date, using several taxa that were not previously sampled in molecular analyses to provide the first quantitative test of the hypothesis put forth by Wheeler et al. (2016). We sampled 281 terminal taxa from 14 families, assembling a matrix with 4380 total base pairs of data from most taxa. We also assembled an atlas of morphological traits with potential significance for both ecology and taxonomy. Our resulting trees indicate that an aquatic habitat association has arisen multiple times within dictynids. Dictynidae and the genus Dictyna are polyphyletic and the genera Lathys and Cicurina remain unplaced. A review of aquatic habitat associations in spiders indicates that it occurs in members of at least 21 families. With our morphological atlas, we explore characters that have been implicated in aiding an aquatic lifestyle, which in the past may have caused confusion regarding taxon placement. Our results indicate that not all spiders with traits thought to be useful for aquatic habitat associations occupy such habitats, and that some spider taxa lacking these traits are nonetheless associated with water. [ABSTRACT FROM AUTHOR]