Repetitive DNA Profiles Reveal Evidence of Rapid Genome Evolution and Reflect Species Boundaries in Ground Beetles.

Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the genome's component parts. Comparative study of entire genome architecture in model organisms is shedding light on mechanisms underlying genome regulation, evolution, and diversification, but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the breve species group of Bembidion, and vary across broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the genome, revealing evidence of rapid genome evolution (including among sister pairs) not evident from analysis of traditional data sources such as multigene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the evolutionary history of Plataphus. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and genome evolution. [Bembidion; Carabidae; copy number variation profiles; rapid genome evolution; ribosomal DNA; species delimitation.].

Phylogeny of the beetle supertribe Trechitae (Coleoptera: Carabidae): Unexpected clades, isolated lineages, and morphological convergence.

Using data from two nuclear ribosomal genes and four nuclear protein-coding genes, we infer a well-resolved phylogeny of major lineages of the carabid beetle supertribe Trechitae, based upon a sampling of 259 species. Patrobini is the sister group of Trechitae, but the genus Lissopogonus appears to be outside of the Patrobini + Trechitae clade. We find that four enigmatic trechite genera from the Southern Hemisphere, Bembidarenas, Argentinatachoides, Andinodontis, and Tasmanitachoides, form a clade that is the sister group of Trechini; we describe this clade as a new tribe, Bembidarenini. Bembidarenini + Trechini form the sister group of remaining trechites. Within Trechini, subtribe Trechodina is not monophyletic, as three trechodine genera from Australia (Trechobembix, Paratrechodes, Cyphotrechodes) are the sister group of subtribe Trechina. Trechini appears to have originated in the continents of the Southern Hemisphere, with almost all Northern Hemisphere lineages representing a single radiation within the subtribe Trechina. We present moderate evidence that the geographically and phylogenetically isolated genera Sinozolus (six species in the mountains of China), Chaltenia (one species in Argentina and Chile), and Phrypeus (one species in western North America) also form a clade, the tribe Sinozolini. The traditionally recognized tribe Bembidiini sens. lat., diagnosed by the presence of a subulate terminal palpomere, is shown to be polyphyletic; subulate palpomeres have arisen five times within Trechitae. Anillini is monophyletic, and the sister group of Tachyini + Pogonini + Bembidiini + Zolini + Sinozolini; within anillines, we confirm earlier results indicating the eyed New Zealand genus Nesamblyops as the sister to the rest. Sampled New World Pogonini are monophyletic, rendering the genus Pogonus non-monophyletic. Tachyina and Xystosomina are sister groups. Within Xystosomina, the New World members are monophyletic, and are sister to an Australia-New Zealand clade. The latter consists of the genus Philipis as well as taxa not previously recognized as xystosomines: Kiwitachys, the "Tachys" ectromioides group, and "Tachys" mulwalensis. Within Tachyina, the subgenus Elaphropus is not closely related to other subgenera previously placed in the genus Elaphropus; we move the other subgenera into the genus Tachyura. Tachyina with a bifoveate mentum do not form a clade; in fact, a bifoveate mentum is found in Xystosomina, Sinozolini, Trechini, Trechitae and its sister group, Patrobini. Extensive homoplasy in the morphological characters previously used as key indicators of relationship is supported by our results: in addition to multiple origins of subulate palpomeres and bifoveate menta, a concave protibial notch has arisen independently in Anillina, Xystosomina, and Tachyina. Phylogenetically and geographically isolated, species-poor lineages in Trechini, Bembidarenini, and Sinozolini may be relicts of more widespread faunas; many of these are found today on gravel or sand shores of creeks and rivers, which may be an ancestral habitat for portions of Trechitae. In addition to the description of Bembidarenini, we present a diagnosis of the newly delimited Sinozolini, and keys to the tribes of Trechitae.

Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error.

The beetle superfamily Dytiscoidea, placed within the suborder Adephaga, comprises six families. The phylogenetic relationships of these families, whose species are aquatic, remain highly contentious. In particular the monophyly of the geographically disjunct Aspidytidae (China and South Africa) remains unclear. Here we use a phylogenomic approach to demonstrate that Aspidytidae are indeed monophyletic, as we inferred this phylogenetic relationship from analyzing nucleotide sequence data filtered for compositional heterogeneity and from analyzing amino-acid sequence data. Our analyses suggest that Aspidytidae are the sister group of Amphizoidae, although the support for this relationship is not unequivocal. A sister group relationship of Hygrobiidae to a clade comprising Amphizoidae, Aspidytidae, and Dytiscidae is supported by analyses in which model assumptions are violated the least. In general, we find that both concatenation and the applied coalescent method are sensitive to the effect of among-species compositional heterogeneity. Four-cluster likelihood-mapping suggests that despite the substantial size of the dataset and the use of advanced analytical methods, statistical support is weak for the inferred phylogenetic placement of Hygrobiidae. These results indicate that other kinds of data (e.g. genomic meta-characters) are possibly required to resolve the above-specified persisting phylogenetic uncertainties. Our study illustrates various data-driven confounding effects in phylogenetic reconstructions and highlights the need for careful monitoring of model violations prior to phylogenomic analysis.

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.

Phylogenetic relationships of the South American ground beetle subgenus Chilioperyphus Jeannel (Coleoptera: Carabidae: Trechinae: Bembidiini: Bembidion Latreille).

The boundaries and relationships of the ground beetle group Chilioperyphus Jeannel (a subgenus of the cosmopolitan genus Bembidion Latreille) are examined using DNA and morphological data. DNA sequence data from seven genes (six nuclear and one mitochondrial) indicates that Chiliopeiyphus (as newly defined) is monophyletic, and is related to the subgenera Antipetyphanes Jeannel and Plocanoperyphus Jeannel, within the South American Antiperyphanes Complex. Chilioperyphus includes two described species, B. iendocinum Jensen-Haarup and B. orregoi Germain. Beinbidion cassinense Roig-Juñent and Gianuca as well as Bembidion cuyanum Roig-Juñent and Scheibler, formerly placed in subgenus Chilioperyphus, are transferred to subgenus Antipetyphanes. Bembidion cuyanum is considered a junior synonym of B. hirtipes Jeannel. The male genitalia of Chilioperyphus is unique in having a very long flagellum that is folded twice, allowing it to fit much of its length within the walls of the median lobe. However, the brush sclerite and basal part of the flagellum are not contained within the median lobe, as they extend anterior to its base.

Re-collected after 55 years: a new species of Bembidion (Coleoptera, Carabidae) from California.

A new species of the carabid beetle genus Bembidion Latreille is described from the Central Valley, Los Angeles Basin, and surrounding areas of California. Bembidionbrownorumsp. nov. is a distinctive species, a relatively large member of the subgenus Notaphus Dejean, and within Notaphus a member of the B.obtusangulum LeConte species group. It has faint spots on the elytra and a large, convex, rounded prothorax. Of the 22 specimens from 11 localities, all but one were collected more than 55 years ago. Although the collection of the holotype in 2021 at UV light suggest the species is still extant, the lack of other recent specimens suggests the species may have a more restricted distribution than in the past, and its populations may be in decline.

Phylogeny of Bembidion and related ground beetles (Coleoptera: Carabidae: Trechinae: Bembidiini: Bembidiina).

The phylogeny of the large genus Bembidion and related genera is inferred from four nuclear protein-coding genes (CAD, wingless, arginine kinase, and topoisomerase I), ribosomal DNA (28S and 18S), and the mitochondrial gene cytochrome oxidase I (COI). 230 of the more than 1200 species of Bembidion are sampled, as well as 26 species of five related genera, and 14 outgroups. Nuclear copies (numts) of COI were found sparsely scattered through sampled species. The resulting phylogeny, based upon individual gene analyses and combined analyses using maximum likelihood and parsimony, is very well supported at most nodes. Additional analyses explored the evidence, and corroborate the phylogeny. Seven analyses, each with one of the seven genes removed from the combined matrix, were also conducted, and yielded maximum likelihood bootstrap trees sharing over 92% of their nodes with the original, well-resolved bootstrap trees based on the complete set of seven genes. All key nodes were present in all seven analyses missing a single gene, indicating that support for these nodes comes from at least two genes. In addition, the inferred maximum likelihood tree based on the combined matrix is well-behaved and self-predicting, in that simulated evolution of sequences on the inferred tree under the inferred model of evolution yields a matrix from which all but one of the model tree's clades are recovered with bootstrap value >50, suggesting that internal branches in the tree may be of a length to yield sequences sufficient to allow their inference. All likelihood analyses were conducted under both a proportion-invariable plus gamma site-to-site rate variation model, as well as a simpler gamma model. The choice of model did not have a major effect on inferred phylogenies or their bootstrap values. The inferred phylogeny shows that Bembidarenas is not closely related to Bembidiina, and Phrypeus is likely distant as well; the remaining genera of Bembidiina form a monophyletic group. Lionepha, formerly considered a subgenus of Bembidion, is shown to be outside of the clade of Asaphidion+Bembidion, and is separated as its own genus. B. (Phyla) obtusum is quite isolated within Bembidion, and there is some evidence that the remaining Bembidion form a clade. Within Bembidion, there are three large clades that are well-supported, the Bembidion, Odontium, and Ocydromus Series. The Bembidion Series contains Bembidion (s. str.), Notaphus, Furcacampa, Emphanes, Trepanedoris, Diplocampa, and related Holarctic species; all species from South America, Australia, New Zealand; and most species from southern Africa and Madagascar. All species in South America, except for members of Notaphus and Nothocys, form a clade, the Antiperyphanes Complex, which has independently radiated into body forms and niches occupied by multiple, independent Northern-Hemisphere forms. All species from New Zealand, including Zecillenus, and Australian species formerly placed in Ananotaphus together form a clade. Bembidion (s. str.) and Cyclolopha are in a clade with the Old World, Southern Hemisphere lineages Notaphocampa, Sloanephila, and Omotaphus. The large subgenus Notaphus appears to have originated in South America, with all Northern Hemisphere Notaphus arising from within a south-temperate grade. All major variation in frontal furrows on the head is contained within the Bembidion Series. The Odontium Series contains subgenera Hirmoplataphus and Hydriomicrus, which together are the sister clade of Odontium, Bracteon, Ochthedromus, Pseudoperyphus, and Microserrullula. The very large Ocydromus Series, dominant in the Holarctic region, includes the Ocydromus Complex, with many subgenera, including Hypsipezum and Leuchydrium; the phylogeny within this group is notably at odds with the current classification. Also included in the Ocydromus Series are Nepha and Bembidionetolitzkya, as well as the Princidium Complex, in which the intertidal B. (Cillenus) laterale falls. Outside these three series are a number of smaller groups, including the Plataphus Complex (containing Blepharoplataphus, Plataphus, the latter including Plataphodes); the Hydrium Complex (Metallina, Chlorodium, and Hydrium, which contains Eurytrachelus), whose sister group might be subgenus Andrewesa; Trechonepha and Liocosmius, which might be sisters; and B. (Melomalus) planatum, which is not close to Plataphus. There is some evidence that these groups plus the Ocydromus and Odontium Series form a clade. A few enigmatic groups were harder to place. The sister group of the pair Philochthus plus Philochthemphanes might be B. wickhami; Eupetedromus is well outside the three major series and not related to Notaphus; the high-elevation Asian group Hoquedela is a very isolated lineage. Notaphiellus is removed from synonymy with Nothocys, and placed in synonymy with Notaphus; Plataphodes is synonymized with Plataphus, as Plataphus is paraphyletic otherwise; Eurytrachelus is synonymized with Hydrium. A new subgenus, Lindrochthus, is described to house the distinctive B. wickhami. The implications of the inferred phylogeny for some morphological characters used in Bembidiina systematics are explored, and some of the most widely used (e.g., location of discal seta ed3 on the elytron, and shape of the shoulder) are shown to be notably homoplastic. For example, the location of elytral seta ed3 has undergone at least nine transitions between two states.

A preliminary phylogeny and review of the genus Tasmanitachoides, with descriptions of two new species (Coleoptera, Carabidae, Bembidarenini).

The genus Tasmanitachoides Erwin, a genus of very small carabid beetle endemic to Australia, is reviewed. Although uncommon in collections, they can be abundant and diverse on banks of fine gravel or coarse sand next to bodies of fresh water; samples from southeastern Australia suggest numerous undescribed species. An initial phylogenetic hypothesis for the genus is presented, including 19 of the 32 known species. The inferred phylogeny, based upon one mitochondrial and four nuclear genes, shows the kingi group to be sister to remaining Tasmanitachoides, with the wattsensis group and T. lutus (Darlington) also being phylogenetically isolated. Two new species are described: T. baehri sp. nov., from the Australian Capital Territory, is a member of the kingi group; T. erwini sp. nov., from Tasmania, is a member of the wattsensis group. Identification tools for described and some undescribed species are presented, including photographs of all known species.

Systematic revision of the trans-Bassian moriomorphine genus Theprisa Moore (Coleoptera, Carabidae).

The Australian genus Theprisa Moore, 1963, is taxonomically revised to comprise five species, two newly described: Theprisadarlingtoni Liebherr & Porch, sp. nov. of Tasmania, and Theprisaotway Liebherr, Porch & Maddison, sp. nov. from the Otway Ranges, Victoria. Two previously described species, T.australis (Castelnau) and T.montana (Castelnau), are distributed in the mountains of Victoria. The third previously described species, T.convexa (Sloane) is found in Tasmania. A lectotype is designated for T.convexa because the various syntypes are ambiguously labelled. Cladistic analysis based on morphological characters establishes monophyly of Theprisa relative to the Australian genera Sitaphe Moore and Spherita Liebherr. This and a second clade of Australian genera (Pterogmus Sloane, Thayerella Baehr, and Neonomius Moore) do not form a natural group, but are cladistically interdigitated among two monophyletic New Zealand lineages (Tarastethus Sharp, and Trichopsida Larochelle and Larivière) suggesting substantial trans-Tasman diversification among these groups. Hypothesized relationships within Theprisa are consistent with two bouts of speciation involving the Bass Strait; an initial event establishing T.convexa as adelphotaxon to the other four species, and a more recent event establishing the sister species T.darlingtoni and T.montana. Geographic restriction of T.otway to the Otway Ranges is paralleled by Otway endemics in several other carabid beetle genera, as well as by endemics in numerous other terrestrial arthropod taxa. Whereas these numerous Otway endemics support the distinctive nature of the Otway Range fauna, their biogeographic relationships are extremely varied, illustrating that the Otways have accrued their distinctive biodiversity via various means.

Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data.

The phylogeny of the carabid beetle supertribe Nebriitae is inferred from analyses of DNA sequence data from eight gene fragments including one nuclear ribosomal gene (28S), four nuclear-protein coding genes (CAD, topoisomerase 1, PEPCK, and wingless), and three mitochondrial gene fragments (16S + tRNA-Leu + ND1, COI ("barcode" region) and COI ("Pat/Jer" region)). Our taxon sample included 264 exemplars representing 241 species and subspecies (25% of the known nebriite fauna), 39 of 41 currently accepted genera and subgenera (all except Notiokasis and Archileistobrius), and eight outgroup taxa. Separate maximum likelihood (ML) analyses of individual genes, combined ML analyses of nuclear, nuclear protein-coding, and mitochondrial genes, and combined ML and Bayesian analyses of the eight-gene-fragment matrix resulted in a well-resolved phylogeny of the supertribe, with most nodes in the tree strongly supported. Within Nebriitae, 167 internal nodes of the tree (out of the maximum possible 255) are supported by maximum-likelihood bootstrap values of 90% or more. The tribes Notiophilini, Opisthiini, Pelophilini, and Nebriini are well supported as monophyletic but relationships among these are not well resolved. Nippononebria is a distinct genus more closely related to Leistus than Nebria. Archastes, Oreonebria, Spelaeonebria, and Eurynebria, previously treated as distinct genera by some authors, are all nested within a monophyletic genus Nebria. Within Nebria, four major clades are recognized: (1) the Oreonebria Series, including eight subgenera arrayed in two subgeneric complexes (the Eonebria and Oreonebria Complexes); (2) the Nebriola Series, including only subgenus Nebriola; (3) the Nebria Series, including ten subgenera arrayed in two subgeneric complexes, the Boreonebria and Nebria Complexes, with the latter further subdivided into three subgeneric subcomplexes (the Nebria, Epinebriola, and Eunebria Subcomplexes)); and (4) the Catonebria Series, including seven subgenera arrayed in two subgeneric complexes (the Reductonebria and Catonebria Complexes). A strong concordance of biogeography with the inferred phylogeny is noted and some evident vicariance patterns are highlighted. A revised classification, mainly within the Nebriini, is proposed to reflect the inferred phylogeny. Three genus-group taxa (Nippononebria, Vancouveria and Archastes) are given revised status and seven are recognized as new synonymies (Nebriorites Jeannel, 1941 and Marggia Huber, 2014 = Oreonebria Daniel, 1903; Pseudonebriola Ledoux & Roux, 1989 = Boreonebria Jeannel, 1937; Patrobonebria Bänninger, 1923, Paranebria Jeannel, 1937 and Barbonebriola Huber & Schmidt, 2017 = Epinebriola Daniel & Daniel, 1904; and Asionebria Shilenkov, 1982 = Psilonebria Andrewes, 1923). Six new subgenera are proposed and described for newly recognized clades: Parepinebriola Kavanaugh subgen. nov. (type species: Nebria delicata Huber & Schmidt, 2017), Insulanebria Kavanaugh subgen. nov. (type species: Nebria carbonaria Eschscholtz, 1829), Erwinebria Kavanaugh subgen. nov. (type species Nebria sahlbergii Fischer von Waldheim, 1828), Nivalonebria Kavanaugh subgen. nov. (type species: Nebria paradisi Darlington, 1931), Neaptenonebria Kavanaugh subgen. nov. (type species: Nebria ovipennis LeConte, 1878), and Palaptenonebria Kavanaugh subgen. nov. (type species: Nebria mellyi Gebler, 1847). Future efforts to better understand relationships within the supertribe should aim to expand the taxon sampling of DNA sequence data, particularly within subgenera Leistus and Evanoleistus of genus Leistus and the Nebria Complex of genus Nebria.

Shards, sequences, and shorelines: two new species of Bembidion from North America (Coleoptera, Carabidae).

Two new species of Bembidion are described from river shores in North America. One, Bembidion mimbres sp. nov., from the Gila River watershed in the lands of the Mimbres culture in New Mexico and Arizona, is closely related to the widespread Bembidion levigatum. DNA sequences from several linkage groups and morphology provide evidence of the distinctiveness of B. mimbres. The second, Bembidion corgenoma sp. nov., has been the subject of recent genomic and transcriptomic studies. It belongs in the Bembidion transversale subgroup, and occurs from California north to British Columbia, east to Montana and Nevada. The B. transversale subgroup as a whole is reviewed, and morphological characters that distinguish B. corgenoma from the similar and sympatric B. transversale and B. erosum are described and illustrated. DNA sequences of these three species show no consistent differences in 28S, COI, CAD, and Topoisomerase, and a coalescent species delimitation analysis reveals no notable structure within the complex. This is the first known trio of species within Bembidion for which those genes provide no clear signal of species boundaries. A neotype is designated for the one name in the group that lacks a primary type, Bembidium haplogonum Chaudoir. Chromosomes of the new species and their relatives are as is typical for Bembidion, with eleven pairs of autosomes and an XY/XX sex chromosome system.

Novelty and emergent patterns in sperm: Morphological diversity and evolution of spermatozoa and sperm conjugation in ground beetles (Coleoptera: Carabidae).

The beetle family Carabidae, with about 40,000 species, exhibits enough diversity in sperm structure and behavior to be an excellent model system for studying patterns and processes of evolution. We explore their potential, documenting sperm form in 177 species of ground beetles using light microscopy and collecting data on one qualitative and seven quantitative phenotypic traits. Our sampling captures 61% of the tribal-level diversity of ground beetles. These data highlight the notable morphological diversity of sperm in ground beetles and suggest that sperm in the group have dynamic evolutionary histories with much morphological innovation and convergence. Sperm vary among species in total length (48-3,400 µm), head length (0.5-270 µm), and head width (0.2-6.3 µm). Most ground beetles make sperm with heads that are indistinct from the flagella at the gross morphological level. However, some or all Omophron, Trachypachus, and Dyschiriini make broad-headed sperm that show morphological differences between species. Most ground beetles package their sperm into groups of sperm, termed conjugates, and ground beetles show variation in conjugate form and in the number and arrangement of sperm in a conjugate. Most ground beetles make sperm conjugates by embedding their sperm in a hyaline rod or spermatostyle. The spermatostyle is remarkably variable among species and varies in length from 17 to 41,000 µm. Several unrelated groups of ground beetles make only singleton sperm, including Nebriinae, Cicindelinae, many Trechinae, and the tribe Paussini. In order to study patterns in sperm evolution, we combine these data with a low-resolution phylogeny of ground beetles. Results from modern comparative analyses suggest the following: (a) sperm differ from conjugates in some aspect of their underlying evolutionary process, (b) sperm have influenced conjugate evolution and vice versa, and (c) conjugation with a spermatostyle likely evolved early within the history of Carabidae and it has been lost independently at least three times.

Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini).

The systematics of sitticine jumping spiders is reviewed, with a focus on the Palearctic and Nearctic regions, in order to revise their generic classification, clarify the species of one region (Canada), and study their chromosomes. A genome-wide molecular phylogeny of 23 sitticine species, using more than 700 loci from the arachnid Ultra-Conserved Element (UCE) probeset, confirms the Neotropical origins of sitticines, whose basal divergence separates the new subtribeAillutticina (a group of five Neotropical genera) from the subtribe Sitticina (five genera of Eurasia and the Americas). The phylogeny shows that most Eurasian sitticines form a relatively recent and rapid radiation, which we unite into the genus Attulus Simon, 1868, consisting of the subgenera Sitticus Simon, 1901 (seven described species), Attulus (41 described species), and Sittilong Prószynski, 2017 (one species). Five species of Attulus occur natively in North America, presumably through dispersals back from the Eurasian radiation, but an additional three species were more recently introduced from Eurasia. Attus palustris Peckham & Peckham, 1883 is considered to be a full synonym of Euophrys floricola C. L. Koch, 1837 (not a distinct subspecies). Attus sylvestris Emerton, 1891 is removed from synonymy and recognized as a senior synonym of Sitticus magnus Chamberlin & Ivie, 1944. Thus, the five native Attulus in North America are Attulus floricola, A. sylvestris, A. cutleri, A. striatus, and A. finschi. The other sitticines of Canada and the U.S.A. are placed in separate genera, all of which arose from a Neotropical radiation including Jollas Simon, 1901 and Tomis F.O.Pickard-Cambridge, 1901: (1) Attinella Banks, 1905 (A. dorsata, A. concolor, A. juniperi), (2) Tomis (T. welchi), and (3) Sittisax Prószynski, 2017 (S. ranieri). All Neotropical and Caribbean "Sitticus" are transferred to either Jollas (12 species total) or Tomis (14 species). Attinella (three species) and Tomis are both removed from synonymy with Sitticus; the synonymy of Sitticus cabellensis Prószynski, 1971 with Pseudattulus kratochvili Caporiacco, 1947 is restored; Pseudattulus Caporiacco, 1947 is synonymized with Tomis. Six generic names are newly synonymized with Attulus and one with Attinella. Two Neotropical species are described as new, Jollas cupreus sp. nov. and Tomis manabita sp. nov. Forty-six new combinations are established and three are restored. Three species synonymies are restored, one is new, and two are rejected. Across this diversity of species is a striking diversification of chromosome complements, with X-autosome fusions occurring at least four times to produce neo-Y sex chromosome systems (X1X2Y and X1X2X3Y), some of which (Sittisax ranieri and S. saxicola) are sufficiently derived as to no longer preserve the simple traces of ancestral X material. The correlated distribution of neo-Y and a base autosome number of 28 suggests that neo-Y origins occurred preferentially in lineages with the presence of an extra pair of autosomes.

After 157 years, a second specimen and species of the phylogenetically enigmatic and previously monobasic genus Nototylus Gemminger & Harold, 1868 (Coleoptera, Carabidae, Nototylini).

The enigmatic beetle tribe Nototylini (Carabidae) is revised and a key to species is provided. Two species from South America are included in the genus. One species, Nototylus fryi (Schaum), is reviewed and a second, Nototylus balli Erwin & Kavanaugh, sp. nov., is described as new. Each species is known from a single specimen, neither of which is in good condition. The possible function of what appears to be a unique antennal grooming structure on the front femur is discussed.

ResumenLa tribu enigmática de escarabajos Nototylini (Carabidae) se revisa y se provee una clave para las especies. Dos especies de América del Sur están incluidas bajo este género. Se revisa una especie, Nototylus fryi (Schaum), y una segunda, Nototylus balli sp. nov., se describe como nueva. Ambas especies se conocen de un solo espécimen, ninguno de los cuales está en buenas condiciones. Se discute la posible función de lo que aparece ser una estructura para acicalamiento antenal el fémur anterior.

RésuméUne révision taxonomique de la tribu énigmatique de coléoptères Nototylini (Carabidae) est présentée et une clé pour l'identification d'espèces est fournie. Deux espèces d'Amérique du Sud sont incluses dans le genre. Une espèce est examinée (Nototylus fryi (Schaum)) et, une deuxième est décrite comme nouvelle espèce (Nototylus balli sp. nov.). Chaque espèce est connue à partir d'un seul spécimen dont aucun est en bon état. La possible fonction de ce qui semble être une structure de toilette antennaire sur le pro-fémur est discutée.

ResumoUma enigmática tribo de besouros, Nototylini (Carabidae), é revisada, e uma chave para as espécies de Nototylus é fornecida. O gênero agora inclui duas espécies: Nototylus fryi (Schaum), aqui redescrita, e Nototylus balli sp. nov., descrita como nova. Ambas são conhecidas por somente um espécimen em mal estado de conservação. Discute-se a função de uma estrutura singular do femur anterior, possivelmente usada na escovagem da antena.

Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera).

Measuring genome size across different species can yield important insights into evolution of the genome and allow for more informed decisions when designing next-generation genomic sequencing projects. New techniques for estimating genome size using shallow genomic sequence data have emerged which have the potential to augment our knowledge of genome sizes, yet these methods have only been used in a limited number of empirical studies. In this project, we compare estimation methods using next-generation sequencing (k-mer methods and average read depth of single-copy genes) to measurements from flow cytometry, a standard method for genome size measures, using ground beetles (Carabidae) and other members of the beetle suborder Adephaga as our test system. We also present a new protocol for using read-depth of single-copy genes to estimate genome size. Additionally, we report flow cytometry measurements for five previously unmeasured carabid species, as well as 21 new draft genomes and six new draft transcriptomes across eight species of adephagan beetles. No single sequence-based method performed well on all species, and all tended to underestimate the genome sizes, although only slightly in most samples. For one species, Bembidion sp. nr. transversale, most sequence-based methods yielded estimates half the size suggested by flow cytometry.

Orange/lemon-scented beetles: opposite enantiomers of limonene as major constituents in the defensive secretion of related carabids.

The major constituent in the pygidial gland defensive fluid of the carabid beetle Ardistomis schaumii is (R)-(+)-limonene, whereas that of Semiardistomis puncticollis is (S)-(-)-limonene. This was an unanticipated result, since it is not very common to find the opposite enantiomers of the same compound among the secondary metabolites of related species. Moreover, the glandular liquid of A. schaumii contains 1,8-cineole, and that of S. puncticollis has beta-pinene, beta-phellandrene, sabinene, and p-cymene. Of about 500 carabid species that have been chemically investigated, this is the first report of the presence of such complex mixtures of monoterpenes in their defensive secretions.

Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples.

Fungi associated with seeds of tropical trees pervasively affect seed survival and germination, and thus are an important, but understudied, component of forest ecology. Here, we examine the diversity and evolutionary origins of fungi isolated from seeds of an important pioneer tree (Cecropia insignis, Cecropiaceae) following burial in soil for five months in a tropical moist forest in Panama. Our approach, which relied on molecular sequence data because most isolates did not sporulate in culture, provides an opportunity to evaluate several methods currently used to analyse environmental samples of fungi. First, intra- and interspecific divergence were estimated for the nu-rITS and 5.8S gene for four genera of Ascomycota that are commonly recovered from seeds. Using these values we estimated species boundaries for 527 isolates, showing that seed-associated fungi are highly diverse, horizontally transmitted, and genotypically congruent with some foliar endophytes from the same site. We then examined methods for inferring the taxonomic placement and phylogenetic relationships of these fungi, evaluating the effects of manual versus automated alignment, model selection, and inference methods, as well as the quality of BLAST-based identification using GenBank. We found that common methods such as neighbor-joining and Bayesian inference differ in their sensitivity to alignment methods; analyses of particular fungal genera differ in their sensitivity to alignments; and numerous and sometimes intricate disparities exist between BLAST-based versus phylogeny-based identification methods. Lastly, we used our most robust methods to infer phylogenetic relationships of seed-associated fungi in four focal genera, and reconstructed ancestral states to generate preliminary hypotheses regarding the evolutionary origins of this guild. Our results illustrate the dynamic evolutionary relationships among endophytic fungi, pathogens, and seed-associated fungi, and the apparent evolutionary distinctiveness of saprotrophs. Our study also elucidates the diversity, taxonomy, and ecology of an important group of plant-associated fungi and highlights some of the advantages and challenges inherent in the use of ITS data for environmental sampling of fungi.

Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization.

Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open-source UCE probe set for beetles of the suborder Adephaga.

Evaluating nuclear protein-coding genes for phylogenetic utility in beetles.

Although nuclear protein-coding genes have proven broadly useful for phylogenetic inference, relatively few such genes are regularly employed in studies of Coleoptera, the most diverse insect order. We increase the number of loci available for beetle systematics by developing protocols for three genes previously unused in beetles (alpha-spectrin, RNA polymerase II and topoisomerase I) and by refining protocols for five genes already in use (arginine kinase, CAD, enolase, PEPCK and wingless). We evaluate the phylogenetic performance of each gene in a Bayesian framework against a presumably known test phylogeny. The test phylogeny covers 31 beetle specimens and two outgroup taxa of varying age, including three of the four extant beetle suborders and a denser sampling in Adephaga and in the carabid genus Bembidion. All eight genes perform well for Cenozoic divergences and accurately separate closely related species within Bembidion, but individual genes differ markedly in accuracy over the older Mesozoic and Permian divergences. The concatenated data reconstruct the test phylogeny with high support in both Bayesian and parsimony analyses, indicating that combining data from multiple nuclear loci will be a fruitful approach for assembling the beetle tree of life.

Phylogenetic relationships of tribes within Harpalinae (Coleoptera: Carabidae) as inferred from 28S ribosomal DNA and the wingless gene.

Harpalinae is a large, monophyletic subfamily of carabid ground beetles containing more than 19,000 species in approximately 40 tribes. The higher level phylogenetic relationships within harpalines were investigated based on nucleotide data from two nuclear genes, wingless and 28S rDNA. Phylogenetic analyses of combined data indicate that many harpaline tribes are monophyletic, however the reconstructed trees showed little support for deeper nodes. In addition, our results suggest that the Lebiomorph Assemblage (tribes Lebiini, Cyclosomini, Graphipterini, Perigonini, Odacanthini, Lachnophorini, Pentagonicini, Catapiesini and Calophaenini), which is united by a morphological synapomorphy, is not monophyletic, and the tribe Lebiini is paraphyletic with respect to members of Cyclosomini. Two unexpected clades of tribes were supported: the Zuphiitae, comprised of Anthiini, Zuphiini, Helluonini, Dryptini, Galeritini, and Physocrotaphini; and a clade comprised of Orthogoniini, Pseudomorphini, and Graphipterini. The data presented in this study represent a dense sample of taxa to examine the molecular phylogeny of Harpalinae and provide a useful framework to examine the origin and evolution of morphological and ecological diversity in this group.