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1. Anchored phylogenomics and revised classification of the Miltogramminae (Diptera: Sarcophagidae)

   https://doi.org/10.1111/syen.12609  

   Johnston, Nikolas P. ; Pape, Thomas ; Piwczyński, Marcin ; Wallman, James F. ; Wiegmann, Brian M. ; Cassel, Brian K. ; Akbarzadeh, Kamran ; Szpila, Krzysztof ( October 2023 , Systematic Entomology)

   The Miltogramminae (Diptera: Sarcophagidae) includes ~600 species across >40 genera, which constitute ~20% of global Sarcophagidae. While molecular phylogenetic hypotheses have been produced for this group, critical problems persist, including the presence of paraphyletic genera, uncertain relationships between genera, a bias of sampling towards Palaearctic taxa, and low support for many branches. The present study remedies these issues through the application of Anchored Hybrid Enrichment (AHE) to a sample including ~60% of the currently recognised genera (16% of known species) representing all biogeographic regions except the Neotropical. An alignment of 1,281 concatenated loci was analysed with maximum likelihood (RAxML, IQ‐TREE), Bayesian inference (ExaBayes) and coalescent‐based approaches (ASTRAL, SVDquartets), which resulted in highly supported and concordant topologies, providing unprecedented insight into the relationships of this subfamily of flesh flies, allowing a major update to miltogrammine classification. The AHE phylogenetic hypothesis supports the monophyly of a large proportion of genera. The monophyly ofMetopiaMeigen is restored by synonymy withAenigmetopiaMalloch,syn.n.To achieve monophyly ofMiltogrammaMeigen, eight species are transferred fromPterellaRobineau‐Desvoidy. The genusPterellais shown to be paraphyletic in its current circumscription, and to restore generic monophylyPterellais restricted to contain onlyPt. grisea(Meigen).ErioproctaEnderlein,stat.rev., is resurrected. The genusSenotainiaMacquart is reconstructed as paraphyletic. The monotypic genusMetopodiaBrauer & Bergenstamm is synonymised withTaxigrammaMacquart,syn.n.In light of our phylogenetic hypotheses, a new Miltogramminae tribal classification is proposed, composed of six tribes.

    

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2. Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera)

   https://doi.org/10.1093/sysbio/syac043  

   Owen, Christopher L. ; Marshall, David C. ; Wade, Elizabeth J. ; Meister, Russ ; Goemans, Geert ; Kunte, Krushnamegh ; Moulds, Max ; Hill, Kathy ; Villet, M. ; Pham, Thai-Hong ; et al ( June 2022 , Systematic Biology)

   Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the anchored hybrid enrichment markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned data set, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after the removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution. [Auchenorrhyncha; base-composition bias; Cicadidae; Cicadoidea; Hemiptera; phylogenetic conflict.]

    

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3. The spider tree of life: phylogeny of Araneae based on target‐gene analyses from an extensive taxon sampling

   https://doi.org/10.1111/cla.12182  

   Wheeler, Ward C. ; Coddington, Jonathan A. ; Crowley, Louise M. ; Dimitrov, Dimitar ; Goloboff, Pablo A. ; Griswold, Charles E. ; Hormiga, Gustavo ; Prendini, Lorenzo ; Ramírez, Martín J. ; Sierwald, Petra ; et al ( December 2016 , Cladistics)

   We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups. The dataset includes six markers from the mitochondrial (12S, 16S,COI) and nuclear (histone H3, 18S, 28S) genomes, and was analysed by multiple methods, including constrained analyses using a highly supported backbone tree from transcriptomic data. We recover most of the higher‐level structure of the spider tree with good support, including Mesothelae, Opisthothelae, Mygalomorphae and Araneomorphae. Several of our analyses recover Hypochilidae and Filistatidae as sister groups, as suggested by previous transcriptomic analyses. The Synspermiata are robustly supported, and the families Trogloraptoridae and Caponiidae are found as sister to the Dysderoidea. Our results support the Lost Tracheae clade, including Pholcidae, Tetrablemmidae, Diguetidae, Plectreuridae and the family Pacullidae (restored status) separate from Tetrablemmidae. The Scytodoidea include Ochyroceratidae along with Sicariidae, Scytodidae, Drymusidae and Periegopidae; our results are inconclusive about the separation of these last two families. We did not recover monophyletic Austrochiloidea and Leptonetidae, but our data suggest that both groups are more closely related to the Cylindrical Gland Spigot clade rather than to Synspermiata. Palpimanoidea is not recovered by our analyses, but also not strongly contradicted. We find support for Entelegynae and Oecobioidea (Oecobiidae plus Hersiliidae), and ambiguous placement of cribellate orb‐weavers, compatible with their non‐monophyly. Nicodamoidea (Nicodamidae plus Megadictynidae) and Araneoidea composition and relationships are consistent with recent analyses. We did not obtain resolution for the titanoecoids (Titanoecidae and Phyxelididae), but the Retrolateral Tibial Apophysis clade is well supported. Penestomidae, and probably Homalonychidae, are part of Zodarioidea, although the latter family was set apart by recent transcriptomic analyses. Our data support a large group that we call the marronoid clade (including the families Amaurobiidae, Desidae, Dictynidae, Hahniidae, Stiphidiidae, Agelenidae and Toxopidae). The circumscription of most marronoid families is redefined here. Amaurobiidae include the Amaurobiinae and provisionally Macrobuninae. We transfer Malenellinae (Malenella, from Anyphaenidae), Chummidae (Chumma) (new syn.) and Tasmarubriinae (Tasmarubrius,TasmabrochusandTeeatta, from Amphinectidae) to Macrobuninae. Cybaeidae are redefined to includeCalymmaria,Cryphoeca,EthobuellaandWillisius(transferred from Hahniidae), andBlabommaandYorima(transferred from Dictynidae). Cycloctenidae are redefined to includeOrepukia(transferred from Agelenidae) andPakehaandParavoca(transferred from Amaurobiidae). Desidae are redefined to include five subfamilies: Amphinectinae, withAmphinecta,Mamoea,Maniho,ParamamoeaandRangitata(transferred from Amphinectidae); Ischaleinae, withBakalaandManjala(transferred from Amaurobiidae) andIschalea(transferred from Stiphidiidae); Metaltellinae, withAustmusia,Buyina,Calacadia,Cunnawarra,Jalkaraburra,Keera,Magua,Metaltella,PenaoolaandQuemusia; Porteriinae (new rank), withBaiami,Cambridgea,CorasoidesandNanocambridgea(transferred from Stiphidiidae); and Desinae, withDesis, and provisionallyPoaka(transferred from Amaurobiidae) andBarahna(transferred from Stiphidiidae).Argyronetais transferred from Cybaeidae to Dictynidae.Cicurinais transferred from Dictynidae to Hahniidae. The generaNeoramia(from Agelenidae) andAorangia,MarplesiaandNeolana(from Amphinectidae) are transferred to Stiphidiidae. The family Toxopidae (restored status) includes two subfamilies: Myroinae, withGasparia,Gohia,Hulua,Neomyro,Myro,OmmatauxesisandOtagoa(transferred from Desidae); and Toxopinae, withMidgeeandJamara, formerly Midgeeinae,new syn.(transferred from Amaurobiidae) andHapona,Laestrygones,Lamina,ToxopsandToxopsoides(transferred from Desidae). We obtain a monophyletic Oval Calamistrum clade and Dionycha; Sparassidae, however, are not dionychans, but probably the sister group of those two clades. The composition of the Oval Calamistrum clade is confirmed (including Zoropsidae, Udubidae, Ctenidae, Oxyopidae, Senoculidae, Pisauridae, Trechaleidae, Lycosidae, Psechridae and Thomisidae), affirming previous findings on the uncertain relationships of the “ctenids”AncylometesandCupiennius, although a core group of Ctenidae are well supported. Our data were ambiguous as to the monophyly of Oxyopidae. In Dionycha, we found a first split of core Prodidomidae, excluding the Australian Molycriinae, which fall distantly from core prodidomids, among gnaphosoids. The rest of the dionychans form two main groups, Dionycha part A and part B. The former includes much of the Oblique Median Tapetum clade (Trochanteriidae, Gnaphosidae, Gallieniellidae, Phrurolithidae, Trachelidae, Gnaphosidae, Ammoxenidae, Lamponidae and the Molycriinae), and also Anyphaenidae and Clubionidae.Orthobulais transferred from Phrurolithidae to Trachelidae. Our data did not allow for complete resolution for the gnaphosoid families. Dionycha part B includes the families Salticidae, Eutichuridae, Miturgidae, Philodromidae, Viridasiidae, Selenopidae, Corinnidae and Xenoctenidae(new fam., includingXenoctenus,ParavulsorandOdo, transferred from Miturgidae, as well asIncasoctenusfrom Ctenidae). We confirm the inclusion ofZora(formerly Zoridae) within Miturgidae.

    

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

   https://doi.org/10.3897/zookeys.925.39691  

   Maddison, Wayne P. ; Maddison, David R. ; Derkarabetian, Shahan ; Hedin, Marshal ( April 2020 , ZooKeys)

   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 subtribe Aillutticina (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 Prószyński, 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 Prószyński, 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 Prószyński, 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 (X 1 X 2 Y and X 1 X 2 X 3 Y), 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. 

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5. Grappling with homoplasy: taxonomic refinements and reassignments in the ant genera Camponotus and Colobopsis (Hymenoptera: Formicidae)

   https://doi.org/10.3897/asp.79.e66978  

   Ward, Philip S. ; Boudinot, Brendon E. ( April 2021 , Arthropod Systematics & Phylogeny)

   null (Ed.)

   Camponotus and Colobopsis are widely distributed and species-rich genera in the ant tribe Camponotini. Molecular phylogenetic studies demonstrate that they are not sister taxa, but several lineages within each genus have converged to a remarkable degree, confounding the taxonomy of these ants. Based on multiple lines of evidence, including worker and male morphology, we demonstrate that: (1) three species of “Camponotus” belonging to the subgenus Myrmotemnus, including its type species, are in fact members of the genus Colobopsis ; (2) four species previously assigned to Colobopsis belong to the subgenus Myrmamblys of Camponotus ; and (3) three Nearctic taxa recently placed in Colobopsis are members of the genus Camponotus and closely related to Camponotus clarithorax . These taxonomic findings yield the following new or revived combinations: Colobopsis moeschi ( comb. nov. ), Colobopsis moeschi lygaea ( comb. nov. ), Colobopsis nutans ( comb. nov. ), Colobopsis nutans cleliae ( comb. nov. ), and Colobopsis reichenspergeri ( comb. nov. ); Camponotus apostemata ( comb. nov. ), Camponotus aurelianus ( comb. rev. ), Camponotus cavibregma ( comb. nov. ), Camponotus horrens ( comb. rev. ), Camponotus politae ( comb. rev. ), Camponotus trajanus ( comb. rev. ), and Camponotus yogi ( comb. rev. ). A further consequence is the following generic synonymy (senior synonym listed first): Colobopsis = Myrmotemnus syn. nov. , and Camponotus = Dolophra syn. rev. At the species level, we argue that Camponotus apostemata and Camponotus cavibregma are junior synonyms ( syn. nov. ) of Camponotus yogi , and Camponotus quercicola is a junior synonym ( syn. nov. ) of Ca. laevigatus . Taxonomic comments are also provided on some members of the Camponotus reticulatus group, with Camponotus adustus ( stat. nov. ) and Ca. leucodiscus ( stat. rev. ) being recognized as distinct species rather than subspecies of Ca. bellus . A male-based diagnosis of the Camponotini is provided, and differences between the males of Colobopsis and Camponotus are documented and illustrated for the first time. This study reveals new character systems of potential value to the systematics of these ants, including features of the male genitalia, and emphasizes the value of reciprocal illumination between phylogenomics and critical morphological analysis. 

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