skip to main content


Title: Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS , and Chloroplast ndhF
Abstract— Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS ( LD ) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndh F data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS ( Dithyrea , Dimorphocarpa , Nerisyrenia , Lyrocarpa , and Synthlipsis ) and PP ( Paysonia and Physaria ). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF .  more » « less
Award ID(s):
1756512
NSF-PAR ID:
10328485
Author(s) / Creator(s):
;
Date Published:
Journal Name:
Systematic Botany
Volume:
46
Issue:
3
ISSN:
0363-6445
Page Range / eLocation ID:
611 to 627
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    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.

     
    more » « less
  2. Abstract

    The family Mutillidae (Hymenoptera) is a species‐rich group of aculeate wasps that occur worldwide. The higher‐level classification of the family has historically been controversial due, in part, to the extreme sexual dimorphism exhibited by these insects and their morphological similarity to other wasp taxa that also have apterous females. Modern hypotheses on the internal higher classification of Mutillidae have been exclusively based on morphology and, further, they include Myrmosinae as a mutillid subfamily. In contrast, several molecular‐based family‐level studies of Aculeata recovered Myrmosinae as a nonmutillid taxon. To test the validity of these morphology‐based classifications and the phylogenetic placement of the controversial taxon Myrmosinae, a phylogenomic study of Mutillidae was conducted using ultraconserved elements (UCEs). All currently recognized subfamilies and tribes of Mutillidae were represented in this study using 140 ingroup taxa. The maximum likelihood criterion (ML) and the maximum parsimony criterion (MP) were used to infer the phylogenetic relationships within the family and related taxa using an aligned data set of 238,764 characters; the topologies of these respective analyses were largely congruent. The modern higher classification of Mutillidae, based on morphology, is largely congruent with the phylogenomic results of this study at the subfamily level, whereas the tribal classification is poorly supported. The subfamily Myrmosinae was recovered as sister to Sapygidae in the ML analysis and sister to Sapygidae + Pompilidae in the MP analysis; it is consequently raised to the family level, Myrmosidae,stat.nov.The two constituent tribes of Myrmosidae are raised to the subfamily level, Kudakrumiinae,stat.nov., and Myrmosinae,stat.nov.All four recognized tribes of Mutillinae were found to be non‐monophyletic; three additional mutilline clades were recovered in addition to Ctenotillini, Mutillini, Smicromyrmini, and Trogaspidiini sensu stricto. Three new tribes are erected for members of these clades: Pristomutillini Waldren,trib.nov., Psammothermini Waldren,trib.nov., and Zeugomutillini Waldren,trib.nov.All three recognized tribes of Sphaeropthalminae were found to be non‐monophyletic; six additional sphaeropthalmine clades were recovered in addition to Dasymutillini, Pseudomethocini, and Sphaeropthalmini sensu stricto. The subtribe Ephutina of Mutillinae: Mutillini was found to be polyphyletic, with theEphutagenus‐group recovered within Sphaeropthalminae and theOdontomutillagenus‐group recovered as sister to Myrmillinae + Mutillinae. Consequently, the subtribe Ephutina is transferred from Mutillinae: Mutillini and is raised to a tribe within Sphaeropthalminae, Ephutini,stat.nov.Further, the taxon Odontomutillinae,stat.nov., is raised from a synonym of Ephutina to the subfamily level. The sphaeropthalmine tribe Pseudomethocini was found to be polyphyletic, with the subtribe Euspinoliina recovered as a separate clade in Sphaeropthalminae; consequently, Euspinoliina is raised to a tribe, Euspinoliini,stat.nov., in Sphaeropthalminae. The dasylabrine tribe Apteromutillini was recovered within Dasylabrini and is proposed as a new synonym of Dasylabrinae. Finally, dating analyses were conducted to infer the ages of the Pompiloidea families (Mutillidae, Myrmosidae, Pompilidae, and Sapygidae) and the ages of the Mutillidae subfamilies and tribes.

     
    more » « less
  3. Abstract

    Distephanus Cass. comprises 43 distinctive species of shrubs and small trees that have been placed historically within the ironweed tribe, Vernonieae (Asteraceae). Using the most expansive sampling of Distephanus to date, this study aims to test the monophyly of this genus and facilitate its classification. Molecular phylogenetic analyses were conducted using four molecular markers from the nuclear and plastid genomes. These data also supported divergence dating analyses that were performed to understand the timing of diversification events within Distephanus and other related genera as well as ancestral area reconstruction analyses to infer the biogegraphic history of species diversity in this group. Results from this study indicate that, as currently circumscribed, Vernonieae is not monophyletic and that Distephanus is, in fact, sister to a clade that comprises Vernonieae and another tribe, Moquinieae, which only includes two species restricted to Brazil. On the basis of these findings, Distephanus is classified in a new tribe that we describe here, Distephaneae. This new tribe comprises 41 species of Distephanus that are easily distinguished from Moquinieae and Vernonieae based on the presence of florets with yellow corollas and trinervate leaves.

     
    more » « less
  4. Abstract

    The Calyptratae, one of the most species‐rich fly clades, only originated and diversified after the Cretaceous–Palaeogene extinction event and yet exhibit high species diversity and a diverse array of life history strategies including predation, phytophagy, saprophagy, haematophagy and parasitism. We present the first phylogenomic analysis of calyptrate relationships. The analysis is based on 40 species representing all calyptrate families and on nucleotide and amino acid data for 1456 single‐copy protein‐coding genes obtained from shotgun sequencing of transcriptomes. Topologies are overall well resolved, robust and largely congruent across trees obtained with different approaches (maximum parsimony, maximum likelihood, coalescent‐based species tree, four‐cluster likelihood mapping). Many nodes have 100% bootstrap and jackknife support, but the true support varies by more than one order of magnitude [Bremer support from 3 to 3427; random addition concatenation analysis (RADICAL) gene concatenation size from 10 to 1456]. Analyses of a Dayhoff‐6 recoded amino acid dataset also support the robustness of many clades. The backbone topology Hippoboscoidea+(Fanniidae+(Muscidae+((Anthomyiidae–Scathophagidae)+Oestroidea))) is strongly supported and most families are monophyletic (exceptions: Anthomyiidae and Calliphoridae). The monotypic Ulurumyiidae is either alone or together with Mesembrinellidae as the sister group to the rest of Oestroidea. The Sarcophagidae are sister to Mystacinobiidae+Oestridae. Polleniinae emerge as sister group to Tachinidae and the monophyly of the clade Calliphorinae+Luciliinae is well supported, but the phylogenomic data cannot confidently place the remaining blowfly subfamilies (Helicoboscinae, Ameniinae, Chrysomyinae). Compared to hypotheses from the Sanger sequencing era, many clades within the muscoid grade are congruent but now have much higher support. Within much of Oestroidea, Sanger era and phylogenomic data struggle equally with regard to finding well‐supported hypotheses.

     
    more » « less
  5. Premise

    Cornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales.

    Methods

    Using the Angiosperms353 probe set and existing data sets, we generated phylogenomic data for 158 samples, representing all families in the Cornales, with intensive sampling in the Cornaceae.

    Results

    We curated an average of 312 genes per sample, constructed maximum likelihood gene trees, and inferred a species tree using the summary approach implemented in ASTRAL‐III, a method statistically consistent with the multispecies coalescent model.

    Conclusions

    The species tree we constructed generally shows high support values and a high degree of concordance among individual nuclear gene trees. Relationships among families are largely congruent with previous molecular studies, except for the placement of the nyssoids and the Grubbiaceae‐Curtisiaceae clades. Furthermore, we were able to place Hydrostachyaceae within Cornales, and within Cornaceae, the monophyly of known morphogroups was well supported. However, patterns of gene tree discordance suggest potential ancient reticulation, gene flow, and/or ILS in the Hydrostachyaceae lineage and the early diversification ofCornus. Our findings reveal new insights into the diversification process across Cornales and demonstrate the utility of the Angiosperms353 probe set.

     
    more » « less