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1. Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights

   https://doi.org/10.1002/ajb2.1695  

   Lee, Aaron K. ; Gilman, Ian S. ; Srivastav, Mansa ; Lerner, Ariel D. ; Donoghue, Michael J. ; Clement, Wendy L. ( July 2021 , American Journal of Botany)

   Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement ofHeptacodiumandZabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb‐Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times.

   Sampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off‐target reads, and 10 fossils were used to calibrate dated trees.

   Varying numbers of targeted loci and off‐target plastomes were recovered from most taxa. Nuclear and plastid data confidently placeHeptacodiumwith Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement ofZabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm‐wide dating analyses, but many major splitting events date to the Eocene.

   The Angiosperms353 probe set facilitated the assembly of a large, single‐copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades.

    

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2. Settling a family feud: a high‐level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes

   https://doi.org/10.1002/ajb2.1697  

   Antonelli, Alexandre ; Clarkson, James J. ; Kainulainen, Kent ; Maurin, Olivier ; Brewer, Grace E. ; Davis, Aaron P. ; Epitawalage, Niroshini ; Goyder, David J. ; Livshultz, Tatyana ; Persson, Claes ; et al ( July 2021 , American Journal of Botany)

   Comprising five families that vastly differ in species richness—ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species—members of the Gentianales are often among the most species‐rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family‐level relationships within Gentianales have been presented in previous studies.

   Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off‐target reads for most taxa and infer phylogenetic trees for comparison with the nuclear‐derived trees.

   We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order’s classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae).

   The higher‐level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.

    

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3. A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

   https://doi.org/10.1002/ajb2.1469  

   Larson, Drew A. ; Walker, Joseph F. ; Vargas, Oscar M. ; Smith, Stephen A. ( April 2020 , American Journal of Botany)

   Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.

   We used a hierarchical clustering approach, with tree‐based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene‐wise edge‐based analyses, concatenation, and coalescent‐based methods, and is summarized in a consensus framework.

   Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole‐genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications.

   We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

    

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4. Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja

   https://doi.org/10.1002/ajb2.1700  

   Wenzell, Katherine E. ; McDonnell, Angela J. ; Wickett, Norman J. ; Fant, Jeremie B. ; Skogen, Krissa A. ( July 2021 , American Journal of Botany)

   Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population‐level differentiation in floral phenotype and genetic sequence variation among recently divergedCastillejato explore patterns of diversification under different scenarios of reproductive isolation.

   Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of fourCastillejaspecies. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespreadC. sessilifloraand the more restrictedC. purpureaspecies complex.

   We document thatC. sessilifloraand theC. purpureacomplex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation withinC. sessilifloraacross floral morphs and geography and less differentiation among species of theC. purpureacomplex.

   Patterns of genetic distance inC. sessiliflorasuggest species cohesion maintained over long distances despite variation in floral traits. In theC. purpureacomplex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco‐evolutionary paths.

    

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5. 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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