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1. Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North American Nyssa (Nyssaceae)

   https://doi.org/10.1111/jse.12599  

   Zhou, Wenbin ; Xiang, Qiu‐Yun ; Wen, Jun ( June 2020 , Journal of Systematics and Evolution)

   Nyssa(Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian–eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographical history, and investigate the evolution of morphology and ecological niches, aiming at a better understanding of the well‐known EA–ENA floristic disjunction. Results showed that the Central American (CAM)Nyssa talamancanawas sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographical history suggested thatNyssahad an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central AmericanN. talamancanarepresents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals ofNyssaand the Neogene dispersals, respectively, as well as the role of Central America as refugia of the Paleogene flora. The total‐evidence‐based dated phylogeny suggested that the pattern of macroevolution ofNyssacoincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA–ENA disjunct, supporting the ecological selection driving trait evolutions after geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene, but “out of Asia” migrations in the Neogene, to explain the present disjunct distribution ofNyssain EA and ENA.

    

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2. Molecular phylogeny of the tribe Candalidini (Lepidoptera: Lycaenidae): systematics, diversification and evolutionary history

   https://doi.org/10.1111/syen.12432  

   Braby, Michael F. ; Espeland, Marianne ; Müller, Chris J. ; Eastwood, Rod ; Lohman, David J. ; Kawahara, Akito Y. ; Maunsell, Sarah C. ; Pierce, Naomi E. ( June 2020 , Systematic Entomology)

   The butterfly tribe Candalidini is geographically restricted to Australia and mainland New Guinea and its adjacent islands. With 60 species and subspecies, it represents a large radiation of Papilionoidea in the Australian region. Although the species‐level taxonomy is relatively well understood, the number of genera is uncertain, varying from two to eight. We reconstructed the phylogeny of the Candalidini based on a 13‐locus hybrid enrichment probe set (12.8 Kbp: COI, Thiolase, CAD, CAT, DDC, EF1‐a, GAPDH, HCL, IDH, MDH, RPS2, RPS5, Wingless), including all previously recognized genera and 76% (28/37) of the species‐level diversity of the tribe. Maximum likelihood analysis recovered the Candalidini as a strongly supported monophyletic group. In conjunction with morphological characters, the phylogeny provided a robust framework for a revised classification in which we recognize four genera, 37 species and 23 subspecies. The genusNesolycaenaWaterhouse & R.E. Turner is considered in synonymy withCandalidesHübner, and four other genera are not recognized, namely,HolochilaC. Felder,AdalumaTindale,ZetonaWaterhouse andMicroscenaTite. Of the four valid genera, theabsimilisgroup (23 species) is placed in the newly described genusEirmocidesBraby, Espeland & Müllergen. nov.(type speciesCandalides consimilisWaterhouse). Theerinusgroup (six species) is assigned toErinaSwainson, which is reinstated.Chrysophanus cyprotusOlliff is assigned toCyprotidesTite, which is also reinstated as a monotypic genus. The remaining seven species are placed inCandalides sensu stricto. Overall, we propose 47 new nomenclatural changes at the species and subspecies levels, including the synonymy ofHolochila biakaTite asEirmocides tringa biaka(Tite)syn. nov. et comb. nov.and recognition ofCandalides hyacinthinus gilesiM.R. Williams & Bollam as a distinct speciesErina gilesi(M.R. Williams & Bollamstat. rev. et comb. nov.A dated phylogeny using Bayesian inference in BEAST2 and biogeographical and habitat analyses based on the DEC model in BioGeoBEARS indicated that the ancestor of the Candalidini most likely evolved in rainforest habitats of the mesic biome in situ on the Australian plate of Southern Gondwana during the Eocene (c. 43 Ma). A major period of diversification occurred in the Miocene, which coincided with aridification of the Australian continent, followed by a further episode of radiation in montane New Guinea during the Plio‐Pleistocene.

   This published work has been registered on ZooBank by the authors: Michael Braby:http://zoobank.org/urn:lsid:zoobank.org:author:4D3A7605‐EBD0‐40F6‐A5F2‐7F67F59E3D60;

   Marianne Espeland:http://zoobank.org/urn:lsid:zoobank.org:author:00D6F9F9‐3902‐4A8B‐846F‐720AB32922A6;

   Chris Müller:http://zoobank.org/urn:lsid:zoobank.org:author:15FE5F26‐7596‐46C2‐9697‐1FD92A692D0D;

   http://zoobank.org/urn:lsid:zoobank.org:pub:47D5CA34‐C294‐4FBD‐84B6‐1C2A82B7CADF.

    

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3. Phylogeny, migration and geographic range size evolution of Anax dragonflies (Anisoptera: Aeshnidae)

   https://doi.org/10.1093/zoolinnean/zlab046  

   Clement, Rebecca A ; Saxton, Natalie A ; Standring, Samantha ; Arnold, Preston R ; Johnson, K Kaihileipihamekeola ; Bybee, David R ; Bybee, Seth M ( August 2021 , Zoological Journal of the Linnean Society)

   Abstract The genus Anax is a group of cosmopolitan dragonflies noted for its conspicuous migratory behaviours and large size. Here we present the first dated, species-level, multigene, molecular phylogeny for the group to test generic and species-limits, as well as the evolution of migration and range size. Using five mitochondrial and nuclear gene regions (COI, COI/COII, CYTB/ND1, ITS1 and PRMT) from 20 species, we reconstructed a phylogeny of Anax using both a Bayesian and maximum likelihood approach. We found that Anax (including its hypothesized sister group Hemianax) forms a monophyletic group, and that 12 out of 20 species tested positive for monophyly were also monophyletic. The monophyly of several species of Anax is less clear. Migratory behaviour, which is known to occur in at least nine species, is recovered as the ancestral behaviour, which was lost and subsequently gained at least three times. Geographic range size seems to be tightly associated with migratory behaviour. 

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4. Phylogeny of the Neotropical tribe Jacarandeae (Bignoniaceae)

   https://doi.org/10.1002/ajb2.1399  

   Ragsac, Audrey C. ; Farias‐Singer, Rosana ; Freitas, Loreta B. ; Lohmann, Lúcia G. ; Olmstead, Richard G. ( December 2019 , American Journal of Botany)

   The tribe Jacarandeae includesJacaranda(49 species) andDigomphia(3 species), two genera of trees and woody shrubs with Neotropical distribution. Jacarandeae is sister to the rest of the Bignoniaceae, but not much is known about interspecific and intergeneric relationships within this group.

   We reconstructed the phylogeny of Jacarandeae using chloroplast (ndhF,rpl32‐trnL,trnL‐F) and nuclear (ETS,PPR62) markers. Evolutionary relationships within Jacarandeae were inferred using Bayesian, Maximum Likelihood, and species tree approaches. The resulting phylogenetic framework was used as the basis to interpret the evolution of key morphological character states (i.e., stamen and calyx traits) and revise the infra‐generic classification of the group.

   JacarandaandDigomphiabelong to a well‐supported clade, withDigomphianested withinJacaranda. We propose the necessary taxonomic changes to recognize monophyletic taxa, including a broadly circumscribedJacarandadivided into four sections: (1)Jacarandasect.Nematopogon, species previously included inDigomphiaand united by divided staminode apices and spathaceous calyces; (2)Jacarandasect.Copaia, species with monothecal anthers and cupular calyces; (3)Jacarandasect.Jacaranda, species with monothecal anthers and campanulate calyces; and (4)Jacarandasect.Dilobos, species with dithecal anthers and cupular calyces, and including more than half of the species of the genus, all restricted to Brazil.

   As circumscribed here, Jacarandeae includes only a broadly definedJacarandadivided into four sections. Each section is defined by a unique combination of anther and calyx morphologies.

    

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5. Phylotranscriptomics reveal the spatio-temporal distribution and morphological evolution of Macrozamia , an Australian endemic genus of Cycadales

   https://doi.org/10.1093/aob/mcac117  

   Habib, Sadaf ; Gong, Yiqing ; Dong, Shanshan ; Lindstrom, Anders ; William Stevenson, Dennis ; Liu, Yang ; Wu, Hong ; Zhang, Shouzhou ( September 2022 , Annals of Botany)

   Abstract Background and Aims Cycads are regarded as an ancient lineage of living seed plants, and hold important clues to understand the early evolutionary trends of seed plants. The molecular phylogeny and spatio-temporal diversification of one of the species-rich genera of cycads, Macrozamia, have not been well reconstructed. Methods We analysed a transcriptome dataset of 4740 single-copy nuclear genes (SCGs) of 39 Macrozamia species and two outgroup taxa. Based on concatenated (maximum parsimony, maximum likelihood) and multispecies coalescent analyses, we first establish a well-resolved phylogenetic tree of Macrozamia. To identify cyto-nuclear incongruence, the plastid protein coding genes (PCGs) from transcriptome data are extracted using the software HybPiper. Furthermore, we explore the biogeographical history of the genus and shed light on the pattern of floristic exchange between three distinct areas of Australia. Six key diagnostic characters are traced on the phylogenetic framework using two comparative methods, and infra-generic classification is investigated. Key Results The tree topologies of concatenated and multi-species coalescent analyses of SCGs are mostly congruent with a few conflicting nodes, while those from plastid PCGs show poorly supported relationships. The genus contains three major clades that correspond to their distinct distributional areas in Australia. The crown group of Macrozamia is estimated to around 11.80 Ma, with a major expansion in the last 5–6 Myr. Six morphological characters show homoplasy, and the traditional phenetic sectional division of the genus is inconsistent with this current phylogeny. Conclusions This first detailed phylogenetic investigation of Macrozamia demonstrates promising prospects of SCGs in resolving phylogenetic relationships within cycads. Our study suggests that Macrozamia, once widely distributed in Australia, underwent major extinctions because of fluctuating climatic conditions such as cooling and mesic biome disappearance in the past. The current close placement of morphologically distinct species in the phylogenetic tree may be related to neotenic events that occurred in the genus. 

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