|Friday, July 09|
New insights into the liverwort and moss backbone phylogeny using the GoFlag probe kit
* Julia Bechteler, University of Bonn, Germany
J. Gordon Burleigh, University of Florida
Stuart McDaniel, University of Florida
Bernard Goffinet, University of Connecticut
David Bell, Royal Botanic Garden Edinburgh
Juan Carlos Villarreal, Laval University
Phylogenomic inferences from large suites of loci are anticipated to resolve the suprafamilial relationships within the three bryophyte lineages, whose diversification spans at least 400 million years. The newly designed GoFlag probe kit for target enrichment provides a universal tool for generating large nuclear datasets to resolve phylogenetic relationships among flagellate land plants. We present ongoing phylogenomic analyses of 444 nuclear loci (exons) from assembling a genus wide molecular phylogeny of mosses and liverworts, with hornworts serving as the outgroup. We inferred relationships among the over 500 bryophyte specimens using Maximum Likelihood (RAxML) and a species tree analysis using ASTRAL. The RAxML and ASTRAL analyses yielded largely congruent results with a highly supported backbone phylogeny for mosses and liverworts. We evaluate the targeted loci and their phylogenetic usefulness and propose a selection of loci that work best for mosses and liverworts including their various subgroups such as rapidly evolving families.
Applying an 802-gene probe set to moss phylogenetics, with an emphasis on the pleurocarp lineage
* Norman Wickett, Chicago Botanic Garden, United States
Matthew Johnson, Texas Tech University
Juan Angulo, New York Botanical Garden
Lisa Pokorny, Centre for Plant Biotechnology and Genomics UPM-INIA
Yang Liu, Fairy Lake Botanical Garden
Rafael Medina, Universidad Complutense de Madrid
Jonathan Shaw, Duke University
Bernard Goffinet, University of Connecticut
Reconstructing relationships within and among major lineages of pleurocarpous mosses remains a significant challenge in plant systematics. The pleurocarp lineage split from their most recent common ancestor shared with acrocarpous (or putatively “proto-pleurocarpous”) mosses well over 100 million years ago and was accompanied by rapid bouts of diversification. Ultimately, this rapid diversification led to over 5200 extant species that are distributed worldwide, comprising 40-50% of all moss species. Unsurprisingly, current molecular phylogenetic analyses suggest that families and genera within Hypnanae are abundantly polyphyletic. Without an accurate circumscription of major lineages in Hypnanae, taxon sampling for phylogenetic analysis, for example within families, may artificially exclude close relatives or include distantly related taxa. To address this challenge, we designed a set of probes representing 802 nuclear genes to be used for target enrichment. Here, we present a phylogenomic approach that uses 802 nuclear genes of 368 species representing all major clades within Hypnanae, as well as a broader discussion of the utility and efficiency of this probe set.
Exploring systematic relationships and morphological evolution in the moss genus Fissidens using data generated from herbarium specimens
* Jessica Budke, University of Tennessee - Knoxville, United States
Mark Wienhold, University of Tennessee - Knoxville
Nikisha Patel, University of Connecticut
Fissidens is a charismatic and morphologically distinct genus of mosses containing over 400 named species that have a distichous leaf arrangement and a leaf lamina that is split into a ‘V’, pocketing the leaf above into the one below. We are using a molecular phylogenetic approach to examine the relationships and test the monophyly of two classification systems for Fissidentaceae Subgenera and Sections proposed by Pursell & Bruggeman-Nannenga in 2004 and Suzuki, Inoue, and Tsubota in 2018. We have assembled two complementary datasets using material sampled from herbarium specimens to examine these relationships. First, in collaboration with the National Science Foundation funded GoFlag project, we have assembled a dataset including over 400 loci for approximately 40 Fissidens species and secondly we have assembled a three loci (trnL-F, trnA-nad7, ITS2) dataset for over 100 samples representing approximately 50 Fissidens species. Preliminary analyses of these data indicate that Subgenus Aloma and Subgenus Pachyfissidens are each monophyletic and that Subgenus Octodiceras is nested within Subgenus Fissidens. Our ongoing studies will use ancestral character state reconstructions and correlation analyses to explore the evolution of and relationships between morphological characters of Fissidentaceae species, focusing on the axillary hyaline nodules, limbidia, costa anatomy, peristome teeth, and sexual systems. The results of this study will help to deepen our understanding of morphological evolution in this diverse lineage of mosses.
A 400-gene phylogeny of the hornworts unveils new relationships and new insights on character evolution and diversification
* Juan Carlos Villarreal A., Université Laval, Canada
Gabriel F. Peñaloza-Bojacá, Departamento de Botânica, Universidade Federal de Minas Gerais
David Bell, Royal Botanic Garden Edinburgh, Scotland
D. Christine Cargill, Australian National Herbarium Canberra, Australia
Loren Endara, University of Florida, USA
Adaíses Maciel-Silva, Universidade Federal de Minas Gerais, Brazil
Gordon Burleigh, University of Florida, USA
Fay-Wei Li, Cornell University
Sahut Chantanaorrapint, Prince of Songkla University, Thailand
Emily B. Sessa, University of Florida, USA
Stuart McDaniel, University of Florida, USA
Noris Salazar Allen, Smithsonian Tropical Research Institute
Karen Renzaglia, Southern Illinois University, Carbondale
Recent plant phylogenomic studies strongly support bryophytes (hornworts, mosses and liverworts) as a clade. Hornworts are the least species-rich bryophyte group (~220 spp.) and they are sister to setaphytes (liverworts plus mosses). A renewed interest in hornworts has been fueled by nuclear genomic analyses of their unique traits such as endophytic cyanobacterial symbiosis and the atavistic presence of pyrenoids, a physical carbon concentrating site found otherwise in algae. In previous analyses based on five organellar loci, hornwort relationships seemed to be stable with Leiosporoceros (Leiosporocerotales) reconstructed as sister to all other species. This solid topology has been the base of multiple ancestral character reconstruction, divergence times and diversification studies. For example, pyrenoids were reconstructed as a derived condition in hornworts simply because Leiosporoceros lacks this trait. We present ongoing phylogenomic analyses of 427 genes from 79 species (ca. 35% of hornwort diversity) encompassing all five orders and eleven hornwort genera. Maximum likelihood and ASTRAL were used to estimate gene and species trees. Our phylogenomic analyses recover two hornwort clades: Leiosporoceros + Anthoceros sensu lato and the rest of the hornwort genera. The position of Leiosporoceros as sister to genus Anthoceros and within the order Anthocerotales is supported by 87% of the quartet trees inferred by ASTRAL. The unexpected relationship is justified by gametophytic morphological characters related to antheridia. This topology requires a reinterpretation of the evolution of the previously considered plesiomorphic features of Leiosporoceros that include Nostoc strands, chloroplast ultrastructure and spore morphology. We will present divergence times and ancestral character reconstructions and propose new scenarios of character evolution, including the pyrenoid.
Trait Evolution and Biogeography of Syntrichia Brid
* Javier Jauregui Lazo, University and Jepson Herbaria, University of California Berkeley, USA., United States
John Brinda, Bryophyte Herbarium, Missouri Botanical Garden, USA.
Sonia Nosratinia, University and Jepson Herbaria, University of California Berkeley, USA.
Jenna Ekwealor, Data Science Lab, Smithsonian Institution, USA.
Melvin Oliver, Division of Plant Sciences, University of Missouri, USA.
Brent Mishler, University and Jepson Herbaria, University of California Berkeley, USA.
Syntrichia is one of the most diverse genera of the family Pottiaceae. It contains around 90 named species distributed in almost all terrestrial ecosystems. It is a dominant group of mosses in habitats ranging from temperate to desert biocrusts across western North America. Yet many taxa occur in the Neotropics, most of which are concentrated in the Andes or polar climates from the southernmost regions of South America. Only a few phylogenetic analyses have been performed in Syntrichia; and these have only focused on a particular subclade or geographic area using a restricted number of molecular markers. The backbone relationships within the genus are still challenging and require careful integration of morphological and molecular analyses. Our research group is undertaking phylogenetic analysis at several scales; here we report results based on target enrichment sequencing data (GoFlag project) that yielded about 450 nuclear loci for most named species of Syntrichia worldwide plus additional outgroups (98 OTUs) to understand (1) the evolutionary history of the group, (2) trait evolution, and (3) global biogeography. We use a newly developed morphological character matrix (42 characters) to distinguish major clades for integration with molecular data in total-evidence phylogenetic analyses. Our results suggested that Syntrichia is a monophyletic group that likely originated in South America. We identified major clades based on morphology and/or geographic range, including a large Northern Hemisphere clade that originated from South America. Functional traits involved in water relations evolved multiple times in the group and are correlated with habitat preference.
Phylogeny of Orthotricheae (Orthotrichaceae, Bryophyta) under the light of the GoFlag data
* Isabel Draper, Autonomous University of Madrid, Spain
Tamara Villaverde, University of Almería
Gordon Burleigh, University of Florida
Suart McDaniel, University of Florida
Ricardo Garilleti, University of Valencia
Vicente Mazimpaka, Autonomous University of Madrid
Juan A. Calleja, Autonomous University of Madrid
Francisco Lara, Autonomous University of Madrid
Over the last two decades, the increase in the knowledge of the moss subfamily Orthotrichoideae has driven important taxonomic changes, including a rearrangement at the generic level. Accordingly, our understanding of the phylogenetic relationships of the main taxa within the subfamily recently have been revised based on molecular data generated by Sanger sequencing. However, in some cases, analyses based on only a few loci can be misleading due to different genetic phenomena such as reticulation and incomplete lineage sorting. We here present a molecular phylogenomic reconstruction of 68 taxa of the tribe Orthotricheae based on approximately 400 nuclear loci generated by target enrichment using the GoFlag 408 probe set. Our preliminary results overall agree with the current phylogenetic proposal. Orthotricheae is divided into two main clades that correspond to the subtribes Orthotrichinae and Lewinskyinae. Orthotrichinae includes the diverse genus Orthotrichum, whereas Lewinskyinae comprises both Lewinskya and Ulota together with some smaller genera including Plenogemma, Pulvigera, and Atlantichella. The genus Atlantichella has been recently segregated from Ulota and now is validated by the target enrichment data. In addition, we provide evidence for the segregation of a new monotypic genus currently included within Ulota. Finally, our results suggest that Nyholmiella should no longer be considered as a member of Orthotrichinae. Further studies are needed to determine whether this genus should be treated as a member of Lewinskyinae or segregated as an additional subtribe.