Bechteler J., G. Peñaloza-Bojacá, D. Bell, G. Burleigh, S. F. McDaniel, E. C. Davis, E. B. Sessa, A. Bippus, D. Christine Cargill, S. Chantanoarrapint, I. Draper, L. Endara, L. L. Forrest, R. Garilleti, S. W. Graham, S. Huttunen, J. Jauregui Lazo, F. Lara, J. Larraín, L. R. Lewis, D. G. Long, D. Quandt, K. Renzaglia, A. Schäfer-Verwimp, G. Ee Lee, A. S. Pinilla, M. von Konrat, C. E. Zartman, M. Regina Pereira, B. Goffinet & J. C. Villarreal. 2023. Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification. American Journal of Botany 110: e16249. pdf GoogleScholar

Abstract reads: 
Premise: Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns and processes of diversification across bryophytes remain unclear.

Methods: Using the GoFlag probe set we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.

Results: The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more, and propose ten new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology.

Conclusions: We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.

Patel N., R. Medina, L.D. Williams, O. Lemieux, B. Goffinet & M.G. Johnson. Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes. Evolution 77: 2561–2575. pdf

Abstract reads: Allopolyploids represent a new frontier in species discovery among embryophytes. Within mosses, allopolyploid discovery is challenged by low morphological complexity. The rapid expansion of sequencing approaches in addition to computational developments to identifying genome merger and whole-genome duplication using variation among nuclear loci representing homeologs has allowed for increased allopolyploid discovery among mosses. Here, we test a novel approach to phasing homeologs within loci and phasing loci across subgenomes, or subgenome assignment, called Homologizer, in the family Funariaceae. We confirm the intergeneric hybrid nature of Entosthodon hungaricus, and the allopolyploid origin of Physcomitrium eurystomum and of one population of P. collenchymatum. We also reveal that hybridization gave rise to P. immersum, as well as to yet unrecognized lineages sharing the phenotype of P. pyriforme, and P. sphaericum. Our findings demonstrate the utility of our approach when working with polyploid genomes, and its value in identifying progenitor species using target capture data.

Hu R., X. Li, Y. Hu, R. Zhang, Q. Lv, M. Zhang, X. Sheng, F. Zhao, Z. Chen, Y. Ding, H. Yuan, X. Wu, S. Xing, X. Yan, F. Bao, P. Wan, L. Xiao, X. Wang, W. Xiao, E.L. Decker, N. van Gessel, H. Renault, G. Wiedemann, N.A. Horst, F.B. Haas, P.K.I. Wilhelmsson, K. Ullrich, E. Neumann, B. Lv, C. Liang, H. Du, H. Lu, Q. Gao, Z. Cheng, H. You, P. Xin, J. Chu, C.-H. Huang, Y. Liu, S. Dong, L. Zhang, F. Chen, L. Deng, F. Duan, W. Zhao, K. Li, Z. Li, X. Li, H. Cui, Y. Zhang, C. Ma, R. Zhu, Y. Jia, M. Wang, M. Hasebe, J. Fu, B. Goffinet, H. Ma, S.A. Rensing, R. Reski, Y. He. 2023. Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet. Cell 186: 3558–3576.  pdf

The most extreme environments are the most vulnerable to transformation under a rapidly changing climate. These ecosystems harbor some of the most specialized species, which will likely suffer the highest extinction rates. We document the steepest temperature increase (2010–2021) on record at altitudes of above 4,000 m, triggering a decline of the relictual and highly adapted moss Takakia lepidozioides. Its de-novo-sequenced genome with 27,467 protein-coding genes includes distinct adaptations to abiotic stresses and comprises the largest number of fast-evolving genes under positive selection. The uplift of the study site in the last 65 million years has resulted in life-threatening UV-B radiation and drastically reduced temperatures, and we detected several of the molecular adaptations of Takakia to these environmental changes. Surprisingly, specific morphological features likely occurred earlier than 165 mya in much warmer environments. Following nearly 400 million years of evolution and resilience, this species is now facing extinction.

Abstract reads: Physcomitrium pygmaeum is an ephemeral moss described in 1871 from a single collection from Utah, currently considered conspecific with Physcomitrium pyriforme. The interpretation of the taxon has been problematic due to its rarity in the field, the elusiveness of the type material, and an extremely scattered and inconsistent collection record. Here we present a comprehensive description and assessment of the taxon following the identification of the original material and lectotype designation, the examination of all existing herbarium specimens to the best of our knowledge, the collection of fresh material in Nevada, and the molecular barcoding of the latter using four plastid and two nuclear loci. Available information, albeit scant, suggests that this member of the North American bryoflora should be considered critically endangered following IUCN criteria.

Abstract reads: Background and Aims — With some 7,300 extant species, liverworts (Marchantiophyta) represent one of the major land plant lineages. The backbone relationships, such as the phylogenetic position of Ptilidiales, and the occurrence and timing of whole genome duplications, are still contentious. Methods – Based on analyses of the newly generated transcriptome data for 38 liverworts and complemented with those publicly available, we reconstructed the evolutionary history of liverworts and inferred gene duplication events along the 55-taxon liverwort species tree. Key Results – Our phylogenomic study provided an ordinal-level liverwort nuclear phylogeny and identified extensive gene tree conflicts and cyto-nuclear incongruences. Gene duplication analyses based on integrated phylogenomics and Ks distributions indicated no evidence of whole genome duplication events along the backbone phylogeny of liverworts. Conclusions – With a broadened sampling of liverwort transcriptomes, we re-evaluated the backbone phylogeny of liverworts, and provided evidence for ancient hybridizations followed by incomplete lineage sorting that shaped the deep evolutionary history of liverworts. The lack of whole genome duplication along the deep evolution of liverworts indicates that liverworts might represent one of the few major embryophyte lineages whose evolution was not driven by whole genome duplications.

Rozzi R., C. S. Quilodrán, E. Botero-Delgadillo, R.D. Crego, C. Napolitano, O. Barroso, R. MacKenzie, J.C. Torres-Mura, C. Bravo, S. Ippi, V. Quirici, J. Rivero-de-Aguilar, C.G. Suazo, B. Goffinet, B. Kempenaers, E. Poulin & R.A. Vásquez. 2022. Aphrastura subantarctica: the Subantarctic Rayadito, a new bird species on the Southernmost islands of the Americas. Scientific Reports 12: 13957. pdf

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Abstract reads: We describe a new taxon of terrestrial bird of the genus Aphrastura (rayaditos) inhabiting the Diego Ramírez Archipelago, the southernmost point of the American continent. This archipelago is geographically isolated and lacks terrestrial mammalian predators as well as woody plants, providing a contrasted habitat to the forests inhabited by the other two Aphrastura spp. Individuals of Diego Ramírez differ morphologically from Aphrastura spinicauda, the taxonomic group they were originally attributed to, by their larger beaks, longer tarsi, shorter tails, and larger body mass. These birds move at shorter distances from ground level, and instead of nesting in cavities in trees, they breed in cavities in the ground, reflecting different life-histories. Both taxa are genetically differentiated based on mitochondrial and autosomal markers, with no evidence of current gene flow. Although further research is required to define how far divergence has proceeded along the speciation continuum, we propose A. subantarctica as a new taxonomic unit, given its unique morphological, genetic, and behavioral attributes in a non-forested habitat. The discovery of this endemic passerine highlights the need to monitor and conserve this still-pristine archipelago devoid of exotic species, which is now protected by the recently created Diego Ramírez Islands-Drake Passage Marine Park.

Zach Muscavitch was awarded a grant from the American Philosophical Society for his project entitled “Resolving symbiont specificity for endemic lichens on the Channel Islands of California.” This project aims to collect Niebla lichens from the Channel Islands and characterize their fungal and algal symbionts applying a novel DNA sampling method: Target Capture. Results will complement those from the mainland to test patterns of isolation and reciprocal specificity between symbionts.