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

In the news: FoxNews Daily Mail

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.

Olivia Lemieux, a graduating honors student who has been in the lab, mentoring by Niki and myself, has been awarded the Margaret F. Ertman Award in recognition of her significant accomplishments at University of Connecticut. Her project is entitled “Whole-range study reveals consistent hybrid nature and conserved progenitors of the North American endemic moss, Physcomitrium immersum.”

Each year, the Margaret F. Ertman Award is awarded to the outstanding senior across all four biology degree programs: Biological Sciences, EEB, MCB, and PNB. The student will have distinguished themselves both through outstanding scholarship in EEB, MCB, and PNB during their undergraduate career, and through original research conducted in biology (broadly defined) at UConn.

The Margaret F. Ertman Award was established in 1983 by Irvin L. Ertman (class of 1939) and Ronnie Ertman (class of 1941) in honor of their daughter Margaret F. Ertman (class of 1974). The award is based not only on your excellent presentation at the research colloquium but also on your superb academic performance throughout your UConn career.

Patiño J., I. Bisang, B. Goffinet, L. Hedenäs, S. McDaniel, S. Pressler, M. Stech, C. Ah-Peng, A. Bergamini, R.T. Caners, C. Cargill, N. Cronberg, J. Duckett, S. Eppley, N. Fenton, K. Fisher, J. M. González-Mancebo, M. Hasebe, J. Heinrichs†, K. Hylander, M.S. Ignatov, J. Martínez-Abaigar, N. Medina, R. Medina, D. Quandt, S. Rensing, K. Renzaglia, M. Renner, R. M. Ros, A. Schäfer-Verwimp, J. Carlos Villarreal & A. Vanderpoorten. 2022. Unveiling the nature of a miniature world: A horizon scan of fundamental questions in bryology. Journal of Bryology 41: 1–34. pdf

Abstract reads: INTRODUCTION Half a century since the creation of the International Association of Bryologists, we carried out a review to identify outstanding challenges and future perspectives in bryology. Specifically, we have identified 50 fundamental questions that are critical in advancing the discipline.
METHODS We have adapted a deep-rooted methodology of horizon scanning to identify key research foci. An initial pool of 258 questions was prepared by a multidisciplinary and international working group of 32 bryologists. A series of online surveys completed by a broader community of researchers in bryology, followed by quality-control steps implemented by the working group, were used to create a list of top-priority questions. This final list was restricted to 50 questions with a broad conceptual scope and answerable through realistic research approaches.
KEY RESULTS The top list of 50 fundamental questions was organised into four general topics: Bryophyte Biodiversity and Biogeography; Bryophyte Ecology, Physiology and Reproductive Biology; Bryophyte Conservation and Management; and Bryophyte Evolution and Systematics. These topics included 9, 19, 14 and 8 questions, respectively.
CONCLUSIONS Although many of the research challenges identified are not newly conceived, our horizon-scanning exercise has established a significant foundation for future bryological research. We suggest analytical and conceptual strategies and novel developments for potential use in advancing the research agenda for bryology.

Olivia presented her undergraduate research project entitled “Conserved progenitors of the hybrid moss Physcomitrium immersum across North America” at the EEEB undergraduate research symposium and was selected to compete at the All Biology undergraduate research symposium on Friday, April 29th. Congrats and good luck!

Liu Y., S. Wang, L. Li, T. Yang, S. Dong, T. Wei, S. Wu, Y. Liu, Y. Gong, X. Feng, J. Ma, G. Chang, J. Huang, Y. Yang, H. Wang, M. Liu, Y. Xu, H. Liang, J. Yu, Y. Cai, Z. Zhang, Y. Fan, W. Mu, S. Kumar Sahu, S. Liu, X. Lang, L. Yang, N. Li, S. Habib, Y. Yang, A.J. Lindstrom, P. Liang, B. Goffinet, S. Zaman, Jill. L. Wegrzyn, D. Li, J. Liu, J. Cui, E.C. Sonnenschein, X. Wang, J. Ruan, J.-Y. Xue, Z.-Q. Shao, C. Song, G. Fan, Z. Li, L. Zhang, J. Liu, Z.-J. Liu, Y. Jiao, X.-Q. Wang, H. Wu, E. Wang, M. Lisby, H. Yang, J. Wang, X. Liu, X. Xu, N. Li, P.S. Soltis, Y. Van de Peer, D.E. Soltis, X. Gong, H. Liu, S. Zhang. 2022. The cycad genome and the early evolution of seed plants. Nature Plants 8: 389–401.  pdf  Google Scholar

Abstract reads: Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this posi- tion. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.