Ciencia habilitada por datos de especímenes

Benson, C. W., M. R. Sheltra, P. J. Maughan, E. N. Jellen, M. D. Robbins, B. S. Bushman, E. L. Patterson, et al. 2023. Homoeologous evolution of the allotetraploid genome of Poa annua L. BMC Genomics 24. https://doi.org/10.1186/s12864-023-09456-5

Background Poa annua (annual bluegrass) is an allotetraploid turfgrass, an agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua’s diploid progenitors, P. infirma and P. supina, and use multi-omic analyses spanning all three species to better understand P. annua’s evolutionary novelty. Results We find that the diploids diverged from their common ancestor 5.5 – 6.3 million years ago and hybridized to form P. annua  ≤ 50,000 years ago. The diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements, leading to a 1.7 × difference in genome size. In allotetraploid P. annua, we find biased movement of retrotransposons from the larger (A) subgenome to the smaller (B) subgenome. We show that P. annua’s B subgenome is preferentially accumulating genes and that its genes are more highly expressed. Whole-genome resequencing of several additional P. annua accessions revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis. Conclusions The divergent evolutions of the diploid progenitors played a central role in conferring onto P. annua its remarkable phenotypic plasticity. We find that plant genes (guided by selection and drift) and transposable elements (mostly guided by host immunity) each respond to polyploidy in unique ways and that P. annua uses whole-genome duplication to purge highly parasitized heterochromatic sequences. The findings and genomic resources presented here will enable the development of homoeolog-specific markers for accelerated weed science and turfgrass breeding .

Chevalier, M. 2022. <i>crestr</i>: an R package to perform probabilistic climate reconstructions from palaeoecological datasets. Climate of the Past 18: 821–844. https://doi.org/10.5194/cp-18-821-2022

Abstract. Statistical climate reconstruction techniques are fundamental tools to study past climate variability from fossil proxy data. In particular, the methods based on probability density functions (or PDFs) can be used in various environments and with different climate proxies because they rely on elementary calibration data (i.e. modern geolocalised presence data). However, the difficulty of accessing and curating these calibration data and the complexity of interpreting probabilistic results have often limited their use in palaeoclimatological studies. Here, I introduce a new R package (crestr) to apply the PDF-based method CREST (Climate REconstruction SofTware) on diverse palaeoecological datasets and address these problems. crestr includes a globally curated calibration dataset for six common climate proxies (i.e. plants, beetles, chironomids, rodents, foraminifera, and dinoflagellate cysts) associated with an extensive range of climate variables (20 terrestrial and 19 marine variables) that enables its use in most terrestrial and marine environments. Private data collections can also be used instead of, or in combination with, the provided calibration dataset. The package includes a suite of graphical diagnostic tools to represent the data at each step of the reconstruction process and provide insights into the effect of the different modelling assumptions and external factors that underlie a reconstruction. With this R package, the CREST method can now be used in a scriptable environment and thus be more easily integrated with existing workflows. It is hoped that crestr will be used to produce the much-needed quantified climate reconstructions from the many regions where they are currently lacking, despite the availability of suitable fossil records. To support this development, the use of the package is illustrated with a step-by-step replication of a 790 000-year-long mean annual temperature reconstruction based on a pollen record from southeastern Africa.

Liang, S., X. Zhang, and R. Wei. 2022. Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity. Molecular Ecology 31: 2679–2697. https://doi.org/10.1111/mec.16420

The formation of spatial genetic structure with the presence of extensive gene flow, an evolutionary force which is generally expected to eliminate population-specific variation and maintain genetic homogeneity, remains poorly understood. Homosporous ferns, which spread by spores through wind and possess long-distance dispersal capacity, provide an ideal system to investigate such a process. Here, using a homoploid fern lineage, the Athyrium sinense complex, we used reduced-representation genomic data to examine spatial genetic structure and explored potential driving forces including geographical distance, environment, climatic history and external dispersal constraints. Our findings showed a clear north-south divergence at the genetic, morphological and ecological levels between both sides of 35°N in East Asia. Fluctuant and heterogeneous climatic condition was demonstrated to play a crucial role during the formation of the divergence. Our results suggested that this lineage was able to migrate southward and colonize new habitat as a result of the Quaternary climatic fluctuation. Furthermore, the present genetic structure is attributed to adaptation to heterogeneous environments, especially temperature difference. In addition to ecological adaptation, we found clues showing that canopy density, wind direction as well as habitat continuity were all likely to constrain the effect of gene flow. These results demonstrated a diversification process without ploidy changes in ferns providing new insights for our present knowledge on ferns’ spatio-temporal evolutionary pattern. In particular, our study highlights the influence of environmental heterogeneity in driving genetic divergence against strong dispersal capacity.

Xue, T., S. R. Gadagkar, T. P. Albright, X. Yang, J. Li, C. Xia, J. Wu, and S. Yu. 2021. Prioritizing conservation of biodiversity in an alpine region: Distribution pattern and conservation status of seed plants in the Qinghai-Tibetan Plateau. Global Ecology and Conservation 32: e01885. https://doi.org/10.1016/j.gecco.2021.e01885

The Qinghai-Tibetan Plateau (QTP) harbors abundant and diverse plant life owing to its high habitat heterogeneity. However, the distribution pattern of biodiversity hotspots and their conservation status remain unclear. Based on 148,283 high-resolution occurrence coordinates of 13,450 seed plants, w…

Wang, C.-J., and J.-Z. Wan. 2021. Functional trait perspective on suitable habitat distribution of invasive plant species at a global scale. Perspectives in Ecology and Conservation 19: 475–486. https://doi.org/10.1016/j.pecon.2021.07.002

Plant invasion has been proved to threaten biodiversity conservation and ecosystem maintenance at a global scale. It is a challenge to project suitable habitat distributions of invasive plant species (IPS) for invasion risk assessment at large spatial scales. Interaction outcomes between native and …

Mairal, M., S. L. Chown, J. Shaw, D. Chala, J. H. Chau, C. Hui, J. M. Kalwij, et al. 2021. Human activity strongly influences genetic dynamics of the most widespread invasive plant in the sub‐Antarctic. Molecular Ecology 31: 1649–1665. https://doi.org/10.1111/mec.16045

The link between the successful establishment of alien species and propagule pressure is well-documented. Less known is how humans influence the post-introduction dynamics of invasive alien populations. The latter requires studying parallel invasions by the same species in habitats that are differen…

Saldaña‐López, A., M. Vilà, F. Lloret, J. Manuel Herrera, and P. González‐Moreno. 2021. Assembly of species’ climatic niches of coastal communities does not shift after invasion Z. Botta‐Dukát [ed.],. Journal of Vegetation Science 32. https://doi.org/10.1111/jvs.12989

Question: Do invasions by invasive plant species with contrasting trait profiles (Arctotheca calendula, Carpobrotus spp., Conyza bonariensis, and Opuntia dillenii) change the climatic niche of coastal plant communities? Location: Atlantic coastal habitats in Huelva (Spain). Methods: We identifi…

Allstädt, F. J., A. Koutsodendris, E. Appel, W. Rösler, T. Reichgelt, S. Kaboth-Bahr, A. A. Prokopenko, and J. Pross. 2021. Late Pliocene to early Pleistocene climate dynamics in western North America based on a new pollen record from paleo-Lake Idaho. Palaeobiodiversity and Palaeoenvironments 101: 177–195. https://doi.org/10.1007/s12549-020-00460-1

Marked by the expansion of ice sheets in the high latitudes, the intensification of Northern Hemisphere glaciation across the Plio/Pleistocene transition at ~ 2.7 Ma represents a critical interval of late Neogene climate evolution. To date, the characteristics of climate change in North America duri…

Yi, S., C.-P. Jun, K. Jo, H. Lee, M.-S. Kim, S. D. Lee, X. Cao, and J. Lim. 2020. Asynchronous multi-decadal time-scale series of biotic and abiotic responses to precipitation during the last 1300 years. Scientific Reports 10. https://doi.org/10.1038/s41598-020-74994-x

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Chase, B. M., A. Boom, A. S. Carr, M. Chevalier, L. J. Quick, G. A. Verboom, and P. J. Reimer. 2019. Extreme hydroclimate response gradients within the western Cape Floristic region of South Africa since the Last Glacial Maximum. Quaternary Science Reviews 219: 297–307. https://doi.org/10.1016/j.quascirev.2019.07.006

The Cape Floristic Region (CFR) is one of the world's major biodiversity hotspots, and much work has gone into identifying the drivers of this diversity. Considered regionally in the context of Quaternary climate change, climate stability is generally accepted as being one of the major factors promo…