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Huang, T., J. Chen, K. E. Hummer, L. A. Alice, W. Wang, Y. He, S. Yu, et al. 2023. Phylogeny of Rubus (Rosaceae): Integrating molecular and morphological evidence into an infrageneric revision. TAXON. https://doi.org/10.1002/tax.12885

Rubus (Rosaceae), one of the most complicated angiosperm genera, contains about 863 species, and is notorious for its taxonomic difficulty. The most recent (1910–1914) global taxonomic treatment of the genus was conducted by Focke, who defined 12 subgenera. Phylogenetic results over the past 25 years suggest that Focke's subdivisions of Rubus are not monophyletic, and large‐scale taxonomic revisions are necessary. Our objective was to provide a comprehensive phylogenetic analysis of the genus based on an integrative evidence approach. Morphological characters, obtained from our own investigation of living plants and examination of herbarium specimens are combined with chloroplast genomic data. Our dataset comprised 196 accessions representing 145 Rubus species (including cultivars and hybrids) and all of Focke's subgenera, including 60 endemic Chinese species. Maximum likelihood analyses inferred phylogenetic relationships. Our analyses concur with previous molecular studies, but with modifications. Our data strongly support the reclassification of several subgenera within Rubus. Our molecular analyses agree with others that only R. subg. Anoplobatus forms a monophyletic group. Other subgenera are para‐ or polyphyletic. We suggest a revised subgeneric framework to accommodate monophyletic groups. Character evolution is reconstructed, and diagnostic morphological characters for different clades are identified and discussed. Based on morphological and molecular evidence, we propose a new classification system with 10 subgenera: R. subg. Anoplobatus, R. subg. Batothamnus, R. subg. Chamaerubus, R. subg. Cylactis, R. subg. Dalibarda, R. subg. Idaeobatus, R. subg. Lineati, R. subg. Malachobatus, R. subg. Melanobatus, and R. subg. Rubus. The revised infrageneric nomenclature inferred from our analyses is provided along with synonymy and type citations. Our new taxonomic backbone is the first systematic and complete global revision of Rubus since Focke's treatment. It offers new insights into deep phylogenetic relationships of Rubus and has important theoretical and practical significance for the development and utilization of these important agronomic crops.

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…

de Oliveira, M. H. V., B. M. Torke, and T. E. Almeida. 2021. An inventory of the ferns and lycophytes of the Lower Tapajós River Basin in the Brazilian Amazon reveals collecting biases, sampling gaps, and previously undocumented diversity. Brittonia 73: 459–480. https://doi.org/10.1007/s12228-021-09668-7

Ferns and lycophytes are an excellent group for conservation and species distribution studies because they are closely related to environmental changes. In this study, we analyzed collection gaps, sampling biases, richness distribution, and the species conservation effectiveness of protected areas i…

Inman, R., J. Franklin, T. Esque, and K. Nussear. 2021. Comparing sample bias correction methods for species distribution modeling using virtual species. Ecosphere 12. https://doi.org/10.1002/ecs2.3422

A key assumption in species distribution modeling (SDM) with presence‐background (PB) methods is that sampling of occurrence localities is unbiased and that any sampling bias is proportional to the background distribution of environmental covariates. This assumption is rarely met when SDM practition…

Goodwin, Z. A., P. Muñoz-Rodríguez, D. J. Harris, T. Wells, J. R. I. Wood, D. Filer, and R. W. Scotland. 2020. How long does it take to discover a species? Systematics and Biodiversity 18: 784–793. https://doi.org/10.1080/14772000.2020.1751339

The description of a new species is a key step in cataloguing the World’s flora. However, this is only a preliminary stage in a long process of understanding what that species represents. We investigated how long the species discovery process takes by focusing on three key stages: 1, the collection …

Peyre, G., J. Lenoir, D. N. Karger, M. Gomez, A. Gonzalez, O. Broennimann, and A. Guisan. 2020. The fate of páramo plant assemblages in the sky islands of the northern Andes B. Jiménez‐Alfaro [ed.],. Journal of Vegetation Science 31: 967–980. https://doi.org/10.1111/jvs.12898

Aims: Assessing climate change impacts on biodiversity is a main scientific challenge, especially in the tropics, therefore, we predicted the future of plant species and communities on the unique páramo sky islands. We implemented the Spatially Explicit Species Assemblage Modelling framework, by i) …

Li, M., J. He, Z. Zhao, R. Lyu, M. Yao, J. Cheng, and L. Xie. 2020. Predictive modelling of the distribution of Clematis sect. Fruticella s. str. under climate change reveals a range expansion during the Last Glacial Maximum. PeerJ 8: e8729. https://doi.org/10.7717/peerj.8729

Background The knowledge of distributional dynamics of living organisms is a prerequisite for protecting biodiversity and for the sustainable use of biotic resources. Clematis sect. Fruticella s. str. is a small group of shrubby, yellow-flowered species distributed mainly in arid and semi-arid areas…

Folk, R. A., R. L. Stubbs, M. E. Mort, N. Cellinese, J. M. Allen, P. S. Soltis, D. E. Soltis, and R. P. Guralnick. 2019. Rates of niche and phenotype evolution lag behind diversification in a temperate radiation. Proceedings of the National Academy of Sciences 116: 10874–10882. https://doi.org/10.1073/pnas.1817999116

Environmental change can create opportunities for increased rates of lineage diversification, but continued species accumulation has been hypothesized to lead to slowdowns via competitive exclusion and niche partitioning. Such density-dependent models imply tight linkages between diversification and…

Inman, R., J. Franklin, T. Esque, and K. Nussear. 2018. Spatial sampling bias in the Neotoma paleoecological archives affects species paleo-distribution models. Quaternary Science Reviews 198: 115–125. https://doi.org/10.1016/j.quascirev.2018.08.015

The ability to infer paleo-distributions with limited knowledge of absence makes species distribution modeling (SDM) a useful tool for exploring paleobiogeographic questions. Spatial sampling bias is a known issue when modeling extant species. Here we quantify the spatial sampling bias in a North Am…