Science Enabled by Specimen Data
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.
Hernández, S., A. G. García, F. Arenas, M. P. Escribano, A. Jueterbock, O. De Clerck, C. A. Maggs, et al. 2023. Range‐edge populations of seaweeds show niche unfilling and poor adaptation to increased temperatures. Journal of Biogeography. https://doi.org/10.1111/jbi.14572
(no abstract available)
Hausdorf, B. 2023. Distribution patterns of established alien land snail species in the Western Palaearctic Region. NeoBiota 81: 1–32. https://doi.org/10.3897/neobiota.81.96360
AbstractEstablished alien land snail species that were introduced into the Western Palaearctic Region from other regions and their spread in the Western Palaearctic are reviewed. Thirteen of the 22 species came from North America, three from Sub-Saharan Africa, two from the Australian region, three probably from the Oriental Region and one from South America. The establishment of outdoor populations of these species was usually first seen at the western or southern rims of the Western Palearctic. Within Europe, the alien species usually spread from south to north and from west to east. The latitudinal ranges of the alien species significantly increased with increasing time since the first record of introduction to the Western Palearctic. The latitudinal mid-points of the Western Palaearctic and native ranges of the species are significantly correlated when one outlier is omitted. There is a general trend of poleward shifts of the ranges of the species in the Western Palaearctic compared to their native ranges. There are three reasons for these shifts: (1) the northward expansion of some species in Western Europe facilitated by the oceanic climate, (2) the impediment to the colonisation of southern latitudes in the Western Palaearctic due to their aridity and (3) the establishment of tropical species in the Mediterranean and the Middle East. Most of the species are small, not carnivorous and unlikely to cause serious ecological or economic damage. In contrast, the recently introduced large veronicellid slugs from Sub-Saharan Africa and the giant African snail Lissachatinafulica could cause economic damage in irrigated agricultural areas or greenhouses in the Mediterranean and the Middle East.
Smith, A. B., S. J. Murphy, D. Henderson, and K. D. Erickson. 2023. Including imprecisely georeferenced specimens improves accuracy of species distribution models and estimates of niche breadth. Global Ecology and Biogeography. https://doi.org/10.1111/geb.13628
Aim Museum and herbarium specimen records are frequently used to assess the conservation status of species and their responses to climate change. Typically, occurrences with imprecise geolocality information are discarded because they cannot be matched confidently to environmental conditions and are thus expected to increase uncertainty in downstream analyses. However, using only precisely georeferenced records risks undersampling of the environmental and geographical distributions of species. We present two related methods to allow the use of imprecisely georeferenced occurrences in biogeographical analysis. Innovation Our two procedures assign imprecise records to the (1) locations or (2) climates that are closest to the geographical or environmental centroid of the precise records of a species. For virtual species, including imprecise records alongside precise records improved the accuracy of ecological niche models projected to the present and the future, especially for species with c. 20 or fewer precise occurrences. Using only precise records underestimated loss of suitable habitat and overestimated the amount of suitable habitat in both the present and the future. Including imprecise records also improves estimates of niche breadth and extent of occurrence. An analysis of 44 species of North American Asclepias (Apocynaceae) yielded similar results. Main conclusions Existing studies examining the effects of spatial imprecision typically compare outcomes based on precise records against the same records with spatial error added to them. However, in real-world cases, analysts possess a mix of precise and imprecise records and must decide whether to retain or discard the latter. Discarding imprecise records can undersample the geographical and environmental distributions of species and lead to mis-estimation of responses to past and future climate change. Our method, for which we provide a software implementation in the enmSdmX package for R, is simple to use and can help leverage the large number of specimen records that are typically deemed “unusable” because of spatial imprecision in their geolocation.
MANCINI, F., A. O. LILLO, R. BARDELLI, S. VIZZINI, and G. MANCINELLI. 2022. Variation in the stable isotope trophic position of the bluefish Pomatomus saltatrix (Linnaeus, 1766) from two Mediterranean sites: insights from a global meta-analysis. Mediterranean Marine Science 23: 850–863. https://doi.org/10.12681/mms.29325
A direct consequence of sea warming is the shift in the distribution range of thermo-tolerant species that have the potential to determine novel inter-specific interactions, ultimately altering food web structures and ecosystem processes. In this study, we investigated the trophic position of the bluefish Pomatomus saltatrix (Linnaeus, 1766), a pelagic predator that has recently expanded its distribution in the Mediterranean basin and for which scant information is available on its functional role in recently-colonised areas. Nitrogen and carbon stable isotopes were determined in muscle tissues of bluefish specimens collected in south-east Italy in the Gulf of Taranto (NW Ionian Sea) and in the Strait of Otranto (SW Adriatic Sea) at two coastal sites showing contrasting oceanographic conditions. The bluefish trophic position (TP) was estimated using locally abundant forage fish species as isotopic baselines. The results indicated for bluefish from the Strait of Otranto a TP value of 5.1, significantly higher than that determined in the Gulf of Taranto (4.2), and exceeding stomach content-based estimations reported by the online database FishBase and by literature sources. A synthesis of 30 publications reporting isotopic data for the bluefish and its potential prey at a global scale indicated that the species’ trophic position varied considerably between 2.7 and 5.2. The observed variability depended on location and on the baseline species used in the estimations. Yet, a significant difference in trophic position was observed for bluefish from transitional and inshore environments as compared with offshore areas, mirroring the results obtained from the Gulf of Taranto and the Strait of Otranto. The findings of the study highlight the high trophic plasticity characterizing the bluefish in recently colonized areas, suggesting that it may play a key role in facilitating the expansion of its distribution range. However, additional investigations are essential to provide an advanced resolution of the bluefish functional role in Mediterranean coastal food webs.
Kroonen, G., A. Jakob, A. I. Palmér, P. van Sluis, and A. Wigman. 2022. Indo-European cereal terminology suggests a Northwest Pontic homeland for the core Indo-European languages S. Wichmann [ed.],. PLOS ONE 17: e0275744. https://doi.org/10.1371/journal.pone.0275744
Questions on the timing and the center of the Indo-European language dispersal are central to debates on the formation of the European and Asian linguistic landscapes and are deeply intertwined with questions on the archaeology and population history of these continents. Recent palaeogenomic studies support scenarios in which the core Indo-European languages spread with the expansion of Early Bronze Age Yamnaya herders that originally inhabited the East European steppes. Questions on the Yamnaya and Pre-Yamnaya locations of the language community that ultimately gave rise to the Indo-European language family are heavily dependent on linguistic reconstruction of the subsistence of Proto-Indo-European speakers. A central question, therefore, is how important the role of agriculture was among the speakers of this protolanguage. In this study, we perform a qualitative etymological analysis of all previously postulated Proto-Indo-European terminology related to cereal cultivation and cereal processing. On the basis of the evolution of the subsistence strategies of consecutive stages of the protolanguage, we find that one or perhaps two cereal terms can be reconstructed for the basal Indo-European stage, also known as Indo-Anatolian, but that core Indo-European, here also including Tocharian, acquired a more elaborate set of terms. Thus, we linguistically document an important economic shift from a mostly non-agricultural to a mixed agro-pastoral economy between the basal and core Indo-European speech communities. It follows that the early, eastern Yamnaya of the Don-Volga steppe, with its lack of evidence for agricultural practices, does not offer a perfect archaeological proxy for the core Indo-European language community and that this stage of the language family more likely reflects a mixed subsistence as proposed for western Yamnaya groups around or to the west of the Dnieper River.
Marcussen, T., H. E. Ballard, J. Danihelka, A. R. Flores, M. V. Nicola, and J. M. Watson. 2022. A Revised Phylogenetic Classification for Viola (Violaceae). Plants 11: 2224. https://doi.org/10.3390/plants11172224
The genus Viola (Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then-known 400 species were distributed among 14 sections and numerous unranked groups. Here, we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We distribute the 664 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, the fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Studies into seed anatomy and morphology are required to understand the fossil record of the genus.
Kendig, A. E., S. Canavan, P. J. Anderson, S. L. Flory, L. A. Gettys, D. R. Gordon, B. V. Iannone III, et al. 2022. Scanning the horizon for invasive plant threats using a data-driven approach. NeoBiota 74: 129–154. https://doi.org/10.3897/neobiota.74.83312
AbstractEarly detection and eradication of invasive plants are more cost-effective than managing well-established invasive plant populations and their impacts. However, there is high uncertainty around which taxa are likely to become invasive in a given area. Horizon scanning that combines a data-driven approach with rapid risk assessment and consensus building among experts can help identify invasion threats. We performed a horizon scan of potential invasive plant threats to Florida, USA—a state with a high influx of introduced species, conditions that are generally favorable for plant establishment, and a history of negative impacts from invasive plants. We began with an initial list of 2128 non-native plant taxa that are known invaders or crop pests. We built on previous invasive species horizon scans by developing data-based criteria to prioritize 100 taxa for rapid risk assessment. The semi-automated prioritization process included selecting taxa “on the horizon” (i.e., not yet in the target location and not on a noxious weed list) with climate matching, naturalization history, “weediness” record, and global commonness. We derived overall invasion risk scores with rapid risk assessment by evaluating the likelihood of each of the taxa arriving, establishing, and having an impact in Florida. Then, following a consensus-building discussion, we identified six plant taxa as high risk, with overall risk scores ranging from 75 to 100 out of a possible 125. The six taxa are globally distributed, easily transported to new areas, found in regions with climates similar to Florida’s, and can impact native plant communities, human health, or agriculture. Finally, we evaluated our initial and final lists for potential biases. Assessors tended to assign higher risk scores to taxa that had more available information. In addition, we identified biases towards four plant families and certain geographical regions of origin. Our horizon scan approach identified taxa conforming to metrics of high invasion risk and used a methodology refined for plants that can be applied to other locations.
Bosso, L., S. Smeraldo, D. Russo, M. L. Chiusano, G. Bertorelle, K. Johannesson, R. K. Butlin, et al. 2022. The rise and fall of an alien: why the successful colonizer Littorina saxatilis failed to invade the Mediterranean Sea. Biological Invasions. https://doi.org/10.1007/s10530-022-02838-y
Understanding what determines range expansion or extinction is crucial to predict the success of biological invaders. We tackled this long-standing question from an unparalleled perspective using the failed expansions in Littorina saxatilis and investigated its present and past habitat suitability in Europe through Ecological Niche Modelling. This intertidal snail is a typically successful Atlantic colonizer and the earliest confirmed alien species in the Mediterranean Sea, where, however, it failed to thrive despite its high dispersal ability and adaptability. We explored the environmental constraints affecting its biogeography, identified potential glacial refugia in Europe that fuelled its post-glacial colonisations and tested whether the current gaps in its distribution are linked to local ecological features. Our results suggested that L. saxatilis is unlikely to be a glacial relict in the Mediterranean basin. Multiple Atlantic glacial refugia occurred in the Last Glacial Maximum, and abiotic environmental features such as salinity and water temperature have influenced the past and current distributions of this snail and limited its invasion of the Mediterranean Sea. The snail showed a significant overlap in geographic space and ecological niche with Carcinus maenas , the Atlantic predator, but distinct from Pachygrapsus marmoratus , the Mediterranean predator, further pointing to Atlantic-like habitat requirements for this species. Abiotic constrains during introduction rather than dispersal abilities have shaped the past and current range of L. saxatilis and help explaining why some invasions have not been successful. Our findings contribute to clarifying the processes constraining or facilitating shifts in species’ distributions and biological invasions.
[NO TITLE AVAILABLE] https://doi.org/10.50826/bnmnsbot.48.2_31
To clarify biogeographic patterns of two mushroom species (Phallus merulinus and Geastrum courtecuissei) previously reported from Myanmar, sequence data of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA were retrieved from GenBank. The BLAST search and phylogenetic analyses of Phallus indicated that P. merulinus and P. atrovolvatus from wide areas, including Australia, Myanmar, Thailand, Brazil, and French Guiana, cannot be distinguished molecularly. The species was, therefore, considered widespread across tropical to subtropical regions. In contrast, G. courtecuissei from Myanmar was tightly clustered exclusively with G. courtecuissei from Central and South America, supporting the idea of its disjunct distribution between Southeast Asia (Myanmar) and Central-South Americas.