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Performance results from species distribution models considering historical occurrences and variables of varying persistency
<p>Occurrence data used to build species distribution models often include historical records from locations in which the species no longer exists. When these records are paired with contemporary environmental values that no longer represent the conditions the species experienced, the model creates false associations that hurt predictive performance. The extent of mismatching increases with the number of historical occurrences and with inclusion of environmental variables that are prone to change over time. Indeed, the mismatch between occurrence data and contemporaneous environmental variables is a common dilemma when modeling rare or cryptic species, especially those of conservation concern that were once more abundant. Herein, we assess (1) the impact of historical occurrences on model performance across three sets of environmental variables of increasing persistency, and (2) the performance of models built using selected-historical occurrences from locations that showed evidence of limited environmental change over time. Concepts are tested on federally listed flatwoods salamanders, reflecting real-world conservation management efforts. We predicted that, compared to other occurrence sets, (1) historical occurrences would perform best with environmental variables that were more persistent, (2) recent occurrences would perform best when the environmental variables were more impersistent, and that (3) our selected-historical occurrences would perform best with a combination of persistent and impersistent variables. Our results showed the expected inversion of model performance of recent and historical occurrences across environmental variables of increasing persistency when evaluated by correct predictions. However, the inversion was not seen in AUC performance, in which historical occurrences outperformed recent occurrence models across all variable sets. Selected-historical occurrences did not notably improve performance over all-historical occurrences in any metric or variable set. To maximize utility and performance, modelers could acknowledge potential tradeoffs from inclusion of historical occurrences and consider number and age of recent and historical occurrences available, the persistency of environmental variables considered, and how their conservation goals are reflected in model design and evaluation, particularly with respect to sensitivity vs. specificity. Our study lends support for inclusion of historical occurrences, with the potential exception of mostly impersistent variables when sensitivity is the highest priority.</p>
Figure 1 from: von Tschirnhaus J, Correa C (2021) The definitive rediscovery of Telmatobius halli (Anura, Telmatobiidae) at its historic type locality and its synonymy with T. dankoi and T. vilamensis. ZooKeys 1079: 1-33. https://doi.org/10.3897/zookeys.1079.69036
Figure 1 Geographic context of this study A distribution of all Telmatobius populations known from the southern range of the genus in Chile (20°55'–22°55'S). Light grey area = Chilean territory, dark grey area = Bolivian territory, grey lines = limits of the sub-basins, star = study site, diamonds = type localities B topographic relief of the surroundings of Miño. Grey lines = limits of the sub-basins. Montt is the name provided by the IHAEC for the Collahuasi Copper Mine C satellite image of Miño. 1) Concrete pool, 2) ruins of mining settlement, 3) sampling point, a) Miño River, b) Nacimiento Creek, c) Loa River.
Supplementary material 1 from: von Tschirnhaus J, Correa C (2021) The definitive rediscovery of Telmatobius halli (Anura, Telmatobiidae) at its historic type locality and its synonymy with T. dankoi and T. vilamensis. ZooKeys 1079: 1-33. https://doi.org/10.3897/zookeys.1079.69036
Video S1. Warm springs swimming bath at source of Río Loa in Chile, 1935.
Figure 6 from: von Tschirnhaus J, Correa C (2021) The definitive rediscovery of Telmatobius halli (Anura, Telmatobiidae) at its historic type locality and its synonymy with T. dankoi and T. vilamensis. ZooKeys 1079: 1-33. https://doi.org/10.3897/zookeys.1079.69036
Figure 6 Adults from the three known populations of Telmatobius halli, as recognized in this study, showing the similarity in their external appearance A Miño B Las Cascadas and C Vilama River. The inlay in the upper right corner of C shows a detail of the keratinous spines. Photograph credits for the Vilama River specimen: Felipe Rabanal. Scale bars: 1 cm.
Figure 5 from: von Tschirnhaus J, Correa C (2021) The definitive rediscovery of Telmatobius halli (Anura, Telmatobiidae) at its historic type locality and its synonymy with T. dankoi and T. vilamensis. ZooKeys 1079: 1-33. https://doi.org/10.3897/zookeys.1079.69036
Figure 5 Selected specimens of Telmatobius halli from Miño A–D dorsal views of adult specimens, showing variation in coloration patterns E ventral view of the specimen from C F tadpole; scale bar: 1 cm (A–F).
Figure 3 from: von Tschirnhaus J, Correa C (2021) The definitive rediscovery of Telmatobius halli (Anura, Telmatobiidae) at its historic type locality and its synonymy with T. dankoi and T. vilamensis. ZooKeys 1079: 1-33. https://doi.org/10.3897/zookeys.1079.69036
Figure 3 Historic and current view of the concrete swimming pool in Miño A panorama extracted from video footage from the IHAEC, 1935. Yellow arrows indicate the upper and lower pool walls B same view in 2020.
Figure 2 from: von Tschirnhaus J, Correa C (2021) The definitive rediscovery of Telmatobius halli (Anura, Telmatobiidae) at its historic type locality and its synonymy with T. dankoi and T. vilamensis. ZooKeys 1079: 1-33. https://doi.org/10.3897/zookeys.1079.69036
Figure 2 Historic and current panoramic view of the area surrounding the concrete swimming pool in Miño A panorama extracted from video footage from the IHAEC, 1935. Yellow arrows indicate rock formations that are easily recognizable B current state of the habitat. Red rectangle = location of the concrete pool. The mountain in the left background is Miño Volcano.
Figure 7 from: von Tschirnhaus J, Correa C (2021) The definitive rediscovery of Telmatobius halli (Anura, Telmatobiidae) at its historic type locality and its synonymy with T. dankoi and T. vilamensis. ZooKeys 1079: 1-33. https://doi.org/10.3897/zookeys.1079.69036
Figure 7 Bayesian consensus tree (50% majority-rule; mitochondrial genes concatenated, treated as two separated partitions), showing the relationships among Chilean Telmatobius and the species groups recovered by Sáez et al. (2014). The specimens of the species and populations of the extreme south of the distribution of the genus in Chile are highlighted with the same colors of the map in Fig. 1A. The values next to the nodes correspond to posterior probabilities and the scale bar below the tree represents the expected substitutions per site along the branches. Identification of populations of Copaquire, Quebrada Chiclla, Quebrada Choja, and Aguas Calientes follows the taxonomy prior to Fibla et al. (2018) and Cuevas et al. (2020). The red box indicates the taxonomic changes proposed in this study.
Long-term shifts in the functional diversity of abandoned wet meadows – Impacts of historical disturbance and successional pathways
<p>Investigating the direction of changes in functional diversity involving successional pathways and historical disturbances may be a promising tool for predictions of the effectiveness of the semi-natural meadows conservation, with great emphasis on formulation of more cost-effective restoration strategies. The goal of this research was to assess the differences in long-term shifts in the functional diversity of plant species in semi-natural wet meadows unmanaged for the last 40 years, under the influence of different successional pathways and historical disturbances. Using ordination techniques, linear mixed-effect models, a set of plant functional traits and parameters of functional diversity, we assessed the importance of habitat filtering, competition and niche partitioning in shaping community assembly changes over time. The most dramatic shifts in functional diversity were found in the <i>Carex acutiformis </i>successional pathway after topsoil removal, where colonization by successional inhibitors was the main driver causing decreases in functional dispersion and divergence. This was expressed as a decrease in the importance of habitat filtering and replacement of specialized species by competitors with heavier seeds and higher specific leaf area. Regarding the <i>C. cespitosa</i> and <i>Salix cinerea </i>pathways, the magnitudes of shifts in functional diversity were milder and differed less between the historical topsoil removal and mowing treatments, thereby maintaining a large role for niche partitioning in shaping the vegetation structure. The results of our study highlight the importance of tussock sedges and shrubs as effective buffers against the biotic homogenization of meadows driven by the simplification of functional composition, even from a long-term perspective.</p>
Figure 4 from: Jusoh WFA, Chua MAH, Bakker PAJ, Kamminga P, Weiler D, Rookmaaker K, Low MEY (2022) A historical specimen of the Fishing Cat, Prionailurus viverrinus (Bennett, 1833) (Carnivora, Felidae) from Singapore in the zoological collection of the Naturalis Biodiversity Center, Leiden. Zoosystematics and Evolution 98(1): 43-53. https://doi.org/10.3897/zse.98.76940
Figure 4 The plate of "Viverine Cat" in the second volume of the "Illustrations" (Gray 1832–1834) which was published between 10 September and 1 October 1834. Reproduced from the Biodiversity Heritage Library (http://biodiversitylibrary.com/).
Supplementary material 1 from: Jusoh WFA, Chua MAH, Bakker PAJ, Kamminga P, Weiler D, Rookmaaker K, Low MEY (2022) A historical specimen of the Fishing Cat, Prionailurus viverrinus (Bennett, 1833) (Carnivora, Felidae) from Singapore in the zoological collection of the Naturalis Biodiversity Center, Leiden. Zoosystematics and Evolution 98(1): 43-53. https://doi.org/10.3897/zse.98.76940
Raw skull measurements and PCA loading matrix
Figure 3 from: Jusoh WFA, Chua MAH, Bakker PAJ, Kamminga P, Weiler D, Rookmaaker K, Low MEY (2022) A historical specimen of the Fishing Cat, Prionailurus viverrinus (Bennett, 1833) (Carnivora, Felidae) from Singapore in the zoological collection of the Naturalis Biodiversity Center, Leiden. Zoosystematics and Evolution 98(1): 43-53. https://doi.org/10.3897/zse.98.76940
Figure 3 A two-page document listing records of specimens sent by Diard to Leiden in March 1830 (A) with the upper part of the first page (B), shows a title of the document "Catalogue des objets d'hist. nat. de l'envoi de Mr Diard arrivé mars 1830", while the bottom part of the page (C), shows "Felis leucopalmis du détroit de Singapour" (translated: Felis leucopalmis from the Strait of Singapore) was among the specimens sent by Diard; at the bottom part of the second page, the document was signed by H. Schlegel (D). Reproduced from Natuurkundige Commissie Archives Online (Gasso et al. 2020)
Figure 2 from: Jusoh WFA, Chua MAH, Bakker PAJ, Kamminga P, Weiler D, Rookmaaker K, Low MEY (2022) A historical specimen of the Fishing Cat, Prionailurus viverrinus (Bennett, 1833) (Carnivora, Felidae) from Singapore in the zoological collection of the Naturalis Biodiversity Center, Leiden. Zoosystematics and Evolution 98(1): 43-53. https://doi.org/10.3897/zse.98.76940
Figure 2 Three labels found in the box labelled "cat. ost. b" (i.e., specimen b of the "Catalogue ostéologique des Mammifères", i.e., Jentink 1887) with a skull specimen in it (A–C) and a label pasted on the pedestal of the mounted skin (D).
Figure 1 from: Jusoh WFA, Chua MAH, Bakker PAJ, Kamminga P, Weiler D, Rookmaaker K, Low MEY (2022) A historical specimen of the Fishing Cat, Prionailurus viverrinus (Bennett, 1833) (Carnivora, Felidae) from Singapore in the zoological collection of the Naturalis Biodiversity Center, Leiden. Zoosystematics and Evolution 98(1): 43-53. https://doi.org/10.3897/zse.98.76940
Figure 1 A specimen of Prionailurus viverrinusRMNH.MAM.59688, referred to as specimen b of Felis viverrina in Jentink's two Catalogues of 1887 and 1892. A–C. The skull from three different angles; D. A specimen box containing the skull; E. The mounted skin.
Figure 5 from: Jusoh WFA, Chua MAH, Bakker PAJ, Kamminga P, Weiler D, Rookmaaker K, Low MEY (2022) A historical specimen of the Fishing Cat, Prionailurus viverrinus (Bennett, 1833) (Carnivora, Felidae) from Singapore in the zoological collection of the Naturalis Biodiversity Center, Leiden. Zoosystematics and Evolution 98(1): 43-53. https://doi.org/10.3897/zse.98.76940
Figure 5 The PCA revealed that the Diard specimen (RMNH.MAM.59688) grouped with Fishing Cats, which were distinctly separated from Leopard Cats from the Malay Peninsula. The specimen grouped more closely with Javan Fishing Cat specimens rather than those of Indochina along the PC2 axis.
Historical earthquake data in northeastern Tibet
<p>This earthquake data is used in my paper submitted to JGR.</p>
Appendix: corpus of historic (18th-21st century) PCM texts
<p>Corpus of historic (18th-21st) PCM texts analyzed for the study.</p>
FIGURE 8 in Taxonomic implications of anatomical characteristics of the genus Tulipa (Liliaceae) in Turkey and their place in the historical subgeneric classifications
FIGURE 8. Results of principle component analysis of subgenus Tulipa.
FIGURE 7 in Taxonomic implications of anatomical characteristics of the genus Tulipa (Liliaceae) in Turkey and their place in the historical subgeneric classifications
FIGURE 7. Results of principle component analysis of subgenus Tulipa+T. clusiana.
FIGURE 5 in Taxonomic implications of anatomical characteristics of the genus Tulipa (Liliaceae) in Turkey and their place in the historical subgeneric classifications
FIGURE 5. Results of principle component analysis of subgenus Eriostemones+T. clusiana.
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