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opencc-by-4.0Mar 2024View details →

Historical tree phenology data reveal the seasonal rhythms of the Congo Basin rainforest

Tropical forest phenology directly affects regional carbon cycles, but the relation between species-specific and whole-canopy phenology remains largely uncharacterized. We present a unique dataset of historical tropical tree phenology collected in the central Congo Basin, before large-scale impacts of human-induced climate change. Historical data was recovered from a phenological study carried out between 1937 and 1956 in the central Congo Basin at the Yangambi Research Station (N00°48’, E24°29’) in what is now the Democratic Republic of Congo (DRC). The data were retrieved from the archives of the INERA (Institut National pour l'Etude et la Recherche Agronomique) herbarium at the Yangambi Research Station. Ground-based phenological observations of local tropical trees were made four times each month on a rotating schedule (resolution of 7.2 days on average) from 1937 until 1956 by the forestry division of the INEAC (Institut National pour l'Étude Agronomique du Congo). The sampling protocol was recovered at the State Archives of Belgium, including details on the observation methods, the observational routes and the training and schedules of the observers. Canopy leaf senescence was defined as a distinct period during which leaves fall and trees remain bare, while canopy turnover was defined as a period during which leaf-fall comes in peaks with concomitant flushes of new leaves (INEAC archives). Summarised data sheets of these long-term observations were digitized using 12 MP resolution cameras. The hand-written notes and annotations depicting phenophases during the observational period were digitized to binary data (yes or no phenophase event at each time-step) through an online citizen science project ‘Jungle Rhythms’ (Hufkens & Kearsley 2023, https://www.zooniverse.org/projects/khufkens/jungle-rhythms).  A selection of species found in the historical forest inventories (Pierlot 1966) are presented, representing 96.0% of the basal area within these inventories. The phenological data comprises 668 individuals covering 140 species (representing 112 genus and 38 families) for a total of 5011 individual observation years (overview of species in Supplementary Table S1). We did not include individuals that were only identified to genus-level. This data accompanies the publication ‘Kearsley, E., Verbeeck, H., Stoffelen, P., Janssens, S. B., Yakusu, E. K., Kosmala, M., De Mil, T., Bauters, M., Kitima, E. R., Ndiapo, J. M., Chuda, A. L., Richardson, A. D., Wingate, L., Ilondea, B. A., Beeckman, H., van den Bulcke, J., Boeckx, P., & Hufkens, K. (2024). Historical tree phenology data reveal the seasonal rhythms of the Congo Basin rainforest. Plant-Environment Interactions, 5, e10136. https://doi.org/10.1002/pei3.10136’. Reference Pierlot, R. (1966). Structure et composition de forêts denses d’Afrique Centrale, spécialement celles du Kivu. Academie Royale des Sciences d’Outre-Mer. Classe des Sciences naturelles et medicales. N.S. XVI-4, Bruxelles, p. 367.

FIGURE 12 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 12. Distribution map based on label information attached to the type specimens in NHMW. Identifications are nominal species as identified by Attems (1951), all here considered to be Lithobius iranicus Attems, 1951, except for L. inquiriendus.

FIGURE 8 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 8. Sternites of ultimate leg-bearing segment and intermediate segment in females, ventral view. A–B. Lithobius iranicus Attems, 1951. A. Lectotype, NHMW MY3963. B. NHMW MY5700. C. Lithobius rhiknus Attems, 1951 syn. nov., syntype, NHMW MY3942. D. Lithobius inquiriendus Attems, 1951, syntype, NHMW MY10386.

FIGURE 1. Lithobius iranicus Attems, 1951 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 1. Lithobius iranicus Attems, 1951, ♀ lectotype NHMW MY3963. A. Habitus, dorsal view. B. Cephalic plate and T1, dorsal view. C. Forcipular segment, ventral view. D. Ocelli and Tömösváry's organ, lateral view. Abbreviation: TO = Tömösváry's organ.

FIGURE 4. Lithobius iranicus Attems, 1951 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 4. Lithobius iranicus Attems, 1951, ♂, new specimen NHMW MY10387. A. Close-up of coxosternal margin showing teeth and porodont. B. TT9-13, dorsal view. C. Posterior segments, ventral view. Abbreviation: Po = porodont.

FIGURE 11 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 11. Maximum Likelihood tree based on all molecular data (28S-16S-COI). Above nodes: bootstrap values>50%, black dot for 100% support.

FIGURE 3. Lithobius iranicus Attems, 1951 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 3. Lithobius iranicus Attems, 1951, ♂, new specimen NHMW MY10387. A. Habitus, dorsal view. B. Cephalic plate and T1, dorsal view. C. Ocelli, lateral view. D. Forcipular segment, ventral view.

FIGURE 9 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 9. Sternites of ultimate leg-bearing segment and first genital segment in males, ventral view. A–C. Lithobius iranicus Attems, 1951. A. Paralectotype, NHMW MY3964. B. NHMW MY5701. C. NHMW MY5700. D–E. Lithobius inaequidens Attems, 1951 syn. nov. D. Syntype, NHMW MY3962. E. Syntype, NHMW MY10385. F. Lithobius rhiknus Attems, 1951 syn. nov., syntype, NHMW MY4044.

FIGURE 5 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 5. Paired sulci on ultimate legs of males, dorsal view. A–B. Lithobius iranicus Attems, 1951. A. Paralectotype NHMW MY10383. B. NHMW MY10387. C. Lithobius rhiknus Attems, 1951 syn. nov., leg 13, syntype NHMW MY4044. D. Lithobius inaequidens Attems, 1951 syn. nov., NHMW MY3962. Arrows pointing to sulci.

FIGURE 6 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 6. Close-up of coxosternal teeth. A–F. Lithobius iranicus Attems, 1951. A. Paralectotype ♂, NHMW MY10383. B. Paralectotype ♂, NHMW MY10384. C. Paralectotype ♂, NHMW MY3964. D. Non-type ♂ NHMW MY5701. E. Non-type ♀, NHMW MY5700. F. Non-type ♂, NHMW MY5700. G–H. Lithobius inaequidens Attems, 1951 syn. nov. G. Syntype ♂, NHMW MY3962. H. Syntype ♂, NHMW MY10385. I. Lithobius inquiriendus Attems, 1951, syntype ♀, NHMW MY10386. J. Lithobius rhiknus Attems, 1951 syn. nov., syntype ♀, NHMW MY3942.

FIGURE 7 in Revision of some historical types of the genus Lithobius Leach, 1814 (Chilopoda, Lithobiomorpha) from the 1949/50 Austrian Iran Expedition, with new molecular data for L. iranicus Attems, 1951

FIGURE 7. Ocellar field in lateral view. A. Lithobius iranicus Attems, 1951, paralectotype ♂, NHMW MY3964. B. Lithobius inaequidens Attems, 1951 syn. nov., syntype ♂, NHMW MY3962. C. Lithobius inaequidens Attems, 1951 syn. nov., syntype ♂, NHMW MY10385. D. Lithobius iranicus Attems, 1951, syntype ♂, NHMW MY10383. E. Lithobius rhiknus Attems, 1951 syn. nov., syntype ♂, NHMW MY4044. Abbreviation: TO = Tömösváry's organ.

opencc-zeroNov 2021View details →

Data for the manuscript: Historical biogeography of Pomaderris (Rhamnaceae): continental vicariance in Australia and repeated independent dispersals to New Zealand

Gondwanan biogeographic patterns include a combination of old vicariance events following the breakup of the supercontinent, and more recent long-distance dispersals across the southern landmasses. Floristic relationships between Australia and New Zealand have mostly been attributed to recent dispersal events rather than vicariance. We assessed the biogeographic history of Pomaderris (Rhamnaceae), which occurs in both Australia and New Zealand, by constructing a time-calibrated molecular phylogeny to infer (1) phylogenetic relationships and (2) the relative contributions of vicariance and dispersal events in the biogeographic history of the genus. Using hybrid capture and high throughput sequencing, we generated nuclear and plastid data sets to estimate phylogenetic relationships and fossil calibrated divergence time estimates for Pomaderris . BioGeoBEARS and biogeographical stochastic mapping (BSM) were used to assess the ancestral area of the genus and the relative contributions of vicariance vs dispersal, and the directionality of dispersal events. Our analyses indicate that Pomaderris originated in the Oligocene and had a widespread Australian distribution. Vicariance of western and eastern Australian clades coincides with the uplift of the Nullarbor Plain c. 14 Ma, followed by subsequent in-situ and within-biome diversification with little exchange across regions. A rapid radiation of southeastern Australian taxa beginning c. 10 Ma was the source for at least six independent long-distance dispersal events to New Zealand during the Pliocene–Pleistocene. Our study demonstrates the importance of dispersal in explaining not only the current cross-Tasman distributions of Pomaderris, but for the New Zealand flora more broadly. The pattern of multiple independent long-distance dispersal events for Pomaderris , without significant radiation within New Zealand, is congruent with other lowland plant groups, suggesting that this biome has a different evolutionary history compared with the younger alpine flora of New Zealand, which exhibits extensive radiations often following single long distance dispersal events.

opencc-zeroFeb 2022View details →

Data from: A diversification relay race from Caribbean-Mesoamerica to the Andes: historical biogeography of Xylophanes hawkmoths

The regions of the Andes and Caribbean-Mesoamerica are both hypothesized to be the cradle for many Neotropical lineages, but few studies have fully investigated the dynamics and interactions between Neotropical bioregions. The NewWorld hawkmoth genus Xylophanes is the most taxonomically diverse genus in the Sphingidae, with the highest endemism and richness in the Andes and Caribbean-Mesoamerica. We integrated phylogenomic and DNA barcode data and generated the first time-calibrated tree for this genus, covering 93.8% of the species diversity. We used event-based likelihood ancestral area estimation and biogeographic stochastic mapping to examine the speciation and dispersal dynamics of Xylophanes across bioregions. We also used trait-dependent diversification models to compare speciation and extinction rates of lineages associated with different bioregions. Our results indicate that Xylophanes originated in Caribbean-Mesoamerica in the Late Miocene, and immediately diverged into five major clades. The current species diversity and distribution of Xylophanes can be explained by two consecutive phases. In the first phase, the highest Xylophanes speciation and emigration rates occurred in the Caribbean-Mesoamerica, and the highest immigration rates occurred in the Andes, whereas in the second phase the highest immigration rates were found in Amazonia, and the Andes had the highest speciation and emigration rates.

opencc-by-4.0Mar 2022View details →

AWI-CM3 version 3.0 historic, 4XCO2, 1% CO2 data

Historical simulation output from AWI-CM3 version 3.0 Years: 1850-2014 Frequency: Annual means Variables: <ul> <li>T2M: near surface (2m) air temperature</li> <li>PRECIP: precipitation</li> <li>SSR: Surface solar radiation</li> <li>STR: Surface thermal radiation</li> <li>SSRD: Surface solar downward radiation</li> <li>TTR: Top thermal radiation</li> <li>TCC: Total cloud cover</li> <li>CI: Sea ice concentration (on atmospheric grid)</li> <li>CP: Convective precipitation</li> <li>LSP: Large scale precipitation</li> <li>U10M: 10meter eastward wind</li> <li>V10M: 10meter northward wind</li> <li>U: 300hPa eastward wind</li> <li>V: 300hPa northward wind</li> <li>Z: 500hPa geopotential height</li> <li>a_ice: sea ice concentration (on ocean mesh)</li> <li>m_ice: sea ice mass per unit area</li> <li>temp: 3D ocean temperature</li> <li>sst: sea surface temperature</li> <li>w: vertical velocity</li> <li>MLD2: Mixed layer depth according to Large et al. (https://doi.org/10.1175/1520-0485(1997)027%3C2418:STSFAB%3E2.0.CO;2)</li> </ul>   4xCO2 simulation output from AWI-CM3 version 3.0 Years: 1850-1970 Frequency: Annual means Variables: <ul> <li>T2M: near surface (2m) air temperature</li> <li>TTR: Top thermal radiation</li> <li>TSR: Top solar radiation</li> </ul>   1% per year increased of CO2 simulation output from AWI-CM3 version 3.0 Years: 1850-2010 Frequency: Annual means Variables: <ul> <li>T2M: near surface (2m) air temperature</li> </ul>

opencc-zeroMar 2022View details →

Data from: Historical mitochondrial genome introgression confounds species delimitation—evidence from phylogenetic inference in the Odorrana grahami species complex

Species delimitation is essential to informing conservation policy and understanding ecological and evolutionary processes. Most of our recent gains in knowledge on animal diversity rely on morphological characteristics and mitochondrial (mt) DNA variation. Concordant results based on both have led to an unprecedented acceleration in the identification of new species and enriched the field of taxonomy. However, discordances are also found commonly between morphological and mtDNA evidence. This confounds species delimitation, especially when gene flow or mitochondrial genome introgression has occurred. Here we illustrate how mitochondrial genome introgression among species of the Odorrana grahami complex confounds species delimitation using the combined evidence of morphological characters, mitochondrial variation, and thousands of nuclear single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). Fifty-eight samples across the distribution of the O. grahami complex were included. The mtDNA matrilineal genealogy indicated two clades, with O. grahami and O. junlianensis clustered together. In contrast, all nuclear evidence including gene trees, species trees, and genetic structure analyses based on GBS data support three species with distinct genetic clusters. These three distinct genetic clusters also correspond to distinct morphological characters. They affirm the distinct taxonomic entities of both O. grahami and O. junlianensis, as well as a third clade distinct from either. Which species the third clade belongs to remains unclear and will require further testing. The nuclear genomic loci contradict the COI evidence, with indications of rampant historical mitochondrial genome introgression among the species of the O. grahami complex. These discordant signals previously confused species delimitation efforts in this group. Based on these findings, we recommend the integration of independent data, especially nuclear genomic evidence, in species delimitation so as to be robust against the pitfalls of mitochondrial introgression.

opencc-zeroApr 2022View details →

Bioclimatic, soil, terrain, distance to Native American settlement, and historical tree taxon relative abundance data at 8-km resolution for the northeastern United States

Researchers have debated impacts of past Native American land use on forests including upon tree species composition in northeastern United States (US), with estimates of impacts ranging from local to regional extent. This study examines tree relative abundances in the northeastern US (approx. 420,000 km2) to assess whether Native Americans influenced geographic distributions of 18 tree taxa prior to Euro-American settlement. We used boosted regression trees to model abundance patterns and to assess the importance of distance-based proxies of Native American land use versus environmental variables. We trained models that included and excluded distance-based proxies. Abundance estimates from original land survey records (1650-1850 CE) were acquired for taxa at 8 km spatial resolution, and related to Native American settlement locations (1500-1800 CE) and 27 environmental variables. When evaluated upon test data, regional-scale models of relative abundance that included distance-based proxies performed only slightly better than models that excluded them, with mean improvements in RMSE of 0.1 percentage points. Models suggest that Native American land use modestly altered the relative abundance of taxa locally, extending no more than 50 km from settlement. Models also suggest slight increases near settlement of a few percentage points in relative abundance for fire-tolerant and/or dietary taxa (e.g. oak, hickory, and pine), and for early-successional taxa (e.g. ash). Past Native American land use had no detectable effect on forest composition across a regional extent, but increased the abundance of fire-tolerant, shade-intolerant, and nut-producing trees locally. The Excel-format (.xlsx) dataset here provides the training and testing data for the BRT models in this publication. It contains relative abundances of the 18 tree taxa expressed as a fraction of total number of trees. It also provides bioclimatic (e.g. annual temperature, annual preciptation), soil (e.g. pH, percent sand), terrain (e.g. slope), and Native American (e.g. distance to settlement) variables developed from multiple sources. A column also indicates whether an observation was part of the training data or the test data. See the publication and its Supporting Information for full details on the acquisition and processing of these data, as well as the original providers of the data. If using these data, please cite both this dataset's corresponding article, as well as the original providers of the data. Also provided are ascii-format (.asc) gridded data layers that were used for making spatial predictions of taxon relative abundances from BRT models. The original creators/providers of the relative abundance, bioclimatic, soil, terrain, and Native American data or layers used for creating the gridded data in this study are: Abel, T. (2016). The Iroquoian occupations of Northern New York: A summary of current research. Ontario Archaeology, 96, 65–75. CIFAS. (2017). Map Of First Nations in New Brunswick. Comitas Institute for Anthropological Study. <a href="http://cifas.us/first-nations-maps/">http://cifas.us/first-nations-maps/</a> Grumet, R. S. (1995). Historic Contact: Indian People and Colonists in Today's Northeastern United States in the Sixteenth through Eighteenth Centuries. University of Oklahoma Press. Jordan, K. A. (2013). Incorporation and colonization: Postcolumbian Iroquois satellite communities and processes of indigenous autonomy. American Anthropologist, 115(1), 29–43. Milner, G. R., & Chaplin, G. (2010). Eastern North American population at ca. A.D. 1500. American Antiquity, 75(4), 707–726. NASA. (2000). SRTM 90m Digital Elevation Database v4.1. <a href="https://cgiarcsi.community/data/srtm-90m-digital-elevation-database-v4-1/">https://cgiarcsi.community/data/srtm-90m-digital-elevation-database-v4-1/</a> O'Donnell, M. S., & Ignizio, D. A. (2012). Bioclimatic Predictors for Supporting Ecological Applications in the Conterminous United States (Data Series 691; p. 10). U.S. Geological Survey. <a href="https://www.sciencebase.gov/catalog/item/4fe0f9f4e4b05d4ed81d9392">https://www.sciencebase.gov/catalog/item/4fe0f9f4e4b05d4ed81d9392</a> Paciorek, C. J., Goring, S. J., Thurman, A. L., Cogbill, C. V., Williams, J. W., Mladenoff, D. J., Peters, J. A., Zhu, J., & McLachlan, J. S. (2016). Statistically-estimated tree composition for the northeastern United States at the time of Euro-American settlement. PLoS ONE, 11(2), e0150087. <a href="https://doi.org/10.1371/journal.pone.0150087">https://doi.org/10.1371/journal.pone.0150087</a> Peters, M. P., Iverson, L. R., Prasad, A. M., & Matthews, S. N. (2013). Integrating Fine-scale Soil Data into Species Distribution Models: Preparing Soil Survey Geographic (SSURGO) Data from Multiple Counties (General Technical Report NRS-122; p. 70). U.S. Forest Service. <a href="https://www.fs.usda.gov/treesearch/pubs/45308">https://www.fs.usda.gov/treesearch/pubs/45308</a>

opencc-zeroApr 2022View details →

Data from: Phylogenomics and historical biogeography of West Indian Rock Iguanas (genus Cyclura)

The genus Cyclura includes nine extant species and six subspecies of West Indian Rock Iguanas and is one of the most imperiled genera of squamate reptiles globally. An understanding of species diversity, evolutionary relationships, diversification, and historical biogeography in this group is crucial for implementing sound long-term conservation strategies. We collected DNA samples from 1–10 individuals per taxon from all Cyclura taxa (n = 70 ingroup individuals), focusing where possible on incorporating individuals from different populations of each species. We also collected 1–2 individuals from each of seven outgroup species of iguanas (Iguana delicatissima; five Ctenosaura species) and Anolis sagrei (n = 12 outgroup individuals). We used targeted genomic sequence capture to isolate and to sequence 1,872 loci comprising of 687,308 base pairs (bp) from each of the 82 individuals from across the nuclear genome. We extracted mitochondrial reads and assembled and annotated mitogenomes for all Cyclura taxa plus outgroup species. We present well-supported phylogenomic gene tree/species tree analyses for all extant species of Cyclura using ASTRAL-III, SVDQuartets, and starBEAST methods, and discuss the taxonomic, biogeographic, and conservation implications of these data. We find a most recent common ancestor of the genus 9.91 million years ago. The earliest divergence within Cyclura separates C. pinguis from a clade comprising all Cyclura except C. pinguis. Within the latter group, a clade comprising C. carinata from the southern Lucayan Islands and C. ricordii from Hispaniola is the sister taxon to a clade comprising the other Cyclura. Among the other Cyclura, the species C. cornuta and C. stejnegeri (from Hispaniola and Isla Mona) form the sister taxon to a clade of species from Jamaica (C. collei), Cuba and Cayman Islands (C. nubila), and the eastern (C. rileyi) and western (C. cychlura) Lucayan Islands. Cyclura cychlura and C. rileyi form a clade whose sister taxon is C. nubila. Cyclura collei is the sister taxon to these three species combined.

opencc-zeroDec 2018View details →

Data from: The influence of historical dispersal on the phylogenetic structure of tree communities in the tropical Andes

We test for evidence of the Tropical Niche Conservatism or the Out of The Tropics hypotheses in structuring patterns of tree community composition along a 2000+ meter elevational gradient in the northern tropical Andes. By collecting and integrating data on the presence-absence of tree species within plots with phylogenetic information, we analyzed: 1) patterns of phylogenetic dispersion and species diversity along the elevational gradient based on indexes of net relatedness, nearest taxon relatedness, and species richness (α-diversity); and 2) the replacement of lineages along the gradient using the PhyloSorensen metric (β-diversity). More specifically, we established 20 0.25-ha permanent tree inventory plots between 750 and 2802 m asl where all individuals with Diameter at Breast Height (DBH) ≥ 10 cm were measured and identified. We then used a series of linear models to test for changes in α and β diversity between plots in relation to elevation. Neither the net relatedness index nor the nearest taxon index showed a significant relationship with elevation. However, there was greater phylogenetic over-dispersion at intermediate elevations; this likely reflects the mixing of species with contrasting origins from tropical and temperate lineages. β-diversity between plots was negatively related to the corresponding difference in elevation, indicating that closely related lineages occupy similar ranges of elevation and temperature. We conclude that the immigration of lineages from extra-tropical regions have significant effects in determining the phylogenetic structure of tree communities in tropical Andean forests.

opencc-by-4.0Jun 2022View details →

Historical data of flash flood and trend analysis information for Uttarakhand, India

Historical data is always useful in interpreting any hazard-affected location. In this article historical data were gathered from various literature reviews, journals, newspapers, reports, and other sources to generate a flash flood map for Uttarakhand state, India. Between 1970 and 2020, a total of 122 sites were identified as being at risk of flash flooding. Moreover, several studies on rainfall trends at various scales have concluded that global warming is increasing extreme precipitation as well as extreme weather-related occurrences and risks. Therefore, high spatial resolution (0.25*0.25 degree) daily gridded rainfall data from the India Meteorological Department (IMD) was utilized to analyse the change in percentage from 1970 to 2020 for annual, pre-monsoon, monsoon, post-monsoon, and winter seasons.