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Fig. 22 in Oosagitta gen. nov. from tropical Africa, with revision of two species and description of four new species (Coleoptera: Chrysomelidae, Galerucinae)

Fig. 22. Holotype of O. geescheae sp. nov. A. Overview with labels. B. Close-up of specimen.

Fig. 13 in Oosagitta gen. nov. from tropical Africa, with revision of two species and description of four new species (Coleoptera: Chrysomelidae, Galerucinae)

Fig. 13. Distribution of O. minuta comb. nov., O. anningae sp. nov. and O. geescheae sp. nov.

Fig. 8 in Oosagitta gen. nov. from tropical Africa, with revision of two species and description of four new species (Coleoptera: Chrysomelidae, Galerucinae)

Fig. 8. Distribution of O. angolensis comb. nov., O. melanopicta sp. nov. and O. thomasi sp. nov.

Fig. 14 in Oosagitta gen. nov. from tropical Africa, with revision of two species and description of four new species (Coleoptera: Chrysomelidae, Galerucinae)

Fig. 14. Lectotype of Oosagitta minuta comb. nov. A. Overview with labels. B. Close-up of specimen.

Fig. 26 in Oosagitta gen. nov. from tropical Africa, with revision of two species and description of four new species (Coleoptera: Chrysomelidae, Galerucinae)

Fig. 26. Holotype of O. thomasi sp. nov. A. Overview with labels. B. Close-up of specimen.

opencc-by-3.0Apr 2014View details →

Fig. 1 in Four Achnanthidium species (Bacillariophyta) formerly identified as Achnanthidium minutissimum from the Antarctic Region

Fig. 1. The Antarctic region with the location of the sampled islands and archipelagos.

opencc-zeroAug 2020View details →

Data from: Shifts in timing and duration of breeding for 73 boreal bird species over four decades

Breeding timed to match optimal resource abundance is vital for the successful reproduction of species, and breeding is therefore sensitive to environmental cues. As the timing of breeding shifts with a changing climate, this may not only affect the onset of breeding, but also its termination, and thus the length of the breeding period. We use an extensive dataset of over 820K nesting records of 73 bird species across the boreal region in Finland to probe for changes in the beginning, end, and duration of the breeding period over four decades (1975-2017). We uncover a general advance of breeding with a strong phylogenetic signal, but no systematic variation over space. Additionally, 31% of species contracted their breeding period in at least one bioclimatic zone, as the end of the breeding period advanced more than the beginning. We did not detect a statistical difference in phenological responses of species with combinations of different migratory strategy or number of broods. Nonetheless, we find systematic differences in species responses, as the contraction in the breeding period was found almost exclusively in resident and short-distance migrating species, which generally breed early in the season. Overall, changes in the timing and duration of reproduction may potentially lead to more broods co-occurring in the early breeding season – a critical time for species' reproductive success. Our findings highlight the importance of quantifying phenological change across species and over the entire season, to reveal shifts in the community-level distribution of bird reproduction.

opencc-zeroAug 2020View details →

Data from: Impact of agricultural weathering on physicochemical properties of biodegradable plastic mulch films: comparison of two diverse climates over four successive years

Biodegradable plastic mulch films (BDMs) are essential in the production of vegetable and specialty crops due to their promotion of increased crop yield and quality. Unlike conventional polyethylene (PE) mulches, BDMs can be tilled into the soil after crop harvest to undergo biodegradation, thereby leading to minimal environmental impact. Agricultural weathering impacts both the performance of BDMs during crop production as a barrier to weeds and biodegradability of BDMs in the soil. To better understand the relative importance of climatic factors, the change of physicochemical properties of BDMs during single-season, 3-4 month, field trials for vegetable production at two diverse climates (Knoxville, TN and Mount Vernon, WA) across four successive years (2015-2018) was evaluated. Mulch treatments consisted of four commercially available BDMs composed primarily of polybutylene co-adipate- co-terephthalate (PBAT) that differed in color and polymeric feedstock, a black experimental BDM prepared from polylactic acid/polyhydroxybutyrate (PLA/PHA) blend, and conventional PE mulch. Mulch deterioration did not vary extensively between years. Solar radiation, an important factor to degradation of mulches, was higher in WA than TN in most sampling years. Yet, degradation occurred more greatly for BDMs in TN, which is attributable to higher temperatures in TN. Loss of mechanical properties and color was greater than chemical property changes. Differences in the extent of molecular weight decrease between years correlated significantly with solar radiation exposure at the two locations. A black-colored PBAT-based BDM was less susceptible to degradation than equivalent clear and white-on-black films, due to carbon black acting as a photostabilizer. The impact of weathering also differed between three commercially available PBAT-based films. The PLA/PHA mulch was more susceptible to degradation than PBAT-based BDMs, particularly in the warmer location, TN, partially due to a leaching out of PHA and lower-molecular weight polymer molecules. The extent of change for physicochemical properties of BDMs due to agricultural weathering is greatly affected by polymeric composition, and is greater in warmer climates.

Figure 20 in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species

Figure 20. Paracaprella carballoi sp. nov. Holotype male mouthparts. Scale bar: 0.05 mm.

Figure 16 in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species

Figure 16. Liropus isabelensis sp. nov. Holotype male mouthparts. Scale bar: 0.1 mm.

Figure 2. Aciconula acanthosoma Chess 1989 in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species

Figure 2. Aciconula acanthosoma Chess 1989. Lateral view. Scale bar: 1 mm.

Figure 1 in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species

Figure 1. Map of study area showing the sampling stations. St5 not shown.

Figure 3. Caprella equilibra Say, 1818 in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species

Figure 3. Caprella equilibra Say, 1818. Lateral view. Scale bar: 1 mm.

opencc-by-4.0Sep 2020View details →

Destructive harvest data collected from four large tropical rainforest trees in Floresta Nacional de Caxiuanã

Title ----- Destructive harvest data collected from four large tropical rainforest trees in Floresta Nacional de Caxiuanã Authors -------  A. Burt M. Boni Vicari A. C. L. da Costa I. Coughlin P. Meir L. Rowland M. Disney Contact ------- a.burt@ucl.ac.uk License ------- These data are distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC BY 4.0) - see the LICENSE file for details. Overview -------- We harvested four large tropical rainforest trees (diameter range: 0.6-1.2m, height range: 30-46m) in a natural closed forest stand in Floresta Nacional de Caxiuanã, Pará, Brazil (approx. coordinates in the WGS-84 datum: -1.798, -51.435 degrees), during August/October 2018. The objective was to measure the green mass of each tree in its entirety, and to measure woody tissue green-to-dry mass and volume ratios, and basic/green/dry woody tissue density.  A complete description of the four trees, these data, and the companion terrestrial lidar data (collected pre-harvest) can be found in our paper entitled: ‘New insights into large tropical tree mass and structure from direct harvest and terrestrial lidar’. Acquisition ----------- Field measurements: Neighbouring vegetation surrounding each tree was removed, including complete clearing of the felling area. Stem diameter was measured using a circumference/diameter tape at either 1.3m above-ground, or 0.5m above-buttress. Each tree was felled onto tarpaulin using a STIHL MS 650 chainsaw with a 20” bar length and 13/64” chain loop. Tree height (incl. stump) was measured with a surveyor's tape measure, and GPS data were acquired from the centre of the stump using a Garmin GPSMAP 64st. The stem (incl. stump) and crown were cut into manageable sections, and the mass of each section was measured via weighing using two Adam LHS 500 crane scales. Mass measurements commenced immediately post-felling, requiring two, four, four and two days to complete measurement of CAX-H_T1 to CAX-H_T4 respectively. Multiple discs (approx. 50mm thick) were also collected from each tree: at 1.3m and 25%, 50% and 75% the length of the stem, and up to 3x discs were taken from the mid-points of 1st, 2nd and 3rd order branches (totalling a minimum of 11 discs per tree). Foliage/fruit samples were retained to confirm taxonomic identity at the Museu Paraense Emílio Goeldi, Belem, Pará, Brazil. Laboratory measurements: All discs were reduced to a set of subsamples using a consistent approach: for any particular disc, they were cut as guided by parallel chords straddling above and below the major axis, each with approximate dimensions of 150mm x 50mm x 50mm (i.e., each set included periderm, phloem, cambium, xylem and pith tissues). Mass and volume measurements were made on each subsample in a green and dry state. Subsamples were considered in a green state after soaking for 48 hours, and a dry state once a constant mass had been attained whilst drying in an oven at 105 degree Celsius. Mass was measured using an Adam NBL4602i Nimbus Precision balance, and volume measurements were made on the same balance via Archimedes’ principle. Processing ---------- Dry mass was estimated from measured green mass and an estimate of whole-tree woody tissue green-to-dry mass ratio.  Whole-tree woody tissue green-to-dry mass ratio was estimated by weighting the mean value from subsamples in each pool (stem and crown), by the green mass in each pool. This mass-weighted approach was also used for estimating whole-tree woody tissue green-to-dry volume ratio and whole-tree basic/green/dry woody tissue density.  File and directory naming convention ------------------------------------ The four trees are identified: CAX-H_T1, CAX-H_T2, CAX-H_T3 and CAX-H_T4. The various files and directories are described as follows:  ./CAXH-H/ ├───overview/ │   ├───cal_cert/                    (Directory: contains balance calibration certificates) │   ├───images/                        (Directory: various photographs illustrating the field and laboratory measurements) │   ├───sentinel-2                    (Directory: contains RGB and NDVI images from Sentinel-2 data over the harvest site during the campaign dates) │   ├───CAX-H.results.xlsx                    (File: top-level results) ├───CAX-H_T1/                        (Directory: tree-level directories) ├───CAX-H_T2/ ├───CAX-H_T3/ ├───CAX-H_T4/ │   ├───fieldsheets/ │   │   ├───CAX-H_T4.fieldsheets.pdf                (File: fieldsheets from the original campaign) │   │   ├───CAX-H_T4.remeasurement.fieldsheets.pdf        (File: fieldsheets from the remeasurement campaign) │   ├───gps/ │   │   ├───CAX-H_T4.gps.txt │   ├───media/                        (Directory: contains various photographs and videos of the field measurements, and the discs and subsamples) │   ├───CAX-H_T4.results.xlsx                    (File: tree-level results)

opencc-zeroSep 2020View details →

Data from: A taxonomic revision of the whitefish radiation of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei: Coregonidae)

The alpha taxonomy of the endemic whitefish of lakes Brienz and Thun, Switzerland, is revised. We evaluate the status of seven known species: Coregonus steinmanni sp. nov., Coregonus profundus sp. nov. and Coregonus acrinasus sp. nov. are endemic to Lake Thun; Coregonus brienzii sp. nov. is endemic to Lake Brienz; and C. alpinus, C. albellus, and C. fatioi from lakes Brienz and Thun are redescribed. One of these species, C. alpinus, is revised, since the lectotype for this species is incongruent with the species description given by Kottelat (1997) and Kottelat and Freyhof (2007). The name C. alpinus is thus retained for the lectotype designated by Kottelat (1997) and a new description of this taxon provided. For the species otherwise described by Kottelat (1997) and Kottelat and Freyhof (2007) as C. alpinus the new name C. profundus is designated. Coregonus acrinasus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance, and we therefore compare it to all recognized species of Lake Constance, C. wartmanni, C. macrophthalmus, C. arenicolus, and C. gutturosus.

opencc-zeroJul 2020View details →

Data from: Changes in age-structure over four decades were a key determinant of population growth rate in a long-lived mammal

1. A changing environment directly influences birth and mortality rates, and thus population growth rates. However, population growth rates in the short-term are also influenced by population age-structure. Despite its importance, the contribution of age-structure to population growth rates has rarely been explored empirically in wildlife populations with long-term demographic data. 2. Here, we assessed how changes in age-structure influenced short-term population dynamics in a semi-captive population of Asian elephants (Elephas maximus). 3. We addressed this question using a demographic dataset of female Asian elephants from timber camps in Myanmar spanning 45 years (1970-2014). First, we explored temporal variation in age-structure. Then, using annual matrix population models, we used a retrospective approach to assess the contributions of age-structure and vital rates to short-term population growth rates with respect to the average environment. 4. Age-structure was highly variable over the study period, with large proportions of juveniles in the years 1970 and 1985, and made a substantial contribution to annual population growth rate deviations. High adult birth rates between 1970-1980 would have resulted in large positive population growth rates, but these were prevented by a low proportion of reproductive-aged females. 5. We highlight that an understanding of both age-specific vital rates and age-structure is needed to assess short-term population dynamics. Furthermore, this example from a human-managed system suggests that the importance of age-structure may be accentuated in populations experiencing human disturbance where age-structure is unstable, such as those in captivity or for endangered species. Ultimately, changes to the environment drive population dynamics by influencing birth and mortality rates, but understanding demographic structure is crucial for assessing population growth.

Genetic structures across a biogeographical barrier reflect dispersal potential of four Southeast Asian mangrove plant species

Aim Biogeographic barriers restrict the movement of individuals, resulting in population divergence, genetic differentiation, endemism and speciation. Yet, some barriers demonstrate unequal effect across species depending on species dispersal, which manifests in varying genetic structure. We test the hypotheses that the genetic structure of four coastal mangrove species would reflect differences in dispersal potential across the Malay Peninsula, a major biogeographic barrier in the Indo-West Pacific region. Location Twelve sites from the east and west coasts of the Malay Peninsula. Taxon Mangrove trees Avicennia alba, Sonneratia alba, Bruguiera gymnorhiza, and Rhizhophora mucronata. Methods For each species, we characterized genetic structure and gene flow using seven to 12 species-specific nuclear microsatellite markers. We tested for east-west genetic differentiation across the peninsula, a stepping-stone migration pattern, and assessed the proportion of recent dispersal and direction of historical migration along the Malacca Strait. Results Significant east-west genetic differentiation across the peninsula was observed in A. alba, S. alba and B. gymnorhiza, and the effect was most pronounced for the two species with lower dispersal potential (A. alba, S. alba). In contrast, the two species with higher dispersal potential (B. gymnorhiza and R. mucronata) exhibited much higher proportion of recent inter-population migration along the Malacca Strait. The signature of historical colonization from refugia in the Andaman Sea (north-to-south migration along the Malacca Strait) predominated for A. alba and S. alba. Historical south-north migration predominated for R. mucronata and B. gymnorhiza. Main conclusions This study is the first to implicate dispersal potential as a causal factor of varying mangrove species genetic structure across a biogeographic barrier. The Malay Peninsula functions as a filter to gene flow rather than a barrier. The genetic structure in mangrove species with a higher dispersal potential is more congruent with contemporary gene flow while that of species with a lower dispersal potential reflects historical processes.Our findings hint at the role of dispersal potential as a predictor of gene flow in mangroves.

Data from: Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups

Background: Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data. Results: We generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda. Conclusions: Our best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal.

Data from: Historical demography of four gecko species specializing in boulder cave habitat – its implications in the evolutionary dead end hypothesis and conservation

Specialization in narrow ecological niches might not only help species to survive in competitive or unique environments but also contribute to their extermination over evolutionary time. Although the "evolutionary dead end" hypothesis has long been debated, empirical evidence from species with detailed information on niche specialization and evolutionary history is still rare. Here we used a group of four closely related Cnemaspis gecko species that highly depend on granite boulder caves in the Mekong Delta to illuminate the potential impact of ecological specialization on their evolution and population dynamics. Isolated by the unsuitable habitat of a flood plain, these boulder-dwelling geckos are among the most narrowly distributed Squamata species in the world. We applied several coalescence-based approaches combined with the RAD-seq technique to estimate their divergence times, gene flow and demographic fluctuations during the speciation and population differentiation processes. Our results showed long-term population shrinkage in the four geckos and limited gene flow during their divergence. The results suggest that the erosion and fragmentation of the granite boulder hills have had great impacts on these populations' divergences and population declines. We argue that the specialist gecko's habitat specialization has facilitated the fine-scaled speciation in these granite rocky hills; in contrast, specialization might also have pushed these species toward the edge of extinction. Our study also emphasizes the conservation urgency of these vulnerable, cave-dependent geckos.

SNP datasets obtained with ddRADseq from four contact zones between Podarcis carbonelli and four other Podarcis species

We used double digestion restriction site associated DNA (ddRAD) sequencing to discover SNPs in samples from four contact zones between Podarcis carbonelli and four other Podarcis species. We obtained a panel of SNPs for each for each contact zone and reference populations and a dataset of diagnostic SNPs between reference populations for each contact zone but excluding private alleles from references, i.e. excluding alleles that are not present in the populations of contact. The final datasets (complete and diagnostic) were obtained after removing loci with depth coverage <8, missing data >20% and removing individuals with more than 35% of missing data. Across complete and diagnostic datasets, mean coverage by individuals ranged from 28 to 47 and by loci from 28 to 44. The analysis of replicate samples (about 6% of samples were replicated, i.e. were amplified and sequenced in independent libraries and SNP calling was performed independently) showed high levels (>99%) of multilocus genotype replicability.