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Fig. 30 in The Mammals Of Paracou, French Guiana: A Neotropical Lowland Rainforest Fauna Part 2. Nonvolant Species

Fig. 30. Dorsal, ventral, and lateral cranial views of FMNH 21720, neotype of Viverra touan Shaw

Fig. 39 in The Mammals Of Paracou, French Guiana: A Neotropical Lowland Rainforest Fauna Part 2. Nonvolant Species

Fig. 39. Left maxillary toothrows (A, B) and right mandibular toothrows (C, D) of Neacomys dubosti

Fig. 65 in The Mammals Of Paracou, French Guiana: A Neotropical Lowland Rainforest Fauna Part 2. Nonvolant Species

Fig. 65. Dorsal and ventral views of the skin of NMW 42010, lectotype of Coendou melanurus

Fig. 69 in The Mammals Of Paracou, French Guiana: A Neotropical Lowland Rainforest Fauna Part 2. Nonvolant Species

Fig. 69. Left lateral cranial views of Coendou melanurus (top, AMNH 94174) and C. insidiosus

Fig. 64 in The Mammals Of Paracou, French Guiana: A Neotropical Lowland Rainforest Fauna Part 2. Nonvolant Species

Fig. 64. Dorsal, ventral, and lateral cranial views of NMW 42010, lectotype of Coendou melanurus

opencc-zeroJan 2023View details →

Data from: Biogeography of curimatid fishes reveals multiple lowland-upland river transitions and differential diversification in the Neotropics (Teleostei, Curimatidae)

The Neotropics harbors a megadiverse ichthyofauna comprising over 6300 species with approximately 80% in just three taxonomic orders within the clade Characiphysi. This highly diverse group has evolved in tropical South America over tens to hundreds of millions of years influenced mostly by re‐arrangements of river drainages in lowland and upland systems. In this study, we investigate patterns of spatial diversification in Neotropical freshwater fishes in the family Curimatidae, a species‐rich clade of the order Characiformes. Specifically, we examined ancestral areas, dispersal events, and shifts in species richness using spatially explicit biogeographic and macroevolutionary models to determine whether lowlands–uplands serve as museums or cradles of diversification for curimatids. We used fossil information to estimate divergence times in BEAST, multiple time‐stratified models of geographic range evolution in BioGeoBEARS, and alternative models of geographic state‐dependent speciation and extinction in GeoHiSSE. Our results suggest that the most recent common ancestor of curimatids originated in the Late Cretaceous likely in lowland paleodrainages of northwestern South America. Dispersals from lowland to upland river basins of the Brazilian and Guiana shields occurred repeatedly across independently evolving lineages in the Cenozoic. Colonization of upland drainages was often coupled with increased rates of net diversification in species‐rich genera such as Cyphocharax and Steindachnerina. Our findings demonstrate that colonization of novel aquatic environments at higher elevations is associated with an increased rate of diversification, although this pattern is clade‐dependent and driven mostly by allopatric speciation. Curimatids reinforce an emerging perspective that Amazonian lowlands act as a museum by accumulating species along time, whereas the transitions to uplands stimulate higher net diversification rates and lineage diversification.

opencc-by-4.0Dec 2022View details →

Map 1 in Impatiens banen and Impatiens etugei (Balsaminaceae), new threatened species from lowland of the Cross-Sanaga Interval, Cameroon

Map 1. Global distributions of Impatiens banen and I. etugei. BY XANDER VAN DER BURGT.

opencc-zeroFeb 2023View details →

Data from: Acoustic indices estimate breeding bird species richness with daily and seasonally variable effectiveness in lowland temperate Białowieża forest

Biodiversity monitoring is important to follow temporal changes of the environment. We examined whether acoustic indices can be used as a rapid and easy-to-apply tool for bird biodiversity estimation in one of the least changed European lowland forests – the Białowieża Forest. We collected soundscape recordings in early and late spring at 84 randomly chosen recording points. At each recording point, we analysed 72 1-min sound samples to evaluate how well acoustic indices predict bird species richness from the perspective of a single sound sample, single survey, and recording point, and how they follow the daily pattern of singing activity. For each 1-min sound sample, we prepared a list of vocalizing bird species and calculated three acoustic indices: Bioacoustic Index (BI), Acoustic Complexity Index (ACI), and Acoustic Diversity Index (ADI). We found that from the perspective of a single 1-min sound sample, BI best predicts the bird species richness, independently of time in the season but variably across the day, while ACI and ADI showed weaker and seasonally and daily variable dependency. The correlation between each index and the number of bird species was stronger in the early survey than in the late survey. All acoustic indices followed daily bird activity patterns, yet they provided greater values before the peak of the species richness estimated by manual spectrogram scanning and listening to recordings. We showed that acoustic indices correlate moderately to strongly with the bird species richness obtained by manual spectrogram scanning and listening to recordings by humans. Therefore, acoustic indices can be used as a tool for rapid estimation of bird biodiversity in temperate forests. However, daily and seasonal variation in effectiveness of acoustic indices should be taken into account in the analysis.

opencc-zeroMar 2023View details →

Alamo x Kanlow genotypic and phenotypic data for biomass yield and yield-related traits in lowland switchgrass (Panicum virgatum L.) crosses

Switchgrass (Panicum virgatum L.) is a model herbaceous bioenergy crop in the USA. It is a native, perennial, warm-season grass, and has broad adaptability. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Significant genetic variation for biomass yield observed in lowland switchgrass hybrids. Due to the quantitative inheritance of biomass yield, varietal improvement for the trait through conventional breeding is slow. Therefore, quantitative trait loci (QTL) mapping is used to discover marker-trait associations and accelerate the breeding process through marker-assisted selection. To identify significant QTL, this study mapped seven biparental crosses and one combined cross of two biparental crosses (30 to 96 F1s) between lowland Alamo and Kanlow genotypes. The crosses were evaluated for biomass yield, plant height, and clonal mass scores in a simulated-sward plot with two replications at two locations in Tennessee from 2019 to 2021. The crosses were genotyped using 17,251 single nucleotide polymorphisms generated through genotyping-by-sequencing. QTL mapping was performed using a single-QTL model in R-QTL. The study identified major QTL for biomass yield, plant height, and clonal mass scores resided on chromosomes 7K, 4K, and 3K and had 0.47, 0.63, and 0.62 heritability, respectively. The dataset contains five files describing the phenotype and genotype of each individual used in the quantitative trait loci (QTL) analysis. <ul> <li>'File 1' contains biomass yield, plant height, and clonal mass data for each genotype and parents evaluated at two locations in Tennessee; the Plateau Research and Education Center (PREC), Crossville and East Tennessee Research and Education Center (ETREC), Knoxville from 2019 to 2021. Plant height and biomass yield were measured at maturity, and clonal mass scores were evaluated after harvesting biomass.</li> <li>'File 2' has the genotype name, library, index, total reads, bases, and the Phred quality score (Q30). Young leaf tissue was collected from each F1 progeny and parent, and DNA was extracted using the cetyltrimethylammonium bromide (CTAB) procedure. The extracted DNA was genotyped at the USDA-ARS Western Regional Research Center laboratory in Albany, CA. Genotyping by sequencing (GBS) was performed on 951 lines (F1s and their parents) using the PstI-MspI GBS protocol. The quality of these sequences showed that 94.4% of the bases were at or above Q30. Reads were mapped to version 5.0 of the switchgrass reference genome. Single nucleotide polymorphism (SNP) calling was performed, and redundant markers were filtered out for linkage map construction. 'File 3' has SNP ID numbers, SNP locations on chromosomes, map positions, and SNP scores. The cross was used as a four-way cross for QTL analysis, where the male parent Kanlow (K) was assigned as '1', and the female parent Alamo (A) was assigned as '2'.</li> <li>The phased output data from the four-way cross, i.e., 11, 12, 21, and 22, were represented by AC, BC, AD, and BD, respectively ('File 3').</li> <li>The progeny file ('File 4') contains the name of the parents used for making crosses and their progenies.</li> <li>A consensus linkage map ('File 5') was produced with Lep-Map3 software. The linkage map contains 18 linkage groups associated with 18 switchgrass chromosomes, marker size (bp), map position (cM) based on male and female maps, and map order.</li> </ul>

opencc-by-4.0Apr 2023View details →

Data for "Trait-based response of deadwood and tree-related microhabitats to decline in temperate lowland and montane forests"

Sampling design and case studies The study was conducted in two French regions, the Loire valley and the French Pyrenees, and one German region, the Bavarian mountains. In the Loire valley, we studied two lowland sites in oak-dominated (both Quercus petraea (Matt.) Liebl. and Quercus robur L.) forests, one in the Orleans State Forest (107-174 m a.s.l.) and one in the Vierzon State Forest (120-190 m a.s.l.). The main secondary species in these forests were hornbeam (Carpinus betulus L.) and Scots pine (Pinus sylvestris L.). In 2020, we selected nine plots to represent a decline gradient in each of these forests. While the Orleans Forest was healthy overall, the Vierzon Forest had undergone several decline events due to successive droughts aggravated by edaphic factors. In the Pyrenees, we studied two sites in montane forests dominated by silver fir (Abies alba Mill.), whose decline is mainly the result of successive droughts occurring since the 1980’s, and with Norway spruce (Picea abies (L.) H. Karst) and European beech (Fagus sylvatica L.) as secondary species. In 2017, we selected 43 plots: (i) 21 plots in the Aure Valley (854-1570 m a.s.l.) and (ii) 22 plots on the Sault Plateau (705-1557 m a.s.l.). The severe summer drought of 2003 had significant effects on tree mortality in oak and fir forests (Cours and others, 2022). Finally, we studied 19 plots of montane forest in the Bavarian Forest National Park, dominated by Norway spruce (Picea abies (L.) H. Karst) with European beech and silver fir as the main secondary species (Bässler and others, 2009). The dieback results from several cycles of windstorms followed by bark beetle (Ips typographus (L.)) outbreaks (Müller and others, 2010), the dominant drivers of forest dynamics in Norway spruce forests in temperate Europe (Zemlerová and others, 2023). This dieback phenomenon was more severe than either of the aforementioned drought-induced declines, and resulted in greater tree mortality (Cours and others, 2021). In the fir and oak forests in France, our plots were set up in managed forests, and the surrounding forest was also predominantly managed. On the other hand, in the German spruce forest, our plots were set up both within the core area of the Bavarian Forest National Park, and in the surrounding zone (BIOKLIM project), with little or no human intervention (Müller and others, 2010). Field measurements Plots were set up with a Bitterlich relascope with an opening angle corresponding to counting factor n° 1 (ratio 1/50), and mean plot area was about 0.3 ha. For each tree within the plot, we recorded its status (i.e. dead, living, snag, log), tree-species and diameter at breast height (DBH; minimum DBH recorded = 17.5 cm for living trees and logs, 7.5 cm for snags, 67.5 cm for very large trees). We took the proportion of dead trees in basal area (i.e. the ratio of the cumulative basal area of standing and lying dead trees to the basal area of all the trees in the plot), hereinafter referred to as “mortality rate”, as a proxy for the level of local stand decline. Note that this “mortality rate” does not reflect true overall mortality rate in managed oak forests, as foresters removed most valuable declining trees. We visually inventoried TreMs on living trees, logs and snags, and included the 47 types described by Larrieu et al. (2018). For each deadwood item (length > 1 m) in the plot, we measured its decay stage (from 1 = hard dead wood fully covered with bark to 4 = soft wood without bark), length, diameter at mid-length for logs and snags < 4 m long, and DBH for dead trees and snags > 4 m. Deadwood was classified in the following categories: ground-lying (logs and uprooted dead trees) vs standing (snags and standing dead trees); small and mid-size (less than 40 cm in diameter) vs large and very large (more than 40 cm in diameter); and fresh (decay class 1 and 2) vs decayed (decay stage 3 and 4). We calculated the total number of items per hectare by allocating a coefficient Nd related to diameter (d) to each item observed in the relascope sampling: (Nd = π 108 [ArcTan(1/50)/(π d)]2). We estimated TreM diversity and the number of deadwood types per plot. We compiled a list of eco-morphological traits for woody elements (i.e., life status (living, dead) and vertical position (downed, standing), decay stage and diameter) and for TreMs detected in the field (TreM nature, association with deadwood (saproxylic, epixylic, mould), type of bearing substrate (i.e., living tree, dead tree or snag, and log), position in the tree (i.e. base, trunk, crown), degree of wetness, life span or ontogenesis).

opencc-zeroJun 2023View details →

Functional-trait based restoration alters nutrient cycling and invasion rates in Hawaiian lowland wet forest

Many degraded ecosystems have altered nutrient dynamics, due to invaders possessing a suite of traits that allow them to both outcompete native species and alter the environment. In ecosystems where invasive species have increased nutrient turnover rates, it can be difficult to reduce nutrient availability. This study examined whether a functional-trait-based restoration approach, involving the planting of species with conservative nutrient-use traits, can slow rates of nutrient cycling and consequently reduce rates of invasion. We examined a functional trait restoration initiative in a heavily-invaded lowland wet forest site in Hilo, Hawai'i. Native and introduced species were chosen to create four experimental hybrid forest communities, in comparison to the invaded forest, with a factorial design in which communities varied in rates of carbon turnover (slow or moderate [SLOW, MOD]), and in the relationship of species in trait space (redundant or complementary [RED, COMP]). After the first five years, we evaluated community-level outcomes related to nutrient cycling: carbon (C), nitrogen (N), and phosphorus (P) via litterfall, litter decomposition, and also outplant productivity and rates of invasion. We found that: (1) regardless of treatment, the experimental communities had low rates of nutrient cycling through litterfall relative to the invaded reference forest, (2) the MOD communities had greater nutrient release via litterfall than the SLOW communities, (3) introduced species had greater nutrient release than native species in the two MOD experimental communities, and (4) within treatments, there was a positive relationship between nutrient levels and outplant basal area, but outplant basal area was negatively associated with rates of invasion. The negative relationships among basal area and weed invasion, particularly for the two COMP treatments, suggest species existing in different parts of trait space may help confer some degree of invasion resistance. The diversification of trait space was facilitated by the use of introduced species; a new concept in Hawaiian forest management. Although challenges remain in endeavors to restore this heavily degraded ecosystem, this study provides evidence that functional trait-based restoration approaches using carefully crafted hybrid communities can reduce rates of nutrient cycling and invasion in order to reach management goals.

opencc-zeroJun 2023View details →

Data from: Resolving a heated debate: the utility of prescribed burning as a management tool for biodiversity on lowland heath

We investigated the impact of prescribed burning and vegetation cutting on a chronisequence of heathland sites (107 in total) in the New Forest National Park, Hampshire, UK. We present data for vegetation cover, canopy active invertebrates collected with sweep nets and ground active invertebrates collected using pitfall traps. Using a multi-trophic approach, we compared the ecological impact of prescribed burning with two types of vegetation cutting (swiping and baling) as management tools for biodiversity outcomes for up to 20 years after management. Indicators included: Common Standards Monitoring assessment (CSM); vegetation species assemblage; invertebrate biodiversity; and available food resources for two characteristic heathland birds – the Dartford Warbler Sylvia undata and the Nightjar Caprimulgus europaeus. When compared with swiped sites, areas managed by prescribed burning resulted in: better habitat condition (assessed by CSM); higher cover of heathers; lower bracken cover; more areas of bare ground. We found no evidence that burning is detrimental for the investigated components of biodiversity. Cutting by swiping did not replicate the benefits of burning. Swiping supported grassland conditions that suit non-heathland species. Baling resulted in habitat conditions similar to prescribed burning but restricted replication of baled sites limited our conclusions. However, swiped sites supported high invertebrate abundance and diversity, including food resources for Dartford Warbler and Nightjar.

opencc-zeroAug 2023View details →

Long-term ecological responses of a lowland dipterocarp forest to climate changes and nutrient availability at Bulusan Lake

This data publication encompasses the datasets generated in a study focusing on reconstructing ecological responses to climatic and nutrient availability changes during the late Holocene in northern Philippines. The data comes from samples taken from sediment cores retrieved from Bulusan Lake, located on Luzon Island, Philippines, in March 2013. In these samples, we analyzed fossil pollen and spores (a proxy for plant taxa abundance), charcoal (a proxy for fire activity), stable carbon isotopic composition of terrestrial-lipid biomarkers (a proxy for vegetation cover), stable nitrogen and phosphate isotope composition of bulk sediments, and elemental composition of sediment cores at a high resolution (proxies for nutrient availability and volcanic activity). The dataset also includes links to records generated in a previous study on the same sediments (Prohaska et al. 2023), where we measured the stable hydrogen isotopic composition of terrestrial-lipid biomarkers to reconstruct past hydrological conditions, as well as the magnetic susceptibility record and AMS dates of plant macrofossils to calculate sediment accumulation ages. The data generation spanned the period from April 2013 to September 2020, and the data files are provided in Excel spreadsheet format.

opencc-zeroAug 2023View details →

Composition of non-volant small mammals inhabiting a degradation gradient in a lowland tropical forest in Uganda

A study aimed at assessing the structure of rodent and shrew assemblages inhabiting a degradation gradient while considering rainfall patterns was conducted in one of the few remaining lowland tropical forests in Eastern Africa. We collected a unique dataset of 1411 rodents and shrews, representing 24 species (19 rodents, 5 shrews). The most abundant species alternated in dominance as species abundance significantly fluctuated across the study period following a degradation gradient, While only generalist species were observed near the degraded forest edge, habitat specialists such as Deomys ferrugineus, Malacomys longipes and Scutisorex congicus, were observed in the primary forest interior suggesting a significant association between species and their associated habitats and habitat attributes. There was also an observed correlation between rainfall patterns and species abundance. Capturing more species in adjacent fallows and along the degraded forest edge suggests that many species are able to live in degraded habitats that offer a variety of food resources. The continued pressure on forest resources, however, may lead to changes in habitat structure. This, coupled with the dependence of forest ecological functions on rainfall, which is typically not the case, may ultimately cause the local extinction of highly specialized but less adaptable species.