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opencc-zeroDec 2022View details →

Seed traits matter—Endozoochoric dispersal through a pervasive mobile linker

Although many plants are dispersed by wind and seeds can travel long distances across unsuitable matrix areas, a large proportion relies on co-evolved zoochorous seed dispersal to connect populations in isolated habitat islands. Particularly in agricultural landscapes, where remaining habitat patches are often very small and highly isolated, mobile linkers as zoochorous seed dispersers are critical for the population dynamics of numerous plant species. However, knowledge about the quali- or quantification of such mobile link processes, especially in agricultural landscapes, is still limited. In a controlled feeding experiment, we recorded the seed intake and germination success after complete digestion by the European brown hare (Lepus europaeus) and explored its mobile link potential as an endozoochoric seed disperser. Utilizing a suite of common, rare, and potentially invasive plant species, we disentangled the effects of seed morphological traits on germination success while controlling for phylogenetic relatedness. Further, we measured the landscape connectivity via hares in two contrasting agricultural landscapes (simple: few natural and semi-natural structures, large fields; complex: high amount of natural and semi-natural structures, small fields) using GPS-based movement data. With 34,710 seeds of 44 plant species fed, one of 200 seeds (0.51%) with seedlings of 33 species germinated from feces. Germination after complete digestion was positively related to denser seeds with comparatively small surface area and a relatively slender and elongated shape, suggesting that, for hares, the most critical seed characteristics for successful endozoochorous seed dispersal minimize exposure of the seed to the stomach and the associated digestive system. Furthermore, we could show that a hare's retention time is long enough to interconnect different habitats, especially grasslands and fields. Thus, besides other seed dispersal mechanisms, this most likely allows hares to act as effective mobile linkers contributing to ecosystem stability in times of agricultural intensification, not only in complex but also in simple landscapes.

opencc-zeroJan 2022View details →

Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences

The data presented here are those used in the paper : CAYUELA H., JACOB S., SCHTICKZELLE N., VERDONCK R., PHILIPPE H., LAPORTE M., HUET M., BERNATCHEZ L., LEGRAND D. Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences. Oikos. DOI: 10.1111/oik.08846 Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species' response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, the genetic control of TGP, its long-term stability, and its potential costs remain largely unknown, mostly because empirical demonstrations of TGP across many generations in several genetic backgrounds are scarce. In the paper of Cayuela et al., we examined how genotype determines the TGP of phenotypic traits related to dispersal, a fundamental process in ecology and evolution. We used an experimental approach in Tetrahymena thermophila, a ciliate model-species, to determine if and how phenotypic changes expressed following a dispersal treatment are inherited over multiple generations. The data include morphological and movement traits, dispersal rates, and cell growth data measured before and after dispersal trials. We considered different genotypes and different populations within each genotype.

opencc-zeroJan 2022View details →

A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long-distance dispersal

Aim: Digitization of herbarium specimens and DNA sequencing efforts in the past decade have enabled integrative analyses of patterns of diversity and endemism in a phylogenetic context. Here, we compare the best available floristic databases to a comprehensive specimen database to examine spatial patterns of moss phylogenetic assembly. We test the hypotheses that 1) mosses exhibit phylogenetic regionalization, 2) islands contain significantly high phylogenetic diversity, and 3) that moss phylogenetic endemism is low on a global scale. Location: Global Taxon: Mosses Methods: We developed a phylogeny of 3,654 moss species using 25 markers and compiled a global specimen database from online repositories. We calculated floristic and phylogenetic measures of diversity and endemism and performed randomizations to test for significant deviations from expectations. We use rarefaction and extrapolation to alleviate substantial differences in sampling effort across the globe. We used both phylogenetic and floristic methods to test for spatial regionalization. We compare our specimen-based results to those obtained using a floristic dataset. Results: Phylogenetic diversity is more robust to missing data than species richness. Mean phylogenetic distance was significantly higher than expected in areas with high species richness, indicating that reported richness in these areas is likely a product of repeated colonization. Phylogenetic endemism is low globally. Phylogenetic regionalizations cluster into a Holarctic/Holantarctic temperate region, a pantropical region, and a region composed of Australia, New Zealand, and South Africa. Main Conclusions: Future efforts for collecting, sequencing, and databasing moss species should focus on the tropics, particularly Africa and Southeast Asia. We provide further evidence to support several important theories developed in moss biogeography, including the role of long-distance dispersal in shaping floristic patterns, the dominance of anagenesis in driving patterns of island diversity, and the role of climatic instability in driving patterns of assembly in the Holarctic.

opencc-zeroJan 2022View details →

Ecology of fear and its effect on seed dispersal by a neotropical rodent by Dumas Gálvez and Marisol Hernández

Predators exert negative effects on prey, besides the act of killing, generating behavioral and physiological costs, a concept known as the ecology of fear. Studies in scatterhoarding rodents in temperate zones suggests that prey use habitat structure to perceive predation risk. Less is known about how tropical forest rodents perceive predation risk. Here, we investigated whether the Central American agouti perceive predation risk by ocelots through olfactory cues and whether it influences the foraging behavior for Attalea butyracea seeds, one of its main food sources. By monitoring tagged seeds, we found that seed dispersal and pilferage was lower in sites with high density of ocelots, in line with the predictions of ecology of fear proposing that scared animals eat less. We also found that pilferage rates in high ocelot density sites seem to be lower during the rainy - transition period but not during dry season when food availability is generally low. However, we did not find evidence that agoutis adjust their cache spacing behavior in response to ocelot density. In an additional experiment to corroborate that agoutis' responses were caused by ocelots' cues, we found lower dispersal rates for seeds placed next to samples of urine and feces of ocelots as compared to controls, during the first seven days. Moreover, agoutis spent less time handling the seeds with ocelots' cues. Here, we discuss potential cascading effects linked to the behavior of agoutis towards predation risk.

Oak galls exhibit ant-dispersal convergent with myrmecochorous seeds

Ants disperse oak galls of some cynipid wasp species similarly to how they disperse seeds with elaiosomes. We conducted choice assays in field and lab settings, with ant-dispersed seeds and wasp-induced galls found in ant nests and found that seed-dispersing ants retrieve these galls as they do myrmecochorous seeds. We also conducted manipulative experiments in which we removed the putative ant-attracting appendages ("kapéllos") from galls and found ants are specifically attracted to kapéllos. Finally, we compared chemical composition and the histology of ant-attracting appendages on seeds and galls, and they both had similar fatty-acid compositions as well as morphology. We also observed seed-dispersing ants retrieve oak galls to their nests, and rodents and birds consuming oak galls that were not retrieved by ants. These results suggest convergence in ant-mediated dispersal between myrmecochorous seeds and oak galls. Based on our observations, a protective advantage for galls retrieved to ant nests seems a more likely benefit than dispersal distance, as also has been suggested for myrmecochorous seeds. These results require reconsideration of established ant-plant research assumptions as ant-mediated seed and gall dispersal appear strongly convergent and galls may be far more abundant in eastern North American deciduous forests than myrmecochorous seeds.

Chimpanzees as ecosystem service providers: Seed dispersal of an economically important plant resource

Vertebrate-mediated seed dispersal is vital to the maintenance of diversity in tropical ecosystems, and seed-dispersing animals are increasingly thought to provide ecosystem services by dispersing the seeds of plant species utilized by people. However, few studies have demonstrated a link between vertebrate frugivores and plants used by people, thus limiting the generalizability of the seed-disperser-as-ecosystem-service-provider concept. We examined the effectiveness of western chimpanzees (Pan troglodytes verus) as seed dispersers (i.e., their influence on seedling recruitment) of an economically important fruit resource, Saba senegalensis, at the site of Fongoli, a savanna-woodland environment in southeastern Senegal. The fruit from the Saba vine is commonly harvested from the wild by local people and is also an important food item for chimpanzees. We conducted germination experiments on gut-passed seeds alongside non-gut-passed seeds and analyzed the germination success of chimpanzee-dispersed seeds in situ. We also analyzed the effect of habitat type and canopy cover at each seed dispersal site to determine which sites are most suitable for Saba germination. Germination trials showed that chimpanzee gut passage and manual pulp removal increased the likelihood of germination over seeds left intact. Nearly a quarter of chimpanzee-dispersed seeds germinated in situ and Saba seeds were distributed non-randomly throughout Fongoli, with more dispersed seeds found in habitats most suitable for Saba germination. These results suggest that chimpanzees aid in the early stages of Saba recruitment and thus provide an ecosystem service via seed dispersal that may contribute to the well-being of local people.

Data from: Dispersion of SARS-CoV-2 in air surrounding COVID-19 infected individuals with mild symptoms

Since the beginning of the pandemic, the transmission modes of SARS-CoV-2—particularly the role of aerosol transmission—has been much debated. Accumulating evidence suggests that SARS-CoV-2 can be transmitted by aerosols, and not only via larger respiratory droplets. In this study, we quantified SARS-CoV-2 in air surrounding 14 test subjects in a controlled setting. All subjects had SARS-CoV-2 infection confirmed by a recent positive PCR test and had mild symptoms when included in the study. RT-PCR and cell culture analyses were performed on air samples collected at distances of one, two, and four meters from test subjects. Oronasopharyngeal samples were taken from consenting test subjects and analyzed by RT-PCR. Additionally, total aerosol particles were quantified during air sampling trials. Air viral concentrations at one-meter distance were significantly correlated with both viral loads in the upper airways, mild coughing, and fever. One sample collected at four-meter distance was RT-PCR positive. No samples were successfully cultured. The results reported here have potential application for SARS-CoV-2 detection and monitoring schemes, and for increasing our understanding of SARS-CoV-2 transmission dynamics.

opencc-by-4.0Feb 2022View details →

Raw data for: Coherent supercontinuum generation in all-normal dispersion Si3N4 waveguides

This document includes the raw data and Matlab/Python scripts to post-process data and plot the figures included in the paper  "Coherent supercontinuum generation in all-normal dispersion Si3N4 waveguides".

The 'Evil Tribe' spreads across the land: A dated molecular phylogeny provides insight into dispersal, expansion, and biogeographic relationships within one of the largest tribes of the sunflower family (Vernonieae: Compositae)

Premise: With over 1500 species, the globally distributed Vernonieae is one of the most successful members of the Compositae. However, due to its morphological complexity and limited geographic representation in previous studies, subtribal and biogeographic relationships are unclear. Here new DNA sequence data spanning the geographical range of the tribe provides a taxonomically robust time-calibrated phylogeny, an estimation of migration pathways and timing of important biogeographical events and allows inference of environmental factors that have contributed to the success of the Vernonieae worldwide. Methods: Phylogenetic relationships were estimated for 368 taxa representing all Vernonieae subtribes. Molecular clock and ancestral range estimation analyses provide a framework for inference of the tribe's biogeographic history. Results: Relationships among the subtribes were established. We confirmed that the Moquinieae are nested in Vernonieae, determined the correct placement of several problematic taxa, and conducted the first model-based assessment of the biogeographical history of the tribe. The . Vernonieae were estimated to have evolved ~50 Ma ago. Africa was the first center of diversity, from which a single dispersal event established the monophyletic New World lineage. Long-distance dispersal from Africa and Brazil established the tribe on five continents and Oceania. Conclusions: Moquinieae are nested in Vernonieae. The New World lineage is monophyletic, but Old World taxa are not. New subtribal taxonomies are needed. Long-distance dispersal from Africa beginning 45 Ma was key to establishing the tribe's near-global distribution. Migration corridors created by volcanic mountain chains and iron-rich soils in Africa and the Americas promoted radiation and range expansion.

Data from: Joint effects of environmental filtering and dispersal limitation on species assemblage of the Tibetan Plateau

Aim Mountains harbour a rich and non-random cluster of species, yet knowledge on the species' biological attributes that support species coexistence in the montane community is limited. Here, we investigated the association of species occurrence on the Tibetan Plateau with species' morphological, ecological or evolutionary constraints. Location Tibetan Plateau (TP) Taxon Mammals and birds Methods We tested whether species occurrence on the TP correlates with morphological, ecological, or evolutionary constraints using the spatial distribution, phylogeny, dispersal ability, and thermal niche property data for 1,353 terrestrial vertebrates (383 mammals and 970 birds). We used standard (non-phylogenetic) and phylogenetic logistic regressions to disentangle the relative contributions of these attributes of species in explaining the species occurrence on the TP. We assessed the geographical patterns of community structures on the TP and fit linear mixed models to explore the underlying eco-evolutionary forces. Results The TP species exhibited a higher cold tolerance, wider thermal niche breadth, and higher rate of niche evolution than the non-TP species. We supported the assumption that the TP species was not a random subset from the species pool, but was structured jointly by environmental filtering and dispersal limitation. While dispersal and ecological processes underlying species assemblages varied spatially and among taxa, we found that species in stressful environments was limited by environmental filtering, whereas dispersal limitation was more pronounced under favourable climatic conditions. Main conclusions Our study finds that environmental filtering and dispersal limitation jointly shape the species assemblage on the TP. These findings provide significant insights into community assembly processes on the TP and other montane ecosystems on Earth, especially those that are sensitive to global warming.

opencc-zeroMar 2022View details →

Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species

Gene flow shapes spatial genetic structure as well as the potential for local adaptation of populations. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats will influence the distribution of biological populations and their pattern of gene flow. We used whole genome sequencing to study demographic history and reduced representation (ddRAD) sequencing data to analyze spatial genetic structure in the broadnosed pipefish (Syngnathus typhle). Its main habitat are seagrass meadows, which along the study coast (SW Norway) have a patchy distribution. Combining the results from several analyses including scans for selection, suggests that stochastic genetic drift has shaped the observed population structure largely due to its patchy habitat distribution. The restricted gene flow is further driven by life history traits such as the presence of parental care combined with no pelagic life stages, resulting in a clear isolation-by-distance pattern spanning 100s of kilometers. The spatial scale of demographic connectivity was inferred from long-term (~30 year) census population counts that uncovered a sharp decline in spatial correlations in abundance with distance (37% decorrelation over 2 km). These findings were contrasted with data from two other fish species sampled along the same coastline, both having pelagic larval stages lasting ~20 days (corkwing wrasse, Symphodus melops, and black goby, Gobus niger) where the population structure is not that evident. For these species, we found a wider spatial scale of demographic connectivity (decorrelation distances of 14 and 28 km, respectively), and weaker isolation-by-distance except at one point along the coast where both species revealed a strong barrier to gene flow, seemingly due to a lack of suitable habitat. Combined, these findings suggest that habitat fragmentation and absence of a pelagic larval stage in pipefish strongly increases geographic structuring, while the pelagic larvae of wrasse and goby increase genetic and demographic connectivity, except over extensive habitat shifts.

opennotspecifiedJan 2022View details →

Figure 4 in A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines

Figure 4. Ancestral biogeographical ranges of Rhinocerotinae, as calculated using BioGeoBEARS package in R (Matzke, 2013; Massana et al., 2015) and mapped on the phylogeny retrieved in Figure 3. Spatial ranges of all terminal taxa included in the phylogenetic and biogeographical analyses were split into eight domains, likely to coalesce: Americas (R), Afro-Arabia (A), Europe + Mediterranean (E), Central Asia (C), South and South-East Asia (M), Indonesia (S), Taiwan (T), Philippines (P).

opennotspecifiedJan 2022View details →

Figure 3 in A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines

Figure 3. Dental and postcranial features characterizing the new genus Nesorhinus in the phylogenetic framework as depicted in Figure 2. Red circles denote synapomorphies of Nesorhinus, whilst green and blue circles correspond to diagnostic characters (autapomorphies) of N. philippinensis and of N. hayasakai, respectively. Nesorhinus philippinensis: A, left upper dental series (D1–M1) in occlusal view (II-2014-J1-294, 095, 409, 427); B, left m2–3 in occlusal view (II-2014-J1-405); C, right p3–m1 in labial view (II-2014-J1-451); D, left scapula in lateral view (II-2014-J1-291). Nesorhinus hayasakai: E, left upper dental series (D1–M3) in occlusal view (DGNTU-FV11b; modified from Hayasaka, 1942); F, right m3 in occlusolabial view (HTR-55); G, left m3 in labial view (HTR-91); H, left fragmentary scapula (HTR-1). Completeness of the skeleton of N. philippinensis found at Kalinga (I): preserved elements appear in dark green. Tentative silhouettes of N philippinensis (J) and N. hayasakai (K) are drawn at a same scale, with a shoulder height of 1.26 m for N. philippinensis. See Supporting Information for further details on body size. Scale bar, 5 cm (A–C, E–G) and 10 cm (D, H).

opennotspecifiedJan 2022View details →

Figure 2 in A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines

Figure 2. Phylogenetic tree of the Rhinocerotidae, built from 278 unweighted craniomandibular, dental and postcranial characters scored in 30 ceratomorph species, and replaced in their stratigraphical context. Tapirus terrestris (Linnaeus, 1758), Hyrachyus eximius Leidy, 1871, Trigonias osborni and Ronzotherium filholi were used as outgroups. Most-parsimonious tree (length: 1315 steps; CI = 0.2821; RI = 0.4858). Node ages were obtained using the approach of Brusatte et al. (2008), as implemented in the paleotree package (Bapst, 2012) in R 4.0.3 (R Core Team, 2020), with the first splitting event set to 60 Mya. Red star and green diamond indicate the earliest occurrences of Dicerorhinus sensu stricto (13 Mya; Heissig, 1972; Antoine et al., 2013) and Teleoceratina (25 Mya; see Supporting Information, Table S2). Aceini, Aceratheriini; DRc, Dicerorhinus–Rhinoceros clade; Dti, Diceroti; Elinae, Elasmotheriinae; Rti, Rhinoceroti; Telina, Teleoceratina. Recent species names are underlined.

opencc-zeroMar 2022View details →

Data from: Factors influencing dispersal initiation and timing in a facultative cooperative breeder

Natal dispersal is a high-risk endeavor where decisions on whether and when to disperse have long-term consequences. Among facultative cooperative breeders, juveniles often forego dispersal and remain philopatric for one or more breeding seasons. This decision is key to the formation of cooperative breeding groups and could have significant effects on reproductive success. We investigated the probability and initiation of dispersal in the cooperatively breeding Brown-headed Nuthatch (Sitta pusilla) to determine the influence that social environments had on dispersal. This study was concurrent with another study where manipulation of population sex ratios increased the prevalence and size of cooperative groups. The concurrent manipulations enabled us to evaluate social effects on dispersal as a plausible mechanism driving the relationship between adult sex ratios and cooperation. We evaluated which factors best predicted whether males dispersed, and the timing of dispersal for both sexes. We considered variables related to the immediate nesting environment as well as characteristics of the local population. Social environments were related to dispersal for both males and females. Juvenile males dispersed earlier when a helper was present in the natal group. Females dispersed earlier in settings with more adult neighbors and when a lower proportion of those neighbors were males. Females with shorter tarsi relative to their siblings dispersed earlier, suggesting that size-based competitive interactions may also affect dispersal decisions. Our results suggest juveniles disperse more readily when they fledge in constrained social environments, and that competition with conspecifics is a major driver of dispersal in the Brown-headed Nuthatch.

opencc-zeroApr 2022View details →

Wind dispersal and 1-year survival of Vataireopsis iglesiasii (Fabaceae) seedlings in a Neotropical lowland rain forest

Populations of many tropical tree species are regulated by negative distance- and density-dependent processes (NDD), yet most studies on the effects of conspecific seedling and adult neighbours on seedling survival have focused on animal-dispersed species. Species with seeds dispersed by wind may not be moved as far on average as seeds dispersed by animals, but some seeds may be dispersed a lot further, suggesting that knowledge of dispersal mechanism may help in our understanding of NDD. In this study, we took advantage of a high-fecundity reproductive event that occurred for an individual isolated canopy tree of Vataireopsis iglesiasii in a tropical lowland rain forest site in Amazonian Ecuador to document seed dispersal and seedling survival to 1-year post-dispersal. Most seeds did not disperse far: 86% of germinated seedlings were found within 100 m. Mortality was high: only 49 of the 1732 monitored seedlings survived one year and only five survived a further four years. We found a significant negative effect of conspecific seedling density (but no effect of distance from the parent tree) on 1-year survival. Rare long-distance dispersal events may increase the probability of a seed reaching specific habitats, such as high-light patches, and surviving beyond one year, thereby shifting the population recruitment curve outwards away from adult trees and maintaining diversity in species-rich forests.

opencc-by-4.0Apr 2022View details →

Supplementary material of "VIGIL: A Python tool for automatized probabilistic VolcanIc Gas dIspersion modeLling"

This dataset includes the Supplementary material of the paper:  Dioguardi F, Massaro S, Chiodini G, Costa A, Folch A, Macedonio G, Sandri L, Selva J, Tamburello G. VIGIL: A Python tool for automatized probabilistic VolcanIc Gas dIspersion modeLling. Ann. Geophys. [Internet]. 2022Apr.3 [cited 2022Apr.7];65(1). Available from: https://www.annalsofgeophysics.eu/index.php/annals/article/view/8796

opencc-zeroApr 2022View details →

Supporting data: Speciation and population divergence in a mutualistic seed dispersing bird

Bird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the evolutionary processes that shaped the diversification of the Eurasian nutcracker (Nucifraga), a seed disperser known for its mutualism with pines (Pinus). Our results show that the divergence and phylogeographic patterns of nutcrackers resemble those of other non-mutualistic passerine birds and suggests that their early diversification was shaped by similar biogeographic and climatic processes. The limited variation in foraging traits indicates that local adaptation to pines likely played a minor role. Our study shows that close mutualistic relationships between bird and plant species might not necessarily act as a primary driver of evolution and diversification in resource-specialized birds. The supporting data include VCF-files for the different population genetic analyses, the morphometric data set, as well as the data set related to the phylogenetic analyses.

opencc-by-4.0Apr 2022View details →

Versatile strategy for homogeneous drying patterns of dispersed particles: Matlab code

Matlab code of "Versatile strategy for homogeneous drying patterns of dispersed particles"