Multispectral canopy reflectance improves spatial distribution models of Amazonian understory species

Species distribution models are required for the research and management of biodiversity in the hyperdiverse tropical forests, but reliable and ecologically relevant digital environmental data layers are not always available. We here assess the usefulness of multispectral canopy reflectance (Landsat) relative to climate data in modelling understory plant species distributions in tropical rainforests. We used a large dataset of quantitative fern and lycophyte species inventories across lowland Amazonia as the basis for species distribution modelling (SDM). As predictors, we used CHELSA climatic variables and canopy reflectance values from a recent basin-wide composite of Landsat TM/ETM+ images both separately and in combination. We also investigated how species accumulate over sites when environmental distances were expressed in terms of climatic or surface reflectance variables. When species accumulation curves were constructed such that differences in Landsat reflectance among the selected plots were maximised, species accumulated faster than when climatic differences were maximised or plots were selected in a random order. Sixty-nine species were sufficiently frequent for species distribution modelling. For most of them, adequate SDMs were obtained whether the models were based on CHELSA data only, Landsat data only or both combined. Model performance was not influenced by species’ prevalence or abundance. Adding Landsat-based environmental data layers overall improved the discriminatory capacity of SDMs compared to climate-only models, especially for soil specialist species. Our results show that canopy surface reflectance obtained by multispectral sensors can provide studies of tropical ecology, as exemplified by SDMs, much higher thematic (taxonomic) detail than is generally assumed. Furthermore, multispectral datasets complement the traditionally used climatic layers in analyses requiring information on environmental site conditions. We demonstrate the utility of freely available, global remote sensing data for biogeographical studies that can aid conservation planning and biodiversity management.     

Mechanistic insights into the role of large carnivores for ecosystem structure and functioning

Large carnivores can exert top–down effects in ecosystems, but the size of these effects are largely unknown. Empirical investigation on the importance of large carnivores for ecosystem structure and functioning presents a number of challenges due to the large spatio-temporal scale and the complexity of such dynamics. Here, we applied a mechanistic global ecosystem model to investigate the influence of large-carnivore removal from undisturbed ecosystems. First, we simulated large-carnivore removal on the global scale to inspect the geographic pattern of top–down control and to disentangle the functional role of large carnivores in top–down control in different environmental contexts. Second, we conducted four small-scale ecosystem simulation experiments to understand direct and indirect changes in food-web structure under different environmental conditions. We found that the removal of top–down control exerted by large carnivores (> 21 kg) can trigger large trophic cascades, leading to an overall decrease in autotroph biomass globally. Furthermore, the loss of large carnivores resulted in an increase of mesopredators. The magnitude of these changes was positively related to primary productivity (NPP), in line with the ‘exploitation ecosystem hypothesis’. In addition, we found that seasonality in NPP dampened the magnitude of change following the removal of large carnivores. Our results reinforce the idea that large carnivores play a fundamental role in shaping ecosystems, and further declines and extinctions can trigger substantial ecosystem responses. Our findings also support previous studies suggesting that natural ecosystem dynamics have been severely modified and are still changing as a result of the widespread decline and extinction of large carnivores.     

Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)

Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions Silene dioica (L.) Clairv. and S. latifolia Poiret. Demographic modelling indicated that the two species diverged with gene flow. The best‐supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (F _ST) and sequence divergence (d _XY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between‐species population pairs, isolation by distance was stronger for genomic regions with low between‐species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated, suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two Silene species, consistent with predictions for speciation in the face of gene flow.     

Beyond the landscape: Resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species’ inherent behavioural variability. There are no functional connectivity analyses using continuous individual‐based sampling across an urban‐rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding rural regions in Brandenburg in order to study genetic structure and dispersal behaviour of a mobile carnivore across the urban‐rural landscape. We assessed functional connectivity by applying an individual‐based landscape genetic optimization procedure. Three commonly used genetic distance measures yielded different model selection results, with only the results of an eigenvector‐based multivariate analysis reasonably explaining genetic differentiation patterns. Genetic clustering methods and landscape resistance modelling supported the presence of an urban population with reduced dispersal across the city border. Artificial structures (railways, motorways) served as main dispersal corridors within the cityscape, yet urban foxes avoided densely built‐up areas. We show that despite their ubiquitous presence in urban areas, their mobility and behavioural plasticity, foxes were affected in their dispersal by anthropogenic presence. Distinguishing between man‐made structures and sites of human activity, rather than between natural and artificial structures, is thus essential for better understanding urban fox dispersal. This differentiation may also help to understand dispersal of other urban wildlife and to predict how behaviour can shape population genetic structure beyond physical barriers.     

Fungal communities living within leaves of native Hawaiian dicots are structured by landscape‐scale variables as well as by host plants

A phylogenetically diverse array of fungi live within healthy leaf tissue of dicotyledonous plants. Many studies have examined these endophytes within a single plant species and/or at small spatial scales, but landscape‐scale variables that determine their community composition are not well understood, either across geographic space, across climatic conditions, or in the context of host plant phylogeny. Here, we evaluate the contributions of these variables to endophyte beta diversity using a survey of foliar endophytic fungi in native Hawaiian dicots sampled across the Hawaiian archipelago. We used Illumina technology to sequence fungal ITS1 amplicons to characterize foliar endophyte communities across five islands and 80 host plant genera. We found that communities of foliar endophytic fungi showed strong geographic structuring between distances of 7 and 36 km. Endophyte community structure was most strongly associated with host plant phylogeny and evapotranspiration, and was also significantly associated with NDVI, elevation and solar radiation. Additionally, our bipartite network analysis revealed that the five islands we sampled each harboured significantly specialized endophyte communities. These results demonstrate how the interaction of factors at large and small spatial and phylogenetic scales shapes fungal symbiont communities.     

Model-based design and control of a small-scale integrated continuous end-to-end mAb platform

A continuous integrated bioprocess available from the earliest stages of process development allows for an easier, more efficient and faster development and characterization of an integrated process as well as production of small-scale drug candidates. The process presented in this article is a proof-of-concept of a continuous end-to-end monoclonal antibody production platform at a very small scale based on a 200 ml alternating tangential flow filtration perfusion bioreactor, integrated with the purification process with a model-based design and control. The downstream process, consisting of a periodic twin-column protein A capture, a virus inactivation, a CEX column and an AEX column, was compactly implemented in a single chromatography system, with a purification time of less than 4 hr. Monoclonal antibodies were produced for 17 days in a high cell density perfusion culture of CHO cells with titers up to 1.0 mg/ml. A digital twin of the downstream process was created by modelling all the chromatography steps. These models were used for real-time decision making by the implementation of control strategies to automatize and optimize the operation of the process. A consistent glycosylation pattern of the purified product was ensured by the steady state operation of the process. Regarding the removal of impurities, at least a 4-log reduction in the HCP levels was achieved. The recovery yield was up to 60%, and a maximum productivity of 0.8 mg/ml/day of purified product was obtained.     

Population modelling and genetics of a critically endangered Madagascan palm Tahina spectabilis

Madagascar is home to 208 indigenous palm species, almost all of them endemic and >80% of which are endangered. We undertook complete population census and sampling for genetic analysis of a relatively recently discovered giant fan palm, the Critically Endangered Tahina spectablis in 2008 and 2016. Our 2016 study included newly discovered populations and added to our genetic study. We incorporated these new populations into species distribution niche model (SDM) and projected these onto maps of the region. We developed population matrix models based on observed demographic data to model population change and predict the species vulnerability to extinction by undertaking population viability analysis (PVA). We investigated the potential conservation value of reintroduced planted populations within the species potential suitable habitat. We found that the population studied in 2008 had grown in size due to seedling regeneration but had declined in the number of reproductively mature plants, and we were able to estimate that the species reproduces and dies after approximately 70 years. Our models suggest that if the habitat where it resides continues to be protected the species is unlikely to go extinct due to inherent population decline and that it will likely experience significant population growth after approximately 80 years due to the reproductive and life cycle attributes of the species. The newly discovered populations contain more genetic diversity than the first discovered southern population which is genetically depauperate. The species appears to demonstrate a pattern of dispersal leading to isolated founder plants which may eventually lead to population development depending on local establishment opportunities. The conservation efforts currently put in place including the reintroduction of plants within the species potential suitable habitat if maintained are thought likely to enable the species to sustain itself but it remains vulnerable to anthropogenic impacts.     

New advances on the Aurignacian in the central Iberian Mediterranean basin

This study aims to obtain a chronological and cultural framework of the Evolved Aurignacian in the central Iberian Mediterranean basin and find agreement between this framework and other sequences of the Iberian southeast. Over the last few years, there has been remarkable progress in the research of the Evolved Aurignacian sites in the Valencian area, making a review of the main characteristics of the technocomplex on a regional scale necessary. The recent fieldwork carried out in Cova de les Malladetes (Valencia) and in Cova de les Cendres (Alicante) have been key to understanding the lithic, osseous and ornament assemblages ascribed to the Evolved Aurignacian. Several Bayesian modelled ages have been constructed from the large dataset of chronological dates obtained at Malladetes and Cendres, as well as in other sites. The Bayesian models have allowed us to chronologically place the characteristics of the analysed assemblages. The present research supports the importance of the Aurignacian as the first technocomplex of the Upper Palaeolithic in this area of the Iberian Peninsula.     

Geoclimatic factors influence the population genetic connectivity of Incarvillea arguta (Bignoniaceae) in the Himalaya–Hengduan Mountains biodiversity hotspot

Geoclimatic factors related to the uplift of the Himalaya and the Quaternary climatic oscillations influence the population genetic connectivity in the Himalaya–Hengduan Mountains (HHM) biodiversity hotspot. Therefore, to explore the relative roles played by these two factors, we examined the population dynamics and dispersal corridors of Incarvillea arguta (Royle) Royle incorporating ensemble species distribution modelling (SDM). Thirty‐seven populations were genotyped using plastid chloroplast DNA and low copy nuclear gene (ncpGS) sequences. Phylogeographic analysis was carried out to reveal the genetic structure and lineage differentiation. Ensemble SDMs were carried out for distributional change in the last glacial maximum, present, and future. Finally, the least cost path method was used to trace out possible dispersal corridors. The haplotypes were divided into four clades with strong geographical structure. The late Miocene origin of I. arguta in the western Himalaya ca. 7.92 Ma indicates lineage diversification related to the uplift of the HHM. The variability in habitat connectivity revealed by SDM is due to change in suitability since the Pleistocene. A putative dispersal corridor was detected along the drainage systems and river valleys, with strong support in the eastern Hengduan Mountains group. Our results support the signature of geoclimatic influence on population genetic connectivity of I. arguta in the HHM. We proposed that the major drainage systems might have assisted the rapid dispersal of isolated riverine plant species I. arguta in the HHM. The population genetic connectivity, using the fine‐tuned ensemble SDMs, enables scientists and policymakers to develop conservation strategies for the species gene pool in the HHM biodiversity hotspots.