Assessing bias and knowledge gaps on seed ecology research: implications for conservation agenda and policy

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%-18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost.

Impact of an IUCN national Red List of threatened flora on scientific attention

Red Lists are thought to attract attention to the conservation of threatened species. Determining the impact of these lists on the attention of scientists is a matter of consequence for biodiversity conservation. We evaluated trends in mentions of Brazilian angiosperm plants in the biodiversity conservation literature and tested the effect of the Red List of Brazilian Flora (RLBF) publication on these mentions. We collected mentions in the literature available in Google Scholar from the years 1990-2020, for 2449 Brazilian angiosperm species assessed in different IUCN categories. We used a Bayesian structural time-series method to test the effect of the RLBF publication on the number of mentions for the set of species in the IUCN categories, angiosperm families, and plants of commercial interest. The results showed a gap in mentions for many threatened and Data Deficient species in the scientific literature. We also found that the mentions were biased toward species of commercial interest and were unrelated to their threat status. Publication of the RLBF positively affected the number of mentions for IUCN threat categories and for more than half of the angiosperm families. These results were obtained after a few species of commercial interest were excluded from each treated group. This study suggests that the Red List assessments are essential to determine priorities for resource allocation to scientific activities. However, this effect was not sufficient to reduce the bias in scientific attention. Our findings support the need to stimulate more effective programs to fund research on threatened plant species.

Biogeographic and fragmentation-related research biases on antbirds and non-flying small mammals in Brazil

Major biogeographic and taxonomic biases are recurrent in biological surveys, including fragmentation studies. Detecting biases and subsequent gaps is crucial to steer future research and suitable conservation policies. We evaluated biogeographic and fragmentation-related biases on antbirds and non-flying small mammals in Brazil, two oversampled and vulnerable taxonomic groups, by surveying papers in the Scielo and the Web of Science. We found 566 articles published from 1945 to 2018, including 55 and 43 fragmentation studies for antbirds and small mammals, respectively. Considering the species richness for each group across the Brazilian biomes, the number of publications for small mammals tended to disproportionately increase while increasing richness. The Atlantic Forest, the most degraded and densely populated biome, contained the highest number of publications. However, the Amazon included a disproportionately high number of papers considering its low population density. Conversely, non-forest biomes such as the Caatinga, Pampa and Pantanal were mostly overlooked. Our results show that research effort for small mammals and antbirds in Brazil is biogeographically biased. We call future research to consider more studies across non-forest biomes and vast unexplored areas within forest biomes to overcome major knowledge gaps on diversity, distribution and ecology of antbirds and small mammals in Brazil.

A brief history of research in campo rupestre: identifying research priorities and revisiting the geographical distribution of an ancient, widespread Neotropical biome

Few ecologists and evolutionary biologists are familiar with the ecology and evolution of the campo rupestre, an ancient azonal peinobiome characterized by a fire-prone, nutrient-impoverished, montane vegetation mosaic, home to thousands of endemics and climate refugia. With the goal of providing a synthetic view of the campo rupestre, we provide a brief historical account of the biological research, revisit its geographical distribution and identify knowledge gaps. The azonal campo rupestre is distributed as isolated and naturally fragmented sky islands, mostly in Central and Eastern Brazil and in the Guyana Shield, with significant areas across the Amazon, Cerrado, Atlantic Forest, Caatinga and Pantanal. Our proposal to elevate campo rupestre to the level of biome is expected to improve communication among scientists and consolidate the use of the term campo rupestre in the ecological and evolutionary literature, as is the case for analogous ecosystems, such as kwongan, fynbos, páramos and tepuis. Based on the identification of knowledge gaps, we propose a research programme comprising ten key topics that can foster our understanding of the ecology and evolution of campo rupestre and, potentially, support conservation strategies.

Intraspecific Variation of Samara Dispersal Traits in the Endangered Tropical Tree Hopea hainanensis (Dipterocarpaceae)

Propagule dispersal is a crucial life history stage, which affects population recruitment and regeneration as well as community structure and functions. The windborne process of samara dispersal is affected not only by samara traits and other plant traits, but also by environmental factors. Therefore, studying samara traits related to its dispersal and intraspecific variation in relation to other plant traits and environmental factors could help to understand population distribution and dynamics. Hopea hainanensis, a Dipterocarpaceae tree species dominant in lowland rainforests in Hainan (China) but endangered due to anthropogenic disturbances, is dispersed mainly by wind because of its sepal-winged samara. Here, we measured dispersal-related intraspecific samara traits of H. hainanensis, and analyzed their variation and correlation in relation to plant height, DBH (diameter at breast height), and elevation plant location. Great variations in the samara traits existed, and the variations were larger within than among individuals, which indicated a "bet-hedging" strategy of this species. Plant height, DBH, and elevation explained slight variation in the samara traits. Samara dispersal potential is mainly affected by the samara mass and morphological traits. Samara settling velocity was significantly positively correlated with fruit mass, seed mass, length and width, as well as samara wing loading, and negatively correlated with wing mass ratio, wing area, and wing aspect ratio. Substantial proportions of intraspecific variation in samara dispersal are explained by the samara mass and morphological traits. Natural regeneration with human-aided dispersal is necessary for recovering the H. hainanensis population. This finding contributes to the generalization of trait-based plant ecology, modeling of seed dispersal in tropical forests, and conservation and recovery of rare and endangered species such as H. hainanensis.

Ex situ conservation of threatened plants in Brazil: a strategic plan to achieve Target 8 of the Global Strategy for Plant Conservation

Abstract With increasing rates of habitat destruction and species loss, ex situ conservation is gaining global momentum and reluctance in relying on ex situ conservation is rapidly giving way to a more optimistic, strategic view. Target 8 of the Global Strategy of Plant Conservation calls for at least 75 percent of threatened plant species in accessible ex situ collections, preferably in the country of origin, and 20 percent of them included in recovery and restoration programs. Here, we provide updated information on Brazil's progress towards Target 8 through a nationwide examination of how many threatened species were conserved in ex situ collections in Brazil. Our data comprised whole plants (living collections), seed (seed banks) and tissue cultures (in vitro). Of the 2,113 threatened species, at least 452 (21.4%) species were conserved in ex situ collections, an increase in 4% of living organisms and 96% of seeds when compared to a previous assessment. Since it is unlikely Brazil will achieve Target 8 by 2020, we also discuss public policies and strategies to help overcome key bottlenecks preventing its achievement and propose revised goals for the GSPC 2020-2030.

Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data

Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.

Phylogeny strongly drives seed dormancy and quality in a climatically buffered hotspot for plant endemism

BACKGROUND AND AIMS

Models of costs and benefits of dormancy (D) predict that the evolutionarily stable strategy in long-term stable environments is for non-dormancy (ND), but this prediction remains to be tested empirically. We reviewed seed traits of species in the climatically buffered, geologically stable and nutrient-impoverished campo rupestre grasslands in Brazil to test the hypothesis that ND is favoured over D. We examined the relative importance of life-history traits and phylogeny in driving the evolution of D and assessed seed viability at the community level.

METHODS

Germination and viability data were retrieved from 67 publications and ND/D was determined for 168 species in 25 angiosperm families. We also obtained the percentage of embryoless, viable and dormant seeds for 74 species. Frequencies of species with dormant and non-dormant seeds were compared with global databases of dormancy distribution.

KEY RESULTS

The majority of campo rupestre taxa (62·5 %) had non-dormant seeds, and the ND/D ratio was the highest for any vegetation type on Earth. Dormancy was unrelated to other species life-history traits, suggesting that contemporary factors are poor predictors of D. We found a significant phylogenetic structure in the dormancy categorical trait. Dormancy diversity was highly skewed towards the root of the phylogenetic tree and there was a strong phylogenetic signal in the data, suggesting a major role of phylogeny in determining the evolution of D versus ND and seed viability. Quantitative analysis of the data revealed that at least half of the seeds produced by 46 % of the surveyed populations were embryoless and/or otherwise non-viable.

CONCLUSIONS

Our results support the view that long-term climatic and geological stability favour ND. Seed viability data show that campo rupestre species have a markedly low investment in regeneration from seeds, highlighting the need for specific in situ and ex situ conservation strategies to avoid loss of biodiversity.