Spatial associations between plants and vegetation community characteristics provide insights into the processes influencing plant rarity

Determining the drivers of plant rarity is a major challenge in ecology. Analysing spatial associations between different plant species can provide an exploratory avenue for understanding the ecological drivers of plant rarity. Here, we examined the different types of spatial associations between rare and common plants to determine if they influence the occurrence patterns of rare species. We completed vegetation surveys at 86 sites in woodland, forest, and heath communities in south-east Australia. We also examined two different rarity measures to quantify how categorisation criteria affected our results. Rare species were more likely to have positive associations with both rare and common species across all three vegetation communities. However, common species had positive or negative associations with rare and other common species, depending on the vegetation community in which they occurred. Rare species were positively associated with species diversity in forest communities. In woodland communities, rare species were associated negatively with species diversity but positively associated with species evenness. Rare species with high habitat specificity were more clustered spatially than expected by chance. Efforts to understand the drivers of plant rarity should use rarity definitions that consider habitat specificity. Our findings suggest that examining spatial associations between plants can help understand the drivers of plant rarity.

Populations of Agrostis diluta Kurcz. and Psathyrostachys caespitosa (Sukaczev) Peschkova in Yakutia: dynamics of vitality

In Yakutia, natural floodplain meadows and steppes have long been involved in economic activities. To develop methods of rational use, one needs to constantly consider the state of vegetation, mainly its constituent populations. Our research focuses on studying the dynamics of the vitality of the populations of the Agrostis diluta Kurcz. and steppe Psathyrostachys caespitosa (Sukaczev) Peschkova cereals. These species play an essential role in the composition of vegetation cover. We determined the vitality coefficient IVC. Our study of populations over several years has revealed the dynamic mobility of the vital structure, which is of adaptive significance and ensures the sustainability of populations. We have found that the vital structure of the cereal populations of the meadow Agrostis diluta and the steppe Psathyrostachys caespitosa during long-term studies (2007–2013 and 2007–2016, respectively) is heterogeneous. In unfavorable humidification conditions, we characterize years as depressive. Under favorable conditions of humidification, they quickly turn into thriving plants. In addition to the weather of the vegetation periods, habitat specificity affects the vitality of species populations that differ in ecological and coenotic characteristics. The Q quality index and IVC correspond to each other by year and form a clear descending order during the transition from a thriving to a depressive state. Currently, the vital state of the populations of both species is satisfactory.

Composition, richness and nestedness of gallery forest bird assemblages in an Amazonian savanna landscape: lessons for conservation

Gallery forests are important to the maintenance of a substantial portion of the biodiversity in neotropical savanna regions, but management guidelines specific to this forest type are limited. Here, we use birds as study group to assess if: (1) functional traits can predict the abundance and occupancy of forest species within a savanna landscape, (2) habitat structures influence the taxonomic, functional, and phylogenetic diversity of forest assemblages, and (3) less diverse gallery forest assemblages are a nested subset of more diverse assemblages living near continuous forests. Then, we propose strategies on how gallery forests can be managed to maintain their species assemblages amidst the fast expansion of human activities across tropical savanna landscapes. We studied 26 sites of gallery forests in an Amazonian savanna landscape and found that: (1) habitat specificity is the only functional trait that predicts species abundance and occupancy across a landscape; (2) phylogenetic diversity is negatively correlated with understory foliage density; (3) the percentage of forests and savannas around sites is positively correlated with both phylogenetic and functional diversity; (4) increasing human activities around gallery forest negatively influences taxonomic and functional diversity; and (5) forest bird assemblages are not distributed at random across the landscape but show a nested pattern caused by selective colonization mediated by habitat filtering. Our combined findings have three implications for the design of conservation strategies for gallery forest bird assemblages. First, maintaining the connectivity between gallery forests and adjacent continuous forests is essential because gallery forest bird assemblages are derived from continuous forest species assemblages. Second, because most species use the savanna matrix to move across the landscape, effectively managing the savanna matrices where gallery forests are embedded is as important to maintaining viable populations of forest bird species as managing the gallery forest themselves. Third, in savanna landscapes planned to be used for agriculture production, protecting gallery forests alone is not enough. Instead, gallery forests should be protected with surrounding savanna buffers to avoid the detrimental effects (edge effects and isolation) of human activities on their biodiversity.

Evaluating firefly extinction risk: Initial red list assessments for North America

Fireflies are a family of charismatic beetles known for their bioluminescent signals. Recent anecdotal reports suggest that firefly populations in North America may be in decline. However, prior to this work, no studies have undertaken a systematic compilation of geographic distribution, habitat specificity, and threats facing North American fireflies. To better understand their extinction risks, we conducted baseline assessments according to the categories and criteria of the International Union for Conservation of Nature (IUCN) Red List for 132 species from the United States and Canada (approximately 79% of described species in the region). We found at least 18 species (14%) are threatened with extinction (e.g. categorized as Critically Endangered, Endangered, or Vulnerable) due to various pressures, including habitat loss, light pollution, and climate change (sea level rise and drought). In addition, more than half of the species (53%) could not be evaluated against the assessment criteria due to insufficient data, highlighting the need for further study. Future research and conservation efforts should prioritize monitoring and protecting populations of at-risk species, preserving and restoring habitat, gathering data on population trends, and filling critical information gaps for data deficient species suspected to be at risk.

Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

The mosquito microbiome includes habitat-specific but rare symbionts

Microbial communities are known to influence mosquito lifestyles by modifying essential metabolic and behavioral processes that affect reproduction, development, immunity, digestion, egg survival, and ability to transmit pathogens. Many studies have used 16S rRNA gene amplicons to characterize mosquito microbiota and investigate factors that influence host-microbiota dynamics. However, a relatively low taxonomic resolution due to clustering methods based on arbitrary threshold and the overall dominance of Wolbachia or Asaia populations obscured the investigation of rare members of mosquito microbiota in previous studies. Here, we used high resolution Shannon entropy-based oligotyping approaches to analyze the microbiota of Culex pipiens, Culex quinquefasciatus and Aedes individuals from continental and overseas regions in Southern France and Guadeloupe as well as from laboratories with or without antibiotics treatment. Our experimental design that resulted in a series of mosquito samples with a gradient of Wolbachia density and relative abundance along with high-resolution analyses of amplicon sequences enabled the recovery of a robust signal from typically less accessible bacterial taxa. Our data confirm species-specific mosquito-bacteria associations with geography as a primary factor that influences bacterial community structure. But interestingly, they also reveal co-occurring symbiotic bacterial variants within single individuals for both Elizabethkingia and Erwinia genera, distinct and specific Asaia and Chryseobacterium in continental and overseas territories and a putative rare Wolbachia variant. Overall, our study reveals the presence of previously-overlooked microdiversity and multiple closely related symbiotic strains within mosquito individuals with a remarkable habitat-specificity.

Fungi in soil and understory have coupled distribution patterns

Ecological processes that control fungal distribution are not well understood because many fungi can persist in a wide variety of dissimilar habitats which are seldom sampled simultaneously. Geographic range size is reflective of species’ resource usage, and for plants and animals, there is a robust positive correlation between niche-breadth and range-size. It remains unknown whether this pattern is true for fungi. To investigate the fungal niche breadth–range size relationship we identified habitat specialists and generalists from two habitats (plant leaves and soil) and asked whether habitat specialization influenced fungal biogeography. We sampled fungi from the soil and phylloplane of tropical forests in Vanuatu and used DNA metabarcoding of the fungal ITS1 region to examine rarity, range size, and habitat connectivity. Fungal communities from the soil and phylloplane are spatially autocorrelated and the spatial distribution of individual fungal OTU are coupled between habitats. Habitat breadth (generalist fungi) did not result in larger range sizes but did correlate positively with occurrence frequency. Fungi that were frequently found were also found in high abundance, a common observation in similar studies of plants and animals. Fungal abundance-occupancy relationships differed by habitat and habitat-specificity. Soil specialists were found to be locally abundant but restricted geographically. In contrast, phylloplane generalists were found to be abundant over a large range in multiple habitats. These results are discussed in the context of differences between habitat characteristics, stability and spatial distribution. Identifying factors that drive spatial variation is key to understanding the mechanisms that maintain biodiversity in forests.

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimoes River, Western Amazon, South America Taxon: Myrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis Methods: We analyzed thousands of UltraConserved Elements to explore spatial patterns of genetic diversity and connectivity between individuals. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species in order to test if the occupation of dynamic habitats could predict spatial patterns of genetic diversity. Results: Our study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusions: Our results suggest that demographic expansions along the Solimoes River might be linked to geographic homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.