Recent declines in once-common species are triggering concern that an environmental crisis point has been reached. Yet, the lack of long abundance time series data for most species can make it difficult to attribute these changes to anthropogenic causes, and to separate them from normal cycles. Genetic diversity, on the other hand, is sensitive to past and recent environmental changes, and reflects a measure of a populations' potential to adapt to future stressors. Here, we consider whether patterns of genetic diversity among aquatic insects can be linked to historical and recent patterns of land use change. We collated mitochondrial cytochrome c oxidase subunit I (COI) variation for >700 aquatic insect species across the United States, where patterns of agricultural expansion and intensification have been documented since the 1800s. We found that genetic diversity was lowest in regions where cropland was historically (pre-1950) most extensive, suggesting a legacy of past environmental harm. Genetic diversity further declined where cropland has since expanded, even after accounting for climate and sampling effects. Notably though, genetic diversity also appeared to rebound where cropland has diminished. Our study suggests that genetic diversity at the community level can be a powerful tool to infer potential population declines and rebounds over longer time spans than is typically possible with ecological data. For the aquatic insects that we considered, patterns of land use many decades ago appear to have left long-lasting damage to genetic diversity that could threaten evolutionary responses to rapid global change.

To understand soil biodiversity we need to know how soil communities are assembled. However, the relationship between soil community assembly and environmental factors, and the linkages between soil microbiota taxonomic groups and their body sizes, remain unexplored in tropical seasonal rainforests. Systematic and stratified random sampling was used to collect 243 soil and organism samples across a 20-ha plot in a tropical seasonal rainforest in southwestern China. High-throughput sequencing, variation analysis and principal coordinates of neighbourhood matrices were performed. Soil community composition, spatial distribution and assembly processes based on propagule size (including archaea, bacteria, fungi and nematodes) were investigated. The results showed that: (i) the community assembly of small soil microorganisms (bacteria, fungi) was mostly influenced by stochastic processes while that of larger soil organisms (nematodes) was more deterministic; (ii) the independent effects of habitat (including soil and topographic variables) and its interaction with plant attributes for community structure significantly decreased with increasing body size; and (iii) plant leaf phosphorus directly influenced the spatial distribution of soil-available phosphorus, which indicates their indirect impact on the assembly of the soil communities. Our data suggest that the assembly of multitrophic soil communities can be explained to some extent by changes in above-ground plant attributes. This highlights the importance of above- and below-ground linkages in influencing multitrophic soil microbiota community assembly.

How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species Lumnitzera littorea and Lumnitzera racemosa provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species Combretum micranthum. While most mangroves have small genomes, the genomes of both Lumnitzera species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, Lumnitzera species have not undergone post-gamma whole-genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, Lumnitzera genomes have reduced transposable elements by constraining the proliferation of new LTR-RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower colour differentiation between the Lumnitzera species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution.

Farmlands are becoming more important as waterfowl foraging habitats, while natural wetlands are being lost globally. However, it is unclear how waterfowl coexist in agricultural landscapes by resource partitioning. We evaluated the diets of seven sympatric dabbling ducks foraging in rice paddy and lotus fields around Lake Kasumigaura, the second largest lake in Japan, during two wintering seasons (from November to February) by faecal DNA metabarcoding using chloroplast trnL and mitochondrial CO1 region sequences. We examined 420 faecal samples and found different patterns of dietary diversity and composition among the duck species. The pattern also differed between plant and invertebrate food. Dietary niche partitioning was clear in plant food. Large-bodied ducks intensively use crop plants, and other ducks might mediate competition by using terrestrial and aquatic plants that are suitable for their foraging behaviours or microhabitats. Dietary segregation among species was the most apparent in February, when the abundance of foraging ducks was the largest. This study illustrated the complex pattern of dietary niche partitioning of dabbling ducks in agricultural landscapes, which might be difficult to evaluate by conventional approaches. The availability of crop plants, as well as other plant food resources in flooted areas and farmland dikes, may enable ducks to coexist by spatial or behavioural resource partitioning.

Islands make up a large proportion of Earth's biodiversity, yet are also some of the most sensitive systems to environmental perturbation. Biogeographic theory predicts that geologic age, area, and isolation typically drive islands' diversity patterns, and thus potentially impact non-native spread and community homogenization across island systems. One limitation in testing such predictions has been the difficulty of performing comprehensive inventories of island biotas and distinguishing native from introduced taxa. Here, we use DNA metabarcoding and statistical modelling as a high throughput method to survey community-wide arthropod richness, the proportion of native and non-native species, and the incursion of non-natives into primary habitats on three archipelagos in the Pacific - the Ryukyus, the Marianas and Hawaii - which vary in age, isolation and area. Diversity patterns largely match expectations based on island biogeography theory, with the oldest and most geographically connected archipelago, the Ryukyus, showing the highest taxonomic richness and lowest proportion of introduced species. Moreover, we find evidence that forest habitats are more resilient to incursions of non-natives in the Ryukyus than in the less taxonomically rich archipelagos. Surprisingly, we do not find evidence for biotic homogenization across these three archipelagos: the assemblage of non-native species on each island is highly distinct. Our study demonstrates the potential of DNA metabarcoding to facilitate rapid estimation of biogeographic patterns, the spread of non-native species, and the resilience of ecosystems.

Cryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and most are probably recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalization and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host-parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.

Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome-level genome assembly and annotation of a female P. qiongdaoensis. Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis, and showed convergent evolution with another tropical poplar, P. ilicifolia, at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis, and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type-A cytokinin response regulator (RR) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus, which may be caused by the translocation and duplication of the RR gene driven by Helitron-like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.

Zooplankton plays an essential role in marine ecosystems as the link between primary producers (phytoplankton) and higher trophic levels in food webs, and as a dynamic pool of recruits for invertebrates and fish. Zooplankton communities are diverse with a patchy distribution at different spatial scales, influenced by oceanographic processes. The continental shelf of eastern South Africa is narrow and exposed to the western-boundary Agulhas Current, with some shelter against strong directional flow provided by the broader KwaZulu-Natal Bight, a coastal offset adjacent to an estuary. We compared zooplankton species richness, diversity and relative abundance of key taxa among sheltered and exposed shelf areas using metabarcoding and community analysis, to explore the ecological role of the bight in a highly dynamic ocean region. Metabarcoding recovered higher richness and diversity at a finer resolution than could previously be achieved with traditional microscopy. Of 271 operational taxonomic units (OTUs) recovered through metabarcoding, 63% could be matched with >95% sequence similarity to reference barcodes. OTUs were dominated by malacostracan crustaceans (161 spp.), ray-finned fishes (45 spp.) and copepods (28 spp.). Species richness, diversity and the relative abundance of key taxa differed between sheltered and exposed shelf areas. Lower species richness in the bight was partly attributed to structurally homogeneous benthic habitats, and an associated reduction of meroplanktonic species originating from local benthic-pelagic exchange. High relative abundance of a ray-finned fish in the bight, as observed based on fish eggs and read counts, confirmed that the bight is an important fish spawning area. Overall, zooplankton metabarcoding outputs were congruent with findings of previous ecological research using more traditional methods of observation.

Habitat fragmentation affects biodiversity, but with unclear effects on pollinators and their interactions with plants in anthropized landscapes. Islands could serve as open air laboratories, suitable to disentangle how land-use alteration impacts pollination ecology. In Maldive islands we investigated how pollinator richness, plant-pollinator interactions and pollination efficiency are influenced by the green area fragmentation (i.e., gardens and semi-natural patches). Moreover, we considered the mediating role of pollinator body size and the plant trait of being invasive in shaping interactions. To do this, we surveyed pollinator insects from 11 islands representing a gradient of green area fragmentation. A DNA metabarcoding approach was adopted to identify the pollen transported by pollinators and characterize the plant-pollinator interactions. We found that intermediate levels of green area fragmentation characterized pollinator communities and increased their species richness, while decreasing interaction network complexity. Invasive plants were more frequently found on pollinator bodies than native or exotic noninvasive ones, indicating a concerningly higher potential for pollen dispersal and reproduction of the former ones. Intriguingly, pollinator body size mediated the effect of landscape alteration on interactions, as only the largest bees expanded the foraging diet in terms of plant richness in the transported pollen at increasing fragmentation. In parallel, the pollination efficiency increased with pollinator species richness in two sentinel plants. This study shows that moderate landscape fragmentation of green areas shapes many aspects of the pollination ecosystem service, where despite interactions being less complex and mediated by pollinator body size, pollinator insect biodiversity and potential plant reproduction are supported.