Regional occupancy increases for widespread species but decreases for narrowly distributed species in metacommunity time series

Prioritizing the multifaceted community and species uniqueness for the conservation of lacustrine fishes in the largest subtropical floodplain, China

Hydrological variations affect habitat characteristics and fish distribution in floodplain lakes. Assessing the contributions of the local community (i.e., LCBD, community uniqueness) and species to overall β diversity (i.e., SCBD, species uniqueness) of fish assemblages is valuable for habitat and species conservation planning, particularly from functional and phylogenetic perspectives. We examined the changes in multifaceted LCBD and SCBD of fish across different hydrological periods in the Poyang Lake, China, and analyzed their responsive mechanisms using regression models, based on which the conservation priorities of habitats and species were evaluated. The findings revealed that taxonomic, functional, and phylogenetic LCBD and SCBD were lowest during the wet season compared to the normal and dry seasons, emphasizing the regulatory effects of hydrological regimes on fish assemblages. Taxonomic and functional LCBD were significantly impacted by the mean abundance of migratory fish, highlighting the importance of specific species combinations on community uniqueness. Taxonomic and functional SCBD exhibited positive correlations primarily with mean abundance, suggesting the potential uniqueness of certain common species. Additionally, we identified the river-lake junction (Hukou station) and natural reserve (Xingzi and Nanjishan stations) with high overall community uniqueness as critical habitats. We also emphasized the necessity for increased conservation efforts for species having high overall species uniqueness during different hydrological periods, including Coilia brachygnathus, Ctenopharyngodon idella, Coilia nasus, Saurogobio dabryi, Hypophthalmichthys molitrix, Megalobrama amblycephala, and Parabramis pekinensis. This research underscores the significance of integrating multiple ecological perspectives to manage biodiversity changes and maintain ecological conservation values effectively.

Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally

Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.

Disproportionate declines of formerly abundant species underlie insect loss

Studies have reported widespread declines in terrestrial insect abundances in recent years1-4, but trends in other biodiversity metrics are less clear-cut5-7. Here we examined long-term trends in 923 terrestrial insect assemblages monitored in 106 studies, and found concomitant declines in abundance and species richness. For studies that were resolved to species level (551 sites in 57 studies), we observed a decline in the number of initially abundant species through time, but not in the number of very rare species. At the population level, we found that species that were most abundant at the start of the time series showed the strongest average declines (corrected for regression-to-the-mean effects). Rarer species were, on average, also declining, but these were offset by increases of other species. Our results suggest that the observed decreases in total insect abundance2 can mostly be explained by widespread declines of formerly abundant species. This counters the common narrative that biodiversity loss is mostly characterized by declines of rare species8,9. Although our results suggest that fundamental changes are occurring in insect assemblages, it is important to recognize that they represent only trends from those locations for which sufficient long-term data are available. Nevertheless, given the importance of abundant species in ecosystems10, their general declines are likely to have broad repercussions for food webs and ecosystem functioning.

Extinction drives recent thermophilization but does not trigger homogenization in forest understorey

The ongoing climate change is triggering plant community thermophilization. This selection process ought to shift community composition towards species adapted to warmer climates but may also lead to biotic homogenization. The link between thermophilization and homogenization and the community dynamics that drive them (colonization and extinction) remain unknown but is critical for understanding community responses under rapid environmental change. We used 14,167 pairs of plots to study shifts in plant community during 10 years of rising temperature in 80 forest ecoregions of France. We computed community mean thermal optimum (thermophilization) and Δβ-diversity (homogenization) for each ecoregion and partitioned these changes into extinction and colonization dynamics of cold- and warm-adapted species. Forest understorey communities thermophilized on average by 0.12 °C per decade and up to 0.20 °C per decade in warm ecoregions. This rate was entirely driven by extinction dynamics. Extinction of cold-adapted species was a driver of homogenization but it was compensated for by the colonization of rare species and the extinction of common species, resulting in the absence of an apparent homogenization trend. Here we show a dieback of present cold-adapted species rather than an adaptation of communities via the arrival of warm-adapted species, with a mutually cancelling effect on β-diversity. These results suggest that a future loss of biodiversity and delayed biotic homogenization should be considered.

Floristic homogenization of South Pacific islands commenced with human arrival

The increasing similarity of plant species composition among distinct areas is leading to the homogenization of ecosystems globally. Human actions such as ecosystem modification, the introduction of non-native plant species and the extinction or extirpation of endemic and native plant species are considered the main drivers of this trend. However, little is known about when floristic homogenization began or about pre-human patterns of floristic similarity. Here we investigate vegetation trends during the past 5,000 years across the tropical, sub-tropical and warm temperate South Pacific using fossil pollen records from 15 sites on 13 islands within the biogeographical realm of Oceania. The site comparisons show that floristic homogenization has increased over the past 5,000 years. Pairwise Bray-Curtis similarity results also show that when two islands were settled by people in a given time interval, their floristic similarity is greater than when one or neither of the islands were settled. Importantly, higher elevation sites, which are less likely to have experienced human impacts, tended to show less floristic homogenization. While biotic homogenization is often referred to as a contemporary issue, we have identified a much earlier trend, likely driven by human colonization of the islands and subsequent impacts.

FISHGLOB_data: an integrated dataset of fish biodiversity sampled with scientific bottom-trawl surveys

Scientific bottom-trawl surveys are ecological observation programs conducted along continental shelves and slopes of seas and oceans that sample marine communities associated with the seafloor. These surveys report taxa occurrence, abundance and/or weight in space and time, and contribute to fisheries management as well as population and biodiversity research. Bottom-trawl surveys are conducted all over the world and represent a unique opportunity to understand ocean biogeography, macroecology, and global change. However, combining these data together for cross-ecosystem analyses remains challenging. Here, we present an integrated dataset of 29 publicly available bottom-trawl surveys conducted in national waters of 18 countries that are standardized and pre-processed, covering a total of 2,170 sampled fish taxa and 216,548 hauls collected from 1963 to 2021. We describe the processing steps to create the dataset, flags, and standardization methods that we developed to assist users in conducting spatio-temporal analyses with stable regional survey footprints. The aim of this dataset is to support research, marine conservation, and management in the context of global change.

Systematic loss in biotic heterogeneity but not biodiversity across multiple trophic levels in Erhai lake, China

Anthropogenic disturbances and climate change have significantly altered the biotic composition across many ecosystems, leading to changes in biodiversity and even ecological collapse. An ecosystem comprises multiple trophic levels, and the issue how these disturbances affect their assembly processes remains unclear. Ecological stability of assemblages was maintained by their structure, and thus, revealing structure changes across trophic levels could improve our understanding of how ecosystems response to disturbances as a whole. In this study, we combined methods from palaeolimnology, ecology and network analysis, and observed the changes of biodiversity and network structure of two trophic levels (algae - diatoms and zoobenthos - chironomids) in Erhai lake, Southwest China over the last century. Results showed nutrient enrichment induced shifts in diatom and chironomid assemblages at ∼2001 CE, suggesting that the shift in Erhai lake may have occurred at multiple trophic levels. We found biodiversity exhibit different trends across trophic levels as it decreased in diatoms but increased in chironomids. However, network skewness declined in both trophic levels, indicating the common loss of biotic heterogeneity. The consistent decline of skewness among trophic levels long before the compositional shift is a potential parameter to warn of the shifts in lake ecosystems.

The vegetation of Holocene coastal dunes of the Cape south coast, South Africa

The vegetation of calcareous coastal dunes of Holocene age along the south coast of South Africa's Cape Floristic Region is poorly described. This vegetation comprises a mosaic of communities associated with two biomes, Fynbos and Subtropical Thicket. Previously, expert knowledge rather than quantitative floristic analysis has been used to identify and delimit vegetation units. In many areas, mapped units conflate vegetation on Holocene sand with that on unconsolidated sediments of late Pleistocene age, despite pronounced species turnover across this edaphic boundary. Despite dominance by Cape lineages and fynbos vegetation, dune vegetation in the eastern part of the region has been included in the Subtropical Thicket Biome rather than the Fynbos Biome. The high levels of local plant endemism associated with this dune vegetation and the small and fragmented configuration of these habitats, makes it an urgent conservation priority especially when placed in the context of rising sea levels, increasing development pressures and numerous other threats. Here we provide a quantitative analysis of 253 plots of the 620 km2 of Holocene dune vegetation of the study area using phytosociological and multivariate methods. We identified six fynbos and two thicket communities based on the occurrences of 500 species. Following a long tradition in Cape vegetation typology, we used the Strandveld (beach vegetation) concept as our first-order vegetation entity and identified six units based on the fynbos floras. These were, from east to west, Southeastern Strandveld, St Francis Strandveld, Goukamma Strandveld, Southwestern Strandveld and Grootbos Strandveld. Each unit was differentiated by a suite of differential species, most being Holocene dune endemics. The two thicket communities-Mesic and Xeric Dune Thicket-showed limited variation across the study area and were subsumed into the Strandveld units. We discussed our findings in terms of vegetation-sediment relationships, emphasizing the need for a greater geographical coverage of sediment ages to facilitate a better understanding of deposition history on vegetation composition. We also discussed the role of soil moisture and fire regime on structuring the relative abundance of fynbos and thicket across the Holocene dune landscape. Finally, we address the conservation implications of our study, arguing that all remaining Holocene dune habitat should be afforded the highest conservation priority in regional land-use planning processes.

Three in four undescribed plant species are threatened with extinction

This article is part of the Special Collection ‘Global plant diversity and distribution’. See https://www.newphytologist.org/global-plant-diversity for more details.

Distinct hybridization modes in wide- and narrow-ranged lineages of Causonis (Vitaceae)

BACKGROUND

Explaining contrasting patterns of distribution between related species is crucial for understanding the dynamics of biodiversity. Despite instances where hybridization and whole genome duplication (WGD) can yield detrimental outcomes, a role in facilitating the expansion of distribution range has been proposed. The Vitaceae genus Causonis exhibits great variations in species' distribution ranges, with most species in the derived lineages having a much wider range than those in the early-diverged lineages. Hybridization and WGD events have been suggested to occur in Causonis based on evidence of phylogenetic discordance. The genus, therefore, provides us with an opportunity to for explore different hybridization and polyploidization modes in lineages with contrasting species' distribution ranges. However, the evolutionary history of Causonis incorporating potential hybridization and WGD events remains to be explored.

RESULTS

With plastid and nuclear data from dense sampling, this study resolved the phylogenetic relationships within Causonis and revealed significant cyto-nuclear discordance. Nuclear gene tree conflicts were detected across the genus, especially in the japonica-corniculata clade, which were mainly attributed to gene flow. This study also inferred the allopolyploid origin of the core Causonis species, which promoted the accumulation of stress-related genes. Causonis was estimated to have originated in continental Asia in the early Eocene, and experienced glaciation in the early Oligocene, shortly after the divergence of the early-divergent lineages. The japonica-corniculata clade mainly diversified in the Miocene, followed by temperature declines that may have facilitated secondary contact. Species distribution modeling based on current climate change predicted that the widespread C. japonica tends to be more invasive, while the endemic C. ciliifera may be at risk of extinction.

CONCLUSIONS

This study presents Causonis, a genus with complex reticulate evolutionary history, as a model of how hybridization and WGD modes differ in lineages of contrasting species' geographic ranges. It is important to consider specific evolutionary histories and genetic properties of the focal species within conservation strategies.

Disentangling spatiotemporal dynamics in metacommunities through a species-patch network approach

Colonization and extinction at local and regional scales, and gains and losses of patches are important processes in the spatiotemporal dynamics of metacommunities. However, analytical challenges remain in quantifying such spatiotemporal dynamics when species extinction-colonization and patch gain and loss processes act simultaneously. Recent advances in network analysis show great potential in disentangling the roles of colonization, extinction, and patch dynamics in metacommunities. Here, we developed a species-patch network approach to quantify metacommunity dynamics including (i) temporal changes in network structure, and (ii) temporal beta diversity of species-patch links and its components that reflect species extinction-colonization and patch gain and loss. Application of the methods to simulated datasets demonstrated that the approach was informative about metacommunity assembly processes. Based on three empirical datasets, our species-patch network approach provided additional information about metacommunity dynamics through distinguishing the effects of species colonization and extinction at different scales from patch gains and losses and how specific environmental factors related to species-patch network structure. In conclusion, our species-patch network framework provides effective methods for monitoring and revealing long-term metacommunity dynamics by quantifying gains and losses of both species and patches under local and global environmental change.