Ecological genetics of isolated loach populations indicate compromised adaptive potential.

Many endangered species live in fragmented and isolated populations with low genetic variability, signs of inbreeding, and small effective population sizes - all features elevating their extinction risk. The flat-headed loach (Oreonectes platycephalus), a small noemacheilid fish, is widely across southern China, but only in the headwaters of hillstreams; as a result, they are spatially isolated from conspecific populations. We surveyed single nucleotide polymorphisms in 16 Hong Kong populations of O. platycephalus to determine whether loach populations from different streams were genetically isolated from each other, showed low levels of genetic diversity, signs of inbreeding, and had small contemporary effective population sizes. Estimates of average observed heterozygosity (HO = 0.0473), average weighted nucleotide diversity (πw = 0.0546) and contemporary effective population sizes (Ne = 10.2 ~ 129.8) were very low, and several populations showed clear signs of inbreeding as judged from relatedness estimates. The degree of genetic differentiation among populations was very high (average FST = 0.668), even over short geographic distances (<1.5 km), with clear patterns of isolation by distance. These results suggest that Hong Kong populations of O. platycephalus have experienced strong genetic drift and loss of genetic variability because sea-level rise after the last glaciation reduced connectedness among paleodrainages, isolating populations in headwaters. All this, together with the fact that the levels of genetic diversity and contemporary effective population sizes within O. platycephalus populations are lower than most other freshwater fishes, suggests that they face high local extinction risk and have limited capacity for future adaptation.

High spatial variability in a species-rich assemblage of diadromous fishes in Hong Kong, southern China.

China has experienced substantial coastal reclamation and damming of rivers. These changes have the potential to impact migrations of diadromous fishes between the sea and fresh waters, but the composition of these fishes and the impacts of barriers to their movement in China have received little attention. We inventoried the species composition and distribution of diadromous fishes, and the impacts of barriers on them, in the Hong Kong Special Administrative Region (HKSAR), southern China. Fish assemblages were surveyed using hand-nets, supplemented by cast-netting and single-pass snorkel surveys, in 24 small coastal streams across three regions. Surveys were undertaken on multiple occasions during the wet and dry seasons to account for the monsoonal tropical climate. Twenty-eight diadromous fishes were collected, mostly gobies, amounting to over half (53%) of the total richness of primary freshwater fishes; four additional species are known from literature records. Diadromous richness was 48% greater during the wet season, when all species were encountered. Richness varied substantially among streams, from a maximum of 17 (2 streams that were diversity hot spots) to none (3 streams). The most widespread diadromous fish was Glossogobius giuris (71% frequency of occurrence), followed by Mugil cephalus (58% occurrence) and Eleotris oxycephala (50% occurrence). The remaining 25 diadromous fishes occurred in fewer than half of the streams; 12 species were confined to a single stream and may be locally threatened. There were conspicuous spatial differences in diadromous assemblages across HKSAR, despite its limited extent (1114 km2), the proximity of the surveyed streams, and the broad geographic distribution of most species. Regional species assemblages were influenced by localized habitat characteristics, with a noticeable distinction between areas with and without large, fast-flowing, and highly oxygenated streams. The presence of in-stream barriers (weirs: 0.3-8.7 m high) did not affect spatial patterns in species assemblages, although, on average, diadromous richness was lower in weir-obstructed streams (4.0 vs. 6.9 species in unobstructed streams). In total, 18 species were confined to unobstructed streams or sections below weirs, whereas the remaining 10 species were recorded both above and below weirs. Only the mottled eel (Anguilla marmorata) and a goby (Stiphodon multisquamus) were able to ascend weirs over 2 m. Although at least 400 m of the lower course of each stream was sampled, diadromous fishes were confined to the first 300 m in 12 of the 13 weir-obstructed streams. Remarkably, the tally of 32 diadromous species in HKSAR exceeds the 19 known from mainland China, highlighting the need for further research on composition and conservation status of diadromous fishes.

A global agenda for advancing freshwater biodiversity research.

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.

Shifts in aquatic insect composition in a tropical forest stream after three decades of climatic warming.

The effects of climatic warming on tropical streams have received little attention, and field studies of such changes are generally lacking. Drifting insects from a Hong Kong forest stream were sampled for 36 months between 2013 and 2016, and compared with samples collected using identical methods in 1983-84. Mean air temperatures rose by ~0.5°C (0.17°C per decade) over this period. The stream drained an uninhabited protected area, so no climate-change effects were confounded by anthropogenic disturbance. In total, 105 taxa and >77,000 individuals were collected. Richness of samples in the historic and contemporary datasets did not differ, but true diversity of drifting insects was highest in 1983-84, and declined between 2013-14 and 2015-16. There was considerable disparity in assemblage composition between 1983-84 and 2013-16, and smaller between-year changes in the contemporary dataset. Nine indicator species of the historic dataset were identified. Most were mayflies, particularly Baetidae, which were greatly reduced in relative abundance in 2013-16. Diptera became more numerous, and tanypodine chironomids were the sole contemporary indicator taxon. Relative abundance of eight of 19 drifting species (comprising 60% of total insects) was lower in 2013-16, when the dominant baetid mayfly during 1983-84 had declined by almost 90%; only one of the 19 species occurred at higher abundance. Eight species were affected by seasonal temperature variability, but these responses were not correlated with any tendency to exhibit long-term changes in abundance. Substantial shifts in composition, including declines in mayfly relative abundance and assemblage diversity, occurred after three decades of warming, despite the broad annual range of stream temperatures (~16°C) in Hong Kong. This contradicts the well-known prediction that organisms from variable climates have evolved wider thermal tolerances that reflect prevailing environmental conditions. The observed compositional reorganization indicates that variability, rather than stability, may be typical of undisturbed tropical stream communities.

Optimal allocation of Red List assessments to guide conservation of biodiversity in a rapidly changing world.

The IUCN Red List is the most extensive source of conservation status assessments for species worldwide, but important gaps in coverage remain. Here, we demonstrate the use of a spatial prioritization approach to efficiently prioritize species assessments to achieve increased and up-to-date coverage efficiently. We focus on freshwater fishes, which constitute a significant portion of vertebrate diversity, although comprehensive assessments are available for only 46% of species. We used marxan to identify ecoregions for future assessments that maximize the coverage of species while accounting for anthropogenic stress. We identified a set of priority regions that would help assess one-third (ca 4000 species) of all freshwater fishes in need of assessment by 2020. Such assessments could be achieved without increasing current investment levels. Our approach is suitable for any taxon and can help ensure that species threat assessments are sufficiently complete to guide global conservation efforts in a rapidly changing world.

Biotic and abiotic variables influencing plant litter breakdown in streams: a global study.

Plant litter breakdown is a key ecological process in terrestrial and freshwater ecosystems. Streams and rivers, in particular, contribute substantially to global carbon fluxes. However, there is little information available on the relative roles of different drivers of plant litter breakdown in fresh waters, particularly at large scales. We present a global-scale study of litter breakdown in streams to compare the roles of biotic, climatic and other environmental factors on breakdown rates. We conducted an experiment in 24 streams encompassing latitudes from 47.8° N to 42.8° S, using litter mixtures of local species differing in quality and phylogenetic diversity (PD), and alder (Alnus glutinosa) to control for variation in litter traits. Our models revealed that breakdown of alder was driven by climate, with some influence of pH, whereas variation in breakdown of litter mixtures was explained mainly by litter quality and PD. Effects of litter quality and PD and stream pH were more positive at higher temperatures, indicating that different mechanisms may operate at different latitudes. These results reflect global variability caused by multiple factors, but unexplained variance points to the need for expanded global-scale comparisons.

Using genetic tools to inform conservation of fragmented populations of Asian elephants (Elephas maximus) across their range in China.

A herd of 15 Chinese elephants attracted international attention during their 2021 northward trek, motivating the government to propose establishment of an Asian elephant national park. However, planning is hampered by a lack of genetic information on the remaining populations in China. We collected DNA from 497 dung samples from all 5 populations encompassing the entire range of elephants in China and used mitochondrial and microsatellite markers to investigate their genetic and demographic structure. We identified 237 unique genotypes (153 females, 84 males), representing 81% of the known population. However, the effective population size was small (28, range 25-32). Historic demographic contraction appeared to account for low haplotype diversity (Hd = 0.235), but moderate nucleotide and nuclear diversity (π = 0.6%, He = 0.55) was attributable to post-bottleneck recovery involving recent population expansion plus historical gene exchange with elephants in Myanmar, Lao PDR, and Vietnam. The 5 populations fell into 3 clusters, with Nangunhe elephants differing consistently from the other 4 populations (FST = 0.23); elephants from Mengyang, Simao, and Jiangcheng belonged to a single population (henceforth, MSJ), and differed from the Shangyong population (FST = 0.11). Interpopulation genetic variation reflected isolation by distance and female-biased dispersal. Chinese elephants should be managed as 2 distinct units: Nangunhe and another combining Shangyong and MSJ; their long-term viability will require restoring gene flow between Shangyong and MSJ, and between elephants in China and neighboring countries. Our results have the potential to inform conservation planning for an iconic megafaunal species.

Anthropogenic pressures increase extinction risk of an isolated Asian elephant (Elephas maximus) population in southwestern China, as revealed by a combination of molecular- and landscape-scale approaches.

Identification of the effect of anthropogenic threats on ecosystem is crucial. We used molecular tools and remote sensing to evaluate the population status of an isolated Asian elephant population in southwestern China in response to changes in habitat suitability between 1989 and 2019. A total of 22 unique genotypes were identified from 117 dung samples collected between March and June 2018 using microsatellite DNA analysis, including 13 males and 9 females. Based on the size of fecal boli, 1 animal was a juvenile, 9 were subadults, and 12 were adults, indicating that recruitment was limited. The effective population size was small (15.3) but there was no signature of a recent population bottleneck. We observed a low genetic diversity (He = 0.46 ± 0.05) and a high level of inbreeding (Fis of 0.43 ± 0.11), suggesting low population viability and high risk of extinction. In total, these elephants lost nearly two thirds (62%) of their habitat in 3 decades. The expansion of agriculture and rubber plantations followed by an increase in human settlements after 1989 increased the isolation of this population. We recommend that resettlement of 800 inhabitants of 2 villages and the abandonment of associated farmland and rubber plantations would make an additional 20 km2 of suitable habitat available. This could allow a population increase of 14 elephants, possibly by translocating individuals from elsewhere in China. Our findings can be applied to the management and conservation of other fragmented populations in China or in other range countries of Asian elephants.

Sex-related differences in aging rate are associated with sex chromosome system in amphibians.

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture-recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the "unguarded X/Z effect") or repeat-rich Y/W chromosome (the "toxic Y/W effect") could accelerate aging in the heterogametic sex in some vertebrate clades.

A global experiment suggests climate warming will not accelerate litter decomposition in streams but might reduce carbon sequestration.

The decomposition of plant litter is one of the most important ecosystem processes in the biosphere and is particularly sensitive to climate warming. Aquatic ecosystems are well suited to studying warming effects on decomposition because the otherwise confounding influence of moisture is constant. By using a latitudinal temperature gradient in an unprecedented global experiment in streams, we found that climate warming will likely hasten microbial litter decomposition and produce an equivalent decline in detritivore-mediated decomposition rates. As a result, overall decomposition rates should remain unchanged. Nevertheless, the process would be profoundly altered, because the shift in importance from detritivores to microbes in warm climates would likely increase CO(2) production and decrease the generation and sequestration of recalcitrant organic particles. In view of recent estimates showing that inland waters are a significant component of the global carbon cycle, this implies consequences for global biogeochemistry and a possible positive climate feedback.

Global distribution of a key trophic guild contrasts with common latitudinal diversity patterns.

Most hypotheses explaining the general gradient of higher diversity toward the equator are implicit or explicit about greater species packing in the tropics. However, global patterns of diversity within guilds, including trophic guilds (i.e., groups of organisms that use similar food resources), are poorly known. We explored global diversity patterns of a key trophic guild in stream ecosystems, the detritivore shredders. This was motivated by the fundamental ecological role of shredders as decomposers of leaf litter and by some records pointing to low shredder diversity and abundance in the tropics, which contrasts with diversity patterns of most major taxa for which broad-scale latitudinal patterns haven been examined. Given this evidence, we hypothesized that shredders are more abundant and diverse in temperate than in tropical streams, and that this pattern is related to the higher temperatures and lower availability of high-quality leaf litter in the tropics. Our comprehensive global survey (129 stream sites from 14 regions on six continents) corroborated the expected latitudinal pattern and showed that shredder distribution (abundance, diversity and assemblage composition) was explained by a combination of factors, including water temperature (some taxa were restricted to cool waters) and biogeography (some taxa were more diverse in particular biogeographic realms). In contrast to our hypothesis, shredder diversity was unrelated to leaf toughness, but it was inversely related to litter diversity. Our findings markedly contrast with global trends of diversity for most taxa, and with the general rule of higher consumer diversity at higher levels of resource diversity. Moreover, they highlight the emerging role of temperature in understanding global patterns of diversity, which is of great relevance in the face of projected global warming.

Recovery of tropical marine benthos after a trawl ban demonstrates linkage between abiotic and biotic changes.

Bottom trawling, which is highly detrimental to seabed habitats, has been banned in some jurisdictions to mitigate the problems of habitat destruction and overfishing. However, most reports of ecosystem responses to trawling impacts originate from temperate latitudes, focusing on commercial species, and recovery of invertebrate macrobenthos from trawl ban has hardly ever been studied in the tropics. In Hong Kong (lat. 22.4°N), a history of intensive trawling with various types of gears has long degraded coastal ecosystems. To facilitate the recovery of fisheries resources and associated benthic ecosystems, the Government of the Hong Kong Special Administrative Region implemented a territory-wide trawl ban on December 31, 2012. Comparison of surveys conducted in June 2012 (before the trawl ban) and June 2015 (2.5 years after the ban) revealed higher organic contents in sediment and lower suspended-solid loads in water column, as well as a significant increase in site-based abundance, species richness, functional diversity and among-site similarity of macrobenthos after the trawl ban. Our results suggest that the imposition of a trawl ban can be an effective measure for biodiversity conservation in tropical coastal waters.

International socioeconomic inequality drives trade patterns in the global wildlife market.

The wildlife trade is a major cause of species loss and a pathway for disease transmission. Socioeconomic drivers of the wildlife trade are influential at the local scale yet rarely accounted for in multinational agreements aimed at curtailing international trade in threatened species. In recent decades (1998-2018), approximately 421,000,000 threatened (i.e., CITES-listed) wild animals were traded between 226 nations/territories. The global trade network was more highly connected under conditions of greater international wealth inequality, when rich importers may have a larger economic advantage over poorer exporting nations/territories. Bilateral trade was driven primarily by socioeconomic factors at the supply end, with wealthier exporters likely to supply more animals to the global market. Our findings suggest that international policies for reducing the global wildlife trade should address inequalities between signatory states, possibly using incentive/compensation-driven programs modeled after other transnational environmental initiatives (e.g., REDD+).

Evidence of rapid shifts in the trophic base of lotic predators using experimental dietary manipulations and assimilation-based analyses.

Assimilation-based techniques such as stoichiometric analysis, bulk tissue stable isotope analysis (SIA), fatty acid (FA) profiling and compound-specific SIA of FAs can be used to resolve ambiguities in consumer-resource relationships, but comparisons of their effectiveness are lacking. Feeding trials and concurrent application of these techniques were used to investigate the trophic base of two shrimps from Hong Kong streams: the atyid Caridina cantonensis, which is a primary consumer, and predatory Macrobrachium hainanense (Palaemonidae). Leaf litter and periphyton were fed to C. cantonensis (CC-LF and CC-PF, respectively) reared in the laboratory for 2 months, when C. cantonensis, that had fed on a mixed diet (CC-WC), were collected from the field. Atyids from each group (CC-LF, CC-PF and CC-WC) were fed to M. hainanense (MH-L, MH-P and MH-W, respectively) during a further 2-month trial, at the end of which M. hainanense were also collected from the field (MH-R). FA biomarkers present in CC-WC and CC-PF indicated that C. cantonensis depended primarily on autochthonous foods, and FA profiles of CC-WC were distinct from those of CC-LF. Differences in C/N ratios and isotope signatures of leaf litter and periphyton were not reflected in tissues of atyids or palaemonid predators. FA profiles of M. hainanense groups were similar, but FA stable C isotope ratio (delta(13)C) signatures of MH-R and MH-W were distinct from those of MH-L and leaf litter. FA delta(13)C signatures of MH-R were similar to those of MH-P and MH-W, indicating that autochthonous resources constituted the trophic base of production for this predator. This is the first study using compound-specific SIA to study stream food chains. Compound-specific SIA and FA profiling allowed accurate elucidation of consumer-resource relationships that were not revealed by stoichiometry or bulk tissue SIA. Compound-specific SIA was particularly sensitive for detecting rapid shifts in the predator trophic base. This tool will have wide applicability for investigating food webs in a range of ecosystems.

Multiple threats imperil freshwater biodiversity in the Anthropocene.

Appropriation of fresh water to meet human needs is growing, and competition among users will intensify in a warmer and more crowded world. This essay explains why freshwater ecosystems are global hotspots of biological richness, despite a panoply of interacting threats that jeopardize biodiversity. The combined effects of these threats will soon become detrimental to humans since provision of ecosystem services, such as protein from capture fisheries, can only be sustained if waters remain healthy. Climate change poses an insidious existential threat to freshwater biodiversity in the Anthropocene, but immediate risks from dams, habitat degradation and pollution could well be far greater.

Correction: Mapping wader biodiversity along the East Asian-Australasian flyway.

[This corrects the article DOI: 10.1371/journal.pone.0210552.].

Mapping wader biodiversity along the East Asian-Australasian flyway.

BACKGROUND AND GOAL: The study is conducted to facilitate conservation of migratory wader species along the East Asian-Australasian Flyway, particularly to 1) Identify hotspots of wader species richness along the flyway and effectively map how these might change between breeding, non-breeding and migratory phases; 2) Determine if the existing network of protected areas (PA) is sufficient to effectively conserve wader biodiversity hotspots along the EAAF; 3) Assess how species distribution models can provide complementary distribution estimates to existing BirdLife range maps. METHODS: We use a species distribution modelling (SDM) approach (MaxEnt) to develop temporally explicit individual range maps of 57 migratory wader species across their annual cycle, including breeding, non-breeding and migratory phases, which in turn provide the first biodiversity hotspot map of migratory waders along the EAAF for each of these phases. We assess the protected area coverage during each migration period, and analyse the dominant environmental drivers of distributions for each period. Additionally, we compare model hotspots to those existing range maps of the same species obtained from the BirdLife Internationals' database. RESULTS: Our model results indicate an overall higher and a spatially different species richness pattern compared to that derived from a wader biodiversity hotspot map based on BirdLife range maps. Field observation records from the eBird database for our 57 study species confirm many of the hotspots revealed by model outputs (especially within the Yellow Sea coastal region), suggesting that current richness of the EAAF may have been underestimated and certain hotspots overlooked. Less than 10% of the terrestrial zones area (inland and coastal) which support waders are protected and, only 5% of areas with the highest 10% species richness is protected. MAIN CONCLUSIONS: The study results suggest the need for new areas for migratory wader research and conservation priorities including Yellow Sea region and Russian far-East. It also suggests a need to increase the coverage and percentage of current PA network to achieve Aichi Target 11 for Flyway countries, including giving stronger consideration to the temporal dynamics of wader migration.

Emerging threats and persistent conservation challenges for freshwater biodiversity.

In the 12 years since Dudgeon et al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in the world's lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only 2.3% of the Earth's surface, these ecosystems host at least 9.5% of the Earth's described animal species. Furthermore, using the World Wide Fund for Nature's Living Planet Index, freshwater population declines (83% between 1970 and 2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii) e-commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation; (xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes, plants, turtles and waterbirds, with potential for ecosystem-level changes through bottom-up and top-down processes. In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However, we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows, environmental DNA) and specific conservation-oriented actions (e.g. dam removal, habitat protection policies, managed relocation of species) that have been met with varying levels of success. Moving forward, we advocate hybrid approaches that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap between the aspirations of conservation biologists and the accelerating rate of species endangerment.

Biodiversity of leaf litter fungi in streams along a latitudinal gradient.

Global patterns of biodiversity have emerged for soil microorganisms, plants and animals, and the extraordinary significance of microbial functions in ecosystems is also well established. Virtually unknown, however, are large-scale patterns of microbial diversity in freshwaters, although these aquatic ecosystems are hotspots of biodiversity and biogeochemical processes. Here we report on the first large-scale study of biodiversity of leaf-litter fungi in streams along a latitudinal gradient unravelled by Illumina sequencing. The study is based on fungal communities colonizing standardized plant litter in 19 globally distributed stream locations between 69°N and 44°S. Fungal richness suggests a hump-shaped distribution along the latitudinal gradient. Strikingly, community composition of fungi was more clearly related to thermal preferences than to biogeography. Our results suggest that identifying differences in key environmental drivers, such as temperature, among taxa and ecosystem types is critical to unravel the global patterns of aquatic fungal diversity.

Integrating the social, hydrological and ecological dimensions of freshwater health: The Freshwater Health Index.

Degradation of freshwater ecosystems and the services they provide is a primary cause of increasing water insecurity, raising the need for integrated solutions to freshwater management. While methods for characterizing the multi-faceted challenges of managing freshwater ecosystems abound, they tend to emphasize either social or ecological dimensions and fall short of being truly integrative. This paper suggests that management for sustainability of freshwater systems needs to consider the linkages between human water uses, freshwater ecosystems and governance. We present a conceptualization of freshwater resources as part of an integrated social-ecological system and propose a set of corresponding indicators to monitor freshwater ecosystem health and to highlight priorities for management. We demonstrate an application of this new framework -the Freshwater Health Index (FHI) - in the Dongjiang River Basin in southern China, where stakeholders are addressing multiple and conflicting freshwater demands. By combining empirical and modeled datasets with surveys to gauge stakeholders' preferences and elicit expert information about governance mechanisms, the FHI helps stakeholders understand the status of freshwater ecosystems in their basin, how ecosystems are being manipulated to enhance or decrease water-related services, and how well the existing water resource management regime is equipped to govern these dynamics over time. This framework helps to operationalize a truly integrated approach to water resource management by recognizing the interplay between governance, stakeholders, freshwater ecosystems and the services they provide.