Explore the vast range of titles available.

Anthropogenic climate change is now in full swing, our global average temperature already having increased by 1°C from preindustrial levels. Many studies have documented individual impacts of the changing climate that are particular to species or regions, but individual impacts are accumulating and being amplified more broadly. Scheffers et al. review the set of impacts that have been observed across genes, species, and ecosystems to reveal a world already undergoing substantial change. Understanding the causes, consequences, and potential mitigation of these changes will be essential as we move forward into a warming world. Science , this issue p. 10.1126/science.aaf7671 Most ecological processes now show responses to anthropogenic climate change. In terrestrial, freshwater, and marine ecosystems, species are changing genetically, physiologically, morphologically, and phenologically and are shifting their distributions, which affects food webs and results in new interactions. Disruptions scale from the gene to the ecosystem and have documented consequences for people, including unpredictable fisheries and crop yields, loss of genetic diversity in wild crop varieties, and increasing impacts of pests and diseases. In addition to the more easily observed changes, such as shifts in flowering phenology, we argue that many hidden dynamics, such as genetic changes, are also taking place. Understanding shifts in ecological processes can guide human adaptation strategies. In addition to reducing greenhouse gases, climate action and policy must therefore focus equally on strategies that safeguard biodiversity and ecosystems.

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. 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. 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. 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.

The construction of large dams will have an impact on the biodeiversity of tropical Asian rivers and their associated wetlands. Attempts to predict the consequences of flow alterations on biodiversity in Asia, however, are confounded by the trend in the region toward more, and bigger, dams.

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

While high efficiency and cost‐effectiveness are two merits of environmental DNA (eDNA) techniques for detecting aquatic organisms, the difficulty of designing species‐specific primers can result in significant expenditure of time and money. During the in silico stage of primer development, primer specificity is predicted with alignment techniques such as BLAST that is based on the number and position of the primer/nontarget template mismatches. However, we speculate that nonspecific amplification is influenced by additional parameters, which lead to inaccuracies of in silico prediction. We performed in vitro specificity tests for 38 species‐specific primers selected for seven fishes and six turtles, using single‐plex conventional PCR (cPCR). A subset of 12 primer pairs were further tested with SYBR Green‐based or TaqMan‐based single‐plex quantitative PCR (qPCR). We disentangle the relative importance of mismatch properties (types and positions), primer properties (length, GC content, and 3′ end stability), PCR conditions (template concentrations and annealing temperatures), and PCR technique (cPCR, TaqMan‐based, or SYBR Green‐based qPCR) in determining the occurrence of amplifications. We then compared the PCR outcomes with the specificity check under two stringency scenarios based on alignment (i.e., BLAST search). We conducted a total of 679 cPCR and 226 qPCR analyses, with 90% of the reactions tested with nontarget templates. Primer pairs predicted by Primer‐BLAST to be specific rarely showed such specificity during the in vitro testing. BLAST searches correctly predicted the outcomes of around 67% of cPCR and qPCR, but had low sensitivity in detection of nontarget amplification (29–57%). Primer specificity increased significantly with total number of mismatches and annealing temperature, but decreased with higher GC content in the primer sequence. Mismatches that consisted of A‐A, G‐A, and C‐C pairings exerted 56% stronger reduction in nonspecific amplification effects than other mismatches. To conclude, we show that the prediction of primer specificity based only on the number and position of mismatches can be misleading. Our findings can be applied to increase the efficiency of the in silico primer selection process to maintain the relatively high efficiency and cost‐effectiveness of eDNA techniques.

The flat-headed loach ( Oreonectes platycephalus) is a small fish inhabiting headwaters of hillstreams of southern China. Its local populations are characterized by low genetic diversity and exceptionally high differentiation, making it an ideal model for studying small population isolates’ persistence and adaptive potential. However, the lack of Oreonectes reference genomes limits endeavours toward these ambitions. We assembled the first haplotype-resolved chromosome-level genome of the genus Oreonectes using PacBio HiFi and Hi-C technologies. This genome consists of two haplotypes (24 pseudo-chromosomes in each), with sizes of 565.68 Mb (haplotype A) and 521.13 Mb (haplotype B) and scaffold N50 lengths of 22.80 Mb and 21.91 Mb, respectively. Chr01 was identified as the likely sex chromosome pair. After masking repetitive elements which accounted for 34.43% to 36.44% of the genome, there are 27,127 protein-coding genes in haplotype A and 25,576 in haplotype B. The availability of this haplotype-resolved chromosome-level reference genome will facilitate the study of population and conservation genetics of the flat-headed loach and other Oreonectes species.

Population genetics is a valuable tool for conservationists to quantify population‐level genetic variation and identify priority conservation units. The Hong Kong newt (Paramesotriton hongkongensis) is a tropical salamander restricted to streams and forests in southern China, facing significant challenges from range‐wide deforestation since the 1600s, and recent rapid urban development. Using species‐specific microsatellite markers, we found surprisingly high genetic diversity within and among P. hongkongensis populations, despite long‐term habitat disturbance and fragmentation. Only 2 out of 10 sites exhibited evidence of recent population bottlenecks. Bayesian clustering revealed four well‐supported genetic clusters within the newt's Hong Kong range, suggesting that these should be managed as separate conservation units. Our findings highlight the resilience of this species to historical and contemporary disturbances and emphasize the importance of considering genetic data in conservation planning for amphibians in human‐modified landscapes. In this paper, we investigated the genetic diversity and population genetic structure of an endangered species of salamander using species‐specific microsatellite markers. Our results indicated that the remaining populations are still genetically diverse and protected areas in place are effective in maintaining both genetic diversity and structure. However, management authorities should consider the genetic origins of animals in any future translocation/relocation efforts.

Freshwater biodiversity is under threat worldwide, but the intensity of threat in the Oriental biogeographic region of tropical Asia is exceptional. Asia is the most densely populated region on Earth. Many rivers in that region are grossly polluted, and significant portions of their drainage basins and floodplains have been deforested or otherwise degraded. Flow regulation has been practiced for centuries, and thousands of dams have been constructed, with the result that most of the rivers are now dammed, often at several points along their course. Irrigation, hydropower, and flood security are among the perceived benefits. Recent water engineering projects in Asia have been exceptionally aggressive; they include the world’s largest and tallest dams in China and a water transfer scheme intended to link India’s major rivers. Some of these projects, i.e., those on the Mekong, have international ramifications that have yet to be fully played out. Overexploitation has exacerbated the effects of habitat alterations on riverine biodiversity, particularly that of fishes. Some fishery stocks have collapsed, and many fish and other vertebrate species are threatened with extinction. The pressure from growing impoverished human populations, increasingly concentrated in cities, has forced governments to focus on economic development rather than environmental protection and conservation. Although legislation has been introduced to control water pollution, which is a danger to human health. it is not explicitly intended to protect biodiversity. Where legislation has been enforced, it can be effective against point-source polluters, but it has not significantly reduced the huge quantities of organic pollution from agricultural and domestic sources that contaminate rivers such as the Ganges and Yangtze. River scientists in Asia appear to have had little influence on policy makers or the implementation of water development projects. Human demands from agriculture and industry dominate water allocation policies, and in-stream flow needs for ecosystems have yet to be widely addressed. Restoration of Asian rivers to their original state is impractical given the constraints prevailing in the region, but some degree of rehabilitation will be possible if relevant legislation and scientific information are promptly applied. Opportunities do exist: enforcement of environmental legislation in China has been strengthened, leading to the suspension of major dam projects. The 2003 introduction of an annual fishing moratorium along the Yangtze River, as well as breeding and restocking programs for endangered fishes in the Yangtze and Mekong, offer the chance to leverage other initiatives that enhance river health and preserve biodiversity, particularly that of fish species. Preliminary data indicate that degraded rivers still retain some biodiversity that can be the focus of rehabilitation efforts. To strengthen these efforts, it is important to identify which ecological features enhance biodiversity and which ones make rivers more vulnerable to human impacts.

The hypotheses that beta diversity should increase with decreasing latitude and increase with spatial extent of a region have rarely been tested based on a comparative analysis of multiple datasets, and no such study has focused on stream insects. We first assessed how well variability in beta diversity of stream insect metacommunities is predicted by insect group, latitude, spatial extent, altitudinal range, and dataset properties across multiple drainage basins throughout the world. Second, we assessed the relative roles of environmental and spatial factors in driving variation in assemblage composition within each drainage basin. Our analyses were based on a dataset of 95 stream insect metacommunities from 31 drainage basins distributed around the world. We used dissimilarity‐based indices to quantify beta diversity for each metacommunity and, subsequently, regressed beta diversity on insect group, latitude, spatial extent, altitudinal range, and dataset properties (e.g., number of sites and percentage of presences). Within each metacommunity, we used a combination of spatial eigenfunction analyses and partial redundancy analysis to partition variation in assemblage structure into environmental, shared, spatial, and unexplained fractions. We found that dataset properties were more important predictors of beta diversity than ecological and geographical factors across multiple drainage basins. In the within‐basin analyses, environmental and spatial variables were generally poor predictors of variation in assemblage composition. Our results revealed deviation from general biodiversity patterns because beta diversity did not show the expected decreasing trend with latitude. Our results also call for reconsideration of just how predictable stream assemblages are along ecological gradients, with implications for environmental assessment and conservation decisions. Our findings may also be applicable to other dynamic systems where predictability is low. Beta diversity should vary along major ecological gradients. We used data for 95 stream insect metacommunities to examine if beta diversity showed general patterns over the world. We did not find clear patterns along latitudinal, altitudinal or environmental gradients, suggesting that stochasticity typical of frequently‐disturbed stream ecosystems may hinder finding clear patterns in stream insect beta diversity.

Human and environmental well-being—including disease resistance or avoidance, good nutrition, and species-appropriate population dynamics—are congruent with sustained healthy conditions. Unfortunately, hydrological alterations designed to benefit human societies often have unintended—and sometimes severe—consequences for the environment and the biodiversity it supports, and hence affecting billions of people. Improving this situation necessitates new water-resource developments, better water-use efficiency, and a reduction of contamination. Overall, the influences of existing and future freshwater (FW) regimes on human and environmental well-being are varied and wide-ranging. Furthermore, the scale is daunting: >1 billion people currently live in basins likely to require river management interventions for climate change alone. Global declines in FW biodiversity, in the nutritional value, and abundance of harvestable FW and riparian products, as well as deterioration in habitat quality for many species, require solutions; as do ongoing increases in the spread of FW-related diseases and non-native species. Modifications to FWs are now manifested in population declines and non-sustainable demographics for many aquatic species, as well as in deterioration of human health. In response, scientists, policy-makers, and water users are beginning to conceptualize FWs in terms of a global water system (GWS) to better understand and manage anthropogenic impacts. This involves identifying the ecological and policy implications of changes to the GWS, establishing international programs to understand and resolve major social and environmental issues arising from those changes, and developing broad-based mitigation or restoration techniques (e.g., environmental flow methodologies). Achieving these goals is paramount for maintaining human health as well as for the FW ecosystems upon which we depend.