U.S. Geological Survey, Wetland and Aquatic Research Center

The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics. Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.

Abstract Background Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully established, with one area being the calculation and interpretation of assay limit of detection (LOD) and limit of quantification (LOQ). Aims Here, we propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies. Materials & Methods/ Results We utilize datasets from multiple cooperating laboratories to demonstrate both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for eDNA qPCR assays. We also provide details of an R script developed and applied for the modeling method. Discussion/Conclusions Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays.

Since amphibian declines were first proposed as a global phenomenon over a quarter century ago, the conservation community has made little progress in halting or reversing these trends. The early search for a "smoking gun" was replaced with the expectation that declines are caused by multiple drivers. While field observations and experiments have identified factors leading to increased local extinction risk, evidence for effects of these drivers is lacking at large spatial scales. Here, we use observations of 389 time-series of 83 species and complexes from 61 study areas across North America to test the effects of 4 of the major hypothesized drivers of declines. While we find that local amphibian populations are being lost from metapopulations at an average rate of 3.79% per year, these declines are not related to any particular threat at the continental scale; likewise the effect of each stressor is variable at regional scales. This result - that exposure to threats varies spatially, and populations vary in their response - provides little generality in the development of conservation strategies. Greater emphasis on local solutions to this globally shared phenomenon is needed.

ABSTRACT Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: ( i ) Genetic Diversity; ( ii ) Genetic Differentiation; ( iii ) Inbreeding; and ( iv ) Effective Population Size ( N e ). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.

Abstract Mangrove forests provide many ecosystem services but are among the world’s most threatened ecosystems. Mangroves vary substantially according to their geomorphic and sedimentary setting; while several conceptual frameworks describe these settings, their spatial distribution has not been quantified. Here, we present a new global mangrove biophysical typology and show that, based on their 2016 extent, 40.5% (54,972 km 2 ) of mangrove systems were deltaic, 27.5% (37,411 km 2 ) were estuarine and 21.0% (28,493 km 2 ) were open coast, with lagoonal mangroves the least abundant (11.0%, 14,993 km 2 ). Mangroves were also classified based on their sedimentary setting, with carbonate mangroves being less abundant than terrigenous, representing just 9.6% of global coverage. Our typology provides a basis for future research to incorporate geomorphic and sedimentary setting in analyses. We present two examples of such applications. Firstly, based on change in extent between 1996 and 2016, we show while all types exhibited considerable declines in area, losses of lagoonal mangroves (− 6.9%) were nearly twice that of other types. Secondly, we quantify differences in aboveground biomass between mangroves of different types, with it being significantly lower in lagoonal mangroves. Overall, our biophysical typology provides a baseline for assessing restoration potential and for quantifying mangrove ecosystem service provision.

BACKGROUND: Many mangrove ecosystems are periodically exposed to high velocity winds and surge from tropical cyclones, and often recover with time and continue to provide numerous societal benefits in the wake of storm events. SCOPE: This review focuses on the drivers and disturbance mechanisms (visible and functional) that tropical cyclones of various intensities have on mangrove ecosystem properties around the world, as well as the potential ecosystem services role offered by mangroves along storm-ravaged coastlines. When viewed together, studies describe repeatable types of impact and a variety of responses of mangroves that make them ecologically resilient to high velocity winds, and which have served to advance the notion that mangroves are disturbance-adapted ecosystems. CONCLUSIONS: Studies have documented massive tree mortality and forest structural shifts as well as high variability of spatial effects associated with proximity and direction of the tropical cyclone trajectory that influence biogeochemical processes, recovery of individual trees, and forest regeneration and succession. Mangroves provide coastal protection through surge and wind suppression during tropical cyclones, and yet are able to overcome wind effects and often recover unless some alternative environmental stress is at play (e.g. hydrological alteration or sedimentation). Structural elements of mangroves are influenced by the legacies imposed by past tropical cyclone injury, which affect their current appearance, and presumably their function, at any point in time. However, much is yet to be discovered about the importance of the effects of tropical cyclones on these fascinating botanical ecosystems, including the role of storm-based sediment subsidies, and much more effort will be needed to predict future recovery patterns as the frequency and intensity of tropical cyclones potentially change.

Abstract Significant efforts have been invested to restore mangrove forests worldwide through reforestation and afforestation. However, blue carbon benefit has not been compared between these two silvicultural pathways at the global scale. Here, we integrated results from direct field measurements of over 370 restoration sites around the world to show that mangrove reforestation (reestablishing mangroves where they previously colonized) had a greater carbon storage potential per hectare than afforestation (establishing mangroves where not previously mangrove). Greater carbon accumulation was mainly attributed to favorable intertidal positioning, higher nitrogen availability, and lower salinity at most reforestation sites. Reforestation of all physically feasible areas in the deforested mangrove regions of the world could promote the uptake of 671.5–688.8 Tg CO 2 -eq globally over a 40-year period, 60% more than afforesting the same global area on tidal flats (more marginal sites). Along with avoiding conflicts of habitat conversion, mangrove reforestation should be given priority when designing nature-based solutions for mitigating global climate change.

In the 21st century, accelerated sea‐level rise and continued coastal development are expected to greatly alter coastal landscapes across the globe. Historically, many coastal ecosystems have responded to sea‐level fluctuations via horizontal and vertical movement on the landscape. However, anthropogenic activities, including urbanization and the construction of flood‐prevention infrastructure, can produce barriers that impede ecosystem migration. Here we show where tidal saline wetlands have the potential to migrate landward along the northern Gulf of Mexico coast, one of the most sea‐level rise sensitive and wetland‐rich regions of the world. Our findings can be used to identify migration corridors and develop sea‐level rise adaptation strategies to help ensure the continued availability of wetland‐associated ecosystem goods and services.

Seagrass meadows provide numerous ecosystem services and their rapid global loss may reduce human welfare as well as ecological integrity. In common with the other 'blue carbon' habitats (mangroves and tidal marshes) seagrasses are thought to provide coastal defence and encourage sediment stabilisation and surface elevation. A sophisticated understanding of sediment elevation dynamics in mangroves and tidal marshes has been gained by monitoring a wide range of different sites, located in varying hydrogeomorphological conditions over long periods. In contrast, similar evidence for seagrasses is sparse; the present study is a contribution towards filling this gap. Surface elevation change pins were deployed in four locations, Scotland, Kenya, Tanzania and Saudi Arabia, in both seagrass and unvegetated control plots in the low intertidal and shallow subtidal zone. The presence of seagrass had a highly significant, positive impact on surface elevation at all sites. Combined data from the current work and the literature show an average difference of 31 mm per year in elevation rates between vegetated and unvegetated areas, which emphasizes the important contribution of seagrass in facilitating sediment surface elevation and reducing erosion. This paper presents the first multi-site study for sediment surface elevation in seagrasses in different settings and species.

Abstract Coastal wetland ecosystems are expected to migrate landwards in response to rising seas. However, due to differences in topography and coastal urbanization, estuaries vary in their ability to accommodate migration. Low‐lying urban areas can constrain migration and lead to wetland loss (i.e. coastal squeeze), especially where existing wetlands cannot keep pace with rising seas via vertical adjustments. In many estuaries, there is a pressing need to identify landward migration corridors and better quantify the potential for landward migration and coastal squeeze. We quantified and compared the area available for landward migration of tidal saline wetlands and the area where urban development is expected to prevent migration for 39 estuaries along the wetland‐rich USA Gulf of Mexico coast. We did so under three sea level rise scenarios (0.5, 1.0, and 1.5 m by 2100). Within the region, the potential for wetland migration is highest within certain estuaries in Louisiana and southern Florida (e.g. Atchafalaya/Vermilion Bays, Mermentau River, Barataria Bay, and the North and South Ten Thousand Islands estuaries). The potential for coastal squeeze is highest in estuaries containing major metropolitan areas that extend into low‐lying lands. The Charlotte Harbor, Tampa Bay, and Crystal‐Pithlachascotee estuaries (Florida) have the highest amounts of urban land expected to constrain wetland migration. Urban barriers to migration are also high in the Galveston Bay (Texas) and Atchafalaya/Vermilion Bays (Louisiana) estuaries. Synthesis and applications . Coastal wetlands provide many ecosystem services that benefit human health and well‐being, including shoreline protection and fish and wildlife habitat. As the rate of sea level rise accelerates in response to climate change, coastal wetland resources could be lost in areas that lack space for landward migration. Migration corridors are particularly important in highly urbanized estuaries where, due to low‐lying coastal development, there is not space for wetlands to move and adapt to sea level rise. Future‐focused landscape conservation plans that incorporate the protection of wetland migration corridors can increase the adaptive capacity of these valuable ecosystems and simultaneously decrease the vulnerability of coastal human communities to the harmful effects of rising seas.

To inform management and conservation decisions, environmental DNA (eDNA) methods are used to detect genetic material shed into the water by imperiled and invasive species. Methodological enhancements are needed to reduce filter clogging, PCR inhibition, and false-negative detections when eDNA is at low concentrations. In the first of three simple experiments, we sought to ameliorate filter clogging from particulates and organic material through a scaled-up, multi-filter protocol. We combined four filters in a 5 mL Phenol-Chloroform-Isoamyl (PCI) procedure to allow for larger volumes of water (~1 L) to be filtered rapidly. Increasing the filtered water volume by four times resulted in 4.4X the yield of target DNA. Next, inhibition from organic material can reduce or block eDNA detections in PCR-based assays. To remove inhibitory compounds retained during eDNA isolation, we tested three methods to chemically strip inhibitors from eDNA molecules. The use of CTAB as a short-term (5-8 day) storage buffer, followed by a PCI isolation, resulted in the highest eDNA yields. Finally, as opposed to a linear relationship among increasing concentrations of filtered genomic eDNA, we observed a sharp change between the lower (70-280 ng) and higher (420-560 ng) amounts. This may be important for effectively precipitating eDNA during protocol testing.

All basic processes of ecological populations involve decisions; when and where to move, when and what to eat, and whether to fight or flee. Yet decisions and the underlying principles of decision-making have been difficult to integrate into the classical population-level models of ecology. Certainly, there is a long history of modeling individuals’ searching behavior, diet selection, or conflict dynamics within social interactions. When all individuals are given certain simple rules to govern their decision-making processes, the resultant population–level models have yielded important generalizations and theory. But it is also recognized that such models do not represent the way real individuals decide on actions. Factors that influence a decision include the organism’s environment with its dynamic rewards and risks, the complex internal state of the organism, and its imperfect knowledge of the environment. In the case of animals, it may also involve complex social factors, and experience and learning, which vary among individuals. The way that all factors are weighed and processed to lead to decisions is a major area of behavioral theory. While classic population-level modeling is limited in its ability to integrate decision-making in its actual complexity, the development of individual- or agent-based models (IBM/ABMs) (we use ABM throughout to designate both ‘agent-based modeling’ and an ‘agent-based model’) has opened the possibility of describing the way that decisions are made, and their effects, in minute detail. Over the years, these models have increased in size and complexity. Current ABMs can simulate thousands of individuals in realistic environments, and with highly detailed internal physiology, perception and ability to process the perceptions and make decisions based on those and their internal states. The implementation of decision-making in ABMs ranges from fairly simple to highly complex; the process of an individual deciding on an action can occur through the use of logical and simple (if-then) rules to more sophisticated neural networks and genetic algorithms. The purpose of this paper is to give an overview of the ways in which decisions are integrated into a variety of ABMs and to give a prospectus on the future of modeling of decisions in ABMs.

A set of universal guidelines is needed to determine the limit of detection (LOD) in PCR-based analyses of low-concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods to detect rare and cryptic species through shed genetic material in environmental samples. Current strategies for assessing detection limits of eDNA are either too stringent or subjective, possibly resulting in biased estimates of species' presence. Here, a conservative LOD analysis grounded in analytical chemistry is proposed to correct for overestimated DNA concentrations predominantly caused by the concentration plateau, a nonlinear relationship between expected and measured DNA concentrations. We have used statistical criteria to establish formal mathematical models for both quantitative and droplet digital PCR. To assess the method, a new Grass Carp (Ctenopharyngodon idella) TaqMan assay was developed and tested on both PCR platforms using eDNA in water samples. The LOD adjustment reduced Grass Carp occupancy and detection estimates while increasing uncertainty-indicating that caution needs to be applied to eDNA data without LOD correction. Compared to quantitative PCR, digital PCR had higher occurrence estimates due to increased sensitivity and dilution of inhibitors at low concentrations. Without accurate LOD correction, species occurrence and detection probabilities based on eDNA estimates are prone to a source of bias that cannot be reduced by an increase in sample size or PCR replicates. Other applications also could benefit from a standardized LOD such as GMO food analysis and forensic and clinical diagnostics.

We present a revised list of freshwater mussels (order Unionida, families Margaritiferidae and Unionidae) of the United States and Canada, incorporating changes in nomenclature and systematic taxonomy since publication of the most recent checklist in 1998. We recognize a total of 298 species in 55 genera in the families Margaritiferidae (one genus, five species) and Unionidae (54 genera, 293 species). We propose one change in the Margaritiferidae: the placement of the formerly monotypic genus Cumberlandia in the synonymy of Margaritifera. In the Unionidae, we recognize three new genera, elevate four genera from synonymy, and place three previously recognized genera in synonymy. We recognize for the first time two species (one native and one nonindigenous) in the Asian genus Sinanodonta as occurring in North America. We recognize four new species and one subspecies and elevate 21 species from synonymy. We elevate 10 subspecies to species status and no longer recognize four subspecies. We change common names for five taxa, correct spelling for eight species, and correct the date of publication of original descriptions for four species.

International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve, and sustainably and equitably use, biodiversity. The CBD is a vital instrument for global conservation because it guides 195 countries and the European Union in setting priorities and allocating resources, and requires regular reporting on progress. However, the CBD and similar policy agreements have often neglected genetic diversity. This is a critical gap because genetic diversity underlies adaptation to environmental change and ecosystem resilience. Here we aim to inform future policy, monitoring, and reporting efforts focused on limiting biodiversity loss by conducting the largest yet evaluation of how Parties to the CBD report on genetic diversity. A large, globally representative sample of 114 CBD National Reports was examined to assess reported actions, progress, values and indicators related to genetic diversity. Although the importance of genetic diversity is recognized by most Parties to the CBD, genetic diversity targets mainly addressed variation within crops and livestock (a small fraction of all species). Reported actions to conserve genetic diversity primarily concerned ex situ facilities and legislation, rather than monitoring and in situ intervention. The most commonly reported status indicators are not well correlated to maintaining genetic diversity. Lastly, few reports mentioned genetic monitoring using DNA data, indigenous use and knowledge of genetic diversity, or development of strategies to conserve genetic diversity. We make several recommendations for the post-2020 CBD Biodiversity Framework, and similar efforts such as IPBES, to improve awareness, assessment, and monitoring of genetic diversity, and facilitate consistent and complete reporting in the future.

Mangrove forests grow on saline, permanently or periodically flooded soils of the tropical and subtropical coasts. The tree species that compose the mangrove are halophytes that have suites of traits that confer differing levels of tolerance of salinity, aridity, inundation and extremes of temperature. Here we review how climate change and elevated levels of atmospheric CO2 will influence mangrove forests. Tolerance of salinity and inundation in mangroves is associated with the efficient use of water for photosynthetic carbon gain which underpins anticipated gains in productivity with increasing levels of CO2. We review evidence of increases in productivity with increasing CO2, finding that enhancements in growth appear to be similar to trees in non-mangrove habitats and that gains in productivity with elevated CO2 are likely due to changes in biomass allocation. High levels of trait plasticity are observed in some mangrove species, which potentially facilitates their responses to climate change. Trait plasticity is associated with broad tolerance of salinity, aridity, low temperatures and nutrient availability. Because low temperatures and aridity place strong limits on mangrove growth at the edge of their current distribution, increasing temperatures over time and changing rainfall patterns are likely to have an important influence on the distribution of mangroves. We provide a global analysis based on plant traits and IPCC scenarios of changing temperature and aridity that indicates substantial global potential for mangrove expansion.

Summary Changing winter climate extremes are expected to result in the poleward migration of mangrove forests at the expense of salt marshes. Although mangroves and marshes are both highly valued ecosystems, the ecological implications of mangrove expansion have not been fully investigated. Here, we examined the effects of mangrove expansion on below‐ground properties related to peat development and carbon storage. We investigated plant – soil interactions in marshes and across mangrove forest structural gradients in three locations in the northern Gulf of Mexico (USA). We compared our results to those from terrestrial grasslands where the effects of woody plant encroachment are often influenced by rainfall and plant traits. Abiotic conditions at our study locations differed, particularly in terms of physicochemical properties related to precipitation. Marsh species composition, marsh above‐ground biomass, and mangrove forest structural complexity also varied across these locations. Marshes in the driest location (Central Texas) had higher salinities and were dominated by low biomass succulent plants and lower soil carbon pools. Marshes in the wetter, less saline locations (Louisiana and North Florida) contained high biomass grasses and higher soil carbon pools. At all locations, above‐ground biomass and above‐ground carbon pools were higher in mangroves than marshes; however, below‐ground soil carbon pools were only higher in mangroves than marshes in the driest location. In the wetter locations, the linkages between mangrove forest structure and soil properties were minimal or not significant. However, in the driest location, there was a significant increase in soil properties related to peat development and carbon storage with increased mangrove forest structural development. Synthesis : Our results indicate that the ecological implications of woody plant encroachment in tidal saline wetlands are dependent upon precipitation controls of plant – soil interactions. Although the above‐ground effects of mangrove expansion are consistently large, below‐ground influences of mangrove expansion appear to be greatest along low‐rainfall coasts where salinities are high and marshes being replaced are carbon poor and dominated by succulent plants. Collectively, these findings complement those from terrestrial ecosystems and reinforce the importance of considering rainfall and plant – soil interactions within predictions of the ecological effects of woody plant encroachment.

Summary Two main sources of data for species distribution models (SDMs) are site‐occupancy (SO) data from planned surveys, and presence‐background (PB) data from opportunistic surveys and other sources. SO surveys give high quality data about presences and absences of the species in a particular area. However, due to their high cost, they often cover a smaller area relative to PB data, and are usually not representative of the geographic range of a species. In contrast, PB data is plentiful, covers a larger area, but is less reliable due to the lack of information on species absences, and is usually characterised by biased sampling. Here we present a new approach for species distribution modelling that integrates these two data types. We have used an inhomogeneous Poisson point process as the basis for constructing an integrated SDM that fits both PB and SO data simultaneously. It is the first implementation of an Integrated SO–PB Model which uses repeated survey occupancy data and also incorporates detection probability. The Integrated Model's performance was evaluated, using simulated data and compared to approaches using PB or SO data alone. It was found to be superior, improving the predictions of species spatial distributions, even when SO data is sparse and collected in a limited area. The Integrated Model was also found effective when environmental covariates were significantly correlated. Our method was demonstrated with real SO and PB data for the Yellow‐bellied glider ( Petaurus australis ) in south‐eastern Australia, with the predictive performance of the Integrated Model again found to be superior. PB models are known to produce biased estimates of species occupancy or abundance. The small sample size of SO datasets often results in poor out‐of‐sample predictions. Integrated models combine data from these two sources, providing superior predictions of species abundance compared to using either data source alone. Unlike conventional SDMs which have restrictive scale‐dependence in their predictions, our Integrated Model is based on a point process model and has no such scale‐dependency. It may be used for predictions of abundance at any spatial‐scale while still maintaining the underlying relationship between abundance and area.

Coastal wetlands are not only among the world's most valued ecosystems but also among the most threatened by high greenhouse gas emissions that lead to accelerated sea level rise. There is intense debate regarding the extent to which landward migration of wetlands might compensate for seaward wetland losses. By integrating data from 166 estuaries across the conterminous United States, we show that landward migration of coastal wetlands will transform coastlines but not counter seaward losses. Two-thirds of potential migration is expected to occur at the expense of coastal freshwater wetlands, while the remaining one-third is expected to occur at the expense of valuable uplands, including croplands, forests, pastures, and grasslands. Our analyses underscore the need to better prepare for coastal transformations and net wetland loss due to rising seas.

Changing climate will impact species' ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local climate, species life-histories, and taxonomic classification. We found that local species richness is most sensitive to changes in water availability during breeding and changes in winter conditions. Based on the relationships we measure, recent changes in climate cannot explain why local species richness of North American amphibians has rapidly declined. However, changing climate does explain why some populations are declining faster than others. Our results provide important insights into how amphibians respond to climate and a general framework for measuring climate impacts on species richness.