Biodiversity and productivity in eastern US forests.

Despite experimental and observational studies demonstrating that biodiversity enhances primary productivity, the best metric for predicting productivity at broad geographic extents-functional trait diversity, phylogenetic diversity, or species richness-remains unknown. Using >1.8 million tree measurements from across eastern US forests, we quantified relationships among functional trait diversity, phylogenetic diversity, species richness, and productivity. Surprisingly, functional trait and phylogenetic diversity explained little variation in productivity that could not be explained by tree species richness. This result was consistent across the entire eastern United States, within ecoprovinces, and within data subsets that controlled for biomass or stand age. Metrics of functional trait and phylogenetic diversity that were independent of species richness were negatively correlated with productivity. This last result suggests that processes that determine species sorting and packing are likely important for the relationships between productivity and biodiversity. This result also demonstrates the potential confusion that can arise when interdependencies among different diversity metrics are ignored. Our findings show the value of species richness as a predictive tool and highlight gaps in knowledge about linkages between functional diversity and ecosystem functioning.

Changes in parrot diversity after human arrival to the Caribbean.

Humans did not arrive on most of the world's islands until relatively recently, making islands favorable places for disentangling the timing and magnitude of natural and anthropogenic impacts on species diversity and distributions. Here, we focus on Amazona parrots in the Caribbean, which have close relationships with humans (e.g., as pets as well as sources of meat and colorful feathers). Caribbean parrots also have substantial fossil and archaeological records that span the Holocene. We leverage this exemplary record to showcase how combining ancient and modern DNA, along with radiometric dating, can shed light on diversification and extinction dynamics and answer long-standing questions about the magnitude of human impacts in the region. Our results reveal a striking loss of parrot diversity, much of which took place during human occupation of the islands. The most widespread species, the Cuban Parrot, exhibits interisland divergences throughout the Pleistocene. Within this radiation, we identified an extinct, genetically distinct lineage that survived on the Turks and Caicos until Indigenous human settlement of the islands. We also found that the narrowly distributed Hispaniolan Parrot had a natural range that once included The Bahamas; it thus became "endemic" to Hispaniola during the late Holocene. The Hispaniolan Parrot also likely was introduced by Indigenous people to Grand Turk and Montserrat, two islands where it is now also extirpated. Our research demonstrates that genetic information spanning paleontological, archaeological, and modern contexts is essential to understand the role of humans in altering the diversity and distribution of biota.

Demographic consequences of phenological asynchrony for North American songbirds.

Changes in phenology in response to ongoing climate change have been observed in numerous taxa around the world. Differing rates of phenological shifts across trophic levels have led to concerns that ecological interactions may become increasingly decoupled in time, with potential negative consequences for populations. Despite widespread evidence of phenological change and a broad body of supporting theory, large-scale multitaxa evidence for demographic consequences of phenological asynchrony remains elusive. Using data from a continental-scale bird-banding program, we assess the impact of phenological dynamics on avian breeding productivity in 41 species of migratory and resident North American birds breeding in and around forested areas. We find strong evidence for a phenological optimum where breeding productivity decreases in years with both particularly early or late phenology and when breeding occurs early or late relative to local vegetation phenology. Moreover, we demonstrate that landbird breeding phenology did not keep pace with shifts in the timing of vegetation green-up over a recent 18-y period, even though avian breeding phenology has tracked green-up with greater sensitivity than arrival for migratory species. Species whose breeding phenology more closely tracked green-up tend to migrate shorter distances (or are resident over the entire year) and breed earlier in the season. These results showcase the broadest-scale evidence yet of the demographic impacts of phenological change. Future climate change-associated phenological shifts will likely result in a decrease in breeding productivity for most species, given that bird breeding phenology is failing to keep pace with climate change.

Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales.

The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.

Rising minimum temperatures contribute to 50 years of occupancy decline among cold-adapted Arctic and boreal butterflies in North America.

Global climate change has been identified as a potential driver of observed insect declines, yet in many regions, there are critical data gaps that make it difficult to assess how communities are responding to climate change. Poleward regions are of particular interest because warming is most rapid while biodiversity data are most sparse. Building on recent advances in occupancy modeling of presence-only data, we reconstructed 50 years (1970-2019) of butterfly occupancy trends in response to rising minimum temperatures in one of the most under-sampled regions of North America. Among 90 modeled species, we found that cold-adapted species are far more often in decline compared with their warm-adapted, more southernly distributed counterparts. Furthermore, in a post hoc analysis using species' traits, we find that species' range-wide average annual temperature is the only consistent predictor of occupancy changes. Species with warmer ranges were most likely to be increasing in occupancy. This trend results in the majority of butterflies increasing in occupancy probability over the last 50 years. Our results provide the first look at macroscale butterfly biodiversity shifts in high-latitude North America. These results highlight the potential of leveraging the wealth of presence-only data, the most abundant source of biodiversity data, for inferring changes in species distributions.

Substantial urbanization-driven declines of larval and adult moths in a subtropical environment.

Recent work has shown the decline of insect abundance, diversity and biomass, with potential implications for ecosystem services. These declines are especially pronounced in regions with high human activity, and urbanization is emerging as a significant contributing factor. However, the scale of these declines and the traits that determine variation in species-specific responses remain less well understood, especially in subtropical and tropical regions, where insect diversity is high and urban footprints are rapidly expanding. Here, we surveyed moths across an entire year in protected forested sites across an urbanization gradient to test how caterpillar and adult life stages of subtropical moths (Lepidoptera) are impacted by urbanization. Specifically, we assess how urban development affects the total biomass of caterpillars, abundance of adult moths and quantify how richness and phylogenetic diversity of macro-moths are impacted by urban development. Additionally, we explore how life-history traits condition species' responses to urban development. At the community level, we find that urban development decreases caterpillar biomass and adult moth abundance. We also find sharp declines of adult macro-moths in response to urban development across the phylogeny, leading to a decrease in species richness and phylogenetic diversity in more urban sites. Finally, our study found that smaller macro-moths are less impacted by urban development than larger macro-moths in subtropical environments, perhaps highlighting the tradeoffs of metabolic costs of urban heat favoring smaller moths over the relative benefits of dispersal for larger moths. In summary, our research underscores the far-reaching consequences of urbanization on moths and provides compelling evidence that urban forests alone may not be sufficient to safeguard biodiversity in cities.

Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method.

Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.].

A cloud-based toolbox for the versatile environmental annotation of biodiversity data.

A vast range of research applications in biodiversity sciences requires integrating primary species, genetic, or ecosystem data with other environmental data. This integration requires a consideration of the spatial and temporal scale appropriate for the data and processes in question. But a versatile and scale flexible environmental annotation of biodiversity data remains constrained by technical hurdles. Existing tools have streamlined the intersection of occurrence records with gridded environmental data but have remained limited in their ability to address a range of spatial and temporal grains, especially for large datasets. We present the Spatiotemporal Observation Annotation Tool (STOAT), a cloud-based toolbox for flexible biodiversity-environment annotations. STOAT is optimized for large biodiversity datasets and allows user-specified spatial and temporal resolution and buffering in support of environmental characterizations that account for the uncertainty and scale of data and of relevant processes. The tool offers these services for a growing set of near global, remotely sensed, or modeled environmental data, including Landsat, MODIS, EarthEnv, and CHELSA. STOAT includes a user-friendly, web-based dashboard that provides tools for annotation task management and result visualization, linked to Map of Life, and a dedicated R package (rstoat) for programmatic access. We demonstrate STOAT functionality with several examples that illustrate phenological variation and spatial and temporal scale dependence of environmental characteristics of birds at a continental scale. We expect STOAT to facilitate broader exploration and assessment of the scale dependence of observations and processes in ecology.

Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus.

PREMISE: Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness. METHODS: Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents. RESULTS: Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway. CONCLUSIONS: Our investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging "mega-radiations." Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species-rich clades.

Challenges and opportunities for using natural history collections to estimate insect population trends.

Natural history collections (NHC) provide a wealth of information that can be used to understand the impacts of global change on biodiversity. As such, there is growing interest in using NHC data to estimate changes in species' distributions and abundance trends over historic time horizons when contemporary survey data are limited or unavailable. However, museum specimens were not collected with the purpose of estimating population trends and thus can exhibit spatiotemporal and collector-specific biases that can impose severe limitations to using NHC data for evaluating population trajectories. Here we review the challenges associated with using museum records to track long-term insect population trends, including spatiotemporal biases in sampling effort and sparse temporal coverage within and across years. We highlight recent methodological advancements that aim to overcome these challenges and discuss emerging research opportunities. Specifically, we examine the potential of integrating museum records and other contemporary data sources (e.g. collected via structured, designed surveys and opportunistic citizen science programs) in a unified analytical framework that accounts for the sampling biases associated with each data source. The emerging field of integrated modelling provides a promising framework for leveraging the wealth of collections data to accurately estimate long-term trends of insect populations and identify cases where that is not possible using existing data sources.

Bridging the Research Gap between Live Collections in Zoos and Preserved Collections in Natural History Museums.

Zoos and natural history museums are both collections-based institutions with important missions in biodiversity research and education. Animals in zoos are a repository and living record of the world's biodiversity, whereas natural history museums are a permanent historical record of snapshots of biodiversity in time. Surprisingly, despite significant overlap in institutional missions, formal partnerships between these institution types are infrequent. Life history information, pedigrees, and medical records maintained at zoos should be seen as complementary to historical records of morphology, genetics, and distribution kept at museums. Through examining both institution types, we synthesize the benefits and challenges of cross-institutional exchanges and propose actions to increase the dialog between zoos and museums. With a growing recognition of the importance of collections to the advancement of scientific research and discovery, a transformational impact could be made with long-term investments in connecting the institutions that are caretakers of living and preserved animals.

Colour scales with climate in North American ratsnakes: a test of the thermal melanism hypothesis using community science images.

Animal colour is a complex trait shaped by multiple selection pressures that can vary across geography. The thermal melanism hypothesis predicts that darker coloration is beneficial to animals in colder regions because it allows for more rapid solar absorption. Here, we use community science images of three closely related species of North American ratsnakes (genus Pantherophis) to examine if climate predicts colour variation across range-wide scales. We predicted that darker individuals are found in colder regions and higher elevations, in accordance with the thermal melanism hypothesis. Using an unprecedented dataset of over 8000 images, we found strong support for temperature as a key predictor of darker colour, supporting thermal melanism. We also found that elevation and precipitation are predictive of colour, but the direction and magnitude of these effects were more variable across species. Our study is the first to quantify colour variation in Pantherophis ratsnakes, highlighting the value of community science images for studying range-wide colour variation.

Rates of niche and phenotype evolution lag behind diversification in a temperate radiation.

Environmental change can create opportunities for increased rates of lineage diversification, but continued species accumulation has been hypothesized to lead to slowdowns via competitive exclusion and niche partitioning. Such density-dependent models imply tight linkages between diversification and trait evolution, but there are plausible alternative models. Little is known about the association between diversification and key ecological and phenotypic traits at broad phylogenetic and spatial scales. Do trait evolutionary rates coincide with rates of diversification, are there lags among these rates, or is diversification niche-neutral? To address these questions, we combine a deeply sampled phylogeny for a major flowering plant clade-Saxifragales-with phenotype and niche data to examine temporal patterns of evolutionary rates. The considerable phenotypic and habitat diversity of Saxifragales is greatest in temperate biomes. Global expansion of these habitats since the mid-Miocene provided ecological opportunities that, with density-dependent adaptive radiation, should result in simultaneous rate increases for diversification, niche, and phenotype, followed by decreases with habitat saturation. Instead, we find that these rates have significantly different timings, with increases in diversification occurring at the mid-Miocene Climatic Optimum (∼15 Mya), followed by increases in niche and phenotypic evolutionary rates by ∼5 Mya; all rates increase exponentially to the present. We attribute this surprising lack of temporal coincidence to initial niche-neutral diversification followed by ecological and phenotypic divergence coincident with more extreme cold and dry habitats that proliferated into the Pleistocene. A lack of density-dependence contrasts with investigations of other cosmopolitan lineages, suggesting alternative patterns may be common in the diversification of temperate lineages.

Climate drivers of adult insect activity are conditioned by life history traits.

Insect phenological lability is key for determining which species will adapt under environmental change. However, little is known about when adult insect activity terminates and overall activity duration. We used community-science and museum specimen data to investigate the effects of climate and urbanisation on timing of adult insect activity for 101 species varying in life history traits. We found detritivores and species with aquatic larval stages extend activity periods most rapidly in response to increasing regional temperature. Conversely, species with subterranean larval stages have relatively constant durations regardless of regional temperature. Species extended their period of adult activity similarly in warmer conditions regardless of voltinism classification. Longer adult durations may represent a general response to warming, but voltinism data in subtropical environments are likely underreported. This effort provides a framework to address the drivers of adult insect phenology at continental scales and a basis for predicting species response to environmental change.

Climate, urbanization, and species traits interactively drive flowering duration.

A wave of green leaves and multi-colored flowers advances from low to high latitudes each spring. However, little is known about how flowering offset (i.e., ending of flowering) and duration of populations of the same species vary along environmental gradients. Understanding these patterns is critical for predicting the effects of future climate and land-use change on plants, pollinators, and herbivores. Here, we investigated potential climatic and landscape drivers of flowering onset, offset, and duration of 52 plant species with varying key traits. We generated phenology estimates using >270,000 community-science photographs and a novel presence-only phenometric estimation method. We found longer flowering durations in warmer areas, which is more obvious for summer-blooming species compared to spring-bloomers driven by their strongly differing offset dynamics. We also found that higher human population density and higher annual precipitation are associated with delayed flowering offset and extended flowering duration. Finally, offset of woody perennials was more sensitive than herbaceous species to both climate and urbanization drivers. Empirical forecast models suggested that flowering durations will be longer in 2030 and 2050 under representative concentration pathway (RCP) 8.5, especially for summer-blooming species. Our study provides critical insight into drivers of key flowering phenophases and confirms that Hopkins' Bioclimatic Law also applies to flowering durations for summer-blooming species and herbaceous spring-blooming species.

Ancient DNA from the extinct Haitian cave-rail (Nesotrochis steganinos) suggests a biogeographic connection between the Caribbean and Old World.

Worldwide decline in biodiversity during the Holocene has impeded a comprehensive understanding of pre-human biodiversity and biogeography. This is especially true on islands, because many recently extinct island taxa were morphologically unique, complicating assessment of their evolutionary relationships using morphology alone. The Caribbean remains an avian hotspot but was more diverse before human arrival in the Holocene. Among the recently extinct lineages is the enigmatic genus Nesotrochis, comprising three flightless species. Based on morphology, Nesotrochis has been considered an aberrant rail (Rallidae) or related to flufftails (Sarothruridae). We recovered a nearly complete mitochondrial genome of Nesotrochis steganinos from fossils, discovering that it is not a rallid but instead is sister to Sarothruridae, volant birds now restricted to Africa and New Guinea, and the recently extinct, flightless Aptornithidae of New Zealand. This result suggests a widespread or highly dispersive most recent common ancestor of the group. Prior to human settlement, the Caribbean avifauna had a far more cosmopolitan origin than is evident from extant species.

Chronic anthropogenic noise disrupts glucocorticoid signaling and has multiple effects on fitness in an avian community.

Anthropogenic noise is a pervasive pollutant that decreases environmental quality by disrupting a suite of behaviors vital to perception and communication. However, even within populations of noise-sensitive species, individuals still select breeding sites located within areas exposed to high noise levels, with largely unknown physiological and fitness consequences. We use a study system in the natural gas fields of northern New Mexico to test the prediction that exposure to noise causes glucocorticoid-signaling dysfunction and decreases fitness in a community of secondary cavity-nesting birds. In accordance with these predictions, and across all species, we find strong support for noise exposure decreasing baseline corticosterone in adults and nestlings and, conversely, increasing acute stressor-induced corticosterone in nestlings. We also document fitness consequences with increased noise in the form of reduced hatching success in the western bluebird (Sialia mexicana), the species most likely to nest in noisiest environments. Nestlings of all three species exhibited accelerated growth of both feathers and body size at intermediate noise amplitudes compared with lower or higher amplitudes. Our results are consistent with recent experimental laboratory studies and show that noise functions as a chronic, inescapable stressor. Anthropogenic noise likely impairs environmental risk perception by species relying on acoustic cues and ultimately leads to impacts on fitness. Our work, when taken together with recent efforts to document noise across the landscape, implies potential widespread, noise-induced chronic stress coupled with reduced fitness for many species reliant on acoustic cues.

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae).

BACKGROUND: Plastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of pseudogenization and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome of Saniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context. RESULTS: We find that the plastid genome of Saniculiphyllum has experienced pseudogenization of five genes of the ndh complex (ndhA, ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with an aquatic habit, as well as the surprising pseudogenization of two genes more central to photosynthesis (ccsA and cemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional. CONCLUSIONS: Saniculiphyllum appears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, perhaps related to its extreme habitat specialization, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.

Corrigendum: The Extended Specimen Network: A Strategy to Enhance US Biodiversity Collections, Promote Research and Education.

[This corrects the article DOI: 10.1093/biosci/biz140.].

Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids.

PREMISE: Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. METHODS: We used a supermatrix for rosids and one well-sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). RESULTS: We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. CONCLUSIONS: We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.