Species Richness at Continental Scales Is Dominated by Ecological Limits

Abstract Explaining variation in species richness among provinces and other large geographic regions remains one of the most challenging problems at the intersection of ecology and evolution. Here we argue that empirical evidence supports a model whereby ecological factors associated with resource availability regulate species richness at continental scales. Any large-scale predictive model for biological diversity must explain three robust patterns in the natural world. First, species richness for evolutionary biotas is highly correlated with resource-associated surrogate variables, including area, temperature, and productivity. Second, species richness across epochal timescales is largely stationary in time. Third, the dynamics of diversity exhibit clear and predictable responses to mass extinctions, key innovations, and other perturbations. Collectively, these patterns are readily explained by a model in which species richness is regulated by diversity-dependent feedback mechanisms. We argue that many purported tests of the ecological limits hypothesis, including branching patterns in molecular phylogenies, are inherently weak and distract from these three core patterns. We have much to learn about the complex hierarchy of processes by which local ecological interactions lead to diversity dependence at the continental scale, but the empirical evidence overwhelmingly suggests that they do

Heterospecific interactions and the proliferation of sexually dimorphic traits

Sexual selection is expected to promote speciation by fostering the evolution of sexual traits that minimize reproductive interactions among existing or incipient species. In species that compete for access to, or attention of, females, sexual selection fosters more elaborate traits in males compared to females. If these traits also minimize reproductive interactions with heterospecifics, then species with enhanced risk of interactions between species might display greater numbers of these sexual dimorphic characters. We tested this prediction in eight families of North American birds. In particular, we evaluated whether the number of sexually dimorphic traits was positively associated with species richness at a given site or with degree of sympatry with congeners. We found no strong evidence of enhanced sexual dimorphism with increasing confamilial species richness at a given site. We also found no overall relationship between the number of sexually dimorphic traits and overlap with congeners across these eight families. However, we found patterns consistent with our prediction within Anatidae (ducks, geese and swans) and, to a lesser degree, Parulidae (New World warblers). Our results suggest that sexually selected plumage traits in these groups potentially play a role in reproductive isolation

On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions

We use a simulation model to examine four of the most common hypotheses for the latitudinal richness gradient and identify patterns that might be diagnostic of those four hypotheses. The hypotheses examined include (1) tropical niche conservatism, or the idea that the tropics are more diverse because a tropical clade origin has allowed more time for diversification in the tropics and has resulted in few species adapted to extra-tropical climates. (2) The ecological limits hypothesis suggests that species richness is limited by the amount of biologically available energy in a region. (3) The speciation rates hypothesis suggests that the latitudinal gradient arises from a gradient in speciation rates. (4) Finally, the tropical stability hypothesis argues that climatic fluctuations and glacial cycles in extratropical regions have led to greater extinction rates and less opportunity for specialization relative to the tropics. We found that tropical niche conservatism can be distinguished from the other three scenarios by phylogenies which are more balanced than expected, no relationship between mean root distance (MRD) and richness across regions, and a homogeneous rate of speciation across clades and through time. The energy gradient, speciation gradient, and disturbance gradient scenarios all produced phylogenies which were more imbalanced than expected, showed a negative relationship between MRD and richness, and diversity-dependence of speciation rate estimates through time. We found that the relationship between speciation rates and latitude could distinguish among these three scenarios, with no relation expected under the ecological limits hypothesis, a negative relationship expected under the speciation rates hypothesis, and a positive relationship expected under the tropical stability hypothesis. We emphasize the importance of considering multiple hypotheses and focusing on diagnostic predictions instead of predictions that are consistent with multiple hypotheses

Multiple dimensions of niche specialization explain changes in species’ range area, occupancy, and population size

In response to environmental change, species may decrease or increase in population size across their range, expand or contract their range limits, or alter how sites are occupied within their existing range. Shifts in range limits and widespread changes in population size have been documented in birds especially in response to changes in climate. Range occupancy, or how patchily or continuously a species is distributed within their range, has been studied less in the context of anthropogenic changes but may be expected to decrease with range-wide population size if abundance-occupancy relationships are generally positive. Determining which properties of species are related to range expansion or contraction or increased range occupancy or decreased range occupancy is useful in developing an understanding of which species become “winners” or “losers” under global change. Species with broader climatic niches may be more likely to successfully expand to new sites as climate changes. Range occupancy can be related to habitat preferences of species, and habitat specialization may predict how species fill in sites within their range. To examine how species niche breadth may explain changes in species distributions, we modeled how changes in range-wide population size, range extent, and range occupancy from 1976 to 2016 were predicted by species’ climate, habitat, and diet niche breadth for 77 North American breeding bird species. We found that climate generalists were more likely to be increasing in range area, while species with declining population trends were likely to be contracting in range area and in occupancy within their range. Understanding how different dimensions of specialization relate to shifts in species distributions may improve predictions of which species are expected to benefit from or be vulnerable to anthropogenic change

3 dimensional proton beam writing for micro electromechanical systems applications.

Proton beam writing is a direct write lithographic technique that uses finely focused MeV proton beams to create structures in a target material. The depth the protons travel in a material is dependent on its energy, this unique property of proton beams allow multi level structures to be created in materials. PBW has been demonstrated successfully on semiconductor materials, glass and polymers. This thesis is a study of the application of PBW in creating Micro Electro-Mechanical Systems (MEMS) in a polymer SU 8 and SU 8 polymer nano composite with silver, and shows experimental steps, theory and computer simulations involved in creating an electrostatic actuated micro-gripping device. Proton beam writing in silver SU 8 composite results in the creation of electrically conducting microstructures. The unique predictability of the range of protons in materials is leveraged in the creating of free standing conducting cantilevers structures which are used as the building blocks for a micro gripping device. The electrostatic actuation has been modelled using a finite element modelling software Sugar 3.1, and the results are comparable with actual actuations in a realized micro-gripping device

The proportion of core species in a community varies with spatial scale and environmental heterogeneity

Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species are both commonly observed in community surveys of a wide range of taxonomic groups, their relative prevalence varies substantially from one community to another depending upon the spatial scale at which the community was characterized and its environmental context. We used a geographically extensive dataset of 968 bird community time series to quantitatively describe how the proportion of core species in a community varies with spatial scale and environmental heterogeneity. We found that the proportion of core species in an assemblage increased with spatial scale in a positive decelerating fashion with a concomitant decrease in the proportion of transient species. Variation in the shape of this scaling relationship between sites was related to regional environmental heterogeneity, with lower proportions of core species at a given scale associated with high environmental heterogeneity. Understanding this influence of scale and environmental heterogeneity on the proportion of core species may help resolve discrepancies between studies of biotic interactions, resource availability, and mass effects conducted at different scales, because the importance of these and other ecological processes are expected to differ substantially between core and transient species

Opportunities and challenges for big data ornithology

Recent advancements in information technology and data acquisition have created both new research opportunities and new challenges for using big data in ornithology. We provide an overview of the past, present, and future of big data in ornithology, and explore the rewards and risks associated with their application. Structured data resources (e.g., North American Breeding Bird Survey) continue to play an important role in advancing our understanding of bird population ecology, and the recent advent of semistructured (e.g., eBird) and unstructured (e.g., weather surveillance radar) big data resources has promoted the development of new empirical perspectives that are generating novel insights. For example, big data have been used to study and model bird diversity and distributions across space and time, explore the patterns and determinants of broad-scale migration strategies, and examine the dynamics and mechanisms associated with geographic and phenological responses to global change. The application of big data also holds a number of challenges wherein high data volume and dimensionality can result in noise accumulation, spurious correlations, and incidental endogeneity. In total, big data resources continue to add empirical breadth and detail to ornithology, often at very broad spatial extents, but how the challenges underlying this approach can best be mitigated to maximize inferential quality and rigor needs to be carefully considered. Los avances recientes en la tecnolog´ıa de la informaci ´on y la adquisici ´on de datos han creado tanto nuevas oportunidades de investigaci ´on como desaf´ıos para el uso de datos masivos (big data) en ornitolog´ıa. Brindamos una visi ´on general del pasado, presente y futuro de los datos masivos en ornitolog´ıa y exploramos las recompensas y desaf´ıos asociados a su aplicaci ´ on. Los recursos de datos estructurados (e.g., Muestreo de Aves Reproductivas de Am´erica del Norte) siguen jugando un rol importante en el avance de nuestro entendimiento de la ecolog´ıa de poblaciones de las aves, y el advenimiento reciente de datos masivos semi-estructurados (e.g., eBird) y desestructurados (e.g., radar de vigilancia clima´tica) han promovido el desarrollo de nuevas perspectivas emp´ıricas que esta´n generando miradas novedosas. Por ejemplo, los datos masivos han sido usados para estudiar y modelar la diversidad y distribuci ´on de las aves a trav´es del tiempo y del espacio, explorar los patrones y los determinantes de las estrategias de migraci ´on a gran escala, y examinar las dina´micas y los mecanismos asociados con las respuestas geogra´ficas y fenol ´ ogicas al cambio global. La aplicaci ´on de datos masivos tambi´en contiene una serie de desaf´ıos donde el gran volumen de datos y la dimensionalidad pueden generar una acumulaci ´on de ruido, correlaciones espurias y endogeneidad incidental. En total, los recursos de datos masivos contin ´uan agregando amplitud y detalle emp´ırico a la ornitolog´ıa, usualmente a escalas espaciales muy amplias, pero necesita considerarse cuidadosamente c ´omo los desaf´ıos que subyacen este enfoque pueden ser mitigados del mejor modo para maximizar su calidad inferencial y rigor

Aligning the Measurement of Microbial Diversity with Macroecological Theory

The number of microbial operational taxonomic units (OTUs) within a community is akin to species richness within plant/animal (“macrobial”) systems. A large literature documents OTU richness patterns, drawing comparisons to macrobial theory. There is, however, an unrecognized fundamental disconnect between OTU richness and macrobial theory: OTU richness is commonly estimated on a per-individual basis, while macrobial richness is estimated per-area. Furthermore, the range or extent of sampled environmental conditions can strongly influence a study's outcomes and conclusions, but this is not commonly addressed when studying OTU richness. Here we (i) propose a new sampling approach that estimates OTU richness per-mass of soil, which results in strong support for species energy theory, (ii) use data reduction to show how support for niche conservatism emerges when sampling across a restricted range of environmental conditions, and (iii) show how additional insights into drivers of OTU richness can be generated by combining different sampling methods while simultaneously considering patterns that emerge by restricting the range of environmental conditions. We propose that a more rigorous connection between microbial ecology and macrobial theory can be facilitated by exploring how changes in OTU richness units and environmental extent influence outcomes of data analysis. While fundamental differences between microbial and macrobial systems persist (e.g., species concepts), we suggest that closer attention to units and scale provide tangible and immediate improvements to our understanding of the processes governing OTU richness and how those processes relate to drivers of macrobial species richness

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL