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Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by ( 1 ) targeting loci with highly degenerate primers or conserved priming sites, ( 2 ) increasing PCR template concentration, ( 3 ) reducing PCR cycle number or ( 4 ) avoiding locus specific amplification by directly sequencing genomic DNA. Amplification bias is reduced considerably by degenerate primers or targeting amplicons with conserved priming sites. Surprisingly, a reduction of PCR cycles did not have a strong effect on amplification bias. The association of taxon abundance and read count was actually less predictable with fewer cycles. Even a complete exclusion of locus specific amplification did not exclude bias. Copy number variation of the target loci may be another explanation for read abundance differences between taxa, which would affect amplicon based and PCR free methods alike. As read abundance biases are taxon specific and predictable, the application of correction factors allows abundance estimates.

Mammalian frugivores are critical seed dispersers, but many are under threat of extinction. Futhermore, the impact of past and future defaunation on plant assemblages has yet to be quantified at the global scale. Here, we integrate palm and mammalian frugivore trait and occurrence data and reveal a global positive relationship between fruit size and frugivore body size. Global variation in fruit size is better explained by present-day frugivore assemblages than by Late Pleistocene assemblages, suggesting ecological and evolutionary reorganization after end-Pleistocene extinctions, except in the Neotropics, where some large-fruited palm species may have outlived their main seed dispersers by thousands of years. Our simulations of frugivore extinction over the next 100 years suggest that the impact of defaunation will be highest in the Old World tropics, and an up to 4% assemblage-level decrease in fruit size would be required to maintain the global body size–fruit size relationship. Overall, our results suggest that while some palm species may be able to keep pace with future defaunation through evolutionary changes in fruit size, large-fruited species may be especially vulnerable to continued defaunation. Extinctions of megafauna can have cascading effects on their ecological communities. Here, Lim et al. investigate the relationships of historical and current mammalian frugivore body size with palm fruit size, then project how further mammal extinctions are likely to affect palm communities.

Adaptive radiations are typically characterized by niche partitioning among their constituent species. Trophic niche partitioning is particularly important in predatory animals, which rely on limited food resources for survival. We test for trophic niche partitioning in an adaptive radiation of Hawaiian Tetragnatha spiders, which have diversified in situ on the Hawaiian Islands. We focus on a community of nine species belonging to two different clades, one web‐building and the other actively hunting, which co‐occur in wet forest on East Maui. We hypothesize that trophic niches differ significantly both: (a) among species within a clade, indicating food resource partitioning, and (b) between the two clades, corresponding to their differences in foraging strategy. To assess niches of the spider species, we measure: (a) web architecture, the structure of the hunting tool, and (b) site choice, the physical placement of the web in the habitat. We then test whether differences in these parameters translate into meaningful differences in trophic niche by measuring (c) stable isotope signatures of carbon and nitrogen in the spiders’ tissues, and (d) gut content of spiders based on metabarcoding data. We find significant interspecific differences in web architecture and site choice. Importantly, these differences are reflected in stable isotope signatures among the five web‐building species, as well as significant isotopic differences between web‐builders and active hunters. Gut content data also show interspecific and inter‐clade differences. Pairwise overlaps of web architecture between species are positively correlated with overlaps of isotopic signature. Our results reveal trophic niche partitioning among species within each clade, as well as between the web‐building and actively hunting clades. Based on the correlation between web architecture and stable isotopes, it appears that the isotopic signatures of spiders’ tissues are influenced by architectural differences among their webs. Our findings indicate an important link between web structure, microhabitat preference and diet in the Hawaiian Tetragnatha. A free Plain Language Summary can be found within the Supporting Information of this article. A free Plain Language Summary can be found within the Supporting Information of this article.

Plant traits are critical to plant form and function —including growth, survival and reproduction— and therefore shape fundamental aspects of population and ecosystem dynamics as well as ecosystem services. Here, we present a global species-level compilation of key functional traits for palms (Arecaceae), a plant family with keystone importance in tropical and subtropical ecosystems. We derived measurements of essential functional traits for all (>2500) palm species from key sources such as monographs, books, other scientific publications, as well as herbarium collections. This includes traits related to growth form, stems, armature, leaves and fruits. Although many species are still lacking trait information, the standardized and global coverage of the data set will be important for supporting future studies in tropical ecology, rainforest evolution, paleoecology, biogeography, macroecology, macroevolution, global change biology and conservation. Potential uses are comparative eco-evolutionary studies, ecological research on community dynamics, plant-animal interactions and ecosystem functioning, studies on plant-based ecosystem services, as well as conservation science concerned with the loss and restoration of functional diversity in a changing world.

Plant–herbivore interactions occur in all ecosystems and provide a major avenue for energy flow to higher trophic levels. A long‐standing hypothesis to explain the latitudinal gradient in species diversity proposes that the relatively stable and frost‐free climate of the tropics should lead to more intense biotic interactions in tropical compared with temperate environments, giving rise to a greater diversity of plants and herbivores. Herbivory rates have been compared across latitudes to test this biotic interactions hypothesis, with herbivory typically being measured from observable leaf damage. However, we argue that a measure of percentage leaf damage alone does not straightforwardly reflect the cost of herbivory to the plant, and on its own does not constitute an appropriate test of the biotic interactions hypothesis. For a given amount of herbivory, the impact of herbivory is dependent upon many factors, such as the construction cost of the leaf, the growth and replacement rates and leaf life span. We investigate the latitudinal gradient in herbivory by analysing a large dataset of herbivory rates for 452 tree species and separating the species into those with short and long leaf life spans. We show that annual herbivory rates tend to be greater at lower latitudes for evergreen species (which have long‐lived leaves), but no trend in herbivory rate with latitude was found for species with short leaf life spans. Phylogenetic least squares regression assuming Ornstein‐Uhlenbeck processes also showed a negative effect of latitude on herbivory rate for evergreen trees, but we caution that viewing herbivory as a species trait is problematic. An integrative approach that incorporates leaf life span, as well as the costs of investment in growth and potential costs of losing leaf tissue, is needed to further our understanding of the ecological and evolutionary dynamics of herbivory.

New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as “DNA barcoding”) and by extension, meta-barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA-based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity.

Angiosperms have been essential components of primate diets for millions of years, but the relative importance of different angiosperm families remains unclear. Here, we assess the contribution and ecological and evolutionary significance of plant families to diets of wild primates by compiling an unprecedented dataset of almost 9000 dietary records from 141 primary sources covering 112 primate species. Of the 205 angiosperm plant families recorded in primate diets, only 10 were consumed by more than half of primate species. Plants of the Moraceae and Fabaceae families were the most widely and frequently consumed, and they likely represent keystone resources for primates. Over 75% of species fed on these two families, and together they made up a median of approximately 13% of primate diets. By analysing the relative proportion of different plant parts consumed, we found that Moraceae was mainly eaten as fruit and Fabaceae as non-fruit parts, with the consumption of these two families not showing a significant phylogenetic signal across primate species. Moraceae consumption was associated with small home range sizes, even though more frugivorous primates tended to have larger home ranges compared to more folivorous species, possibly due to the year-round availability of moraceous fruits and the asynchrony in their phenology. Our results suggest that primates may be intricately and subtly shaped by the plant families that they have consumed over millions of years, and highlight the importance of detailed dietary studies to better understand primate ecology and evolution.

Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along two elevational gradients across two volcanoes on the island of Hawai‘i. We find that arthropod communities between the two transects become increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.

The arboreal ecosystem is vitally important to global and local biogeochemical processes, the maintenance of biodiversity in natural systems, and human health in urban environments. The ability to collect samples, observations, and data to conduct meaningful scientific research is similarly vital. The primary methods and modes of access remain limited and difficult. In an online survey, canopy researchers ( n = 219) reported a range of challenges in obtaining adequate samples, including ∼10% who found it impossible to procure what they needed. Currently, these samples are collected using a combination of four primary methods: (1) sampling from the ground; (2) tree climbing; (3) constructing fixed infrastructure; and (4) using mobile aerial platforms, primarily rotorcraft drones. An important distinction between instantaneous and continuous sampling was identified, allowing more targeted engineering and development strategies. The combination of methods for sampling the arboreal ecosystem provides a range of possibilities and opportunities, particularly in the context of the rapid development of robotics and other engineering advances. In this study, we aim to identify the strategies that would provide the benefits to a broad range of scientists, arborists, and professional climbers and facilitate basic discovery and applied management. Priorities for advancing these efforts are (1) to expand participation, both geographically and professionally; (2) to define 2–3 common needs across the community; (3) to form and motivate focal teams of biologists, tree professionals, and engineers in the development of solutions to these needs; and (4) to establish multidisciplinary communication platforms to share information about innovations and opportunities for studying arboreal ecosystems.

The diversity of the biota of any place and time is often the product of a long and complex history of ecological and evolutionary assembly through the fundamental processes of immigration, speciation and extinction. This biotic assembly typically occurs amid a backdrop of constant abiotic and biotic change at multiple spatiotemporal scales. Given this potentially complex abiotic and biotic history, investigating the core processes that underlie the assembly of regional biotas, as well as the abiotic, biotic and historical factors that influence them, is a major challenge at the intersection of biogeography, macroevolution and ecology. Oceanic islands provide ideal opportunities to investigate the processes underlying the assembly of regional biotas. Given their volcanic origins, their landscapes represent initial blank slates that are then populated by successful long-distance dispersal events by various organisms, and the subsequent diversification of some of these colonist lineages. Furthermore, their relatively predictable geologic histories and lifespans make the study of how the diversification of lineages are shaped over geologic time-scales especially tractable, compared to the more complex abiotic and biotic histories that often shape continental, mainland biotas. Remote hotspot archipelagoes such as that of Hawaii are especially exciting case studies, as they are composed of islands formed in sequence through the movement of the Pacific tectonic plate over a relatively stationary mantle hotspot, and so that each island captures a record of diversification at different stages. The multiple “snapshots” of diversity provided by the differently-aged islands of the Hawaiian archipelago, as well as their well-defined and quantifiable ontogenies, allow the diversities observed on each of the main islands to be leveraged to understand how diversity on islands change through the lifespan of an island, as if each island were a different point on a time series. In Chapter 1, I investigate whether, and how, the changing geologic backdrop has shaped the diversification of Hawaiian plant and animal lineages on each of the islands. I used a geologically informed diversity-dependent model of species richness change that incorporates estimates of how island area has changed through time, while also taking into account island-specific ontogenetic differences among the four current main islands / island complexes of the Hawaiian archipelago, and tested my models against alternative models that do not account for island ontogenetic changes. I find that, at the broadest temporal scales, the geologic dynamics of the Hawaiian Islands have had a profound influence on the macroevolutionary history of most of the 14 endemic lineages examined, with all lineages undergoing radiations as islands grow, and most of them now undergoing long-term evolutionary declines as the islands undergo subsidence and erosion with age. As mentioned above, the isolation and de novo formation of the Hawaiian Islands imposes a strong filter, limiting successful colonization of the islands to a subset of mainland plant and animal groups that have the traits necessary for long-distance dispersal. As a result, it has often been assumed that the Hawaiian Islands often represent a biogeographic sink for many lineages, with colonization of the remote islands representing “dead ends” in the history of dispersal of lineages that prove successful. In some cases, this is certainly true, with some lineages evolving characteristics that reduce dispersal ability relatively quickly upon successful colonization. However, molecular phylogenetic data are slowly challenging this narrative, and it is increasingly demonstrated that the Hawaiian archipelago may instead also play a fundamental role as a biogeographic source for other parts of the Pacific and even mainland areas. In Chapter 2, testing this more nuanced view of the biogeographic history of Hawaiian lineages in the context of the greater Pacific, I constructed a molecular phylogeny of one of the most species-rich angiosperm radiations in the Pacific, Peperomia (Piperaceae), using full plastome sequences generated via a high-throughput shotgun sequencing approach. The final tree consisted of about half the total number of species described in the Pacific. Incredibly, I found that the Pacific has played host to four separate and distinct colonist lineages that originated from the Neotropics, although whether these colonization events occurred through direct dispersal from South and Central America, or via indirect routes of dispersal through the Afro and Paleotropics remain unclear. Nonetheless, in support of the newer view of the role of the Hawaiian Islands in Pacific biogeography, my molecular phylogeny paints a picture of frequent dispersal within the south Pacific, with two independent radiations of Peperomia on Hawaii, and subsequent southwards dispersal of some individuals derived from one of these radiations to the Marquesas Islands. (Abstract shortened by ProQuest.)