Browsing by Author "Emerson, Brent C."
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- Building a robust, densely-sampled spider tree of life for ecosystem researchPublication . Macías-Hernández, Nuria; Domènech, Marc; Cardoso, Pedro; Emerson, Brent C.; Borges, Paulo A. V.; Lozano-Fernandez, Jesús; Paulo, Octávio S.; Vieira, Ana; Enguídanos, Alba; Rigal, François; Rosário, Isabel Amorim do; Arnedo, Miquel A.Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.
- Challenges, advances and perspectives in Island BiogeographyPublication . Borges, Paulo A. V.; Cardoso, Pedro; Gabriel, Rosalina; Ah-Peng, Claudine; Emerson, Brent C.Island biogeographical research is becoming more and more fashionable, with the continuous identification of new challenges that are critical for the advancement of science. In this contribution we identify biases and limitations associated with island biogeographical studies, and also describe recent advances and propose new perspectives. The main proposals include: 1) downscaling island biogeographical studies to local/plot scale; 2) investigating geographical patterns of intra-specific genetic variation to infer dispersal processes among and within islands; 3) using applied biogeographical research to respond to the current island biodiversity crisis; and 4) applying new computer-intensive methods such as artificial intelligence (AI) approaches.
- Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islandsPublication . Emerson, Brent C.; Borges, Paulo A. V.; Cardoso, Pedro; Convey, Peter; deWaard, Jeremy R.; Economo, Evan P.; Gillespie, Rosemary G.; Kennedy, Susan; Krehenwinkel, Henrik; Meier, Rudolf; Roderick, George K.; Strasberg, Dominique; Thébaud, Christophe; Traveset, Anna; Creedy, Thomas J.; Meramveliotakis, Emmanouil; Noguerales, Víctor; Overcast, Isaac; Morlon, Hélène; Papadopoulou, Anna; Vogler, Alfried P.; Arribas, Paula; Andújar, CarmeloABSTRACT: Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.
- A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scalesPublication . Emerson, Brent C.; Casquet, Juliane; López, Heriberto; Cardoso, Pedro; Borges, Paulo A. V.; Mollaret, Noémy; Oromí, Pedro; Strasberg, Dominique; Thébaud, ChristopheObtaining fundamental biodiversity metrics such as alpha, beta and gamma diversity for arthropods is often complicated by a lack of prior taxonomic information and/or taxonomic expertise, which can result in unreliable morphologically based estimates. We provide a set of standardized ecological and molecular sampling protocols that can be employed by researchers whose taxonomic skills may be limited, and where there may be a lack of robust a priori information regarding the regional pool of species. These protocols combine mass sampling of arthropods, classification of samples into parataxonomic units (PUs) and selective sampling of individuals for mtDNA sequencing to infer biological species. We sampled ten lowland rainforest plots located on the volcanic oceanic island of R eunion (Mascarene archipelago) for spiders, a group with limited taxonomic and distributional data for this region. We classified adults and juveniles into PUs and then demonstrated the reconciliation of these units with presumed biological species using mtDNA sequence data, ecological data and distributional data. Because our species assignment protocol is not reliant upon prior taxonomic information, or taxonomic expertise, it minimizes the problem of the Linnean shortfall to yield diversity estimates that can be directly compared across independent studies. Field sampling can be extended to other arthropod groups and habitats by adapting our field sampling protocol accordingly.
- Cryptic diversity in Azorean beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae) : An integrative taxonomic approach with description of four new speciesPublication . Borges, Paulo A. V.; Amorim, Isabel R.; Terzopoulou, Sofia; Rigal, François; Emerson, Brent C.; Serrano, Artur R. M.Recent findings based on molecular data support the occurrence in the Azores of several independently evolving lineages of the beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae Solier, 1834) and higher species richness masked by cryptic diversity, needing formal taxonomic description. All Tarphius from the Azores are revised using an integrative taxonomic approach, using evidence from morphology, morphometrics and molecular data to delimit species. Our results reveal that Azorean Tarphius comprise at least five phyletic lineages, two of which share a similar morphology, despite being divergent at the molecular level. A total of four new species are described grouped into two complexes: i) two new species in the “complex tornvalli” with the new taxa Tarphius relictus sp. nov. (Terceira) and Tarphius furtadoi sp. nov. (São BORGES ET AL. 402 · Zootaxa 4236 (3) © 2017 Magnolia Press Jorge, Faial and Pico) and; ii) two new species in the “complex azoricus-wollastoni-depressus” with the new taxa Tarphius gabrielae sp. nov. (Pico) and Tarphius floresensis sp. nov. (Flores). Descriptions, photographs of holotypes and morphological details, and remarks on diagnostic features comparing similar species are presented. Additional information on the distribution and conservation status of the 12 described species in the archipelago is also provided.
- A database of functional traits for spiders from native forests of the Iberian Peninsula and MacaronesiaPublication . Macías Hernández, Nuria; Ramos, Cândida; Domènech, Marc; Febles, Sara; Santos, Irene; Arnedo, Miquel A.; Borges, Paulo A. V.; Emerson, Brent C.; Cardoso, PedroThere is an increasing demand for databases including species trait information for biodiversity and community ecology studies. The existence of trait databases is useful for comparative studies within taxa or geographical regions, but there is low availability of databases for certain organisms. Here we present an open access functional trait database for spiders from Macaronesia and the Iberian Peninsula, recording several morphological and ecological traits related to the species life histories, microhabitat and trophic preferences.
- Evidence for multiple founding lineages and genetic admixture in the evolution of species within an oceanic island weevil (Coleoptera, Curculionidae) super-radiationPublication . Faria, Christiana; Machado, António; Amorim, Isabel R.; Gage, Matthew J. G.; Borges, Paulo A. V.; Emerson, Brent C.AIM: To infer colonization and speciation history for a closely related complex of nine species within the enigmatic Canary Island Laparocerus weevil radiation of 128 species. Using molecular dating and the spatial and temporal context that islands provide, we evaluate the possible explanations of incomplete lineage sorting and gene flow for the origin of shared genetic variation among species from different islands. LOCATION: Canary Islands (Gran Canaria, Tenerife, La Palma and El Hierro). METHODS: We collected a total of 173 specimens from 37 sites distributed across the four islands. Phylogenetic analyses of mitochondrial (COII) and nuclear (ITS2) sequence data and molecular dating techniques were used to infer the origin of the group in the archipelago and their history of colonization and differentiation. RESULTS: Gran Canaria appeared to be the geographical origin of the complex. An unexpected result was that mtDNA revealed each of the single species on La Palma and El Hierro to be the product of more than one colonization event from more than one source island. In both cases nuclear ITS2 data revealed these multiple colonizations to have been followed by admixture. MAIN CONCLUSIONS: The two gene trees present very different topologies, with a rather simple colonization history required to explain the pattern of nuclear gene relationships, while the mtDNA gene tree implicates a much more complex history of colonization. Explanations of incomplete lineage sorting are ruled out and a history of colonization and speciation for the L. tessellatus complex involving genetic admixture is inferred.
- Habitat filtering and inferred dispersal ability condition across‐scale species turnover and rarity in Macaronesian island spider assemblagesPublication . Malumbres-Olarte, Jagoba; Rigal, François; Girardello, Marco; Cardoso, Pedro; Crespo, Luís C.; Amorim, Isabel R.; Arnedo, Miquel A.; Boieiro, Mário; Carvalho, José Carlos; Carvalho, Rui; Gabriel, Rosalina; Lamelas-López, Lucas; López, Heriberto; Paulo, Octávio S.; Pereira, Fernando; Pérez‐Delgado, Antonio J.; Rego, Carla; Romeiras, Maria M.; Ros-Prieto, Alejandra; Oromí, Pedro; Vieira, Ana; Emerson, Brent C.; Borges, Paulo A. V.AIM: Habitat diversity has been linked to the diversity and structure of island communities, however, little is known about patterns and processes within habitats. Here we aim to determine the contributions of habitat type and inferred dispersal frequency to the differences in taxonomic structure between assemblages in the same island habitat. LOCATION: The Macaronesian archipelagos (Azores, Madeira, the Canary Islands and Cabo Verde). TAXON: Spiders (Araneae). METHODS: We established forest and dry habitat sites (each with five plots) on two islands per archipelago. We collected spiders using standardised sampling protocols. We tested the differences in beta diversity separately for each habitat and for each inferred category of ballooning (an aerial dispersal strategy) frequency across geographic scales through nested non-parametric permutational multivariate analyses of variance. We then tested whether ballooning and habitat influenced heterogeneity in species composition (dispersion in beta diversity) in the two habitat types. We analysed the effects of habitat and ballooning on species abundance distribution (SAD) and rarity by fitting Gambin models and evaluating the contribution of ballooning categories to SAD. RESULTS: Communities of the same archipelago and habitat were taxonomically more similar, and beta diversity increased with geographic scale, being greater in dry habitats. There was greater species replacement among assemblages in dry habitats than in forests, with greater differences for rare ballooners. There were no differences in SAD between habitats although dry habitat sites seemed to harbour more species with low abundances (rare species) than forests. MAIN CONCLUSIONS: Habitat type does not only condition the differences between spider assemblages of the same habitat but also the scale at which they occur. These differences may be determined by the heterogeneity in the physical structure of each habitat as well as how much this structure facilitates aerial dispersal (ballooning), and should be considered in theories/hypotheses on island community assembly as well as in conservation strategies.
- MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced speciesPublication . Cicconardi, Francesco; Borges, Paulo A. V.; Strasberg, Dominique; Oromí, Pedro; López, Heriberto; Pérez-Delgado, Antonio J.; Casquet, Juliane; Caujapé-Castells, Juli; Fernández-Palacios, José María; Thébaud, Christophe; Emerson, Brent C.Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large-scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil-dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate humanmediated species introductions, with minimum estimates for the proportion of introducedspecies on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.
- Phylogeography and molecular phylogeny of Macaronesian island Tarphius (Coleoptera: Zopheridae): why so few species in the Azores?Publication . Amorim, Isabel R.; Emerson, Brent C.; Borges, Paulo A. V.; Wayne, Robert K.AIM: We used a phylogenetic framework to examine island colonization and predictions pertaining to differentiation within Macaronesian Tarphius (Insecta, Coleoptera, Zopheridae), and explain the paucity of endemics in the Azores compared with other Macaronesian archipelagos. Specifically, we test whether low diversity in the Azores could be due to recent colonization (phylogenetic lineage youth), cryptic speciation (distinct phylogenetic entities within species) or the young geological age of the archipelago. LOCATION: Macaronesian archipelagos (Azores, Madeira and the Canary Islands), northern Portugal and Morocco. METHODS: Phylogenetic analyses of mitochondrial and nuclear genes of Tarphius beetles of the Azores, other Macaronesian islands and neighbouring continental areas were used to investigate the origin of island biodiversity and to compare patterns of colonization and differentiation. A comparative nucleotide substitution rate test was used to select the appropriate substitution rate to infer clade divergence times. RESULTS: Madeiran and Canarian Tarphius species were found to be more closely related to each other, while Azorean taxa grouped separately. Azorean taxa showed concordance between species and phylogenetic clades, except for species that occur on multiple islands, which segregated by island of origin. Divergence time estimates revealed that Azorean Tarphius are an old group and that the most recent intra-island speciation event on Santa Maria, the oldest island, occurred between 3.7 and 6.1 Ma. MAIN CONCLUSIONS: Our phylogenetic approach provides new evidence to understand the impoverishment of Azorean endemics: (1) Tarphius have had a long evolutionary history within the Azores, which does not support the hypothesis of fewer radiation events due to recent colonization; (2) the current taxonomy of Azorean Tarphius does not reflect common ancestry and cryptic speciation is responsible for the underestimation of endemics; (3) intra-island differentiation in the Azores was found only in the oldest island, supporting the idea that young geological age of the archipelago limits the number of endemics; and (4) the lack of evidence for recent intra-island diversification in Santa Maria could also explain the paucity of Azorean endemics. Phylogenetic reconstructions of other species-rich taxa that occur on multiple Macaronesian archipelagos will reveal whether our conclusions are taxon specific, or of a more general nature.