Publications by authors named "Brent Emerson"

78 Publications

Biodiversity monitoring using environmental DNA.

Mol Ecol Resour 2021 07 24;21(5):1405-1409. Epub 2021 May 24.

Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, University of Idaho, Hagerman, ID, USA.

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http://dx.doi.org/10.1111/1755-0998.13399DOI Listing
July 2021

Genomic variation, population history and within-archipelago adaptation between island bird populations.

R Soc Open Sci 2021 Feb 3;8(2):201146. Epub 2021 Feb 3.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.

Oceanic island archipelagos provide excellent models to understand evolutionary processes. Colonization events and gene flow can interact with selection to shape genetic variation at different spatial scales. Landscape-scale variation in biotic and abiotic factors may drive fine-scale selection within islands, while long-term evolutionary processes may drive divergence between distantly related populations. Here, we examine patterns of population history and selection between recently diverged populations of the Berthelot's pipit (), a passerine endemic to three North Atlantic archipelagos. First, we use demographic trees and statistics to show that genome-wide divergence across the species range is largely shaped by colonization and bottlenecks, with evidence of very weak gene flow between populations. Then, using a genome scan approach, we identify signatures of divergent selection within archipelagos at single nucleotide polymorphisms (SNPs) in genes potentially associated with craniofacial development and DNA repair. We did not detect within-archipelago selection at the same SNPs as were detected previously at broader spatial scales between archipelagos, but did identify signatures of selection at loci associated with similar biological functions. These findings suggest that similar ecological factors may repeatedly drive selection between recently separated populations, as well as at broad spatial scales across varied landscapes.
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http://dx.doi.org/10.1098/rsos.201146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8074581PMC
February 2021

Sustained resiliency building and burnout reduction for healthcare professionals via organizational sponsored mindfulness programming.

Explore (NY) 2021 Apr 16. Epub 2021 Apr 16.

Division of Health Behavior and Health Promotion, College of Public Health, The Ohio State University, Columbus, OH, United States.

Purpose: To measure healthcare professional (HCP) result sustainability following implementation of an organizationally sponsored Mindfulness Based Intervention (MBI), Mindfulness in Motion (MIM), in areas of burnout, perceived stress, resilience, and work engagement.

Methods: A follow-up survey was sent via email to healthcare professionals (n = 220) who previously participated in the 8-week MIM intervention. Survey assessed burnout, perceived stress, resilience, work engagement, and included open-ended questions pertaining to barriers, facilitators, and sustained impact of practicing mindfulness after program end.

Results: Analysis included 66 healthcare professionals with sustainability time frames ranging from 3 to 28 months from initial program finish. Average time since intervention end was 12.2 months. Based on 12.2 months sustained results post MIM, there were significant differences from pre-MIM to sustainability follow-up in burnout (*p = 0.0047), perceived stress (*p = 0.00001), and resilience (*p = 0.0004). Work engagement benefits were non-significant from pre-test to follow-up (p = 0.4008). There were no significant differences in results when comparing the length of time since participant was enrolled in the initial study. Additionally, analysis of the qualitative data revealed multiple subthemes relating to facilitators of sustained mindfulness, barriers to practicing mindfulness, and lasting impacts of the MIM intervention.

Conclusions: For Healthcare Professionals, the organizationally sponsored mindfulness intervention outcomes were sustained beyond the 8-weeks of the initial MIM intervention for all but one outcome variable. Post 8-week intervention end, participants were given the option of receiving weekly "Mindful Moment" emails and attending monthly mindfulness booster sessions. Organizational support may be a pivotal factor in sustaining positive results achieved via mindfulness programming.
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http://dx.doi.org/10.1016/j.explore.2021.04.004DOI Listing
April 2021

Flightlessness in insects enhances diversification and determines assemblage structure across whole communities.

Proc Biol Sci 2021 02 17;288(1945):20202646. Epub 2021 Feb 17.

Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands 38206, Spain.

Dispersal limitation has been recurrently suggested to shape both macroecological patterns and microevolutionary processes within invertebrates. However, because of potential interactions among biological, environmental, temporal, and spatial variables, causal links among flight-related traits, diversification and spatial patterns of community assembly remain elusive. Integrating genetic variation within species across whole insect assemblages, within a simplified spatial and environmental framework, can be used to reduce the impact of these potentially confounding variables. Here, we used standardized sampling and mitochondrial DNA sequencing for a whole-community characterization of the beetle fauna inhabiting a singular forested habitat (laurel forest) within an oceanic archipelago setting (Canary Islands). The spatial structure of species assemblages together with species-level genetic diversity was compared at the archipelago and island scales for 104 winged and 110 wingless beetle lineages. We found that wingless beetle lineages have: (i) smaller range sizes at the archipelago scale, (ii) lower representation in younger island communities, (iii) stronger population genetic structure, and (iv) greater spatial structuring of species assemblages between and within islands. Our results reveal that dispersal limitation is a fundamental trait driving diversity patterns at multiple hierarchical levels by promoting spatial diversification and affecting the spatial configuration of entire assemblages at both island and archipelago scales.
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http://dx.doi.org/10.1098/rspb.2020.2646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7935046PMC
February 2021

Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data.

Mol Ecol Resour 2021 Aug 24;21(6):1772-1787. Epub 2021 Feb 24.

Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC, San Cristóbal de la Laguna, Spain.

Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. metaMATE requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mitochondrial DNA haplotypes) or nonauthentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. metaMATE (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of nonauthentic ASVs and the collateral effects on the removal of authentic ASVs. The output from metaMATE facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the metaMATE software (available at https://github.com/tjcreedy/metamate).
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http://dx.doi.org/10.1111/1755-0998.13337DOI Listing
August 2021

Revealing community assembly through barcoding: Mediterranean butterflies and dispersal variation.

J Anim Ecol 2020 09;89(9):1992-1996

Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Spain.

In Focus: Scalercio, S., Cini, A., Menchetti, M., Vodă, R., Bonelli, S., Bordoni, A., … Dapporto, L. (2020). How long is 3 km for a butterfly? Ecological constraints and functional traits explain high mitochondrial genetic diversity between Sicily and the Italian Peninsula. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.13196. Biotic and abiotic factors can shape geographical patterns of genetic variation within species, but few studies have addressed how this might generate common patterns at the level of communities of species. Scalercio et al. (2020) have combined mtDNA sequence data and life-history traits, to reveal a repeated pattern of genetic structure between Sicilian and southern Italian butterfly populations, which are separated by only 3 km of ocean. They reveal how intrinsic species traits and extrinsic environmental constraints explain this pattern, demonstrating an important role for wind. Moreover, the inclusion of almost 8,000 georeferenced sequences reveals that, in spite of also being present in southern Italy, almost half of Sicilian butterfly species are more closely related to populations from other parts of Europe, Asia or North Africa. We provide further discussion on the biogeographic barrier they identify, and the potential of community-level DNA barcoding to identify processes that structure genetic variation across communities.
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http://dx.doi.org/10.1111/1365-2656.13316DOI Listing
September 2020

Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis.

Mol Ecol 2021 03 2;30(5):1120-1135. Epub 2021 Feb 2.

Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain.

High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.
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http://dx.doi.org/10.1111/mec.15797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7986105PMC
March 2021

Long-term cloud forest response to climate warming revealed by insect speciation history.

Evolution 2021 Feb 1;75(2):231-244. Epub 2020 Nov 1.

Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, 38206, Spain.

Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change.
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http://dx.doi.org/10.1111/evo.14111DOI Listing
February 2021

The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding.

Mol Ecol 2021 01 30;30(1):48-61. Epub 2020 Aug 30.

Department of Life Sciences, Natural History Museum, London, UK.

Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly are scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multihierarchical approach was performed using haplotype-level COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1,000 codistributed species and nearly 3,000 haplotypes. Local assemblage composition differed greatly between grasslands and forests and, within each habitat, showed strong spatial structure and high endemicity. Distance decay was high at all levels, even at the scale of a few kilometres or less. The local distance decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity on Earth.
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http://dx.doi.org/10.1111/mec.15591DOI Listing
January 2021

A database of functional traits for spiders from native forests of the Iberian Peninsula and Macaronesia.

Biodivers Data J 2020 30;8:e49159. Epub 2020 Apr 30.

Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, University of Helsinki Helsinki Finland.

Background: There 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.

New Information: We present a database that includes 12 biological traits for 506 spider species present in natural forests of the Iberian Peninsula (Spain) and three Macaronesian archipelagoes (Azores, Madeira and Canary Islands). The functional trait database consists of two sections:individual-level data for six morphological traits (total body size, prosoma length, prosoma width, prosoma height, tibia I length and fang length), based on direct measurements of 2844 specimens of all spider species; andspecies-level aggregate data for 12 traits (same 6 morphological traits as in the previous section plus dispersal ability, vertical stratification, circadian activity, foraging strategy, trophic specialization and colonization status), based on either the average of the direct measurements or bibliographic searches.This functional trait database will serve as a data standard for currently ongoing analyses that require trait and functional diversity statistics.
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http://dx.doi.org/10.3897/BDJ.8.e49159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7205838PMC
April 2020

A Teachable Moment: Colorectal Cancer Screening Among Companions Waiting for Outpatients Undergoing a Colonoscopy.

J Cancer Educ 2020 Apr 21. Epub 2020 Apr 21.

Comprehensive Cancer Center, The Ohio State University, Suite 525, 1590 North High Street, Columbus, OH, 43201, USA.

To determine colorectal cancer (CRC) screening knowledge, attitudes, behaviors, and preferences for a future CRC screening educational intervention among adults (companions) waiting for outpatients undergoing a colonoscopy. We approached 384 companions at three endoscopy centers associated with one healthcare system to complete a survey from March to July 2017. The survey assessed CRC and CRC screening knowledge, attitudes, behaviors, and preferences for a future CRC screening educational intervention. There were 164 companions at average risk for CRC that completed a self-administered survey. Among average-risk companions, 23% were not within screening guidelines. Additionally, 74% of those not within guidelines reported that they had never completed a CRC screening test. The most frequently reported barriers to CRC screening were the perception of not needing screening because they were asymptomatic and lack of a provider recommendation for screening. Companions suggested that a future CRC screening intervention include a brochure and/or a brief video, featuring men and women from different races/ethnicities, a CRC survivor, and a healthcare professional. Almost one-fourth of average-risk companions waiting at endoscopy centers were not within CRC screening guidelines, providing a teachable moment to recruit companions to participate in an educational intervention to encourage screening. Companions provided suggestions (e.g., content and channel) for a future intervention to promote CRC screening in this population.
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http://dx.doi.org/10.1007/s13187-020-01745-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7575613PMC
April 2020

Climate drives community-wide divergence within species over a limited spatial scale: evidence from an oceanic island.

Ecol Lett 2020 Feb 25;23(2):305-315. Epub 2019 Nov 25.

Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain.

Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the spatial scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance are restricted, microclimatic variation over distances of only a few kilometres can maintain strong geographic isolation extending back several millions of years. Further to this, we demonstrate congruent diversification with gene flow across species, mediated by Quaternary climate oscillations that have facilitated a dynamic of isolation and secondary contact. The unprecedented scale of parallel species responses to a common environmental driver for evolutionary change has profound consequences for understanding past and future species responses to climate variation.
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http://dx.doi.org/10.1111/ele.13433DOI Listing
February 2020

Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari.

Mol Biol Evol 2020 03;37(3):683-694

Department of Life Sciences, Natural History Museum, London, United Kingdom.

High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.
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http://dx.doi.org/10.1093/molbev/msz255DOI Listing
March 2020

Dispersal limitation: Evolutionary origins and consequences in arthropods.

Mol Ecol 2019 07 16;28(13):3137-3140. Epub 2019 Jul 16.

Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.

Niche and dispersal ability are key traits for explaining the geographical structuring of species into discrete populations, and its evolutionary significance. Beyond their individual effects, the interplay between species niche and its geographic limits, together with the evolutionary lability of dispersal ability, can underpin trait diversification and speciation when exposed to gradients of selection. In this issue of Molecular Ecology, two complementary papers demonstrate how evolutionary lability for dispersal ability linked to niche shift can drive such a model in a context that includes selection. Both papers investigate the evolution of dispersal limitation in arthropods across altitudinal gradients, but using taxa with contrasting ecologies. McCulloch et al. (2019) investigate the evolution of wing loss at higher altitudes in stoneflies, a taxon inhabiting freshwater systems. Suzuki et al. (2019) report a similar phenomenon, but involving wing reduction at higher altitudes in scorpionflies, a taxon associated with moist terrestrial habitats. Here, we compare and contrast the results of both studies to explore their broader implications for understanding diversification and speciation within arthropods.
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http://dx.doi.org/10.1111/mec.15152DOI Listing
July 2019

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles.

Genome Biol 2019 05 17;20(1):98. Epub 2019 May 17.

Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.

Background: The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing.

Results: We explore the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representative of the two most species-rich beetle suborders. We contrast the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We find gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant feeding, we identify families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There is notable support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes.

Conclusions: Our explicit modeling of the evolution of gene repertoires across 18 species identifies putative adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant feeding in general, in driving beetle diversification.
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http://dx.doi.org/10.1186/s13059-019-1704-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6525341PMC
May 2019

Introgressive hybridization in a Spiny-Tailed Iguana, , and its implications for taxonomy and conservation.

PeerJ 2019 23;7:e6744. Epub 2019 Apr 23.

Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, Spain.

Introgression, the transmission of genetic material of one taxon into another through hybridization, can have various evolutionary outcomes. Previous studies have detected signs of introgression between western populations of the Mexican endemic and threatened spiny-tailed iguana, . However, the extent of this phenomenon along the geographic distribution of the species is unknown. Here, we use multilocus data together with detailed geographic sampling to (1) define genotypic clusters within ; (2) evaluate geographic concordance between maternally and biparentally inherited markers; (3) examine levels of introgression between genotypic clusters, and (4) suggest taxonomic modifications in light of this information. Applying clustering methods to genotypes of 341 individuals from 49 localities of and the closely related , we inferred the existence of five genotypic clusters. Contact zones between genotypic clusters with signatures of interbreeding were detected, showing different levels of geographic discordance with mtDNA lineages. In northern localities, mtDNA and microsatellites exhibit concordant distributions, supporting the resurrection of . Similar concordance is observed along the distribution of , confirming its unique taxonomic identity. Genetic and geographic concordance is also observed for populations within southwestern Mexico, where the recognition of a new species awaits in depth taxonomic revision. In contrast, in western localities a striking pattern of discordance was detected where up to six mtDNA lineages co-occur with only two genotypic clusters. Given that the type specimen originated from this area, we suggest that individuals from western Mexico keep the name . Our results have profound implications for conservation, management, and forensics of Mexican iguanas.
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http://dx.doi.org/10.7717/peerj.6744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485205PMC
April 2019

Evolution of host plant use and diversification in a species complex of parasitic weevils (Coleoptera: Curculionidae).

PeerJ 2019 20;7:e6625. Epub 2019 Mar 20.

Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Canary Islands, Spain.

Weevils (Coleoptera: Curculionoidea) represent one of the most diverse groups of organisms on Earth; interactions with their host plants have been recognized to play a central role in their remarkable diversity, yet the exact mechanisms and factors still remain poorly understood. Using phylogenetic comparative analyses, here we investigate the evolution of host use and its possible role in diversification processes of and , two closely related groups of weevils that feed and develop inside plant tissues of hosts within the families Scrophulariaceae and Plantaginaceae. We found strong evidence for phylogenetic conservatism of host use at the plant family level, most likely due to substantial differences in the chemical composition of hosts, reducing the probability of shifts between host families. In contrast, the use of different plant organs represents a more labile ecological trait and ecological niche expansion that allows a finer partitioning of resources. and weevils initially specialized on plants within Scrophulariaceae and then shifted to the closely related Plantaginaceae; likewise, a gall inducing behavior evolved from non-galler weevils, possibly in response to resource competition, as galls facilitate larval development by providing enhanced nutrition and a favorable microhabitat. Results from trait-dependent diversification analyses suggest that both use of hosts within Plantaginaceae and parasitism on fruits and seed capsules are associated with enhanced diversification of and via low extinction rates. Our study provides quantitative evidence and insights on the ecological factors that can promote diversification in phytophagous insects that feed and develop inside plant tissues.
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http://dx.doi.org/10.7717/peerj.6625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431137PMC
March 2019

Babies, Bathwater, and Straw Men? Not Quite: A Response to Meiri et al.

Trends Ecol Evol 2018 12 25;33(12):896-897. Epub 2018 Sep 25.

Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206, Spain; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA; Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, La Laguna, 38071, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.tree.2018.09.004DOI Listing
December 2018

Why the COI barcode should be the community DNA metabarcode for the metazoa.

Mol Ecol 2018 10 17;27(20):3968-3975. Epub 2018 Sep 17.

Grupo de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain.

Metabarcoding of complex metazoan communities is increasingly being used to measure biodiversity in terrestrial, freshwater and marine ecosystems, revolutionizing our ability to observe patterns and infer processes regarding the origin and conservation of biodiversity. A fundamentally important question is which genetic marker to amplify, and although the mitochondrial cytochrome oxidase subunit I (COI) gene is one of the more widely used markers in metabarcoding for the Metazoa, doubts have recently been raised about its suitability. We argue that (a) the extensive coverage of reference sequence databases for COI; (b) the variation it presents; (c) the comparative advantages for denoising protein-coding genes; and (d) recent advances in DNA sequencing protocols argue in favour of standardizing for the use of COI for metazoan community samples. We also highlight where research efforts should focus to maximize the utility of metabarcoding.
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http://dx.doi.org/10.1111/mec.14844DOI Listing
October 2018

Anagenesis, Cladogenesis, and Speciation on Islands.

Trends Ecol Evol 2018 07 3;33(7):488-491. Epub 2018 May 3.

Island Ecology and Evolution Research Group, IPNA-CSIC, C/Astrofísico Francisco Sánchez 3, 38206 La Laguna, Santa Cruz de Tenerife, Spain; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA; Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, La Laguna, 38071, Spain. Electronic address:

Anagenesis and cladogenesis are fundamental evolutionary concepts, but are increasingly being adopted as speciation models in the field of island biogeography. Here, we review the origin of the terms 'anagenetic' and 'cladogenetic' speciation, critique their utility, and finally suggest alternative terminology that better describes the geographical relationships of insular sister species.
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http://dx.doi.org/10.1016/j.tree.2018.04.006DOI Listing
July 2018

Long-term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics.

Mol Ecol 2018 01 16;27(2):432-448. Epub 2018 Jan 16.

Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Santa Cruz de Tenerife, Spain.

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (i) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation and (ii) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky islands (the Trans-Mexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow.
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http://dx.doi.org/10.1111/mec.14461DOI Listing
January 2018

Connecting Earth observation to high-throughput biodiversity data.

Nat Ecol Evol 2017 Jun 22;1(7):176. Epub 2017 Jun 22.

Department of Geography, King's College London, Strand Campus, London WC2R 2LS, UK.

Understandably, given the fast pace of biodiversity loss, there is much interest in using Earth observation technology to track biodiversity, ecosystem functions and ecosystem services. However, because most biodiversity is invisible to Earth observation, indicators based on Earth observation could be misleading and reduce the effectiveness of nature conservation and even unintentionally decrease conservation effort. We describe an approach that combines automated recording devices, high-throughput DNA sequencing and modern ecological modelling to extract much more of the information available in Earth observation data. This approach is achievable now, offering efficient and near-real-time monitoring of management impacts on biodiversity and its functions and services.
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http://dx.doi.org/10.1038/s41559-017-0176DOI Listing
June 2017

Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.

Mol Phylogenet Evol 2017 09 21;114:189-198. Epub 2017 Jun 21.

Department of Ecology and Evolution, University of Lausanne, Switzerland. Electronic address:

Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last couple of years. Here we examine the potential and limitations of one of such techniques-Restriction-site Associated DNA (RAD) sequencing, a method that produces thousands of (mostly) anonymous nuclear markers, in disentangling the phylogeny of the fly genus Chiastocheta (Diptera: Anthomyiidae). In Europe, this genus encompasses seven species of seed predators, which have been widely studied in the context of their ecological and evolutionary interactions with the plant Trollius europaeus (Ranunculaceae). So far, phylogenetic analyses using mitochondrial markers failed to resolve monophyly of most of the species from this recently diversified genus, suggesting that their taxonomy may need a revision. However, relying on a single, non-recombining marker and ignoring potential incongruences between mitochondrial and nuclear loci may provide an incomplete account of the lineage history. In this study, we applied both classical Sanger sequencing of three mtDNA regions and RAD-sequencing, for reconstructing the phylogeny of the genus. Contrasting with results based on mitochondrial markers, RAD-sequencing analyses retrieved the monophyly of all seven species, in agreement with the morphological species assignment. We found robust nuclear-based species assignment of individual samples, and low levels of estimated contemporary gene flow among them. However, despite recovering species' monophyly, interspecific relationships varied depending on the set of RAD loci considered, producing contradictory topologies. Moreover, coalescence-based phylogenetic analyses revealed low supports for most of the interspecific relationships. Our results indicate that despite the higher performance of RAD-sequencing in terms of species trees resolution compared to cytoplasmic markers, reconstructing inter-specific relationships among recently-diverged lineages may lie beyond the possibilities offered by large sets of RAD-sequencing markers in cases of strong gene tree incongruence.
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http://dx.doi.org/10.1016/j.ympev.2017.06.012DOI Listing
September 2017

Cryptic diversity in the Azorean beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae): An integrative taxonomic approach with description of four new species.

Zootaxa 2017 Feb 23;4236(3):zootaxa.4236.3.1. Epub 2017 Feb 23.

cE3c-Centre for Ecology, Evolution and Environmental Changes/ Azorean Biodiversity Group and Universidade dos Açores-Departamento de Ciências e Engenharia do Ambiente, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal..

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 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.
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http://dx.doi.org/10.11646/zootaxa.4236.3.1DOI Listing
February 2017

MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species.

Mol Ecol 2017 Jun 6;26(12):3104-3115. Epub 2017 Mar 6.

Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain.

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 human-mediated species introductions, with minimum estimates for the proportion of introduced species 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.
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http://dx.doi.org/10.1111/mec.14037DOI Listing
June 2017

Comment on Rieux and Balloux: calibration from tip-dating can compromise topological accuracy and evolutionary inference.

Mol Ecol 2017 05 31;26(10):2623-2624. Epub 2016 Dec 31.

Biology Department, City College of New York, New York, NY, 10031, USA.

We contribute to the recent review of Rieux & Balloux, 2016, Mol. Ecol., 25, 1911 on inferences from tip-dated phylogenies by developing their discussion on the influence of population size (N ) under panmixia for the estimation of substitution rate (μ). We highlight how phylogenetic trees inferred with tip-dated sequences under large panmictic N tend to erroneously enforce an age-based coalescent pattern on the posterior distribution of trees, which in turn results in systematically inflated estimates of μ. We discuss the consequences of this and suggest how to accommodate the issue in the short term and long term.
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http://dx.doi.org/10.1111/mec.13951DOI Listing
May 2017

A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scales.

Mol Ecol Resour 2017 Jul 20;17(4):694-707. Epub 2016 Nov 20.

Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France.

Obtaining 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 Réunion (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.
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http://dx.doi.org/10.1111/1755-0998.12617DOI Listing
July 2017

Post-copulatory opportunities for sperm competition and cryptic female choice provide no offspring fitness benefits in externally fertilizing salmon.

R Soc Open Sci 2016 Mar 2;3(3):150709. Epub 2016 Mar 2.

School of Biological Sciences , University of East Anglia , Norwich Research Park, Norwich NR4 7TJ, UK.

There is increasing evidence that females can somehow improve their offspring fitness by mating with multiple males, but we understand little about the exact stage(s) at which such benefits are gained. Here, we measure whether offspring fitness is influenced by mechanisms operating solely between sperm and egg. Using externally fertilizing and polyandrous Atlantic salmon (Salmo salar), we employed split-clutch and split-ejaculate in vitro fertilization experiments to generate offspring using designs that either denied or applied opportunities for sperm competition and cryptic female choice. Following fertilizations, we measured 140 days of offspring fitness after hatch, through growth and survival in hatchery and near-natural conditions. Despite an average composite mortality of 61%, offspring fitness at every life stage was near-identical between groups fertilized under the absence versus presence of opportunities for sperm competition and cryptic female choice. Of the 21 551 and 21 771 eggs from 24 females fertilized under monandrous versus polyandrous conditions, 68% versus 67.8% survived to the 100-day juvenile stage; sub-samples showed similar hatching success (73.1% versus 74.3%), had similar survival over 40 days in near-natural streams (57.3% versus 56.2%) and grew at similar rates throughout. We therefore found no evidence that gamete-specific interactions allow offspring fitness benefits when polyandrous fertilization conditions provide opportunities for sperm competition and cryptic female choice.
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http://dx.doi.org/10.1098/rsos.150709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821276PMC
March 2016

Model misspecification confounds the estimation of rates and exaggerates their time dependency.

Mol Ecol 2015 Dec;24(24):6013-20

Biology Department, City College of New York, New York, NY, 10031, USA.

While welcoming the comment of Ho et al. (2015), we find little that undermines the strength of our criticism, and it would appear they have misunderstood our central argument. Here we respond with the purpose of reiterating that we are (i) generally critical of much of the evidence presented in support of the time-dependent molecular rate (TDMR) hypothesis and (ii) specifically critical of estimates of μ derived from tip-dated sequences that exaggerate the importance of purifying selection as an explanation for TDMR over extended timescales. In response to assertions put forward by Ho et al. (2015), we use panmictic coalescent simulations of temporal data to explore a fundamental assumption for tip-dated tree shape and associated mutation rate estimates, and the appropriateness and utility of the date randomization test. The results reveal problems for the joint estimation of tree topology, effective population size and μ with tip-dated sequences using BEAST. Given the simulations, BEAST consistently obtains incorrect topological tree structures that are consistent with the substantial overestimation of μ and underestimation of effective population size. Data generated from lower effective population sizes were less likely to fail the date randomization test yet still resulted in substantially upwardly biased estimates of rates, bringing previous estimates of μ from temporally sampled DNA sequences into question. We find that our general criticisms of both the hypothesis of time-dependent molecular evolution and Bayesian methods to estimate μ from temporally sampled DNA sequences are further reinforced.
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http://dx.doi.org/10.1111/mec.13451DOI Listing
December 2015
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