25 Works

Data from: Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari

Paula Arribas, Carmelo Andújar, María Lourdes Moraza, Benjamin Linard, Brent C. Emerson & Alfried P. Vogler
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...

Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation

Jason J. Kolbe, Richard E. Glor, Marta López‐Darias, C. Verónica Gómez Pourroy, Alexis S. Harrison, Kevin De Queiroz, Liam J. Revell, Jonathan B. Losos & Robert Graham Reynolds
Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis...

Demographic consequences of dispersal-related trait shift in two recently diverged taxa of montane grasshoppers

Joaquín Ortego, Jorge Gutiérrez-Rodríguez & Víctor Noguerales
Although the pervasiveness of intraspecific wing-size polymorphism and transitions to flightlessness have long captivated biologists, the demographic outcomes of shifts in dispersal ability are not yet well understood and have been seldom studied at early stages of diversification. Here, we use genomic data to infer the consequences of dispersal-related trait variation in the taxonomically controversial short-winged (Chorthippus corsicus corsicus) and long-winged (Chorthippus corsicus pascuorum) Corsican grasshoppers. Our analyses revealed lack of contemporary hybridization between sympatric...

Data from: Dispersal limitations and long-term persistence drive differentiation from haplotypes to communities within a tropical sky-island: evidence from community metabarcoding

Nancy Gálvez-Reyes, Paula Arribas, Carmelo Andújar, Brent C. Emerson, Daniel Piñero & Alicia Mastretta-Yanes
Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes-level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species-level diversity, and higher. However, empirical data is still limited, with the few studies to date coming from temperate latitudes. Here, we focus on a tropical mountain within the Transmexican Volcanic Belt to evaluate spatially fine-scale...

Data from: Long-term in situ persistence of biodiversity in tropical sky-islands revealed by landscape genomics

Alicia Mastretta-Yanes, Alexander T. Xue, Alejandra Moreno-Letelier, Tove H. Jørgensen, Nadir Alvarez, Daniel Piñero, Brent C. Emerson & Tove H. Jorgensen
Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) 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...

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

Antonia Salces-Castellano, Sean Stankowski, Paula Arribas, Jairo Patiño, Dirk N. Karger, Roger Butlin & Brent C. Emerson
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...

Datasets from: Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode

Carmelo Andujar, Paula Arribas & Thomas Creedy
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,...

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

Antonia Salces-Castellano, Carmelo Andújar, Heriberto López, Antonio José Pérez-Delgado, Paula Arribas & Brente Charles Emerson
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 standardised sampling...

Data from: Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island

Carmelo Andújar Fernández, Paula Arribas, Heriberto López, Yurena Arjona, Antonio José Pérez-Delgado, Pedro Oromí, Alfried P. Vogler & Brent C. Emerson
Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here we take advantage of a relatively young and dynamic oceanic island to advance our understanding of eco-evolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable...

Data from: Sex-specific responses of phenotypic diversity to environmental variation

Adam C. Algar & Marta Lopez-Darias
Identifying the factors generating ecomorphological diversity within species can provide a window into the nascent stages of ecological radiation. Sexual dimorphism is an obvious axis of intraspecific morphological diversity that could affect how environmental variation leads to ecological divergence among populations. In this paper we test for sex-specific responses in how environmental variation generates phenotypic diversity within species, using the generalist lizard Gallotia galloti on Tenerife (Canary Islands). We evaluate two hypotheses: the first proposes...

Image-based taxonomic classification of bulk biodiversity samples using deep learning and domain adaptation

Tomochika Fujisawa, Víctor Noguerales, Emmanouil Meramveliotakis, Anna Papadopoulou & Alfried Vogler
Complex bulk samples of insects from biodiversity surveys present a challenge for taxonomic identification, which could be overcome by high-throughput imaging combined with machine learning for rapid classification of specimens. These procedures require that taxonomic labels from an existing source data set are used for model training and prediction of an unknown target sample. However, such transfer learning may be problematic for the study of new samples not previously encountered in an image set, e.g....

Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island

Jun Ying Lim, Jairo Patiño, Suzuki Noriyuki, Henrik Krehenwinkel, Luis Simmari, Rosemary Gillespie, Luis Cayetano & Rosemary G. Gillespie
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...

Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest

Yurena Arjona, Paula Arribas, Antonia Salces-Castellano, Heriberto López, Brent C. Emerson & Carmelo Andújar
Soils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall), and the distribution of those already described is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies of mitochondrial genes, and other artefacts lead to taxonomic inflation, which compromises the reliability of biodiversity inventories. Here we explore the potential of a bioinformatic approach to jointly “denoise” and filter non-authentic mitochondrial sequences from metabarcode...

Genomic evidence of speciation by fusion in a recent radiation of grasshoppers

Víctor Noguerales & Joaquín Ortego
Post-divergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). While neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the...

Data from: Model misspecification confounds the estimation of rates and exaggerates their time dependency

Brent Emerson, Diego Alvarado-Serrano, Michael Hickerson, Brent C. Emerson & Michael J. Hickerson
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...

Evidence for an extreme founding effect in a highly successful invasive species: data and R code

Jane Waterman, Kateryna Kratzer, Annemarie Van Der Marel, Colin Garroway, Marta López-Darias & Stephen Petersen
The adaptive potential of invasive species is thought to decrease during founding events due to reduced genetic diversity, limiting the new population’s ability to colonize novel habitats. Barbary ground squirrels (Atlantoxerus getulus) were purportedly introduced as a single breeding pair to the island of Fuerteventura but have expanded to over a million individuals spread across the island in just over 50 years. We estimated the number of founders and measured the level of genetic diversity...

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

Paula Arribas, Carmelo Andújar, Antonia Salces-Castellano, Brent Emerson & Alfried Vogler
Soil mesofauna communities are hyperdiverse and critical for ecosystem functioning. However, our knowledge on spatial structure and underlying processes of community assembly for soil arthropods is 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...

Dispersal ability and its consequences for population genetic differentiation and diversification

Daniel Suárez, Paula Arribas, Eduardo Jiménez-García & Brent Emerson
Dispersal ability is known to influence geographic structuring of genetic variation within species, with a direct relationship between low vagility and population genetic structure, which can potentially give rise to allopatric speciation. However, our general understanding of the relationship between dispersal ability, population differentiation and lineage diversification is limited. To address this issue, we sampled mitochondrial DNA variation within lineages of beetles and spiders across the Canary Islands to explore the relationships between dispersal ability,...

Data from: Hidden island endemic species, and their implications for cryptic speciation within soil arthropods

Carmelo Andújar Fernández, Antonio Perez Delgado, Brent Emerson, Paula Arribas, Yurena Arjona, Daniel Suárez Ramos, Carles Hernando & Heriberto López
Aim: Specialisation to the soil environment is expected to constrain the spatial scale of diversification within animal lineages. In this context, the existence of flightless arthropod lineages, adapted to soil environments, but with broad geographic ranges, represent something of an anomaly. Here we investigate the diversification process within one such ‘anomalous’ soil specialist: Geomitopsis franzi Coiffait, 1978, an eyeless and flightless beetle species strongly adapted to the endogean environment but distributed across several oceanic islands....

Data from: Evidence for mega-landslides as drivers of island colonization

Víctor García-Olivares, Heriberto López, Jairo Patiño, Nadir Alvarez, Antonio Machado, Juan Carlos Carrecedo, Vicente Soler, Brent C. Emerson & Juan Carlos Carracedo
Aim: How non-dispersive taxa colonize islands is generalized as being by wind, or rafting, with the implicit assumption that such events involve one (wind) or a few (rafting) individuals. However, because of the evolutionary time-scale for colonization events, the fit of individual species to a conceptual model of wind or rafting is difficult to assess. Here, we describe an alternative testable geological model for inter-island colonization that can result in larger effective founding population sizes...

Data from: Beta diversity and specialization in plant-pollinator networks along an elevational gradient

Carlos Lara-Romero, Jaume Seguí, Antonio Pérez Delgado, Manuel Nogales & Anna Traveset
Aim: To assess whether the reduced nutritional resources available for pollinators due to plant community simplification along an elevational plant-diversity gradient changes pollinator niche breadth and richness. Additionally, we evaluated how body size and proboscis length of pollinators shifted along the gradient, and whether these changes were related to pollinator niche breadth. Location: An elevational gradient (2,350-3,520 m a.s.l.) on the oceanic high-mountain strato-volcano of El Teide (Tenerife, Canary Islands). Taxon: Flowering plant and pollinator...

Irreversible habitat specialization does not constrain diversification in hypersaline water beetles

Adrián Villastrigo, Paula Arribas & Ignacio Ribera
Specialization to extreme environments is often considered an evolutionary dead-end, leading to irreversible adaptations and reduced evolvability. There is, however, mixed evidence of this macroevolutionary pattern, and limited data from speciose lineages. Here, we tested the effect of habitat specialization to hypersaline waters in the diversification rates of aquatic beetles of the genus Ochthebius (Coleoptera, Hydraenidae), using a molecular phylogeny with more than 50% of the 546 recognized species, including representatives of all subgenus and...

Data from: Trophic strategies of two sympatric endemic pigeons in insular ecosystems: a framework for understanding spatiotemporal frugivory interactions

Patricia Marrero & Manuel Nogales
Pigeons are considered to play key ecological roles in frugivory and seed dispersal. They have colonised numerous oceanic islands and diversified into several species in sympatry. How these species coexist in similar niches is poorly understood, although dietary separation is among the mechanisms suggested to avoid trophic overlap. We investigated the trophic ecology of the two endemic Columba species co-occurring in the laurel forest and thermosclerophyllous relicts of two of the Canary Islands. This study...

Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests

Víctor Noguerales, Emmanouil Meramveliotakis, Adrián Castro-Insua, Carmelo Andújar, Paula Arribas, Thomas Creedy, Isaac Overcast, Hélène Morlon, Brent C. Emerson, Alfried P. Vogler & Anna Papadopoulou
Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical datasets are required to account for taxon- and context-dependency but relevant research in understudied areas is often compromised by the taxonomic impediment. We here employed haplotype-level community DNA metabarcoding, enabled by stringent filtering...

Data from: The role of nutritional impairment in carbon-water balance of silver fir drought-induced dieback

Ester González De Andrés, Antonio Gazol, José Ignacio Querejeta, José M. Igual, Michele Colangelo, Raúl Sánchez-Salguero, Juan Carlos Linares & J. Julio Camarero
Rear-edge populations at the xeric distribution limit of tree species are particularly vulnerable to forest dieback triggered by drought. This is the case of silver fir (Abies alba) forests located in the southwestern of Europe. While silver fir drought-induced dieback patterns have been previously explored, information on the role played by nutritional impairment is lacking despite its potential interactions with tree carbon-water balances. We performed a comparative analysis of radial growth, intrinsic water-use efficiency (iWUE),...

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