Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider

Ortiz, David; Pekár, Stano; Bilat, Julia; Álvarez, Nadir

doi:10.1016/j.ympev.2020.106997

Cited by 20 publications

(24 citation statements)

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“…Therefore, they have been far less explored for estimating supra-specific relationships. However, empirical and simulation-based studies have shown that employing bioinformatic filtering strategies that maximize the number of loci at the expense of allowing very high proportions of missing data (retaining loci missing in up to 90% of the samples) results in reliable, more resolved phylogenies with higher support values than those obtained from more stringent filtering (Crotti et al, 2019;Hodel et al, 2017;Huang & Knowles, 2016;Lee et al, 2018;Ortiz et al, 2021;Rubin et al, 2012). Therefore, RAD matrices have shown high performance when simultaneously resolving relationships from shallow to middle levels of time divergence in a number of groups: e.g., Viburnum flowering plants ( $ 50 Myr; Eaton et al, 2016), phrynosomatid lizards ( $ 55 Myr;Leach e et al, 2015), Drosophila flies ( $ 60 Myr; Rubin et al, 2012), deepsea corals ( $ 80 Myr; Herrera & Shank, 2016), and primates ( $ 90 Myr; Collins & Hrbek, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…Within the genus, 12 groups of species have been established on the basis of genital features, mainly the female epigynum, and the male retrolateral apophysis, bulbal embolus and median apophysis (Bosmans, 1997(Bosmans, , 2009. So far, the only approaches to the supraspecific relationships of the genus are those of Pek ar et al (2018), who obtained a three-marker phylogeny of six Iberian Zodarion species in order to study shifts in their trophic niche, and Ortiz et al (2021), who used five nominal Zodarion species as outgroups while assessing the species delimitation of Z. styliferum using RAD data. Therefore, the deep evolution of Zodarion has never been investigated, and given the lack of documented fossils, the timeline of its diversification also remains obscure.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant‐eating spiders suggest a high potential of RAD‐seq for genus‐level spider phylogenetics

2021

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RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxonspecific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant‐eating spiders suggest a high potential of RAD‐seq for genus‐level spider phylogenetics

2021

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“…The number of ITS2 copies is very high in the genome, and the individual copies usually show no variation among each other because DNA repair mechanisms homogenise their sequences within the genome ( Zimmer et al 1980 ; Elder and Turner 1995 ; Álvarez 2003 ). Ortiz et al (2021) found the pattern of over-splitting CO1 when testing ddRAD sequencing in an ant-eating Zodarion species. The species was assumed to consists of two cryptic lineages based on ecological traits.…”

Section: Discussionmentioning

confidence: 97%

Incongruent molecular and morphological variation in the crab spider Synema globosum (Araneae, Thomisidae) in Europe

Urfer¹,

Spasojevic²,

Klopfstein³

et al. 2021

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Establishing species boundaries is one of the challenges taxonomists around the world have been tackling for centuries. The relation between intraspecific and interspecific variability is still under discussion and in many taxa it remains understudied. Here the hypothesis of single versus multiple species of the crab spider Synema globosum (Fabricius) is tested. The wide distribution range as well as its high morphological variability makes this species an interesting candidate for re-evaluation using an integrative approach. This study combines information from barcoding, phylogenetic reconstruction based on mitochondrial CO1 and ITS2 of more than 60 specimens collected over a wide range of European localities, and morphology. The findings show deep clades with up to 6% mean pairwise distance in the CO1 barcode without any biogeographical pattern. The nuclear ITS2 gene did not support the CO1 clades. Morphological assessment of somatic and genital characters in males and females and a morphometric analysis of the male palp uncovered high intraspecific variation that does not match the CO1 or ITS2 phylogenies or biogeography either. Screening for endosymbiotic Wolbachia bacteria was conducted and only a single infected specimen was found. Several scenarios might explain these inconsistent patterns. While the deep divergences in the barcoding marker might suggest cryptic or ongoing speciation or geographical isolation in the past, the lack of congruent variation in the nuclear ITS2 gene or the studied morphological character systems, especially the male palp, indicates that S. globosum might simply be highly polymorphic both in terms of its mtDNA and morphology. Therefore, more data on ecology and behaviour and full genome sequences are necessary to ultimately resolve this taxonomically intriguing case.

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“…For example, Messor species are widespread and abundant ants across the Iberian Peninsula (Azcárate et al, 2005), and M. barbarus is especially common in grasslands, scrublands (Azcárate et al, 2005(Azcárate et al, , 2007L opez et al, 1993), and some agrobiocenoses, playing an important role (as a top seed predator) in weed control at least in cereal fields (Westerman et al, 2012) and citrus orchards (Atanackovic et al, 2015). In those environments, Z. styliferum and Z. alacre thrive, especially the former one (Ortiz et al, 2021;Pekár, Cardoso, et al, 2011;Pekár, Šmerda, et al, 2012). Additionally, Messor ants live in large colonies and individuals are highly polymorphic, potentially providing suitable targets for spiders at different stages of development (Pekár, Martišová, & Bilde, 2011).…”

Section: Discussionmentioning

confidence: 99%

Gut content metabarcoding of three widespread Iberian ant‐eating spiders reveals specialisation on the same abundant harvester ants

Ortiz

Dušátková

Pekár

2021

Ecological Entomology

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1. Trophic specialists often follow unique evolutionary pathways, show potential applications in biological control, and suffer from increased ecological vulnerability.The myrmecophagous spider genus Zodarion, highly diversified across the Mediterranean, is among the few predatory groups showing strict stenophagy. Most Zodarion species display narrow distributions, but a few of them occur across hundreds to thousands of kilometres, raising questions on the causes of their comparatively higher distributional success.2. In this study, through extensive geographic sampling and the metabarcoding of gut contents, we explored the diets of the three most widely distributed Iberian species of Zodarion: Zodarion alacre and the two lineages of Zodarion styliferum.3. Our data support the three species as strictly myrmecophagous, showing diets largely based on the granivorous Messor ants. Auxiliary prey includes other ants of the subfamilies Myrmicinae, Formicinae, and Dolichoderinae. The diet breadth of both Z. styliferum lineages was slightly narrower than that of Z. alacre, coinciding with their higher physiological and behavioural efficiency for predating on Messor.4. We discard that the relatively large distribution range of our three focal Zodarion species is related to breaking the boundaries of myrmecophagy, and instead argue that such success could be favoured by their specialisation on Messor ants, which are also abundant and widespread across the Iberian Peninsula.

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Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider

Cited by 20 publications

References 129 publications

Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant‐eating spiders suggest a high potential of RAD‐seq for genus‐level spider phylogenetics

Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant‐eating spiders suggest a high potential of RAD‐seq for genus‐level spider phylogenetics

Incongruent molecular and morphological variation in the crab spider Synema globosum (Araneae, Thomisidae) in Europe

Gut content metabarcoding of three widespread Iberian ant‐eating spiders reveals specialisation on the same abundant harvester ants

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Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider

Cited by 20 publications

References 129 publications

Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant‐eating spiders suggest a high potential of RAD‐seq for genus‐level spider phylogenetics

Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant‐eating spiders suggest a high potential of RAD‐seq for genus‐level spider phylogenetics

﻿Incongruent molecular and morphological variation in the crab spider Synema globosum (Araneae, Thomisidae) in Europe

Gut content metabarcoding of three widespread Iberian ant‐eating spiders reveals specialisation on the same abundant harvester ants

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Product

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Incongruent molecular and morphological variation in the crab spider Synema globosum (Araneae, Thomisidae) in Europe