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Factors affecting species delimitations with the GMYC model: Insights from a butterfly survey

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Abstract

1. The generalized mixed Yule-coalescent (GMYC) model has become one of the most popular approaches for species delimitation based on single-locus data, and it is widely used in biodiversity assessments and phylogenetic community ecology. We here examine an array of factors affecting GMYC resolution (tree reconstruction method, taxon sampling coverage/taxon richness, and geographic sampling intensity/geographic scale). 2. We test GMYC performance based on empirical data (DNA barcoding of the Romanian butterflies) on a solid taxonomic framework (i.e. all species are thought to be described and can be determined with independent sources of evidence). The dataset is comprehensive (176 species), and intensely and homogeneously sampled (1303 samples representing the main populations of butterflies in this country). Taxonomy was assessed based on morphology, including linear and geometric morphometry when needed. 3. The number of GMYC entities obtained constantly exceeds the total number of morphospecies in the dataset. We show that approximately 80% of the species studied are recognised as entities by GMYC. Interestingly, we show that this percentage is practically the maximum that a single threshold method can provide for this dataset. Thus the ca. 20% of failures are attributable to intrinsic properties of the COI polymorphism: overlap in inter- and intraspecific divergences and non-monophyly of the species likely because of introgression or lack of independent lineage sorting. 4. Our results demonstrate that this method is remarkably stable under a wide array of circumstances, including most phylogenetic reconstruction methods, high singleton presence (up to 95%), taxon richness (above five species), and presence of gaps in intraspecific sampling coverage (removal of intermediate haplotypes). Hence, the method is useful to designate an optimal divergence threshold in an objective manner, and to pinpoint potential cryptic species that are worth being studied in detail. However, the existence of a substantial percentage of species wrongly delimited indicates that GMYC cannot be used as sufficient evidence for evaluating the specific status of particular cases without additional data. 5. Finally, we provide a set of guidelines to maximize efficiency in GMYC analyses and discuss the range of studies that can take advantage of the method.

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... Model assumptions include that (1) species are monophyletic, (2) there is no intraspecific geographical structuring, and (3) there is no extinction (Fujisawa & Barraclough, 2013). The method has become very popular in ecology because it does not require prior knowledge of the target study group, which makes it a particularly useful tool for studies involving species for which taxonomic knowledge is limited or non-existent (Talavera et al., 2013). ...
... The performance of the GMYC model has been predominantly tested on simulated data where the effects of factors are controlled, and the model's assumptions are not violated (Esselstyn et al., 2012;Fujisawa & Barraclough, 2013;Papadopoulou et al., 2009;Talavera et al., 2013). Most applications of the GMYC using empirical data will, however, likely violate these assumptions. ...
... Applying a multiple threshold method may be useful in large data sets where there is significant variation in intra-and interspecific genetic divergences. Generally, however, a single-threshold approach is recommended as it is less likely to oversplit (Blair and Bryson Jr, 2017;Fujisawa & Barraclough, 2013;Talavera et al., 2013). ...
Article
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Species delimitation tools are vital to taxonomy and the discovery of new species. These tools can make use of genetic data to estimate species boundaries, where one of the most widely-used methods is the Generalised Mixed Yule Coalescent (GMYC) model. Despite its popularity, a number of factors are known to influence the performance and resulting inferences of the GMYC. Moreover, the few studies that have assessed model performance to date have been predominantly based on simulated datasets, where model assumptions are not violated. Here, we present a user-friendly R Shiny application, “SPEDE-sampler” (SPEcies DElimitation sampler), that assesses the effect of computational and methodological choices, in combination with sampling effects, on the GMYC model. Output phylogenies are used to test the effect that 1) sample size, 2) BEAST and GMYC parameters (e.g. prior settings, single vs multiple threshold, clock model), and 3) singletons has on GMYC output. Optional predefined grouping information (e.g. morphospecies/ecotypes) can be uploaded in order to compare it to GMYC species and estimate percentage match scores. Additionally, predefined groups that contribute to inflated species richness estimates are identified by SPEDE-sampler, allowing for the further investigation of potential cryptic species or geographic sub-structuring in those groups. Merging by the GMYC is also recorded to identify where traditional taxonomy has overestimated species numbers. Four worked examples are provided to illustrate the functionality of the program’s workflow, and the variation that can arise when applying the GMYC model to empirical datasets. The R Shiny program is available for download on GitHub. Link: https://onlinelibrary.wiley.com/share/author/PV2UXQJRPJXG4CZRQFY2?target=10.1111/1755-0998.13591
... Testing the factors affecting species delimitation on real data can help to define practical guidelines to establish the most reliable experimental design and/or to account for biases when reading delimitation results. Some studies in this direction are available (Talavera, Dinca, & Vila, 2013, Ahrens et al., 2016, Pentinsaari, Vos, & Mutanen, 2017, but further factors and methods should be considered to obtain a complete overview on the potential biases of the methods. ...
... This article is protected by copyright. All rights reserved sampling could cause oversplit (Lohse, 2009;Talavera et al., 2013;Mason et al., 2020), a limited sampling could favour delimitation efficiency (Pentinsaari et al., 2017), whereas wider sampling could result in both split of species or better delimitation possibly depending on species population structure. iii) The taxonomic rank of the dataset, in this work considered at the genus, subfamily and family level, could be viewed as a proxy of the overall phylogenetic distance among the analysed species. ...
... GMYC resulted also the only method whose efficiency could be significantly affected by the taxonomic rank, in particular a decrease in the efficiency was observed with genus level data (Fig. 2B). In accordance to what was already observed by Talavera et al. (2013), the lack of significance of GMYC analyses in separating species within a genus could be related to the very low number of species included in some datasets, rather than to the taxonomic rank of the dataset itself. For our datasets, the majority of the not significant GMYC analyses (41 over 43) were indeed related to datasets including ≤ 3 species (39 genus datasets, 2 subfamily datasets). ...
Article
In the contest of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single‐marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested on more than 90 empirical datasets, derived from a set of 7,237 COI sequences attributed to 542 leaf beetles species (Coleoptera: Chrysomelidae). The considered factors were: i) the number of haplotypes per species (as a proxy for genetic diversity); ii) the geographic distance among conspecific collection localities (as a proxy of sampling width); iii) the difficulty related to morphological identification of species; iv) the taxonomic rank. Distance‐based methods, with on average more than 70% of match with morphological identification, outperformed those relying on phylogenetic trees, with less than 59%. A high number of haplotypes per species was found to have a negative effect on delimitation efficiency, whereas large geographic distances within species had a positive effect. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. Finally, the only method influenced by the taxonomic rank of the dataset was GMYC, showing lower efficiency in datasets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input datasets for species delimitation analyses to obtain a more reliable representation of biological diversity.
... All DNA-based methods incorporate models that are imperfect imitations of biological reality and, as such, make a number of simplifying assumptions, any one of which could be violated in a particular system (Carstens et al., 2013). Many authors therefore agree that taxonomic changes should not be made solely on the results of these methods (Lohse, 2009;Esselstyn et al., 2012;Puillandre et al., 2012b;Talavera et al., 2013;Zhang et al., 2013;Blair & Bryson, 2017). ...
... giganteus G1 (in the ML tree used for mPTP; see Supporting Information, Fig. S3.C) as monophyletic, preventing their delimitation as single putative species by tree-based methods (Fig. 2). These results further exemplify that, although the DNA barcode region was generally found useful for 'quick start' taxonomic exploration (Hebert et al., 2003;Kekkonen & Hebert, 2014;Martínez-Arce et al., 2020), species delineation based solely on single-locus mitochondrial DNA data is exposed to interpretational risk (Funk & Omland, 2003;Lohse, 2009;Dupuis et al., 2012;Talavera et al., 2013). ...
Article
Among Antarctic amphipods of the genus Eusirus, a highly distinctive clade of giant species is characterized by a dorsal, blade-shaped tooth on pereionites 5-7 and pleonites 1-3. This lineage, herein named 'crested Eusirus', includes two potential species complexes, the Eusirus perdentatus and Eusirus giganteus complexes, in addition to the more distinctive Eusirus propeperdentatus. Molecular phylogenies and statistical parsimony networks (COI, CytB and ITS2) of crested Eusirus are herein reconstructed. This study aims to formally revise species diversity within crested Eusirus by applying several species delimitation methods (Bayesian implementation of the Poisson tree processes model, general mixed Yule coalescent, multi-rate Poisson tree processes and automatic barcode gap discovery) on the resulting phylogenies. In addition, results from the DNA-based methods are benchmarked against a detailed morphological analysis of all available specimens of the E. perdentatus complex. Our results indicate that species diversity of crested Eusirus is underestimated. Overall, DNA-based methods suggest that the E. perdentatus complex is composed of three putative species and that the E. giganteus complex includes four or five putative species. The morphological analysis of available specimens from the E. perdentatus complex corroborates molecular results by identifying two differentiable species, the genuine E. perdentatus and a new species, herein described as Eusirus pontomedon sp. nov.
... A certain discordance among methods is reported for groups A to D. For these groups, the most conservative methods (ABGD and mPTP) indicate one species, while GMYC and PTP indicate seven species. These results are in line with many studies reporting the tendency of ABGD and mPTP to collapse multiple taxa into one [29,30], as well as the tendency of GMYC and PTP to split [23,31]. ...
... neapolitanum, C. rectoides, C. xylophilum, C. tenuissimum, C. colocasiae, C. oxysporum, C. vignae, C. angustisporum, C. anthropophilum, C. subuliforme and C. cucumerinum) and to C. hillianum, which was used as the outgroup (Table 2). These species were included in order (1) to provide the taxonomic assignment for C. cladosporioides isolates in the GenBank database and (2) to better fit in the context of species delimitation methods (such as the general mixed Yule-coalescent model), which can be destabilized when less than 5 species are included in the analysis [31]. ...
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Cladosporium cladosporioides is an extremely widespread fungus involved in associations ranging from mutualistic to pathogenic and is the most frequently represented Cladosporium species in sequence databases, such as Genbank. The taxonomy of Cladosporium species, currently based on the integration of molecular data with morphological and cultural characters, is in frequent need of revision. Hence, the recently developed species delimitation methods can be helpful to explore cryptic diversity in this genus. Considering a previous study that reported several hypothetical species within C. cladosporioides, we tested four methods of species delimitation using the combined DNA barcodes internal transcribed spacers, translation elongation factor 1-� and actin 1. The analyses involved 105 isolates, revealing that currently available sequences of C. cladosporioides in GenBank actually represent more than one species. Moreover, we found that eight isolates from this set should be ascribed to Cladosporium anthropophilum. Our results revealed a certain degree of discordance among species delimitation methods, which can be efficiently treated using conservative approaches in order to minimize the risk of considering false positives.
... The delimitation methods allowed us to define primary species hypotheses (PSHs), while searching for congruence between markers and methods led us to select secondary species hypotheses (SSHs), which were then confirmed or not using morphoanatomic information. Besides, comparing molecular-based hypotheses to non-genetic data (e.g., morpho-anatomic, ecological) is recommended to corroborate species boundaries , Wiens 2007, Fujita et al. 2012, Carstens et al. 2013, Talavera et al. 2013. ...
... Comparing different methods is important to counterbalance the bias of starting hypotheses, concepts or models, and to overcome the limits inherent in each method, and finally, to define the most likely species hypotheses , Dupuis et al. 2012, Puillandre et al, 2012b, Carstens et al. 2013, Leliaert et al. 2014, Rannala 2015. In addition, taking into account data of different types makes possible the identification of possible differences in the evolutionary signal and is therefore particularly recommended to compare molecular results to non-genetic data, such as the morphologic observations used here , Wiens 2007, Fujita et al. 2012, Carstens et al. 2013, Talavera et al. 2013. ...
Article
Genera and species of the tribes Rhipileae and Rhipiliopsideae are abundant in most coral reef ecosystems worldwide. However, the group has been largely overlooked, and very little genetic data is available to accurately assess its diversity, phylogenetic relationships, and geographical distribution. Our study provided an in‐depth reassessment of tribes Rhipileae and Rhipiliopsideae based on a species‐rich dataset and the combination of molecular species delimitation, multilocus phylogenetic analyses (tufA, rbcL and 18S rDNA), and morpho‐anatomical observations. Our results revealed an unexpected diversity of 38 morphologically‐validated species hypotheses, including 20 new species, two of which are described in this paper and one resurrected species (Rhipilia diaphana). Based on our phylogenetic results we proposed to redefine the genera Rhipilia and Rhipiliopsis and described two new genera, Kraftalia gen. nov. (Rhipileae) and Rhipiliospina gen. nov. (Rhipiliopsideae). Finally, we validated Rhipiliella Kraft and included it in tribe Rhipileae. Although Rhipilia and Rhipiliopsis have a pantropical distribution, none of the species studied here appeared cosmopolitan; instead, they have restricted distributions.
... Molecular species delimitation analyses have been used both as a standalone approach to delimit species and as part of integrative taxonomic studies along with other sources of evidence (Garc ıa-Melo et al., 2019;Titus et al., 2018;Vitecek et al., 2017). Several analytical approaches for molecular species delimitation exist, but only a few of these are suitable for analysis of a single locus, and they all have variable performance depending on factors such as sampling design and methods of phylogenetic inference (in cases where a guided tree is needed) (Ahrens et al., 2016;Talavera et al., 2013). Nevertheless, these analyses have been helpful to estimate species boundaries in sigmodontine taxa, particularly in genera with high levels of cryptic speciesdiversity (Hurtado & D'El ıa, 2019;Prado et al., 2021;Su arez-Villota et al., 2018). ...
... A single-threshold GMYC analysis was performed in the R package splits v1.0-19 (Ezard et al., 2009). We chose the single-threshold model considering limited improvements achievable with the multiple-threshold model (Fujisawa & Barraclough, 2013;Talavera et al., 2013). ...
Article
The genus Brucepattersonius currently includes eight valid species from the Atlantic Forest of south-eastern Brazil and north-eastern Argentina. Most of those species were described in the past 20 years, based on very small sample sizes: four species are known only from their type localities. Concerns on the taxonomic validity of some Brucepattersonius species have been raised in the recent literature. In this study, we present a phylogenetic hypothesis including samples throughout the distribution of the genus (among them the holotypes of two species) and employed single-locus molecular species delimitation analyses to provide a new hypothesis for species limits within Brucepattersonius. We also analysed intra- and interpopulation morphological and morphometric variation to apply an integrative taxonomic approach to species delimitation. Our phylogenetic inference of molecular data recovered four strongly supported clades within Brucepattersonius, which were recognized as distinct operational taxonomic units in all species delimitation analyses. The first two clades represent the Caparaó mountain range endemic B. griserufescens and its sister-group, the recently described species B. nebulosus. The third clade comprises several specimens assigned to B. soricinus but also includes the holotype of B. igniventris; we revise these species limits accordingly. The last clade is composed of samples from southern Brazil assigned to B. iheringi. Based on morphological and morphometric analyses, we find no clear structure among the three described species from Misiones Province, Argentina (B. guarani, B. misionensis and B. paradisus) and B. inheringi from southern Brazil, suggesting that those samples represent a single species. Therefore, in the present study we propose that the genus Brucepattersonius comprises only four diagnosable species: B. griserufescens (including B. albinasus), B. nebulosus, B. soricinus (including B. igniventris) and B. iheringi (including B. guarani, B. misionensis and B. paradisus).
... According to the distance analysis (OT), each specimen represents one different MOTU. Talavera et al. (2013) argue that the presence of a high number of singletons could considerably reduce the result's biological meaningfulness. Thus, we view this result as unlikely for now, but it is necessary to ascertain the presence of Rhamdia divergent lineages from the Amazonas region. ...
... The GMYC has been used in numerous empirical studies (Machado et al., 2017;Ramirez et al., 2017Ramirez et al., , 2020Melo et al., 2018), and simulation and empirical data suggest that the method is robust to different assumptions (Esselstyn et al., 2012;Reid and Carstens, 2012;Talavera et al., 2013). The method detected nine lineages from cis-Andean hydrographic basins in the present study: two belong to valid species R. voulezi and R. branneri, and seven divergence lineages currently identified as R. quelen. ...
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The wide distribution of the Neotropical freshwater catfish Rhamdia offers an excellent opportunity to investigate the historical processes responsible for modeling South America's hydrogeological structure. We used sequences from cis-Andean and Mesoamerican Rhamdia species to reconstruct and estimate divergence times among cis-Andean lineages, correlating the results with known geological events. Species delimitation methods based on distance (DNA barcoding and BIN) and coalescence (GMYC) approaches identified nine well-supported lineages from the cis-Andean region from sequences available in the BOLD dataset. The cis-Andean Rhamdia lineages diversification process began in Eocene and represented the split between cis-Andean and Mesoamerican clades. The cis-Andean clade contains two principal groups: Northwest clade (MOTUs from Amazon, Essequibo, Paraguay, and Itapecuru basins) and Southeast clade (Eastern Brazilian shield basins (Paraná, Uruguay, Iguaçu, and São Francisco) plus eastern coastal basins). The diversification of the cis-Andean Rhamdia lineages results from vicariance and geodispersion events, which played a key role in the current intricate distribution pattern of the Rhamdia lineages. The wide geographical distribution and large size of the specimens make it attractive to cultivate in different countries of the Neotropical region. The lineages delimitation minimizes identification mistakes, unintentional crossings by aquaculture, and reduces natural stocks contamination.
... All DNA-based methods incorporate models that are imperfect imitations of biological reality and, as such, make a number of simplifying assumptions, any one of which could be violated in a particular system (Carstens et al., 2013). Many authors therefore agree that taxonomic changes should not be made solely on the results of these methods (Lohse, 2009;Esselstyn et al., 2012;Puillandre et al., 2012b;Talavera et al., 2013;Zhang et al., 2013;Blair & Bryson, 2017). ...
... giganteus G1 (in the ML tree used for mPTP; see Supporting Information, Fig. S3.C) as monophyletic, preventing their delimitation as single putative species by tree-based methods (Fig. 2). These results further exemplify that, although the DNA barcode region was generally found useful for 'quick start' taxonomic exploration (Hebert et al., 2003;Kekkonen & Hebert, 2014;Martínez-Arce et al., 2020), species delineation based solely on single-locus mitochondrial DNA data is exposed to interpretational risk (Funk & Omland, 2003;Lohse, 2009;Dupuis et al., 2012;Talavera et al., 2013). ...
Article
Among Antarctic amphipods of the genus Eusirus, a highly distinctive clade of giant species is characterized by a dorsal, blade-shaped tooth on pereionites 5–7 and pleonites 1–3. This lineage, herein named ‘crested Eusirus’, includes two potential species complexes, the Eusirus perdentatus and Eusirus giganteus complexes, in addition to the more distinctive Eusirus propeperdentatus. Molecular phylogenies and statistical parsimony networks (COI, CytB and ITS2) of crested Eusirus are herein reconstructed. This study aims to formally revise species diversity within crested Eusirus by applying several species delimitation methods (Bayesian implementation of the Poisson tree processes model, general mixed Yule coalescent, multi-rate Poisson tree processes and automatic barcode gap discovery) on the resulting phylogenies. In addition, results from the DNA-based methods are benchmarked against a detailed morphological analysis of all available specimens of the E. perdentatus complex. Our results indicate that species diversity of crested Eusirus is underestimated. Overall, DNA-based methods suggest that the E. perdentatus complex is composed of three putative species and that the E. giganteus complex includes four or five putative species. The morphological analysis of available specimens from the E. perdentatus complex corroborates molecular results by identifying two differentiable species, the genuine E. perdentatus and a new species, herein described as Eusirus pontomedon sp. nov.
... The Bayesian implementation (bGMYC) has the advantage of accounting for uncertainty in phylogenetic estimation (Reid and Carstens, 2012;Fujisawa and Barraclough, 2013). The R package Splits (SPecies' LImits by Threshold Statistics; Ezard et al., 2009) was used to run the singlethreshold mlGMYC, using the MCC tree obtained with BEAST 2. We assume a single threshold in mlGMYC due to better performance for simulated data compared to the multiple threshold approach (Fujisawa and Barraclough, 2013;Talavera et al., 2013;Luo et al., 2018). Next, we resampled 1000 random trees from the posterior distribution of BEAST 2 analysis and subjected them to the R package bGMYC (Reid and Carstens, 2012) to estimate the uncertainties in delimitation due to the phylogenetic estimation. ...
... Taking into account the shortcomings inherent to each method, taxonomic changes should not be made solely on these type of analyses; instead, we suggest that these algorithms be used to generate preliminary species hypotheses, which will then be cross-compared with results based on other data sets (i.e. independent nuclear markers, morphometric data, etc.), following integrative taxonomic practices (Dayrat, 2005;Knowles and Carstens, 2007;Fujita et al., 2012;Talavera et al., 2013;Zhang et al., 2013;Sukumaran and Knowles, 2017;Dellicour and Flot, 2018; Fig. 1). The linear and meristic datasets resolved the highest number of differences between L. baguali and L. escarchadosi, two species that seem to be completely allopatric from each other (Figs. 2 and 4). ...
Article
Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.
... The GMYC is thought to oversplit species when undersampling affects maximum intraspecific distance (e.g. Talavera et al. 2013) and to underperform with big or uneven population sizes (Fujisawa and Barraclough 2013). The mPTP by contrast has been suggested to outperform other delimitation methods in the presence of uneven sampling or large differences in effective population sizes of species (Blair and Bryson 2017). ...
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Our study seeks to: (1) reduce biodiversity knowledge gaps in amphibians from desert and arid regions; (2) quantify species diversity and detect potential cryptic diversity; (3) identify environmental correlates of amphibian richness distribution, and (4) identify diversity hotspots. DNA barcoding and spatial modelling were integrated to map observed and predicted amphibian richness in Mauritania, Africa. We built two DNA barcoding libraries using one mitochondrial (COI) and one nuclear marker (RAG1). Taxon richness was calculated using species delimitation methods. A generalised linear model was employed to identify environmental correlates of amphibian richness and the distribution of diversity hotspots was predicted. We found a total of 16 anuran taxa with Afrotropic affinities, and two genera and four species were added for the amphibian list of Mauritania. Potential cryptic diversity was detected in Hoplobatrachus occipitalis. Amphibian richness was positively correlated with proximity to savannah, gravel floodplains, and with presence of seasonal wetlands, and negatively with proximity to dunes. Major diversity hotspots were predicted in southern Mauritania. Barcoding methods for both genetic markers successfully identified the taxonomic identity of specimens, also uncovering cryptic diversity in the amphibians of the Sahara-Sahel ecoregions. Amphibian richness in Mauritania increases southwards and it is mostly concentrated in areas under pressure due to habitat conversion, lacking legal protection. The combination of DNA barcoding with spatial modelling can be easily applied to any desert system to address pressing needs for research on biodiversity distribution.
... In this study we used a Bayesian implementation of the evolutionary model-based method, bGMYC (Reid and Carstens, 2012). The bGMYC approach outperforms existing GMYC implementations by accomodating different uncertainties in the model, e.g. the quality of the ultra-metric tree has less influence on the outcome (Esselstyn et al., 2012;Reid and Carstens, 2012;Talavera et al., 2013;Zhang et al., 2013). The input trees were generated by BEAST2 using the mtDNA partition. ...
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One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ∼2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high genetic diversity within Occidozyga based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages defined using the >5% uncorrected p-distance criterion for the 16S rRNA gene, showing that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that the lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether the observed diversity of Puddle frog lineages warrants taxonomic recognition.
... Parsimony character state reconstructions were done using the Bayesian Coalescent tree reconstructed using the program BEAST for: 1) bristle abundance, 2) band conspicuousness, 3) watershed designation, 4) river-side, and 5) adjacent stream corridor designation for each genetic sample using the program Mesquite. Species were delimitated based on the Bayesian General Mixed Yule Coalescent 12 procedure using the program bGMYC (Reid and Carstens 2012;Talavera et al. 2014), which accounts for uncertainty in the phylogeny. Generally, the program bGMYC tries to detect the shift in branching pattern from a Yule process, characteristic of intraspecific variation, to a birth-death process more characteristic of interspecies variation. ...
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The Trinity bristle snail (Monadenia setosa) is listed as a threatened species under the California Endangered Species Act (CESA). In northern California, populations of this endemic terrestrial gastropod occur in rare, isolated, and highly fragmented locations within the greater Trinity Basin. Since 1952 when it was originally described, the taxonomic status of the Trinity bristle snail has been questioned based on unpublished information limited in geographic scope and sample size, which resulted in the taxon being reduced from species status (M. setosa) to subspecific status (M. i. setosa) within the Redwood sideband (M. infumata) species complex. Primary objectives of the present study were to: 1) use DNA extraction and PCR sequencing to gain insight into patterns of genetic variation and phylogenetic relationships among a larger sample of en-demic populations of the Trinity bristle snail; 2) re-evaluate the systematic and taxonomic status of the species using outgroup analysis and references samples from sympatric ecologically co-occurring taxa within the genus Monadenia; and 3) evaluate the potential biogeographic effects of major riverine systems on genetic differentiation among relic and disjunct populations within the Trinity Basin. Results of the DNA sequence analysis using several different tree reconstruction methods revealed that subspecies of the Redwood sideband (M. i. subcarinata), Yellow-based sideband (M. i. ochromphalus), and the Trinity bristle (M. i. setosa) exhibited a phylogenetic signal at > 95% species probability. Except for the Yellow-based sideband, molecular evidence detected the presence of several morphologically cryptic subclades within each species clade formerly undescribed by the scientific community. Syntopic 1 ecological relationships between subclades of the Trinity bristle snail and the Redwood sideband occurred in several areas within the geographic range of the Trinity bristle snail, which indicated that these subclades were conservatively differentiated at the subspecific level. A Bayesian coalescent tree showed that genetic variation 1 Syntopy refers to the joint occurrence of two species in the same habitat at the same time, which may result in hybridization between closely related taxa or sister species. In contrast, sympatric species occur together in the same region, but do not necessarily share the same localities as syntopic species do (Futuma 2009).
... With emerging global comprehensiveness from the global iBOL project (International Barcode of Life), researchers became aware of the problems that arise with the use of cox1 (i.e., mitochondrial DNA) as taxonomic marker (Ballard & Whitlock, 2004;Dasmahapatra & Mallet, 2006;Dowton et al., 2014;Dupuis et al., 2012;Eberle et al., 2019;Funk & Omland, 2003;Nicholls et al., 2012;Ross, 2014;Smith et al., 2012), but also the effects of geographic scale on accuracy and performance of barcoding (Bergsten et al., 2012;Gaytán et al., 2020;Lohse, 2009). Therefore, geographic sampling has been a central debate Lim et al., 2012;Reid & Carstens, 2012;Talavera et al., 2013), in particular with respect to DNA barcoding, one of the major tools of DNA taxonomy. ...
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DNA barcoding and DNA-based species delimitation are major tools in DNA tax-onomy. Sampling has been a central debate in this context, because the geographical composition of samples affects the accuracy and performance of DNA barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical dataset sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivorous chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analyzed for a total of 186 individuals of 56 morphospecies. Tree-based and distance-based species delimita-tion methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. Poisson tree process (PTP) and statistical parsimony network analysis (TCS) prevailingly over-splitted morphospecies, while 3% clustering and Automatic Barcode Gap Discovery (ABGD) also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospe-cies and MOTUs have to be explained by historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation. K E Y W O R D S barcoding, cox1, geographic sampling bias, Laos, species delimitation
... GMYC may over-split species when there is low genetic divergence between lineages and overlap of inter-and intraspecific divergences, or a lack of reciprocal monophyly between species. In addition, sampling bias, differences in population size and speciation rates might also cause GMYC to overestimate species richness (Esselstyn et al. 2012;Talavera et al. 2013;Pentinsaari et al. 2016). PTP generates results that are highly congruent with GMYC (Tang et al. 2014;Pentinsaari et al. 2016). ...
Article
Nephotettix leafhoppers are widely distributed and some members of this genus are important vectors of rice pathogens. Species delimitation in this group has proven difficult because traditional morphological characters tend to exhibit substantial variation within populations, and the morphology-based species classification of this genus has not previously been tested using molecular data. This study analysed DNA sequence data from three mitochondrial genes (COI, Cytb and 16S) and two nuclear genes (ITS2, H3) to infer the phylogenetic relationships and status of five previously recognized Nephotettix species and compare the performance of different molecular species-delimitation methods using single loci and multiple loci. The analysis supports the monophyly of Nephotettix and divided the included haplotypes into five well-supported subclades. Data from the three mitochondrial genes were usually consistent with morphology in supporting recognition of five species. However, data from the two nuclear genes usually lumped the haplotypes into a single species, probably due to the relatively small numbers of variable and parsimony-informative nucleotide positions present in these loci. The jMOTU and ABGD analyses of single mitochondrial loci gave the most consistent results with morphology. Considering the variable results yielded by various methods employing single loci, the BPP method, which combines data from multiple loci, may be more reliable in Nephotettix.
... However, the GYMC analysis showed three putative species, specifically in the Antarctic clade. The GYMC analysis may suggest a population genetic structure or a more complex lineage classification (Pons et al. 2006;Reid and Carstens 2012;Talavera et al. 2013;Tang et al. 2014). Furthermore, when a single specimen that differs from the others by one nucleotide substitution is found, GMYC tends to diverge in the presence of a low intraspecific divergence (Pentinsaari et al. 2017;Luo et al. 2018). ...
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The systematics of Subantarctic and Antarctic near-shore marine benthic invertebrates requires major revision and highlights the necessity to incorporate additional sources of information in the specimen identification chart in the Southern Ocean (SO). In this study, we aim to improve our understanding of the biodiversity of Kidderia (Dall 1876) through molecular and morphological comparisons of Antarctic and Subantarctic taxa. The microbivalves of the genus Kidderia are small brooding organisms that inhabit intertidal and shallow subtidal rocky ecosystems. This genus represents an interesting model to test the vicariance and dispersal hypothesis in the biogeography of the SO. However, the description of Kidderia species relies on a few morphological characters and biogeographic records that raise questions about the true diversity in the group. Here we will define the specimens collected with genetic tools, delimiting their respective boundaries across provinces of the SO, validating the presence of two species of Kidderia. Through the revision of taxonomic issues and species delimitation, it was possible to report that the Antarctic species is Kidderia subquadrata and the species recorded in the Subantarctic islands Diego Ramirez, South Georgia and the Kerguelen Archipelago is Kidderia minuta. The divergence time estimation suggests the origin and diversification of Kidderia lineages are related to historical vicariant processes probably associated with the separation of the continental landmasses close to the late Eocene. Supplementary information: The online version contains supplementary material available at 10.1007/s00300-021-02885-6.
... GMYC estimated a slightly higher number of OTUs than CROP (Table S3). We chose to use OTUs derived from CROP for further analyses, because of concerns that GMYC tends to overestimate the number of units (Carstens et al., 2013;Talavera et al., 2013). ...
Article
Aim To (a) evaluate whether colonization of newly emerged high-elevation habitats occurred from neighbouring highlands (allopatric divergence and niche conservatism) or from within the same mountain (peripatric or parapatric divergence and niche shift) and (b) test for the effect of past landscape configurations in geographically structuring biodiversity (a West–East structure spanning the central part of the Transmexican Volcanic Belt). Location Transmexican Volcanic Belt, Mexico. Taxa Coleoptera and Araneae. Methods Coleoptera and Araneae communities were collected in a comparative sampling framework. Seven sky-islands were sampled within two high-elevation habitats separated by altitude. Samples were individually sequenced for a region of the mtDNA COI gene to delimit Operational Taxonomic Units (OTUs) and haplotypes within them. Richness was estimated at the community level, as well as genetic diversity within and among mountains and habitats. The West–East structure was tested with a null model and an analysis of variance with permutations. Results Few OTUs were shared between the Abies forests and alpine grasslands. High beta diversity was found across mountains. Beta diversity between the West and East grouping is higher than expected by chance. Main conclusions Our results indicate that colonization from other mountains followed by allopatric divergence dominates as a source of OTU formation, and that despite some probable connectivity during glacial periods existed, ancient communities and genetic structures persist.
... DNA barcodes are also widely applied in phylogeography and surveys of intraspecific variability. After much initial debate, it is now well established that DNA barcoding (and any other single-marker approach) can be a useful tool to identify potential cryptic species, although an integrative approach is necessary for confirmation (e.g., nuclear markers, morphology, and ecology) DeSalle et al. 2005;Talavera et al. 2013b;Dincǎ et al. 2015;Hernández-Roldán et al. 2016;Lukhtanov et al. 2016;Gaunet et al. 2019). ...
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Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multi-locus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multi-gene sequencing (approximately one per simulated genus), the addition of this multi-gene backbone DNA data for as few as 5-10% of the specimens in the total dataset can produce high-quality phylogenies, comparable to those resulting from 100% multi-gene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen dataset of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multi-gene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for insertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large datasets.
... Priors: coalescent constant population model, uniform frequency parameter, exponential gamma rate, population size 1/X, uniform rates from 1 to 100. Single threshold was used for the GMYC run 110 . ...
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Although species delimitation is often controversial, emerging DNA-based and classical morphology-based methods are rarely compared using large-scale samplings, even less in the case of widely distributed species that have distant, allopatric populations. In the current study, we examined species boundaries within two wolf spider species of the genus Pardosa (Araneae, Lycosidae), P. riparia and P. palustris. Wolf spiders constitute an excellent model for testing the relevance of traditional vs. modern methods in species and population delimitation because several closely related species are distributed over cross-continental geographic ranges. Allopatric populations of the two Pardosa species were sampled across Europe to Far East Russia (latitudinal range > 150°) and several dozen individuals were studied using morphological characters (morphometry of three measures for both sexes, plus five in males only and two in females only), DNA barcoding (COI sequencing) and double-digest restriction site associated DNA sequencing (ddRADseq). The results obtained allow for changing the taxonomic status of two Far East Russian populations to subspecies and ddRADseq proved to be a powerful tool for taxonomic research despite scarce sampling and inherent subjectivity of species delimitation in allopatry. Overall, this study pleads for both multi-criteria and more population-based studies in taxonomy.
... Species delimitation employing the coalescent, such as GMYC, have previously been criticized for a tendency to over-split when applied to structured populations (Lohse 2009). This, in turn, suggests that a single-threshold delimitation model may be inappropriate for use with hierarchically structured data (Talavera et al. 2013). Strong intraspecific structure in Aspidoscelis, similar to that found in other desert reptiles Douglas 2007, Douglas et al. 2002), may explain the over-fitting of GMYC. ...
... employing the single (GMYCs) threshold method following parameters in the SPLITS package manual (Supplementary Material File S2). We applied the single-threshold version of GMYC since it has been shown to outperform the multiple-threshold version (Fujisawa & Barraclough 2013;Talavera et al. 2013;Luo et al. 2018). ...
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In recent years, several species that have long been considered to belong in Bacidia s. lat. have been transferred to other genera such as Bellicidia , Bibbya , Scutula , and also to Toniniopsis , accommodating species previously placed in Bacidia and Toninia . One of its widespread species, Toniniopsis subincompta , can be recognized by its thinly granular thallus, dark brown to black apothecia, green epithecium, red-brown hypothecium, and bacilliform ascospores. However, it shows considerable variation in thallus structure, and coloration of apothecia, hypothecium and exciple. We sequenced 20 specimens of T. subincompta to investigate whether there is phylogenetic support for the delimitation of species in accordance with the variability of the observed characters. For phylogenetic analyses, we used newly generated sequence data from the nuclear internal transcribed spacer (nrITS), mitochondrial small subunit (mtSSU) and DNA-directed RNA polymerase II subunit ( RPB 2). Maximum likelihood and Bayesian inference analyses, as well as three species delimitation programs, provided consistent evidence that T. subincompta forms two separate lineages, to be recognized at the species level. The complex nomenclature of T. subincompta (basionym Lecidea subincompta ) shows it to be a synonym of Bellicidia incompta . For the most common taxon previously called Bacidia ( Toniniopsis ) subincompta , the new combination T. separabilis is made, rather than proposing a conserved type for Lecidea subincompta . Toniniopsis dissimilis is newly described to accommodate the less common taxon. Toniniopsis dissimilis is characterized by a predominantly wrinkled to warted to subsquamulose thallus; generally grey-brown to dark brown apothecia, often with a lighter margin; a dark brown hypothecium, frequently gradually merging into the coloration of the exciple below and the lateral part of the exciple attached to the hymenium; a mostly colourless rim and lateral part of the exciple. The closely related T. separabilis is characterized by a thallus of mostly single or contiguous ±loose granules, often forming short, coralloid, isidium-like bulges; darker apothecia, with a margin mostly of the same colour or darker than the disc; a comparatively thinner hypothecium easily separated from the exciple below. The rim and lateral part of the exciple often contain either a blue, brown or mixed blue-brown colour in the upper part or along the whole margin. Lectotypes of Bacidia vegeta , Lecidea bacillifera f. melanotica and Secoliga atrosanguinea var. affinis (the synonyms of T. separabilis ) are selected. Cyanotrophy and the occurrence of albino morphs in T. separabilis are discussed.
... Results from single-gene (or gene cluster) species delineations may be misleading as they may be affected by introgression (Cong et al., 2017) and incomplete lineage sorting (Mallo & Posada, 2016). Moreover, population sampling effects might cause the GMYC model to overestimate species numbers, because geographic structuring may be mistaken for species limits (but see Talavera et al., 2013). These delineations should therefore be viewed as prima facie estimates of species boundaries to be re-evaluated and refined when new lines of evidence become available (Yeates et al., 2011). ...
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Many nominal species of microscopic animals traditionally fitting the ‘everything is everywhere’ paradigm have been revealed to be complexes of cryptic species. Here, we explore species diversity within the micrometazoan flatworm Gyratrix hermaphroditus—unique among meiofauna because of its global occurrence in a wide variety of brackish, freshwater and marine environments. With maximum likelihood and Bayesian approaches, we analysed 18S, 28S, 5.8S and ITS2 rDNA sequences from 401 specimens across the global distribution of G. hermaphroditus. Generalized Mixed Yule Coalescent (GMYC) and Automatic Barcode Gap Discovery (ABGD) methods delineated 78 and 62 putative species, respectively. This renders G. hermaphroditus one of the most species‐rich complexes known to date. Based on shape variations of the male copulatory organ, 14 morphotypes corresponding with molecular clades were identified within the species complex. Within morphotypes, morphometric measurements were able to further discriminate between GMYC species using discriminant analyses. While most putative species occur on local or regional scales, over 10% are distributed over vast distances (>500 km apart) and two GMYC and six ABGD species have colonised multiple continents. This suggests that the cosmopolitanism of the G. hermaphroditus species complex is not just caused by mixing cryptic species with a more limited geographic distribution, but is due to the presence of previously unrecognised cosmopolitan taxa. The wide variation in distribution patterns between putative species indicates that meiofaunal biogeography should not be simplified into ‘everything is everywhere’, but rather entails every ecological state, extending from local endemism to true cosmopolitanism.
... Errors in the framework underpinning the analysis may affect the final results (Kekkonen and Hebert 2014). Also, GMYC usually over-splits species, mainly due to low genetic divergence between lineages and overlap of interspecific and intraspecific divergences, or due to lack of reciprocal monophyly between sister clades (Talavera et al. 2013;Pentinsaari et al. 2016;Stokkan et al. 2018). Evaluations of the accuracy and efficiency of ABGD conducted by different researchers reached a consensus that ABGD is more conservative and faster than other methods (Puillandre et al. 2012a;Puillandre et al. 2012b;Kekkonen and Hebert 2014;Guillemin et al. 2016). ...
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Cyclommatus scutellaris Möllenkamp, 1912, Cyclommatus elsae Kriesche, 1921 and Cyclommatus tamdaoensis Fujita, 2010 are East Asian stag beetle species with long-debated taxonomic relationships due to high intraspecific morphological variability. In this study, we applied multilocus phylogenetic analyses to reassess their relationships. Two mitochondrial genes (16S rDNA, COI) and two nuclear genes (28S rDNA, Wingless) were used to reconstruct the phylogeny through the Bayesian inference (BI) and Maximum Likelihood (ML) methods. Both topologies supported two clades: the clade C. scutellaris was sister to the clade ( C. elsae + C. tamdaoensis ) with the subclade C. tamdaoensis embedded in the subclade C. elsae . The Kimura 2-parameter (K2P) genetic distance analysis yielded a low mean value (≤0.035) among the three taxa, which was well below the minimum mean value between other Cyclommatus species (≥0.122). We also compared the accuracy and efficiency of two approaches, GMYC and ABGD, in delimitating the three lineages. The result shows that ABGD is a better approach than GMYC. Our molecular data recognizes the three species as different populations of a single species, ranging from Taiwan Island to the continent. Therefore, we propose two new junior synonyms for C. scutellaris : C. tamdaoensis , syn. nov. and C. elsae syn. nov.
... With emerging global comprehensiveness from the global iBOL project (International Barcode of Life), researchers became aware of the problems that arise with the use of cox1 (i.e., mitochondrial DNA) as taxonomic marker (Funk & Omland 2003;Ballard & Whitlock, 2004;Dasmahapatra & Mallet, 2006;Dupuis et al., 2012;Nicholls et al., 2012;Smith et al., 2012;Dowton et al., 2014;Ross, 2014;Eberle et al., 2019), but also the effects of geographic scale on accuracy and performance of barcoding (Lohse, 2009;Bergsten et al., 2012;Gaytán et al., 2020). Therefore, geographic sampling has been a central debate (Lim et al., 2012;Reid & Carstens, 2012;Talavera et al., 2013;Ahrens et al., 2016), in particular with respect to DNA barcoding, one of the major tools of DNA taxonomy. ...
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DNA-barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affect the accuracy and performance of DNA-barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical data set sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivore chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analysed for a total of 186 individuals of 56 morphospecies. Tree based and distance based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. PTP and TCS prevailingly over-splitted morphospecies, while 3% clustering and ABGD also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs were discussed in the context of historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.
... GMYC delimitation based on both Yule and coalescent models split the O. striagatus lineage into three species, but it was estimated to be one species in the morphological and other delimitation methods (Fig. 2). GMYC is known to overestimate the number of species, and its performance can be affected by several factors, such as the accuracy of phylogeny, completeness of sampling, and level of population structure (Lohse 2009;Papadopoulou et al. 2009;Esselstyn et al. 2012;Reid & Carstens 2012;Prévot et al. 2013;Talavera et al. 2013;Hamilton et al. 2014;xu et al. 2015). The multispecies coalescent approach of GMYC possibly detects genetic structure rather than species, and it could misidentify population structure as putative species (Sukumaran & Knowles 2017). ...
Article
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This study revised the spider genus Oxyopes Latreille, 1804 in Taiwan and delineated the species boundaries based on morphological and molecular characters. A total of seven Oxyopes spiders were recognized, including two newly described species, O. hasta sp. nov. and O. taiwanensis sp. nov. Oxyopes fujianicus Song & Zhu 1993 from Yilan County, Nantou County, and Kaohsuing City, and O. striagatus Song 1999 from New Taipei City, Taichung City, Nantou County, and Kaohsiung City were recorded for the first time in Taiwan. An identification key and a distributional map of Taiwanese Oxyopes species were provided. Partial COI sequences were obtained for molecular phylogenetic and species delimitation analyses. Maximum likelihood and Bayesian phylogenies, and DNA barcoding gap analysis supported morphologically defined species. However, molecular species delimitation based on Automatic Barcode Gap Discovery (ABGD), PID (Liberal), and generalized mixed Yule coalescent (GMYC) were incongruent in species assignment. The results showed that the interspecific genetic divergence between O. sertatus and O. taiwanensis was relatively low (1.28 ± 0.43%), and the intraspecific genetic divergence of O. striagatus was relatively high (1.69 ± 0.35%). Ecological data, additional samples and genetic loci are required to further examine the level of reproductive isolation and patterns of population genetic structure in Taiwanese Oxyopes.
... Our findings, therefore, echo the growing consensus that, while it remains a popular approach, in comparison with traditional taxonomy and/or other such approaches, GMYC results in a much higher, and somewhat unrealistic, number of species (e.g. Carstens et al., 2013;Talavera et al., 2013;Dellicour & Flot, 2018). In particular, the GMYC approach tends to perform poorly when effective population sizes are large and speciation rates are high (Dellicour & Flot, 2018), both of which are likely characteristics of Hermeuptychia. ...
Article
DNA ‘barcoding’ has contributed greatly to resolving species limits in rapidly diverging tropical insect groups. Here, we explored species diversity in the widespread, cryptic Neotropical butterfly genus Hermeuptychia by generating 601 new sequences of the cytochrome c oxidase I (COI) barcode, tripling available information. Our dataset focused in particular on Ecuador, a biogeographically pivotal country, with additional sequences from Brazil, Costa Rica, French Guiana, Guatemala, Mexico, Panama and Peru. We examined the performance of two phylogeny-based approaches for objectively delineating species, Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP), as well as a clustering-based approach, Automatic Barcode Gap Discovery (ABGD), on the combined dataset, including our data and 302 published sequences. In general, GMYC and PTP tended to cluster or split likely species as assessed from morphology, depending on model settings, whereas ABGD was less sensitive and produced a more plausible classification. Numerous sequences formed well-supported clades, putative species, that were unrepresented in previously published datasets. The average diversity across all methods was 45 species, in contrast to the 11 species recognized in the current taxonomy. The resulting COI dataset, in combination with ongoing genomic and morphological research, should significantly clarify our understanding of Hermeuptychia species diversity.
... The GMYC species delimitation independently recovered FMNH 265806, 255454, 270492 and VNUF R.2014.50 and C. ngati (IBER 4829 and VNUF R.2020.12) as conspecific. However, the likelihood ratio test was insignificant (p=0.10000) which is not surprising given the high percentage of singletons in the data set (Talavera et al. 2013). The bPTP analysis also recovered these specimens as conspecific with a 0.84 posterior probability. ...
Article
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Convergent morphological specializations for an arboreal lifestyle in most species of the Cyrtodactylus brevipalmatus group have been a confounding factor for establishing a stable taxonomy among its species. Recent references to C. interdigitalis from throughout Thailand and Laos were made without comparisons to the type material from Tham Yai Nam Nao, Nam Nao National Park, Phetchabun Province, Thailand, but instead, were based on general morphological similarity and distribution. The taxonomy of C. interdigitalis is stabilized here by comparing the paratypes to other specimens from Thailand and Laos and recovering their phylogenetic relationships based on newly acquired genetic data, including those from the type locality. The phylogeny recovered all specimens outside the type locality to be either C. ngati from Vietnam or new species closely related to C. ngati . Cyrtodactylus interdigitalis is shown here to be a range-restricted upland endemic on the Phetchabun massif of northern Thailand. The phylogeny also indicates that C. ngati extends hundreds of kilometers farther south into northern Thailand and central Laos. We hypothesize that the significant morphological divergence in body shape of the types of C. ngati , compared to that of the Lao and Thai populations, may be due to local adaptions for utilizing karst ( C. ngati ) rather than vegetation (Lao and Thai populations). Additionally, phylogenetic and multivariate analyses identified a potentially new species from Phu Hin Rong Kla National Park, Phitsanulok Province, in northern Thailand and another from the Khlong Naka Wildlife Sanctuary, Ranong Province, in southern Thailand. A series of newly examined specimens from Kaeng Krachan National Park, Phetchaburi Province, Thailand represents a possible ~82 km range extension to the southeast of C. rukhadeva . This research continues to underscore the high diversity of range-restricted upland endemics in Thailand and the importance of examining type material (if possible) in the context of a phylogeny so as to construct proper taxonomies that reveal, rather than obscure, diversity.
... A FASTA alignment was used as input file. For the GMYC analysis, non-unique haplotypes were removed from the alignments (Talavera et al. 2013). Ultrametric tree was generated in BEAST v1.10.4 . ...
... With small datasets, ABGD, PTP and TCS, when employed in an integrative fashion, are more stable approaches in inferring OTUs than GMYC (Hamilton et al., 2014). The GMYC method is susceptible to tree reconstruction method, sampling bias and taxon coverage (Talavera et al., 2013). Regarding the ABGD method, Meier et al. (2008) argued in favour of choosing the smallest interspecific genetic distance for determining the 'barcode gap', but in our samples, this method failed to recognize two species that are well supported morphologically, M. fuscus and M. gallicus. ...
Article
Previously considered as a thelytokous parthenogenetic species, the widespread ant cricket Myrmecophilus acervorum actually turns out to have a mixed reproductive system: our recent surveys in the central part of its distribution area has revealed the presence of both sexes. Detailed morphological and morphometric descriptions of the previously unknown males are here provided. New data on species distribution in south-eastern Europe are presented, including the first records of M. balcanicus in Bulgaria and of M. nonveilleri in Bulgaria and Hungary. Phylogenetic and phylogeographic analyses have revealed several haplotypes of M. acervorum in Europe, with six of them forming a parthenogenetic clade in populations distributed west of the Carpathians. We tested our samples for bacterial infection by Wolbachia and, surprisingly, Wolbachia was identified only in populations with both sexes and no amplification was obtained from parthenogenetic populations. Phylogenetic analyses performed with sequences pertaining to five nominal species related to M. acervorum, yielded topological congruent trees with four well-supported groups: one group with M. acervorum samples, the second group with M. nonveilleri samples, the third group with M. fuscus and M. gallicus samples, and the fourth group with samples of M. balcanicus. We performed species delineation tests on our sequences, which delimited between four to seven putative species.
... r-project.org/projects/splits/). The single-threshold model of bGMYC was preferred since it has been demonstrated to outperform the multiple-threshold model (Fujisawa & Barraclough, 2013;Talavera & al., 2013). ...
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The genus Arthrorhaphis is a group of ascomycetes comprising lichenised and non‐lichenised taxa from temperate to arctic‐alpine regions in both hemispheres. Nine species and two infraspecific taxa are currently recognised. Their delimitation, inter‐relationships, and phylogenetic placement remain poorly understood. We have used an integrative taxonomic approach to assess taxon limits, phylogenetic placement of the family, and to test the hypothesis that transition to lichenisation has happened only once. We present a first molecular phylogenetic hypothesis of all but one known Arthrorhaphis species based on Bayesian inference and maximum likelihood analyses of multilocus DNA sequence data. Our results support monophyly of Arthrorhaphis, phylogenetic placement in the Ostropomycetidae, and lichenisation having evolved from lichenicolous ancestors only once. The lichenicolous Arthrorhaphis species are well‐defined both morphologically and genetically. The lichenised A. alpina s.l. and A. citrinella s.l., however, include multiple genetic clades that are partly supported by phenotypic data. We split A. citrinella s.l. into the following five species: (1) A. bullata sp. nov., (2) A. catolechioides comb. & stat. nov., (3) A. citrinella, (4) A. farinosa sp. nov., and (5) A. vulgaris comb. & stat. nov. A sixth phylogenetic clade from the Neotropics remains undescribed herein due to insufficient data. Five circumarctic accessions of A. alpina s.l. form a genetically distinct but morphologically poorly understood clade sister to the alpina‐vacillans clade, which we preliminarily name “A. septentrionalis”. Jointly, our multispecies coalescence analyses, of both single‐locus (bGMYC) and multilocus (bPtP, bP&P) datasets, largely support our proposed species hypotheses in Arthrorhaphis.
... However, the GMYC method is known often to oversplit, especially when compared to the PTP, and this has usually been explained with errors in time calibration of the tree (Pentinsaari et al., 2017). Unfortunately, the reltime method we used for time calibration was not included in the comparative analysis by Talavera et al. (2013), who tested alternative methods for dating ML phylogenies to be used for GMYC. Even when different Table 1) on the first and second principal components (bgPC 1 and bgPC 2) obtained from a between-group principal components analysis of the symmetric component of the shape. ...
Article
The investigation of species boundaries in strictly endogeic animals is challenging because they are prone to fine-scale genetic and phenotypic geographical differentiation owing to low dispersal ability. An integrative approach exploiting different sources of information has seldom been adopted in these animals and even more rarely by treating all data sources equally. We investigated species boundaries in the endogeic centipede Clinopodes carinthiacus across the south-eastern Alps by studying genetic and morphological differentiation in a sample of 66 specimens from 27 sites, complemented by the morphological examination of more than 1100 specimens from other sites. Hypotheses of species delimitation were obtained independently from the molecular sequences of three markers (mitochondrial 16S and COI and nuclear 28S) by means of different species discovery methods (automatic barcode gap discovery, assemble species by automatic partitioning, general mixed Yule coalescent and the Poisson tree process) and from ten morphological characters by means of a model-based cluster analysis and Bayesian model selection. We found strong support for the existence of at least two species: C. carinthiacus s.s. and Clinopodes strasseri, which was formerly described as a subspecies of another species, and later placed in synonymy with C. carinthiacus. The two species coexist in syntopy in at least one site.
... One source of support is often from coalescent analyses in fast-evolving genes, which often provide the most direct evidence of evolutionarily independent lineages (Monaghan et al., 2005(Monaghan et al., , 2009Zhang et al., 2013). Methods for recognizing species from gene coalescents necessarily depend on obtaining a representative gene tree for at least five genuine species (Reid & Carstens, 2012;Fujisawa & Barraclough, 2013;Talavera et al., 2013;Zhang et al., 2013;Leliaert et al., 2014;Dellicour & Flot, 2015) and on the correct rooting of the tree (Zhang et al., 2013), and also require accounting for any: (1) 'numts' (nuclear paralogous copies of mitochondrial genes: Magnacca & Brown, 2010;Song et al., 2014); (2) heteroplasmy (Magnacca & Brown, 2010;Francoso et al., 2016;Williams et al., 2019); (3) other forms of incomplete lineage sorting (Maddison & Knowles, 2006); and (4) introgression (Ballard & Whitlock, 2004;Monaghan et al., 2005). A lack of interbreeding now became a necessary, but not sufficient, criterion for recognizing separate species, with species sometimes accepted as showing a possibly temporary lack of interbreeding between parts of their populations when dispersal barriers were introduced (Goulson et al., 2011). ...
Article
Splitting or lumping of species is a concern because of its potential confounding effect on comparisons of biodiversity and on conservation assessments. By comparing global lists of species reported by previous authors to lists of the presently recognized species that were known to those authors, a simple ratio can be used to describe their relative splitting or lumping of species. One group of 'model' organisms claimed for the study of what species are and how to recognize them is bumblebees. A comparison of four bumblebee subgenera shows: (1) an early phase (up to and including 1931) showing splitting, in which taxonomy was dominated by a typological concept of invariant species with heavy reliance on colour-pattern characters; (2) a middle phase (1935-98) showing lumping, associated with a shift to a polytypic concept of species emphasizing morphological characters, often justified with an interbreeding concept of species, but only rarely associated directly with process-related characters; and (3) a recent phase (after 2000), using a concept of species as evolutionarily independent lineages, as evidenced by corroboration from integrative assessment, usually including evidence for coalescents of species in fast-evolving genes compared with morphology. Analysis of splitting or lumping should help to improve biodiversity comparisons and conservation.
... In the current study, the GMYC approach was more adept at recognizing species than the bPTP and ABGD approaches. This result is consistent with previous findings, which showed that the GMYC method provided more usable taxonomic units than other species delimitation methodologies [91,92,97,99,[101][102][103]. Furthermore, one functional pattern analysis (ITS secondary structure) of the 16S-23S ITS dataset was applied in this study. ...
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Simple trichal types constitute a group of cyanobacteria with an abundance of novel, often cryptic taxa. Here, we investigated material collected from wet surface-soil in a saline environment in Petchaburi Province, central Thailand. A morphological comparison of the isolated strain with similar known species, as well as its phylogenetic and species delimitation analyses based on the combined datasets of other related organisms, especially simple trichal cyanobacteria, revealed that the material of this study represented an independent taxon. Using a multifaceted method, we propose that this material represents a new genus, Thainema gen. nov., belonging to the family Leptolyngbyaceae, with the type species Thainema salinarum sp. nov. This novel taxon shares similar ecological habitats with strains previously placed in the same lineage.
... The GMYC method is sometimes considered prone to oversplitting (Lohse 2009, Talavera et al. 2013, but it did not oversplit the datasets in our previous study on the section Nidulantes (Sklen a r et al. 2020), neither the dataset in this study. The method delimiting the highest number of species was bPTP and the most conservative method (resulting in the lowest number of delimited species) was bGMYC. ...
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Since the last revision in 2015, the taxonomy of section Flavipedes evolved rapidly along with the availability of new species delimitation techniques. This study aims to re-evaluate the species boundaries of section Flavipedes members using modern delimitation methods applied to an extended set of strains (n = 90) collected from various environments. The analysis used DNA sequences of three housekeeping genes (benA, CaM, RPB2) and consisted of two steps: application of several single-locus (GMYC, bGMYC, PTP, bPTP) and multi-locus (STACEY) species delimitation methods to sort the isolates into putative species, which were subsequently validated using DELINEATE software that was applied for the first time in fungal taxonomy. As a result, four new species are introduced, i.e. A. alboluteus, A. alboviridis, A. inusitatus and A. lanuginosus, and A. capensis is synonymized with A. iizukae. Phenotypic analyses were performed for the new species and their relatives, and the results showed that the growth parameters at different temperatures and colonies characteristics were useful for differentiation of these taxa. The revised section harbors 18 species, most of them are known from soil. However, the most common species from the section are ecologically diverse, occurring in the indoor environment (six species), clinical samples (five species), food and feed (four species), droppings (four species) and other less common substrates/environments. Due to the occurrence of section Flavipedes species in the clinical material/hospital environment, we also evaluated the susceptibility of 67 strains to six antifungals (amphotericin B, itra-conazole, posaconazole, voriconazole, isavuconazole, terbinafine) using the reference EUCAST method. These results showed some potentially clinically relevant differences in susceptibility between species. For example, MICs higher than those observed for A. fumigatus wild-type were found for both triazoles and amphotericin B for A. ardalensis, A. iizukae, and A. spelaeus whereas A. lanuginosus, A. luppiae, A. movilensis, A. neoflavipes, A. olivimuriae and A. suttoniae were comparable to or more susceptible as A. fumigatus. Finally, terbinafine was in vitro active against all species except A. alboviridis.
... The phylogenetic analysis and species delimitation presented here have important limitations, as they assessed only one locus, represented by part of the mitochondrial DNA. Additionally, literature strongly recommends that GMYC results should not be considered alone to guide taxonomic reviews, but should be discussed in the light of other evidences and biological information (Talavera et al., 2013;Tang et al., 2014). The elucidation of the phylogenetic relationships and species delimitation in the M. americana complex depends not only of an advance in molecular analysis, but also an advance in Amazonian populations sampling, which are still underrepresented. ...
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The red brocket deer Mazama americana Erxleben, 1777 is considered a polyphyletic complex of cryptic species with wide chromosomal divergence. Evidence indicates that the observed chromosomal divergences result in reproductive isolation. The description of a neotype for M. americana allowed its genetic characterization and represented a comparative basis to resolve the taxonomic uncertainties of the group. Thus, we designated a neotype for the synonym Mazama rufa Illiger, 1815 and tested its recognition as a distinct species from the M. americana complex with the analysis of morphological, cytogenetic and molecular data. We also evaluated its distribution by sampling fecal DNA in the wild. Morphological data from craniometry and body biometry indicated an overlap of quantitative measurements between M. rufa and the entire M. americana complex. The phylogenetic hypothesis obtained through mtDNA confirmed the reciprocal monophyly relationship between M. americana and M. rufa , and both were identified as distinct molecular operational taxonomic units by the General Mixed Yule Coalescent species delimitation analysis. Finally, classic cytogenetic data and fluorescence in situ hybridization with whole chromosome painting probes showed M. rufa with a karyotype of 2n = 52, FN = 56. Comparative analysis indicate that at least fifteen rearrangements separate M. rufa and M. americana ( sensu stricto ) karyotypes, which confirmed their substantial chromosomal divergence. This divergence should represent an important reproductive barrier and allow its characterization as a distinct and valid species. Genetic analysis of fecal samples demonstrated a wide distribution of M. rufa in the South American continent through the Atlantic Forest, Cerrado and south region of Amazon. Thus, we conclude for the revalidation of M. rufa as a distinct species under the concept of biological isolation, with its karyotype as the main diagnostic character. The present work serves as a basis for the taxonomic review of the M. americana complex, which should be mainly based on cytogenetic characterization and directed towards a better sampling of the Amazon region, the evaluation of available names in the species synonymy and a multi-locus phylogenetic analysis.
... Therefore, the number of species depends on the method used, although all of them pointed to undescribed cryptic species in the region. Some studies argue that in some cases GMYC can lead to an overestimation of the number of species (e.g., Talavera et al., 2013;García-Melo et al., 2019). Despite that in our study the GMYC analysis delimited the highest number of species, the results of this method were corroborated by the WP and ABGD result 2. Therefore, we cannot state that the GMYC analysis overestimated the number of delimited species in our study. ...
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Recent studies in eastern Amazon coastal drainages and their surroundings have revealed new fish species that sometimes exhibit little morphological differentiation (cryptic species). Thus, we used a DNA-based species delimitation approach to test if populations showing the morphotype and typical character states of the Aphyocharax avary holotype correspond either to A. avary or A. brevicaudatus, two known species from the region, or if they form independent lineages, indicating cryptic speciation. WP and GMYC analyses recovered five lineages (species) in the ingroup, while a bPTP analysis delimited three lineages. ABGD analyses produced two possible results: one corroborating the WP and GMYC methods and another corroborating the bPTP method. All methods indicate undescribed cryptic species in the region and show variation from at least 1 to 4 species in the ingroup, depending on the approach, corroborating previous studies, and revealing this region as a possible hotspot for discovering undescribed fish species.
... Many authors have discussed the oversplitting behaviour of the GMYC model due to several different circumstances (e.g. Talavera et al. 2013), and we are convinced that the convergence of the results of all of the analyses except GMYC strongly suggests that our data set includes haplotypes of two well-distinct taxa only. Both taxa show a certain degree of intra-specific variation that, among other factors, could also be related to the flightless characteristic of these insects. ...
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The trophic ecology of Chiloneus weevil species from Sicily was unknown until recently when the host plant of these closely related species was discovered. The opportunity to collect many samples of these elusive species allowed us to re-evaluate the morphology and the genetic relationships among the three closest of the four species inhabiting Sicily and the adjoining islands. We analysed a fragment of the cox1 mitochondrial gene of adult specimens collected from the host plant Drimia pancration in Sicily, Pantelleria, Pelagie Islands and Malta to study the population structure and the relationships among the different nominal species known so far. Both morphological and genetic results suggest that the previous three species are actually two species with disjunct distribution, for which the new synonymy C. hoffmanni (González, 1970) (= C. solarii Pesarini, 1970, syn. nov.) is established. Chiloneus meridionalis (Boheman, 1840) inhabits the main island of Sicily and Pantelleria island, while C. hoffmanni is restricted to Malta and Pelagie islands. Adults of the two species are very similar in general appearance but still distinguishable by a set of well-established characters presented here in a key to their identification. The genetic approach provided evidence of a certain degree of structure of the genetic variation within the two species that would be worth addressing from a phylogeographic perspective in future work. urn:lsid:zoobank.org:pub:1F03BA05-B7A9-44B7-8225-321174A1E3FB
... This data filtering is necessary due to limitations of the species delimitation algorithms besides saving computational efforts. Moreover, in genealogical inference using BEAST, identical sequences are interpreted as coalescent alleles, generating branch lengths different from zero, probably affecting the GMYC estimates (Reid & Carstens, 2012;Talavera et al., 2013). ...
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Hypostomus Lacépède, 1803, is a species-rich and widespread fish genus from the Neotropical region, but its evolutionary history and systematics remain largely unclear. In addition, species from regions with high levels of species richness and endemism such as the Northeastern Mata Atlântica (NMA) and São Francisco (SF) hydrographic freshwater ecoregions are underrepresented in phylogenetic studies so far. In this study, we performed a broad sampling of Hypostomus in NMA and SF to investigate the interspecific boundaries and phylogenetic relationships using a multilocus approach based on one mitochondrial and three nuclear markers. Seven genetic groups were found for both ecoregions, in addition to one lineage exclusive to the SF represented by populations of the species Hypostomus velhochico. Moreover, multilocus analyses validated 16 formally described species and two new lineages for the NMA and SF ecoregions, as well as putative cases of species complexes. In general, lineages with independent evolutionary histories were revealed within the same ecoregion alongside genetically related groups between NMA, SF, and other ecoregions. These data reinforce the intricate scenario of this group of Neotropical fish and are useful to outline further phylogeographic studies in Hypostomus.
... Initially, GMYC was proposed by Pons et al. (2006) as a molecular method for species delimitation in a Maximum Likelihood context and based on ultrametric trees. The method was found to be robust in a range of departures from its simplifying assumptions (Fujisawa & Barraclough 2013;Talavera et al. 2013). Herein, this species delimitation method was robust and concordant for the analyzed species of Pseudocellus, recovering the new species based on traditional morphology (Fig. 2). ...
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A new species of epigean ricinuleid of the genus Pseudocellus Platnick, 1980 from El Triunfo Biosphere Reserve, Chiapas, Mexico is described. DNA barcoding utilizing mitochondrial cytochrome c oxidase subunit 1 (CO1) and morphology were used for species delimitation. Molecular analyses and species delimitation included four methods: 1) General Mixed Yule Coalescent model (GMYC), 2) Automatic Barcode Gap Discovery (ABGD), 3) Bayesian Poisson Tree Process (bPTP), and 4) Assemble Species by Automatic Partitioning (ASAP). All molecular methods and morphology were consistent in delimiting and recognizing the new species described herein. The average interspecific genetic distance (p-distance) among analyzed species of Pseudocellus was 11.6%. The species is described based on adult males and females: Pseudocellus giribeti sp. nov. This is the seventh species described from Chiapas, which holds the highest number of ricinuleids species for the country. The total number of described species of Pseudocellus from Mexico increases to 21, having the highest species diversity of known ricinuleids worldwide.
... With small datasets, ABGD, PTP and TCS, when employed in an integrative fashion, are more stable approaches in inferring OTUs than GMYC (Hamilton et al., 2014). The GMYC method is susceptible to tree reconstruction method, sampling bias and taxon coverage (Talavera et al., 2013). Regarding the ABGD method, Meier et al. (2008) argued in favour of choosing the smallest interspecific genetic distance for determining the 'barcode gap', but in our samples, this method failed to recognize two species that are well supported morphologically, M. fuscus and M. gallicus. ...
Article
Previously considered as a thelytokous parthenogenetic species, the widespread ant cricket Myrmecophilus acervorum actually turns out to have a mixed reproductive system: our recent surveys in the central part of its distribution area has revealed the presence of both sexes. Detailed morphological and morphometric descriptions of the previously unknown males are here provided. New data on species distribution in southeastern Europe are presented, including the first records of M. balcanicus in Bulgaria and of M. nonveilleri in Bulgaria and Hungary. Phylogenetic and phylogeographic analyses have revealed several haplotypes of M. acervorum in Europe, with six of them forming a parthenogenetic clade in populations distributed west of the Carpathians. We tested our samples for bacterial infection by Wolbachia and, surprisingly, Wolbachia was identified only in populations with both sexes and no amplification was obtained from parthenogenetic populations. Phylogenetic analyses performed with sequences pertaining to five nominal species related to M. acervorum, yielded topological congruent trees with four well-supported groups: one group with M. acervorum samples, the second group with M. nonveilleri samples, the third group with M. fuscus and M. gallicus samples, and the fourth group with samples of M. balcanicus. We performed species delineation tests on our sequences, which delimited between four to seven putative species.
... These methods aim to identify putative species by discriminating betweenspecies coalescence from within-species coalescence using information from branching rates. Because it is not uncommon that different species delimitation analyses result in incongruent results (Carstens et al. 2013), it is important that putative species delimited by GMYC and PTP are validated with other lines of evidence (Talavera et al. 2013;Zhang et al. 2013). Therefore, we used a conservative, multifaceted approach to species delimitation in which putative GMYCand PTP-delimited species are only accepted as species if they are also diagnosably morphologically distinct. ...
Article
Tetrastigma loheri (Vitaceae) is a vine species native to Borneo and the Philippines. Because it is a commonly encountered forest species in the Philippines, T. loheri is potentially suitable for studying patterns of genetic diversity and connectivity among fragmented forestecosystems in various parts of this country. However, previous research suggests that T. loheri is part of a species complex in the Philippines (i.e. the T. loheri s. l. complex) that potentially also contains Philippine plants identified as T. diepenhorstii , T. philippinense , T. stenophyllum , and T. trifoliolatum . This uncertainty about its taxonomic delimitation can make it challenging to draw conclusions that are relevant to conservation from genetic studies using this species. Here, we tested the hypothesis that T. loheri s. l. is composed of more than one species in the Philippines.For this, we used generalized mixed Yule coalescent (GMYC) and Poisson tree process (PTP) species delimitation models to identify clades within DNA sequence phylogenies of T. loheri s. l. that might constitute species within this complex. Although these methods identified several putative species, these are statistically poorly supported and subsequent random forest analyses using a geometric morphometric leafshape dataset and several other vegetative characters did not result in the identification of characters that can be used to discriminate these putative species morphologically. Furthermore, the results of principal component and principal coordinates analyses of these data suggest the absence of morphological discontinuities within the species complex. Under a unified species concept that uses phylogenetic and morphological distinction as operational criteria for species recognition, we therefore conclude that the currently available data do not support recognizing multiple species in the T. loheri s. l. complex. This implies that T. loheri is best considered as a single, morphologically variable specieswhen used for studying patterns of genetic diversity and connectivity in the Philippines.
... The 18S BI could not discriminate between these two species and many other species well delimited by morphological characters (e.g., Teredo navalis and Lyrodus pedicellatus) as this gene evolves at a slower rate than mitochondrial genes (Stage and Eickbush, 2007) and thus is a poor choice for species delimitation. However, 18S, when combined with COI, helps to avoid the pitfalls that can occur when using single COI sequences, such as the co-amplification of pseudogenes (Song et al., 2008), introgression, or incomplete lineage sorting (Talavera et al., 2013). ...
Article
Cryptic species are a common phenomenon in cosmopolitan marine species. The use of molecular tools has often uncovered cryptic species occupying a fraction of the geographic range of the original morphospecies. Ship-worms (Teredinidae) are marine bivalves, living in drift and fixed wood, many of which have a conserved morphology across cosmopolitan distributions. Herein novel and GenBank mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S rRNA) DNA sequences are employed to produce a phylogeny of the Teredinidae and delimit a cryptic species pair in the Psiloteredo megotara complex. The anatomy, biogeography, and ecology of P. megotara, Psiloteredo sp. and Nototeredo edax are compared based on private and historic museum collections and a thorough literature review. Morphological and anatomical characters of P. megotara from the North Atlantic and Psiloteredo sp. from Japan were morphologically indistinguishable, and differ in pallet architecture and soft tissue anatomy from N. edax. The two Psiloteredo species were then delimited as genetically distinct species using four molecular-based methods. Consequently, the Northwest Pacific species, Psiloteredo pentago-nalis, first synonymized with N. edax and then with P. megotara, is resurrected. Nototeredo edax, P. megotara and P. pentagonalis are redescribed based upon morphological and molecular characters. Phylogenetic analysis further revealed cryptic species complexes within the cosmopolitan species Bankia carinata and possibly additional cryptic lineages within the cosmopolitan Lyrodus pedicellatus.
... En revanche, la méthode PTP considère la longueur des branches proportionnelle au nombre de substitutions (Zhang et al, 2013), sans nécessité d'arbres ultra-métriques, rendant la méthode plus rapide et tout aussi efficace selon des études de modélisation (Dellicour and Flot, 2018). De plus, la méthode GMYC peut parfois surestimer le nombre d'espèces suite à un biais de certains paramètres de l'analyse, comme les différences dans la taille de la population ou les taux de spéciation (Dellicour and Flot, 2015;Esselstyn et al, 2012;Fujisawa and Barraclough, 2013;Talavera et al, 2013). Des implémentations bayésiennes de la méthode GMYC, (bGMYC) (Reid and Carstens, 2012) (Dellicour and Flot, 2015). ...
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Depuis 2006, des épizooties importantes de fièvre catarrhale ovine et de virus (FCO) de Schmallenberg (SB) sont observées dans la région ouest paléarctique, ces deux virus étant transmis par des moucherons hématophages autochtones du genre Culicoides (Diptera : Ceratopogonidae). Ces virus affectent les bovins, les ovins, les caprins et les ruminants sauvages. La dispersion des Culicoides correspond à ce que les écologues appellent dispersion stratifiée ou « stratified dispersal ». Elle résulte de la combinaison de dispersion active de proche en proche, sur de courtes distances, et de sauts sur de longues distances via le vent de manière passive ou semi-passive, permettant des sauts de dispersion de plusieurs centaines de kilomètres. Culicoides obsoletus est une espèce vectrice importante pour les virus de la FCO et de SB et abondante en région paléarctique. Si la dispersion des Culicoides par le vent au-dessus des masses d’eaux est bien établie, il est aussi important d’évaluer la dispersion au-dessus des terres et de déterminer l'influence des facteurs biotiques et abiotiques influant sur celle-ci.L'objectif de ce travail de thèse est de déterminer, par l'observation des patrons de distribution des fréquences alléliques, comment la dispersion a pu façonner l'arrangement spatial de la diversité génétique et comment elle est influencée par les paysages et par les caractéristiques des habitats qui peuvent favoriser ou limiter les mouvements des Culicoides. Pour cela, deux plans d’échantillonnage ont été utilisés : un échantillonnage populationnel à l’échelle de l’Europe (de la Scandinavie aux îles Canaries, à la Turquie), et un échantillonnage individuel à l’échelle française. L’utilisation complémentaire de marqueurs mitochondriaux et nucléaires à ces différentes échelles spatiales nous ont permis (i) de clarifier la distribution et de réviser le schéma taxonomique du Complexe Obsoletus/Scoticus, (ii) de mettre en évidence des flux de gènes importants permettant d'homogénéiser la structure génétique des populations à l'échelle d'un pays et d’un continent, (iii) de quantifier l’impact d’un large éventail de facteurs environnementaux et météorologiques sur la dispersion des Culicoides et de mettre en évidence l’importance de la densité d’hôtes, (iv) et de proposer un scénario présentant l’histoire évolutive récente des populations européennes de C. obsoletus. L’hypothèse retenue est une recolonisation post-glaciaire récente depuis le refuge glaciaire des Balkans et un refuge plus au nord-est. Ces populations auraient recolonisé ensemble l’ouest de l’Europe, engendrant une admixture des populations.Nos résultats démontrent une capacité de dispersion de C. obsoletus à l'intérieur des terres très importante, qui doit être prise en compte pour les travaux à venir sur la compétence des vecteurs et la modélisation épidémiologique de la transmission des virus transmis.
... To test the taxonomic status of recovered clades, we used two species delimitations methods, which are commonly used for detection of species-level clusters in taxonomic studies of various groups of insects, including butterflies (Talavera et al., 2013a;Dincă et al., 2015): the automatic barcode gap discovery (ABGD) method (Puillandre et al., 2012) and the generalized mixed Yule coalescent (GMYC) model (Pons et al., 2006;Fujisawa & Barraclough, 2013). For the ABGD test, we used COI alignment from the phylogenetic analysis, excluding outgroups, that was trimmed to the length of the shortest sequence (610 bp) in MEGA7 (Kumar et al., 2016). ...
Article
The tribe Tomarini is represented by the sole genus Tomares, comprising about eight species distributed from the western Mediterranean to Central Asia. We carried out a multilocus phylogenetic and a biogeographical analysis to test the taxonomy of the genus by several molecular species delimitation methods and reveal patterns shaping the current distribution of Tomares. The phylogenetic analysis based on four molecular markers recovered the monophyly of the genus and recovered two deep-branching lineages: an African clade and an Asian clade. Species delimitation analyses suggested six or ten putative species depending on the method applied. The haplotype network analysis of the Tomares nogelii clade revealed no phylogeographical and taxonomic structure. We consider the taxon Tomares nesimachus (syn. nov.) a synonym of T. nogelii and reinstate Tomares callimachus dentata stat. rev. for populations from southeastern Turkey. Tomares originated between the early Oligocene and the early Miocene, most probably in southwest Asia. The split of the most recent common ancestor of Tomares occurred between the middle-late Miocene and middle-late Pliocene, probably as a response to increasing aridification and habitat fragmentation. Differentiation of the Asian clade took place in southwest Asia during the Pliocene and Pleistocene and coincided temporally with the evolution of Tomares host plants of the genus Astragalus (Fabaceae).
... To test the taxonomic status of recovered clades, we used two species delimitations methods, which are commonly used for detection of species-level clusters in taxonomic studies of various groups of insects, including butterflies (Talavera et al., 2013a;Dincă et al., 2015): the automatic barcode gap discovery (ABGD) method (Puillandre et al., 2012) and the generalized mixed Yule coalescent (GMYC) model (Pons et al., 2006;Fujisawa & Barraclough, 2013). For the ABGD test, we used COI alignment from the phylogenetic analysis, excluding outgroups, that was trimmed to the length of the shortest sequence (610 bp) in MEGA7 (Kumar et al., 2016). ...
Article
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The tribe Tomarini is represented by the sole genus Tomares, comprising about eight species distributed from the western Mediterranean to Central Asia. We carried out a multilocus phylogenetic and a biogeographical analysis to test the taxonomy of the genus by several molecular species delimitation methods and reveal patterns shaping the current distribution of Tomares. The phylogenetic analysis based on four molecular markers recovered the monophyly of the genus and recovered two deep-branching lineages: an African clade and an Asian clade. Species delimitation analyses suggested six or ten putative species depending on the method applied. The haplotype network analysis of the Tomares nogelii clade revealed no phylogeographical and taxonomic structure. We consider the taxon Tomares nesimachus (syn. nov.) a synonym of T. nogelii and reinstate Tomares callimachus dentata stat. rev. for populations from south-eastern Turkey. Tomares originated between the early Oligocene and the early Miocene, most probably in south-west Asia. The split of the most recent common ancestor of Tomares occurred between the middle-late Miocene and middle-late Pliocene, probably as a response to increasing aridification and habitat fragmentation. Differentiation of the Asian clade took place in south-west Asia during the Pliocene and Pleistocene and coincided temporally with the evolution of Tomares host plants of the genus Astragalus (Fabaceae).
... As it is seen in the Figure 2, divergence time of S. asperum and S. savvalense (and also divergence time of other Symphytum species studied herein) is relatively recent. Genetic variation among species that diverged recently cannot be enough to detect real relationships among species and cause misevaluation in species delimitation (Talavera et al. 2013). ...
Article
Symphytum is regarded one of the most complicated genera in terms of the classification of its members among the Boraginaceae. In addition to different infrageneric classification methods, several species complex or aggregates have been proposed to deal with the taxonomical problem of genus members. Symphytum asperum aggregate was first introduced by Kurtto, who proposed six taxa within this aggregate. However, according to further studies by different researchers based on morphological data, total number of species of the complex was variable. The number of species was reduced to three, comprising S. asperum, S. savvalense, and S. sylvaticum, after the phylogenetic and morphological studies of Tarıkahya-Hacıoğlu and Erik. However, the taxonomical status of some of these species (i.e., S. savvalense and S. sylvaticum, and S. sepulcrale), which was assigned as a member of this complex by Kurtto, has been regarded as unresolved. To solve this uncertainty, different species delimitation methods were used, including statistical parsimony network analysis (TCS), generalized mixed Yule coalescent (GMYC), and Bayesian Phylogenetics and Phylogeography (BPP) of the ITS, trnL-F and trnS-G sequence data. In addition to members of this complex, S. ibericum, which is phylogenetically nested within the S. asperum aggregate, was also used. The TCS and GMYC analyses demonstrated more complicated clusters, whereas high posterior probabilities of BPP clusters were more compatible with the morphological data. In accordance with the morphological approach of Tarıkahya-Hacıoğlu and Erik, the species delimitation analyses based on molecular data support the recognition of S. asperum, S. ibericum, S. savvalense, and S. sylvaticum as different species.
... Five partitions were delimited using ABGD and mPTP and six with bGMYC. Previous studies have shown that the Generalized Mixed Yule Coalescent model is useful in detecting incipient speciation events 85 , when the threshold of intra-and interspecific distances is low, but on certain occasions it can overestimate the number of species due to pronounced intraspecific genetic variability 86,87 . The tree recovered in our analysis shows large branch lengths between the main clades, but short within each lineage, which is also noticeable in the haplotype network. ...
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Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
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DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single threshold version of the method outperforms the multiple threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.
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Many cold adapted species occur in both montane settings and in the subarctic. Their disjunct distributions create taxonomic complexity because there is no standardized method to establish whether their allopatric populations represent single or different species. This study employs DNA barcoding to gain new perspectives on the levels and patterns of sequence divergence among populations of 122 arctic-alpine species of Lepidoptera from the Alps, Fennoscandia and North America. It reveals intraspecific variability in the barcode region ranging from 0.00-10.08%. Eleven supposedly different species pairs or groups show close genetic similarity, suggesting possible synonymy in many cases. However, a total of 33 species show evidence of cryptic diversity as evidenced by the presence of lineages with over 2% maximum barcode divergence in Europe, in North America or between the two continents. Our study also reveals cases where taxonomic names have been used inconsistently between regions and exposes misidentifications. Overall, DNA barcodes have great potential to both increase taxonomic resolution and to make decisions concerning the taxonomic status of allopatric populations more objective.
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Background Species are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to identify them are often unavailable to researchers. In such cases DNA sequence-based species delimitation has been proposed as a means of estimating species boundaries for further analysis. Several methods have been proposed to accomplish this. Here we present a Bayesian implementation of an evolutionary model-based method, the general mixed Yule-coalescent model (GMYC). Our implementation integrates over the parameters of the model and uncertainty in phylogenetic relationships using the output of widely available phylogenetic models and Markov-Chain Monte Carlo (MCMC) simulation in order to produce marginal probabilities of species identities. Results We conducted simulations testing the effects of species evolutionary history, levels of intraspecific sampling and number of nucleotides sequenced. We also re-analyze the dataset used to introduce the original GMYC model. We found that the model results are improved with addition of DNA sequence and increased sampling, although these improvements have limits. The most important factor in the success of the model is the underlying phylogenetic history of the species under consideration. Recent and rapid divergences result in higher amounts of uncertainty in the model and eventually cause the model to fail to accurately assess uncertainty in species limits. Conclusion Our results suggest that the GMYC model can be useful under a wide variety of circumstances, particularly in cases where divergences are deeper, or taxon sampling is incomplete, as in many studies of ecological communities, but that, in accordance with expectations from coalescent theory, rapid, recent radiations may yield inaccurate results. Our implementation differs from existing ones in two ways: it allows for the accounting for important sources of uncertainty in the model (phylogenetic and in parameters specific to the model) and in the specification of informative prior distributions that can increase the precision of the model. We have incorporated this model into a user-friendly R package available on the authors’ websites.
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Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule-coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries suggested by GMYC. In our simulations, GMYC performed relatively well (errors in estimated species diversity less than 25%) when the product of the haploid effective population size (N(e)) and speciation rate (SR; per lineage per million years) was less than or equal to 10(5), while interspecific variation in N(e) was twofold or less. However, at higher but also biologically relevant values of N(e) × SR and when N(e) varied tenfold among species, performance was very poor. GMYC analyses of mitochondrial DNA sequences from Philippine Hipposideros suggest actual diversity may be approximately twice the current estimate, and available echolocation call data are mostly consistent with GMYC delimitations. In conclusion, we consider the GMYC model useful under some conditions, but additional information on N(e), SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results.
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Integrative taxonomy is a recently developed approach that uses multiple lines of evidence such as molecular, morphological, ecological and geographical data to test species limits, and it stands as one of the most promising approaches to species delimitation in taxonomically difficult groups. The Pnigalio soemius complex (Hymenoptera: Eulophidae) represents an interesting taxonomical and ecological study case, as it is characterized by a lack of informative morphological characters, deep mitochondrial divergence, and is susceptible to infection by parthenogenesis-inducing Rickettsia. We tested the effectiveness of an integrative taxonomy approach in delimiting species within the P. soemius complex. We analysed two molecular markers (COI and ITS2) using different methods, performed multivariate analysis on morphometric data and exploited ecological data such as host-plant system associations, geographical separation, and the prevalence, type and effects of endosymbiont infection. The challenge of resolving different levels of resolution in the data was met by setting up a formal procedure of data integration within and between conflicting independent lines of evidence. An iterative corroboration process of multiple sources of data eventually indicated the existence of several cryptic species that can be treated as stable taxonomic hypotheses. Furthermore, the integrative approach confirmed a trend towards host specificity within the presumed polyphagous P. soemius and suggested that Rickettsia could have played a major role in the reproductive isolation and genetic diversification of at least two species.
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Eight years after DNA barcoding was formally proposed on a large scale, CO1 sequences are rapidly accumulating from around the world. While studies to date have mostly targeted local or regional species assemblages, the recent launch of the global iBOL project (International Barcode of Life), highlights the need to understand the effects of geographical scale on Barcoding's goals. Sampling has been central in the debate on DNA Barcoding, but the effect of the geographical scale of sampling has not yet been thoroughly and explicitly tested with empirical data. Here, we present a CO1 data set of aquatic predaceous diving beetles of the tribe Agabini, sampled throughout Europe, and use it to investigate how the geographic scale of sampling affects 1) the estimated intraspecific variation of species, 2) the genetic distance to the most closely related heterospecific, 3) the ratio of intraspecific and interspecific variation, 4) the frequency of taxonomically recognized species found to be monophyletic, and 5) query identification performance based on 6 different species assignment methods. Intraspecific variation was significantly correlated with the geographical scale of sampling (R-square = 0.7), and more than half of the species with 10 or more sampled individuals (N = 29) showed higher intraspecific variation than 1% sequence divergence. In contrast, the distance to the closest heterospecific showed a significant decrease with increasing geographical scale of sampling. The average genetic distance dropped from > 7% for samples within 1 km, to < 3.5% for samples up to > 6000 km apart. Over a third of the species were not monophyletic, and the proportion increased through locally, nationally, regionally, and continentally restricted subsets of the data. The success of identifying queries decreased with increasing spatial scale of sampling; liberal methods declined from 100% to around 90%, whereas strict methods dropped to below 50% at continental scales. The proportion of query identifications considered uncertain (more than one species < 1% distance from query) escalated from zero at local, to 50% at continental scale. Finally, by resampling the most widely sampled species we show that even if samples are collected to maximize the geographical coverage, up to 70 individuals are required to sample 95% of intraspecific variation. The results show that the geographical scale of sampling has a critical impact on the global application of DNA barcoding. Scale-effects result from the relative importance of different processes determining the composition of regional species assemblages (dispersal and ecological assembly) and global clades (demography, speciation, and extinction). The incorporation of geographical information, where available, will be required to obtain identification rates at global scales equivalent to those in regional barcoding studies. Our result hence provides an impetus for both smarter barcoding tools and sprouting national barcoding initiatives-smaller geographical scales deliver higher accuracy.
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Uncovering cryptic biodiversity is essential for understanding evolutionary processes and patterns of ecosystem functioning, as well as for nature conservation. As European butterflies are arguably the best-studied group of invertebrates in the world, the discovery of a cryptic species, twenty years ago, within the common wood white Leptidea sinapis was a significant event, and these butterflies have become a model to study speciation. Here we show that the so-called 'sibling' Leptidea actually consist of three species. The new species can be discriminated on the basis of either DNA or karyological data. Such an unexpected discovery challenges our current knowledge on biodiversity, exemplifying how a widespread species can remain unnoticed even within an intensely studied natural model system for speciation.
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Singletons—species only known from a single specimen—and uniques—species that have only been collected once—are very common in biodiversity samples. Recent reviews suggest that in tropical arthropod samples, 30% of all species are represented by only one specimen (Bickel 1999; Novotny and Basset 2000; Coddington et al. 2009), with additional sampling helping little with eliminating rarity. Usually, such sampling only converts some of the singleton species to doubletons, with new singleton species being discovered in the process (Scharff et al. 2003; Coddington et al. 2009). Here, we first demonstrate that rare species are similarly common in specimen samples used for taxonomic research before we argue that the phenomenon of rarity has been insufficiently considered by the new quantitative techniques for species delimitation. Addressing this disconnect between theory and reality is pressing given that the last decade has seen a renewed interest in methods for species identification and delimitation (Sites and Marshall 2004; O’Meara 2010). Much of this interest has been fuelled by the availability of DNA sequences (Meier 2008). However, many newly proposed techniques implicitly or explicitly assume that all populations and species can be well sampled. But what is the value of these techniques if many species have only been collected once and/or are only known from one specimen? Here, we argue that all existing techniques need to be modified to accommodate the commonness of rarity and that all future techniques should be explicit about how rare species can be discovered and treated.
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Sample size has long been one of the basic issues since the start of the DNA barcoding initiative and the global biodiversity investigation. As a contribution to resolving this problem, we propose a simple resampling approach to estimate several key sampling sizes for a DNA barcoding project. We illustrate our approach using both structured populations simulated under coalescent and real species of skipper butterflies. We found that sample sizes widely used in DNA barcoding are insufficient to assess the genetic diversity of a species, population structure impacts the estimation of the sample sizes, and hence will bias the species identification potentially.
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Comparative phylogeographical studies in island archipelagos can reveal lineage-specific differential responses to the geological and climatic history. We analysed patterns of genetic diversity in six codistributed lineages of darkling beetles (Tenebrionidae) in the central Aegean archipelago which differ in wing development and habitat preferences. A total of 600 specimens from 30 islands and eight adjacent mainland regions were sequenced for mitochondrial cytochrome oxidase I and nuclear Muscular protein 20. Individual gene genealogies were assessed for the presence of groups that obey an independent coalescent process using a mixed Yule coalescent model. The six focal taxa differed greatly in the number of coalescent groups and depth of lineage subdivision, which was closely mirrored by the degree of geographical structuring. The most severe subdivision at both mitochondrial DNA and nuclear DNA level was found in flightless lineages associated with presumed stable compact-soil habitats (phrygana, maquis), in contrast to sand-obligate lineages inhabiting ephemeral coastal areas that displayed greater homogeneity across the archipelago. A winged lineage, although associated with stable habitats, showed no significant phylogenetic or geographical structuring. Patterns of nucleotide diversity and local genetic differentiation, as measured using PhiST and hierarchical AMOVA, were consistent with high levels of ongoing gene flow in the winged taxon; frequent local extinction and island recolonisation for flightless sand-obligate taxa; and very low gene flow and geographical structure largely defined by the palaeogeographical history of the region in flightless compact-soil taxa. These results show that differences in dispersal rate, mediated by habitat persistence, greatly influence the levels of phylogeographical subdivision in lineages that are otherwise subjected to the same geological events and palaeoclimatic changes.
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By far the greatest challenge for diversity studies is to characterize the diversity of prokaryotes, which probably encompasses billions of species, most of which are unculturable. Recent advances in theory and analysis have focused on multi-locus approaches and on combined analysis of molecular and ecological data. However, broad environmental surveys of bacterial diversity still rely on single-locus data, notably 16S ribosomal DNA, and little other detailed information. Evolutionary methods of delimiting species from single-locus data alone need to consider population genetic and macroevolutionary theories for the expected levels of interspecific and intraspecific variation. We discuss the use of a recent evolutionary method, based on the theory of coalescence within independently evolving populations, compared with a traditional approach that uses a fixed threshold divergence to delimit species.
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Phylogenies reconstructed from contemporary taxa do not contain information about lineages that have gone extinct. We derive probability models for such phylogenies, allowing real data to be compared with specified null models of evolution, and lineage birth and death rates to be estimated.
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Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
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With millions of species and their life-stage transformations, the animal kingdom provides a challenging target for taxonomy. Recent work has suggested that a DNA-based identification system, founded on the mitochondrial gene, cytochrome c oxidase subunit 1 (COI), can aid the resolution of this diversity. While past work has validated the ability of COI sequences to diagnose species in certain taxonomic groups, the present study extends these analyses across the animal kingdom. The results indicate that sequence divergences at COI regularly enable the discrimination of closely allied species in all animal phyla except the Cnidaria. This success in species diagnosis reflects both the high rates of sequence change at COI in most animal groups and constraints on intraspecific mitochondrial DNA divergence arising, at least in part, through selective sweeps mediated via interactions with the nuclear genome.
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Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. Availability: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
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Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10x average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens.