Species limits in butterflies (Lepidoptera: Nymphalidae): Reconciling classical taxonomy with the multispecies coalescent

AbstractSpecies delimitation is at the core of biological sciences. During the last decade, molecular-based approaches have advanced the field by providing additional sources of evidence to classical, morphology-based taxonomy. However, taxonomy has not yet fully embraced molecular species delimitation beyond threshold-based, single-gene approaches, and taxonomic knowledge is not commonly integrated to multi-locus species delimitation models. Here we aim to bridge empirical data (taxonomic and genetic) with recently developed coalescent-based species delimitation approaches. We use the multispecies coalescent model as implemented in two Bayesian methods (DISSECT/STACEY and BP&P) to infer species hypotheses. In both cases, we account for phylogenetic uncertainty (by not using any guide tree) and taxonomic uncertainty (by measuring the impact of using or not a priori taxonomic assignment to specimens). We focus on an entire Neotropical tribe of butterflies, the Haeterini (Nymphalidae: Satyrinae). We contrast divergent taxonomic opinion—splitting, lumping and misclassifying species—in the light of different phenotypic classifications proposed to date. Our results provide a solid background for the recognition of 22 species. The synergistic approach presented here overcomes limitations in both traditional taxonomy (e.g. by recognizing cryptic species) and molecular-based methods (e.g. by recognizing structured populations, and not raise them to species). Our framework provides a step forward towards standardization and increasing reproducibility of species delimitations.

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The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa

Systematic Biology ◽

10.1093/sysbio/syz042 ◽

2019 ◽

Vol 69 (1) ◽

pp. 184-193 ◽

Cited By ~ 16

Author(s):

E Anne Chambers ◽

David M Hillis

Keyword(s):

Species Delimitation ◽

Isolation By Distance ◽

A Priori ◽

Genetic Data ◽

Species Group ◽

Recent Analysis ◽

Multispecies Coalescent ◽

Species Complexes ◽

Taxonomic Changes ◽

Recent Species

AbstractMany recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic–nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.

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DNA Barcoding of Penaeidae (Decapoda; Crustacea): Non-Distance-Based Species Delimitation of the Most Economically Important Shrimp Family

Diversity ◽

10.3390/d13100460 ◽

2021 ◽

Vol 13 (10) ◽

pp. 460

Author(s):

Jorge L. Ramirez ◽

Luisa Simbine ◽

Carla G. Marques ◽

Eliana Zelada-Mázmela ◽

Lorenzo E. Reyes-Flores ◽

...

Keyword(s):

Dna Barcoding ◽

Species Delimitation ◽

Mitochondrial Gene ◽

Single Gene ◽

Penaeid Shrimp ◽

Genetic Distances ◽

Structured Populations ◽

Nominal Species ◽

Data Set ◽

Shrimp Fishery

The Penaeidae family includes some of the most economic and ecological important marine shrimp, comprising hundreds of species. Despite this importance and diversity, the taxonomic classification for penaeid shrimp has constantly been revised, and issues related to the species identification are common. In this study, we implemented DNA barcoding analyses in addition to single-gene species delimitation analyses in order to identify molecular operational taxonomy units (MOTUs) and to generate robust molecular information for penaeid shrimp based on the cytochrome oxidase subunit I (COI) mitochondrial gene. Our final data set includes COI sequences from 112 taxa distributed in 23 genera of penaeids. We employed the general mixed Yule coalescent (GMYC) model, the Poisson tree processes (PTP), and the Bayesian PTP model (bPTP) for MOTUs delimitation. Intraspecific and interspecific genetic distances were also calculated. Our findings evidenced a high level of hidden diversity, showing 143 MOTUs, with 27 nominal species not agreeing with the genetic delimitation obtained here. These data represent potential new species or highly structured populations, showing the importance of including a non-distance-based species delimitation approach in biodiversity studies. The results raised by this study shed light on the Penaeidae biodiversity, addressing important issues about taxonomy and mislabeling in databases and contributing to a better comprehension of the group, which can certainly help management policies for shrimp fishery activity in addition to conservation programs.

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Molecular diversity and species delimitation in the family Gasteruptiidae (Hymenoptera: Evanioidea)

Genome ◽

10.1139/gen-2019-0186 ◽

2020 ◽

pp. 1-12

Author(s):

Ben A. Parslow ◽

Michael P. Schwarz ◽

Mark I. Stevens

Keyword(s):

Species Delimitation ◽

Sequence Data ◽

Molecular Data ◽

Multiple Parameters ◽

Operational Taxonomic Units ◽

The Family ◽

Molecular Phylogenetic ◽

Taxonomic Uncertainty ◽

Traditional Taxonomy ◽

Morphological Species

Gasteruptiidae Ashmead is an easily recognised family of wasps with ∼589 described species worldwide. Although well characterised by traditional taxonomy, multiple authors have commented on the extreme morphological uniformity of the group, making species-level identification difficult. This problem is enhanced by the lack of molecular data and molecular phylogenetic research for the group. We used 187 cytochrome c oxidase subunit I (COI) barcodes to explore the efficiency of sequence data to delimitate species in Gasteruptiidae. We undertook a graphical and discussion-based comparison of six methods for species delimitation, with the success of methods judged based on known species boundaries and morphology. Both distance-based (ABGD and jMOTU threshold analysis) and tree-based (GMYC and PTP) methods compared across multiple parameters recovered variable molecular operational taxonomic units (MOTUs), ranging from 55 to 123 MOTUs. Tree-based methods tended to split known morphological species less than distance-based methods, with the single-threshold GMYC method the most concordant with known morphospecies. Our results suggest that the incorporation of molecular species delimitation techniques provides a powerful tool to assist in the interpretation of species and help direct informed decisions with taxonomic uncertainty in the family.

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Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology

PeerJ ◽

10.7717/peerj.3724 ◽

2017 ◽

Vol 5 ◽

pp. e3724 ◽

Cited By ~ 7

Author(s):

Ana C. Afonso Silva ◽

Natali Santos ◽

Huw A. Ogilvie ◽

Craig Moritz

Keyword(s):

Species Delimitation ◽

A Priori ◽

Integrated Approach ◽

Morphological Characters ◽

Integrative Taxonomy ◽

Gene Trees ◽

Separate Species ◽

Data Set ◽

Multispecies Coalescent ◽

Alternative Species

While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography, in an integrative taxonomy framework. Deep phylogeographic divergences have been reported for several species ofCarliaskinks, but only for some eastern taxa have species boundaries been formally tested. The present study does this and revises the taxonomy for two species from northern Australia,Carlia johnstoneiandC. triacantha. We introduce an approach that is based on the recently published method StarBEAST2, which uses multilocus data to explore the support for alternative species delimitation hypotheses using Bayes Factors (BFD). We apply this method, jointly with two other multispecies coalescent methods, using an extensive (from 2,163 exons) data set along with measures of 11 morphological characters. We use this integrated approach to evaluate two new candidate species previously revealed in phylogeographic analyses of rainbow skinks (genusCarlia) in Western Australia. The results based on BFD StarBEAST2, BFD* SNAPP and BPP genetic delimitation, together with morphology, support each of the four recently identifiedCarlialineages as separate species. The BFD StarBEAST2 approach yielded results highly congruent with those from BFD* SNAPP and BPP. This supports use of the robust multilocus multispecies coalescent StarBEAST2 method for species delimitation, which does not requirea prioriresolved species or gene trees. Compared to the situation inC. triacantha, morphological divergence was greater between the two lineages within Kimberley endemicC. johnstonei, which also had deeper divergent histories. This congruence supports recognition of two species withinC. johnstonei. Nevertheless, the combined evidence also supports recognition of two taxa within the more widespreadC. triacantha. With this work, we describe two new species,Carlia insularissp. nov andCarlia isostriacanthasp. nov. in the northwest of Australia. This contributes to increasing recognition that this region of tropical Australia has a rich and unique fauna.

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Species delimitation and phylogeny estimation under the multispecies coalescent

10.1101/010199 ◽

2014 ◽

Cited By ~ 12

Author(s):

Graham R Jones

Keyword(s):

Dna Sequences ◽

Species Delimitation ◽

A Priori ◽

Simulated Data ◽

Species Trees ◽

Data Set ◽

Multispecies Coalescent ◽

Multiple Loci ◽

Population Sizes ◽

Phylogeny Estimation

This article describes a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using DNA sequences from multiple loci. The focus here is on species delimitation with no a priori assignment of individuals to species, and no guide tree. The method uses a new model for the population sizes along the branches of the species tree, and three new operators for sampling from the posterior using the Markov chain Monte Carlo (MCMC) algorithm. The correctness of the moves is demonstrated both by proofs and by tests of the implementation. Current practice, using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data (Olave et al, 2014). The same simulated data set is used to demonstrate the accuracy and efficiency of the present method. The method is implemented in a package called STACEY for BEAST2.

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The Impact of Competitive Quasi-Market on Service Delivery in Benue State University, Makurdi Nigeria

GIS Business ◽

10.26643/gis.v14i4.5120 ◽

2019 ◽

Vol 14 (4) ◽

pp. 85-98

Author(s):

Idoko Peter

Keyword(s):

Service Delivery ◽

A Priori ◽

Least Square ◽

Secondary Source ◽

State University ◽

Ordinary Least Square ◽

Negative Effect ◽

The Impact ◽

The Relationship

This research the impact of competitive quasi market on service delivery in Benue State University, Makurdi Nigeria. Both primary and secondary source of data and information were used for the study and questionnaire was used to extract information from the purposively selected respondents. The population for this study is one hundred and seventy three (173) administrative staff of Benue State University selected at random. The statistical tools employed was the classical ordinary least square (OLS) and the probability value of the estimates was used to tests hypotheses of the study. The result of the study indicates that a positive relationship exist between Competitive quasi marketing in Benue State University, Makurdi Nigeria (CQM) and Transparency in the service delivery (TRSP) and the relationship is statistically significant (p<0.05). Competitive quasi marketing (CQM) has a negative effect on Observe Competence in Benue State University, Makurdi Nigeria (OBCP) and the relationship is not statistically significant (p>0.05). Competitive quasi marketing (CQM) has a positive effect on Innovation in Benue State University, Makurdi Nigeria (INVO) and the relationship is statistically significant (p<0.05) and in line with a priori expectation. This means that a unit increases in Competitive quasi marketing (CQM) will result to a corresponding increase in innovation in Benue State University, Makurdi Nigeria (INVO) by a margin of 22.5%. It was concluded that government monopoly in the provision of certain types of services has greatly affected the quality of service experience in the institution. It was recommended among others that the stakeholders in the market has to be transparent so that the system will be productive to serve the society effectively

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Frame me if you must: PrEP framing and the impact on adherence to HIV Pre-exposure Prophylaxis

Open Forum Infectious Diseases ◽

10.1093/ofid/ofx163.1113 ◽

2017 ◽

Vol 4 (suppl_1) ◽

pp. S439-S439

Author(s):

Eric Ellorin ◽

Jill Blumenthal ◽

Sonia Jain ◽

Xiaoying Sun ◽

Katya Corado ◽

...

Keyword(s):

A Priori ◽

Social Groups ◽

Continuous Measure ◽

Gay Community ◽

Randomized Controlled ◽

Exposure Prophylaxis ◽

The Impact ◽

Actual Prevalence ◽

Tenofovir Diphosphate

Abstract Background “PrEP whore” has been used both as a pejorative by PrEP opponents in the gay community and, reactively, by PrEP advocates as a method to reclaim the label from stigmatization and “slut-shaming.” The actual prevalence and impact of such PrEP-directed stigma on adherence have been insufficiently studied. Methods CCTG 595 was a randomized controlled PrEP demonstration project in 398 HIV-uninfected MSM and transwomen. Intracellular tenofovir-diphosphate (TFV-DP) levels at weeks 12 and 48 were used as a continuous measure of adherence. At study visits, participants were asked to describe how they perceived others’ reactions to them being on PrEP. These perceptions were categorized a priori as either “positively framed,” “negatively framed,” or both. We used Wilcoxon rank-sum to determine the association between positive and negative framing and TFV-DP levels at weeks 12 and 48. Results By week 4, 29% of participants reported perceiving positive reactions from members of their social groups, 5% negative, and 6% both. Reporting decreased over 48 weeks, but positive reactions were consistently reported more than negative. At week 12, no differences in mean TFV-DP levels were observed in participants with positively-framed reactions compared with those reporting no outcome or only negatively-framed (1338 [IQR, 1036-1609] vs. 1281 [946-1489] fmol/punch, P = 0.17). Additionally, no differences were observed in those with negative reactions vs. those without (1209 [977–1427] vs. 1303 [964–1545], P = 0.58). At week 48, mean TFV-DP levels trended toward being higher among those that report any reaction, regardless if positive (1335 [909–1665] vs. 1179 [841–1455], P = 0.09) or negative (1377 [1054–1603] vs. 1192 [838–1486], P = 0.10) than those reporting no reaction. At week 48, 46% of participants reported experiencing some form of PrEP-directed judgment, 23% reported being called “PrEP whore,” and 21% avoiding disclosing PrEP use. Conclusion Over 48 weeks, nearly half of participants reported some form of judgment or stigmatization as a consequence of PrEP use. However, individuals more frequently perceived positively framed reactions to being on PrEP than negative. Importantly, long-term PrEP adherence does not appear to suffer as a result of negative PrEP framing. Disclosures All authors: No reported disclosures.

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Using Unstated Cases to Correct for COVID-19 Pandemic Outbreak and Its Impact on Easing the Intervention for Qatar

Biology ◽

10.3390/biology10060463 ◽

2021 ◽

Vol 10 (6) ◽

pp. 463

Author(s):

Narjiss Sallahi ◽

Heesoo Park ◽

Fedwa El Mellouhi ◽

Mustapha Rachdi ◽

Idir Ouassou ◽

...

Keyword(s):

Public Health ◽

A Priori ◽

Epidemiological Models ◽

Sir Epidemic Model ◽

Gulf Region ◽

Epidemiological Modeling ◽

Public Health Policies ◽

Sir Epidemic ◽

The Impact ◽

Case Data

Epidemiological Modeling supports the evaluation of various disease management activities. The value of epidemiological models lies in their ability to study various scenarios and to provide governments with a priori knowledge of the consequence of disease incursions and the impact of preventive strategies. A prevalent method of modeling the spread of pandemics is to categorize individuals in the population as belonging to one of several distinct compartments, which represents their health status with regard to the pandemic. In this work, a modified SIR epidemic model is proposed and analyzed with respect to the identification of its parameters and initial values based on stated or recorded case data from public health sources to estimate the unreported cases and the effectiveness of public health policies such as social distancing in slowing the spread of the epidemic. The analysis aims to highlight the importance of unreported cases for correcting the underestimated basic reproduction number. In many epidemic outbreaks, the number of reported infections is likely much lower than the actual number of infections which can be calculated from the model’s parameters derived from reported case data. The analysis is applied to the COVID-19 pandemic for several countries in the Gulf region and Europe.

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Survey Data Quality in Analyzing Harmonized Indicators of Protest Behavior: A Survey Data Recycling Approach

American Behavioral Scientist ◽

10.1177/00027642211021623 ◽

2021 ◽

pp. 000276422110216

Author(s):

Kazimierz M. Slomczynski ◽

Irina Tomescu-Dubrow ◽

Ilona Wysmulek

Keyword(s):

Data Processing ◽

Data Quality ◽

Survey Data ◽

A Priori ◽

Data Sets ◽

New Approach ◽

Survey Quality ◽

Survey Error ◽

Ex Post ◽

The Impact

This article proposes a new approach to analyze protest participation measured in surveys of uneven quality. Because single international survey projects cover only a fraction of the world’s nations in specific periods, researchers increasingly turn to ex-post harmonization of different survey data sets not a priori designed as comparable. However, very few scholars systematically examine the impact of the survey data quality on substantive results. We argue that the variation in source data, especially deviations from standards of survey documentation, data processing, and computer files—proposed by methodologists of Total Survey Error, Survey Quality Monitoring, and Fitness for Intended Use—is important for analyzing protest behavior. In particular, we apply the Survey Data Recycling framework to investigate the extent to which indicators of attending demonstrations and signing petitions in 1,184 national survey projects are associated with measures of data quality, controlling for variability in the questionnaire items. We demonstrate that the null hypothesis of no impact of measures of survey quality on indicators of protest participation must be rejected. Measures of survey documentation, data processing, and computer records, taken together, explain over 5% of the intersurvey variance in the proportions of the populations attending demonstrations or signing petitions.

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Implementation of a Rapid Phenotypic Susceptibility Platform for Gram-Negative Bloodstream Infections With Paired Antimicrobial Stewardship Intervention: Is the Juice Worth the Squeeze?

Clinical Infectious Diseases ◽

10.1093/cid/ciab126 ◽

2021 ◽

Author(s):

Evan D Robinson ◽

Allison M Stilwell ◽

April E Attai ◽

Lindsay E Donohue ◽

Megan D Shah ◽

...

Keyword(s):

Median Time ◽

Antimicrobial Stewardship ◽

A Priori ◽

Bloodstream Infections ◽

Standard Of Care ◽

Post Intervention ◽

Gram Negative ◽

Stewardship Program ◽

Days Of Therapy ◽

The Impact

Abstract Background Implementation of the Accelerate PhenoTM Gram-negative platform (RDT) paired with antimicrobial stewardship program (ASP) intervention projects to improve time to institutional-preferred antimicrobial therapy (IPT) for Gram-negative bacilli (GNB) bloodstream infections (BSIs). However, few data describe the impact of discrepant RDT results from standard of care (SOC) methods on antimicrobial prescribing. Methods A single-center, pre-/post-intervention study of consecutive, nonduplicate blood cultures for adult inpatients with GNB BSI following combined RDT + ASP intervention was performed. The primary outcome was time to IPT. An a priori definition of IPT was utilized to limit bias and to allow for an assessment of the impact of discrepant RDT results with the SOC reference standard. Results Five hundred fourteen patients (PRE 264; POST 250) were included. Median time to antimicrobial susceptibility testing (AST) results decreased 29.4 hours (P < .001) post-intervention, and median time to IPT was reduced by 21.2 hours (P < .001). Utilization (days of therapy [DOTs]/1000 days present) of broad-spectrum agents decreased (PRE 655.2 vs POST 585.8; P = .043) and narrow-spectrum beta-lactams increased (69.1 vs 141.7; P < .001). Discrepant results occurred in 69/250 (28%) post-intervention episodes, resulting in incorrect ASP recommendations in 10/69 (14%). No differences in clinical outcomes were observed. Conclusions While implementation of a phenotypic RDT + ASP can improve time to IPT, close coordination with Clinical Microbiology and continued ASP follow up are needed to optimize therapy. Although uncommon, the potential for erroneous ASP recommendations to de-escalate to inactive therapy following RDT results warrants further investigation.

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