Towards an integrative taxonomy ofPhyllopsora(Ramalinaceae)

2019 ◽  
Vol 51 (4) ◽  
pp. 323-392 ◽  
Author(s):  
Sonja KISTENICH ◽  
Mika BENDIKSBY ◽  
Stefan EKMAN ◽  
Marcela E. S. CÁCERES ◽  
Jesús E. HERNÁNDEZ M. ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Integrative Approach ◽  
Gene Trees ◽  
Multiple Sources ◽  
Type Specimens ◽  
Secondary Chemistry ◽  
Sister Relationships

AbstractSpecies identification in the tropical lichen genusPhyllopsorais generally challenging and is based on ascospore morphology, vegetative dispersal units, thallus structure and secondary chemistry. As several type specimens are in poor condition and difficult to interpret, it is often unclear how these old names fit with the currently used taxonomy. In the present study, we aim to identify species boundaries inPhyllopsoras. str. supported by an integrative approach using multiple sources of evidence. We investigated a substantial amount of herbarium as well as freshly collected material and generated mtSSU and ITS sequence data from most of the described species, including several types. Species delimitation analyses are applied on the gene trees using mPTP and we construct a species tree of both markers with *BEAST, facilitating discussion of species delimitation and sister-relationships. Comparing morphology, chemistry and molecular data, we found that the mPTP analyses split established species repeatedly. Based on our integrative results, we exclude nine species from the genus, resurrect one (P. melanoglaucaZahlbr.), reduce two into synonymy with otherPhyllopsoraspecies and describe five as new to science:Phyllopsora amazonicaKistenich & Timdal (which shares the secondary chemistry (atranorin and terpenoid pattern) withP. haleichemotype 1, but differs, e.g., in having smaller areolae that are attached to a thinner, white prothallus, and in having more persistently marginate and less convex apothecia),Phyllopsora concinnaKistenich & Timdal (which shares the secondary chemistry (atranorin and parvifoliellin) withP. parvifoliellaandP. rappiana, but differs from both in forming larger isidia, having a white prothallus, apothecial margin paler than the disc, and longer and broader ascospores),Phyllopsora furfurellaKistenich & Timdal (which is here segregated fromP. furfuraceabased on having a white prothallus and in containing skyrin in the hypothecium (K+ red)),Phyllopsora isidosaKistenich & Timdal (which differs fromP. byssisedain forming a more crustose thallus with more delicate isidia, and fromP. isidiotylain forming somewhat coarser, less branched isidia) andPhyllopsora neotinicaKistenich & Timdal (a neotropical species here segregated from the now exclusively paleotropicalP. chodatinica, differing in containing an unknown xanthone (not chodatin)). Lectotypes are designated forBiatora pyrrhomelaenaTuck.,Lecidea leucophyllinaNyl.,L. pertextaNyl., andP. brachysporaMüll. Arg. In total, we accept 54 species in the genusPhyllopsora.

Species delimitation and nematode biodiversity: phylogenies rule

Nematology ◽  
2002 ◽  
Vol 4 (5) ◽  
pp. 615-625 ◽  
Author(s):  
Steven Nadler
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Molecular Data ◽  
Gene Trees ◽  
California Sea Lions ◽  
Separate Species ◽  
Nucleotide Sequence Data ◽  
Sea Lions ◽  
Multiple Loci ◽  
Fur Seals

AbstractPractitioners of nematode taxonomy have rarely been explicit about what species represent or how data are being used to delimit species prior to their description. This lack of explicitness reflects the broader species problem common to all biology: there is no universally accepted idea of what species are and, as a consequence, scientists disagree on how to go about finding species in nature. However, like other biologists, nematologists seem to agree that species are real and discrete units in nature, and that they result from descent with modification. This evolutionary perspective provides a conceptual framework for nematologists to view species as independent evolutionary lineages, and provides approaches for their delimitation. Specifically, species may be delimited scientifically by methods that can test the hypothesis of lineage independence. For sequence data, such hypothesis testing should be based on sampling many individual organisms for multiple loci to avoid mistaking tokogeny and gene trees as evidence of species. Evolutionary approaches to analysing data and delimiting species avoid the inherent pitfalls in approaches that use all observed sequence differences to define species through calculation of a genetic distance. To illustrate evolutionary species delimitation, molecular data are used to test the hypothesis that hookworms parasitic in northern fur seals and in California sea lions represent separate species. The advantages and potential caveats of employing nucleotide sequence data for species delimitation are discussed, and the merits of evolutionary approaches are contrasted to inherent problems in similarity-based methods.

scholarly journals Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

2019 ◽  
Vol 42 (1) ◽  
pp. 75-100 ◽  
Author(s):  
C.G. Boluda ◽  
V.J. Rico ◽  
P.K. Divakar ◽  
O. Nadyeina ◽  
L. Myllys ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Delimitation ◽  
Sequence Data ◽  
Species Recognition ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Haplotype Network ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Molecular Sequence Data

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

scholarly journals Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)

2018 ◽  
Vol 32 (6) ◽  
pp. 1298 ◽  
Author(s):  
Feng Zhang ◽  
Daoyuan Yu ◽  
Mark I. Stevens ◽  
Yinhuan Ding
Keyword(s):  
Species Complex ◽  
Instar Larva ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Species Level ◽  
Integrative Approach ◽  
Gene Markers ◽  
Late Neogene ◽  
Taxonomic Approach ◽  
Colour Patterns

Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.

Species delimitation of the northeastern Anatolian Symphytum (Boraginaceae) taxa

Phytotaxa ◽  
2021 ◽  
Vol 516 (3) ◽  
Author(s):  
KURTULUŞ ÖZGİŞİ ◽  
BURCU TARIKAHYA-HACIOĞLU
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Infrageneric Classification ◽  
Number Of Species ◽  
Morphological Studies ◽  
Statistical Parsimony ◽  
Taxonomical Status ◽  
Parsimony Network Analysis

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.

Multi-instar descriptions of cave dwelling Erythraeidae (Trombidiformes: Parasitengona) employing an integrative approach

Zootaxa ◽  
2019 ◽  
Vol 4717 (1) ◽  
pp. 137-184 ◽  
Author(s):  
SAMUEL GEREMIAS DOS SANTOS COSTA ◽  
HANS KLOMPEN ◽  
LEOPOLDO FERREIRA DE OLIVEIRA BERNARDI ◽  
LUCIANA CARDOSO GONÇALVES ◽  
DANTE BATISTA RIBEIRO ◽  
...  
Keyword(s):  
Life Cycle ◽  
Cytochrome Oxidase ◽  
Molecular Analysis ◽  
Species Delimitation ◽  
Morphological Changes ◽  
Molecular Data ◽  
Coi Gene ◽  
Integrative Approach ◽  
Larval Instars ◽  
Individual Host

The life cycle of Parasitengona includes major morphological changes precluding an instar association based only on the morphology. This makes rearing and/or molecular data necessary to associate the heteromorphic instars. Most of the described species are known from either post larval instars or larva. Following a previous study on Palearctic Erythraeidae, in the present study the instar association was made through an integrative approach including rearing trials and molecular analysis of the cytochrome oxidase I (COI) gene with the Bayesian Generalized Mixed Yule Coalescent (bGMYC) algorithm for species delimitation. Two new cave dwelling Erythraeidae (Trombidiformes: Parasitengona) species are described Lasioerythraeus jessicae sp. nov. and Leptus sidorchukae sp. nov. including all active instars. Additionally, a complete description of the previously unknown adults of Charletonia rocciai Treat & Flechtmann, 1979 is provided with notes on the larva and deutonymph. We also demonstrate experimentally that Ch. rocciai larvae are not attached to the same individual host during the entire feeding stage. We discuss the presence of troglomorphisms in Le. sidorchukae sp. nov.; and the distribution of the species. 

A revision of the genus Seligeria (Seligeriaceae, Bryophyta) in Russia inferred from molecular data

Phytotaxa ◽  
2017 ◽  
Vol 323 (1) ◽  
pp. 27 ◽  
Author(s):  
VLADIMIR E. FEDOSOV ◽  
ALINA V. FEDOROVA ◽  
ELENA A. IGNATOVA ◽  
MICHAEL S. IGNATOV
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Phylogenetic Group ◽  
Undescribed Species ◽  
Dna Sequence Data ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Sister Relationships ◽  
Central Strand

The genus Seligeria is revised based on morphological and DNA sequence data of nuclear ITS and chloroplastic trnL-F. Fifteen species from most infrageneric units of the genus are recovered in two well supported phylogenetic clusters that are also distinctive in morphology. The clade with the type species of the genus, S. pusilla, includes also S. donniana, S. brevifolia, S. calcarea, S. patula, S. tristichoides, S. trifaria, and S. oelandica. These species are characterized by short, cupulate or turbinate capsules widened towards the mouth, and the lack of a stem central strand. Another clade includes species with rather long, mainly ovate to cylindrical capsules and more or less developed stem central strand: S. campylopoda, S. recurvata, S. subimmersa, S. diversifolia, and S. polaris. These two clusters do not show sister relationships, but the second one appears more closely related to the Blindia clade. To resolve the apparent paraphyly, the latter phylogenetic group is segregated in a genus Blindiadelphus. In some aspects of morphology and ecology it is intermediate between Seligeria s. str. and Blindia, but differs from both genera in subquadrate upper leaf cells and thin- to moderately thick-walled rectangular exothecial cells. Molecular phylogenetic analyses revealed heterogeneity within the specimens previously referred to Blindiadelphus campylopodus, indicating a presence in Asian Russia of an undescribed species that is described here as Blindiadelphus sibiricus. It differs from B. campylopodus by the larger spores and typically rounded leaf apices. The isotype specimen of S. galinae appeared to be nearly identical to S. donniana in the sequences of ITS and trnL-F, and examination of morphology revealed no substantial differences between these species. Thus, we consider S. galinae as a synonym of S. donniana. The genus Blindiadelphus includes species of Seligeria subg. Blindiadelphus and S. subg. Cyrtoseligeria, which however are found intermingled in the molecular phylogenetic analysis. Thus the genus Blindiadelphus is accepted without any infrageneric taxa. The phylogenetic tree is congruent with the subdivision of the genus Seligeria s.str into subg. Seligeria, subg. Anodon, subg. Megalosporia and one newly established subgenus Robustidontia for S. brevifolia.

scholarly journals Perlidae (Plecoptera) from the Paranapiacaba Mountains, Atlantic Forest, Brazil: Diversity and implications of the integrative approach and teneral specimens on taxonomy

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243393
Author(s):  
Lucas Henrique de Almeida ◽  
Pitágoras da Conceição Bispo
Keyword(s):  
New Record ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Coi Gene ◽  
Southeastern Brazil ◽  
Integrative Approach ◽  
South American ◽  
Neighbor Joining ◽  
Previous Record ◽  
Coi Sequences

The study of complementary sources of biological variation (e.g. morphological, molecular) has allowed a better understanding of biodiversity through the construction of an integrative taxonomy. Using this approach, specimens from the Paranapiacaba Mountains, southeastern Brazil, were studied to update the knowledge on the stonefly family Perlidae from the region, characterize the species, and make associations between nymphs and adults using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. The study also discusses the implications of integrative taxonomy and teneral specimens for the study of South American Perlidae. The molecular data were analyzed using Bayesian inference, Neighbor-joining, and delimiting species methods. Our results revealed that, in general, there was a morphological and molecular congruence between species. In the Paranapiacaba Mountains, three genera and 15 species were recorded: Anacroneuria boraceiensis Froehlich 2004, A. debilis (Pictet 1841) (new record), A. fiorentini De Ribeiro and Froehlich 2007 (new record), A. flintorum Froehlich 2002, A. iporanga Bispo and Froehlich 2004, A. itajaimirim Bispo and Froehlich 2004, A. polita (Burmeister 1913), A. subcostalis Klapálek 1921, A. tupi Bispo and Froehlich 2004 (with a description of the nymph), Kempnyia auberti Froehlich 1996, K. colossica (Navás 1934), K. flava Klapálek 1916, K. neotropica (Jacobson and Bianchi 1905) (including its new junior synonym K. petersorum Froehlich 1996), Kempnyia sp., and Macrogynoplax veneranda Froehlich 1984. COI sequences were obtained for 11 species, five of which had nymphs associated with adults. Among the five associated nymphs, the nymph of A. tupi is described here. The results of this study indicate that the color of adult teneral specimens differs from that of mature specimens. Given this, the synonym of K. neotropica and K. petersorum was proposed since these species have high morphological and molecular similarities and differ only in color patterns. In addition, the previous record of A. petersi Froehlich 2002 from the Paranapiacaba Mountains was invalidated since it was considered a teneral specimen of A. flintorum. These results suggest that the development of an integrative taxonomy is essential to continue advancing the study of Perlidae diversity in South America.

Guidelines for DNA barcoding of coralline algae, focusing on Lithophylloideae (Corallinales) from Brazil

2018 ◽  
Vol 61 (2) ◽  
pp. 127-140 ◽  
Author(s):  
Beatriz N. Torrano-Silva ◽  
Bruno R. Vieira ◽  
Rafael Riosmena-Rodríguez ◽  
Mariana C. Oliveira
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Morphological Traits ◽  
Dna Barcode ◽  
Molecular Data ◽  
Coralline Algae ◽  
Integrative Approach ◽  
Interspecific Divergence ◽  
Algorithmic Approaches ◽  
Barcode Gap

AbstractMultiple-marker (COI-5P, UPA,psbA andrbcL-3P) and two algorithmic approaches [automatic barcode gap discovery (ABGD) and Poisson tree process (PTP)] were used for species delimitation of Lithophylloideae in Brazil. The integrative approach was mostly congruent between markers and algorithmic methods of species delimitation, suggesting the occurrence of 24 species. Based on morphology and molecular data,Amphiroa rigida,Amphiroa vanbosseae,Lithophyllum atlanticum,Lithophyllum kaiseri,Lithophyllum margaritae,Titanoderma pustulatum,Titanoderma prototypumandPaulsilvella huveorum, which were previously reported for Brazil, are confirmed in this work. Six new species are distinguished by both molecular and morphological traits, and they are provisionally named asAmphiroasp. 1,Amphiroasp. 2,Amphiroasp. 3,Lithophyllumsp. 1,Lithophyllumsp. 2 andLithophyllumsp. 3. Another 10 species are cryptic and cannot be distinguished based on traditionally used morphological traits. These includeAmphiroasp. 4,Lithophyllumsp. 4, three species that are morphologically named underAmphiroa beauvoisii, and six that share the morphology described forAmphiroa fragilissima. All four markers used were useful for species delimitation. However, a combination of practical aspects and levels of intra- and interspecific divergence values led us to propose the use ofrbcL-3P as a standard DNA barcode marker for the Corallinales.

Discovery of the second European Amalopis species: an integrative survey of the widespread Pedicia (Amalopis) occulta (Meigen, 1830) (Insecta, Diptera, Pediciidae)

Zootaxa ◽  
2012 ◽  
Vol 3189 (1) ◽  
pp. 1 ◽  
Author(s):  
LUJZA UJVÁROSI ◽  
MIKLÓS BÁLINT
Keyword(s):  
Sequence Data ◽  
Far East ◽  
Sequence Divergence ◽  
Integrative Taxonomy ◽  
Type Specimens ◽  
Species Discovery ◽  
Dna Sequence Data ◽  
Close Relationship ◽  
Male Genital ◽  
Comprehensive Study

Integrative taxonomy enhances species discovery and facilitates species delimitation by combining DNA sequence data,morphology, and distributional and ecological information. In this paper we use complementary methods of morphologyand DNA barcoding to delineate species boundaries in a widespread European spring-dwelling crane-fly, Pedicia (Amalo-pis) occulta (Meigen). We describe a previously overlooked large cryptic dipteran as Pedicia (Amalopis) fusca n. sp. Wealso designate the lectotype of P. occulta of the basis of a comprehensive study of relevant type specimens. Morphologicaldifferences between the two species are delicate but detectable, and comprise mostly male genital structures. However,the sequence divergence of 13.1% reflects an ancient divergence, which plausibly pre-dates the Pleistocene. The EuropeanAmalopis species differ significantly from all the rest of Amalopis species with Far East distributions, but share a numberof similarities with a species identified from the Himalayas, India and described as Pedicia (Tricyphona) ericarum Alexander, 1966. We also discuss a possible close relationship between P. ericarum and the European Amalopis species.

scholarly journals Taxonomic resolution of Stylonychia notophora (Alveolata, Ciliophora, Hypotricha) sensu Sapra and Dass 1970 using an integrative approach

2020 ◽  
Vol 70 (6) ◽  
pp. 3939-3952
Author(s):  
Harpreet Kaur ◽  
Shashi ◽  
Alan Warren ◽  
Ram Krishan Negi ◽  
Komal Kamra
Keyword(s):  
18S Rdna ◽  
Species Delimitation ◽  
Indian Population ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Taxonomic Resolution ◽  
Integrative Approach ◽  
Rdna Sequences ◽  
18S Rdna Sequences ◽  
River Yamuna

The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although the descriptions are lacking in detail. It has been suggested several times that the Indian population, S. notophora sensu Sapra and Dass, 1970 collected along the Delhi stretch of the River Yamuna, is identical to Tetmemena pustulata, but this has never been confirmed due to insufficient data for the former. The present study includes detailed descriptions (classical and molecular) of populations of Tetmemena isolated from six locations along the River Yamuna, India. These include four from the Delhi stretch including that from which Sapra and Dass, 1970 isolated their population of S. notophora. Due to the lack of a sufficiently detailed description, the taxonomic status of S. notophora sensu Sapra and Dass, 1970 was not clear. Comparisons among the populations isolated in the present study with previous descriptions of T. pustulata and S. notophora sensu Sapra and Dass, 1970 show only minor differences in morphometry, morphogenesis and in 18S rDNA sequences. The 18S rDNA sequences of all six populations had 99% similarity to both T. pustulata and S. notophora. These findings support the contention that S. notophora sensu Sapra and Dass, 1970 was misidentified and is a population of T. pustulata. This study supports the need for adopting an integrative approach based on morphological, morphogenetic and molecular data in order to understand species delimitation in ciliated protists.

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