Journal articles: 'Molecular species delimitation'

1

Košuthová, Alica, Martin Westberg, Mónica A. G. Otálora, and Mats Wedin. "Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes)." MycoKeys 47 (February 20, 2019): 17–33. http://dx.doi.org/10.3897/mycokeys.47.32227.

Full text

Abstract:

Here, we test the current generic delimitation of Rostania (Collemataceae, Peltigerales, Ascomycota) utilizing molecular phylogeny and morphological investigations. Using DNA sequence data from the mitochondrial SSU rDNA and two nuclear protein-coding genes (MCM7 and β-tubulin) and utilizing parsimony, maximum likelihood and Bayesian phylogenetic methods, Rostania is shown to be non-monophyletic in the current sense. A new generic delimitation of Rostania is thus proposed, in which the genus is monophyletic, and three species (Rostaniacoccophylla, R.paramensis, R.quadrifida) are excluded and transferred to other genera. Rostaniaoccultata is further non-monophyletic, and a more detailed investigation of species delimitations in Rostania s. str. is needed. The new combinations Leptogiumparamense and Scytiniumquadrifidum are proposed.

APA, Harvard, Vancouver, ISO, and other styles

2

Najafian, Sakine, Iraj Mehregan, Alireza Iranbakhsh, Mostafa Assadi, and Silvio Fici. "Species delimitation in Capparis (Capparaceae): Morphological and molecular." Genetika 53, no. 2 (2021): 609–27. http://dx.doi.org/10.2298/gensr2102609n.

Full text

Abstract:

Capparis spinosa L. (Capparidaceae) is the largest genus of the family Capparaceae, distributed in pantropical region. C. spinosa is known as a medicinal plant species. In Iran, different parts of caper bush plants are used as diuretics, tonics and in treatment of malaria and joint disease. Till present time, there has been no detailed information available on molecular phylogeny and genetic structure of these species in the country. Therefore, the present study was conducted with the aim to investigate species delimitation by both morphological and molecular data and to reveal genetic diversity and population structure in these five of Capparis species. For this study, 108 randomly collected plants from 20 geographical populations in of Capparis species were used. We encountered extensive within species genetic and morphological diversity. ISSR molecular markers could delimit the studied species. STRUCTURE analysis revealed the occurrence gene flow between these species. The Mantel test showed correlation between genetic distance and geographical distance of the populations studied. Phylogenetic tree was constructed based on ITS data set which separated out-groups from the studied species. Genetic affinity of the studied species have been discussed.

APA, Harvard, Vancouver, ISO, and other styles

3

Khodami, Sahar, Pedro Martinez Arbizu, Sabine Stöhr, and Silke Laakmann. "Molecular Species Delimitation of Icelandic Brittle Stars (Ophiuroidea)." Polish Polar Research 35, no. 2 (July 29, 2014): 243–60. http://dx.doi.org/10.2478/popore-2014-0011.

Full text

Abstract:

Abstract Brittle stars (Echinodermata: Ophiuroidea) comprise over 2, 000 species, all of which inhabit marine environments and can be abundant in the deep sea. Morphological plasticity in number and shape of skeletal parts, as well as variable colors, can complicate correct species identification. Consequently, DNA sequence analysis can play an important role in species identification. In this study we compared the genetic variability of the mitochondrial cytochrome c subunit I gene (COI) and the nuclear small subunit ribosomal DNA (SSU, 18S rDNA) to morphological identification of 66 specimens of 11 species collected from the North Atlantic in Icelandic waters. Also two species delimitation tools, Automatic Barcode Gap Discovery (ABGD) and General Mixed Yule Coalescence Method (GMYC) were performed to test species hypotheses. The analysis of both gene fragments was successful to discriminate between species and provided new insights into some morphological species hypothesis. Although less divergent than COI, it is helpful to use the SSU region as a complementary fragment to the barcoding gene.

APA, Harvard, Vancouver, ISO, and other styles

4

Chroni, A., M. Djan, D. Obreht Vidaković, T. Petanidou, and A. Vujić. "Molecular species delimitation in the genusEumerus(Diptera: Syrphidae)." Bulletin of Entomological Research 107, no. 1 (August 30, 2016): 126–38. http://dx.doi.org/10.1017/s0007485316000729.

Full text

Abstract:

AbstractEumerusis one of the most diverse genera of hoverfly worldwide. Species delimitation within genus is considered to be difficult due to: (a) lack of an efficient key; (b) non-defined taxonomical status of a large number of species; and (c) blurred nomenclature. Here, we present the first molecular study to delimit species of the genus by using a fragment of the mitochondrial cytochrome-c oxidase subunit I gene (COI) gene. We assessed 75 specimens assigned to 28 taxa originating from two biogeographic zones: 22 from the western Palaearctic and six from the Afrotropical region. Two datasets were generated based on different sequence lengths to explore the significance of availability of more polymorphic sites for species delimitation; dataset A with a total length of 647 bp and dataset B with 746 bp. Various tree inference approaches and Poisson tree processes models were applied to evaluate the putative ‘taxonomical’ vs. ‘molecular’ taxa clusters. All analyses resulted in high taxonomic resolution and clear species delimitation for both the dataset lengths. Furthermore, we revealed a high number of mitochondrial haplotypes and high intraspecific variability. We report two major monophyletic clades, and seven ‘molecular’ groups of taxa formed, which are congruent with morphology-based taxonomy. Our results support the use of the mitochondrial COI gene in species diagnosis ofEumerus.

APA, Harvard, Vancouver, ISO, and other styles

5

Özgişi, Kurtuluş, Burcu Tarıkahya-Hacıoğlu, and Atilla Ocak. "Species delimitation in Noccaea densiflora species complex (Brassicaceae) based on morphological and molecular data." Botany 99, no. 7 (July 2021): 389–402. http://dx.doi.org/10.1139/cjb-2020-0184.

Full text

Abstract:

The accurate identification of an organism is the basis of all biological disciplines. Although there have been many different species concepts and methods proposed, researchers generally choose the most appropriate concept according to their interests. However, each species concept has both advantages and disadvantages. In such cases, an integrated concept based on evidence obtained from different species concepts and methods is suitable for the accurate delimitation of a species. The biggest dilemma of integrated species delimitation methods is the inconsistency between species concepts and methods. Herein, the congruency of the different concepts and methods was tested to reveal the relationship of the Noccaea densiflora species complex. Nuclear ribosomal internal transcribed spacer, chloroplast trnL-F, and trnQ-5′rps16 regions were used for species delimitation using the multispecies coalescent model as implemented in two developed Bayesian methods. Internal transcribed spacer and trnL-F regions were also used for Templeton, Crandall, and Singh haplotype network analyses. In addition to morphological measurements from different populations and vouchers, specific bioclimatic data values were also used for the principal component analysis. Based on the analyses, it was determined that only one population of N. densiflora (Boiss. & Kotschy) F.K. Mey. and one of Noccaea microstyla (Boiss.) F.K. Mey. were clearly distinct, whereas the rest of the specimens remain taxonomically uncertain.

APA, Harvard, Vancouver, ISO, and other styles

6

Ellepola, Gajaba, Jayampathi Herath, Kelum Manamendra-Arachchi, Nayana Wijayathilaka, Gayani Senevirathne, Rohan Pethiyagoda, and Madhava Meegaskumbura. "Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae)." PLOS ONE 16, no. 10 (October 19, 2021): e0258594. http://dx.doi.org/10.1371/journal.pone.0258594.

Full text

Abstract:

Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA–Rag-1; mt-DNA– 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island’s aseasonal ‘wet zone’ and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges–ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.

APA, Harvard, Vancouver, ISO, and other styles

7

Esfandani Bozchaloyi, S., M. Sheidai, M. Keshavarzi, and Z. Noormohammadi. "Species delimitation in Geranium sect. Batrachioidea: morphological and molecular." Acta Botanica Hungarica 59, no. 3-4 (September 2017): 319–34. http://dx.doi.org/10.1556/034.59.2017.3-4.3.

Full text

APA, Harvard, Vancouver, ISO, and other styles

8

Barcenas-Peña, Alejandrina, Steven D. Leavitt, Felix Grewe, and H. Thorsten Lumbsch. "Diversity of Xanthoparmelia (Parmeliaceae) species in Mexican xerophytic scrub vegetation, evidenced by molecular, morphological and chemistry data." Anales del Jardín Botánico de Madrid 78, no. 1 (June 15, 2021): e107. http://dx.doi.org/10.3989/ajbm.2564.

Full text

Abstract:

The genus Xanthoparmelia is the largest genus of lichen- forming fungi with about 800 species worldwide. Xanthoparmelia is also common in the deserts of central Mexico, but only a few molecular studies exist on its species’ diversity in this region. In this study, we sampled 38 Xanthoparmelia species from around the world including species from the xerophytic scrubs of central Mexico to assess the diversity using an integrative approach. Molecular phylogenetic analyses were performed using a combination of the ITS, mtSSU and nuLSU genetic markers. We evaluated our phylogenetic results in a context of traditional morphological and chemical characters. The combined evidence of molecular, morphological, and chemical data identified a total of 18 Xanthoparmelia species-level lineages occurring in central Mexico. However, numerous traditionally circumscribed species did not form monophyletic groups in the molecular phylogenetic reconstructions. This conflict indicates that taxonomy and species delimitation in the genus Xanthoparmelia requires revision and emphasizes the importance of molecular evidence for more robust species delimitations in this genus.

APA, Harvard, Vancouver, ISO, and other styles

9

Singh, Sohana P., Johan C. Groeneveld, Abdulaziz Al-Marzouqi, and Sandi Willows-Munro. "A molecular phylogeny of the spiny lobster Panulirus homarus highlights a separately evolving lineage from the Southwest Indian Ocean." PeerJ 5 (May 25, 2017): e3356. http://dx.doi.org/10.7717/peerj.3356.

Full text

Abstract:

Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.

APA, Harvard, Vancouver, ISO, and other styles

10

Nolasco, Samuel, and Alejandro Valdez-Mondragón. "To be or not to be… Integrative taxonomy and species delimitation in the daddy long-legs spiders of the genus Physocyclus (Araneae, Pholcidae) using DNA barcoding and morphology." ZooKeys 1135 (December 12, 2022): 93–118. http://dx.doi.org/10.3897/zookeys.1135.94628.

Full text

Abstract:

Integrative taxonomy is crucial for discovery, recognition, and species delimitation, especially in underestimated species complex or cryptic species, by incorporating different sources of evidence to construct rigorous species hypotheses. The spider genus Physocyclus Simon, 1893 (Pholcidae, Arteminae) is composed of 37 species, mainly from North America. In this study, traditional morphology was compared with three DNA barcoding markers regarding their utility in species delimitation within the genus: 1) Cytochrome c Oxidase subunit 1 (CO1), 2) Internal Transcribed Spacer 2 (ITS2), and 3) Ribosomal large subunit (28S). The molecular species delimitation analyses were carried out using four methods under the corrected p-distances Neighbor-Joining (NJ) criteria: 1) Automatic Barcode Gap Discovery (ABGD), 2) Assemble Species by Automatic Partitioning (ASAP), 3) General Mixed Yule Coalescent model (GMYC), and 4) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 75 terminals from 22 putative species of Physocyclus. The average intraspecific genetic distance (p-distance) was found to be < 2%, whereas the average interspecific genetic distance was 20.6%. The ABGD, ASAP, and GMYC methods were the most congruent, delimiting 26 or 27 species, while the bPTP method delimited 33 species. The use of traditional morphology for species delimitation was congruent with most molecular methods, with the male palp, male chelicerae, and female genitalia shown to be robust characters that support species-level identification. The barcoding with CO1 and 28S had better resolution for species delimitation in comparison with ITS2. The concatenated matrix and traditional morphology were found to be more robust and informative for species delimitation within Physocyclus.

APA, Harvard, Vancouver, ISO, and other styles

11

Edwards, Danielle L., and L. Lacey Knowles. "Species detection and individual assignment in species delimitation: can integrative data increase efficacy?" Proceedings of the Royal Society B: Biological Sciences 281, no. 1777 (February 22, 2014): 20132765. http://dx.doi.org/10.1098/rspb.2013.2765.

Full text

Abstract:

Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning individuals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation—species detection and individual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how individuals are initially assigned, and the practices and statistical issues surrounding individual assignment warrant careful consideration.

APA, Harvard, Vancouver, ISO, and other styles

12

Li, Dengqing, Zhaoyang Chen, Fengxiang Liu, Daiqin Li, and Xin Xu. "An integrative approach reveals high species diversity in the primitively segmented spider genus." Invertebrate Systematics 36, no. 2 (February 22, 2022): 160–98. http://dx.doi.org/10.1071/is21058.

Full text

Abstract:

Accurate species delimitation is crucial for our understanding of evolution, biodiversity and conservation. However, morphology-based species delimitation alone appears to be prone to taxonomic errors and ineffective for taxa with high interspecific morphological homogeneity or intraspecific morphological variations, as is the case for mesothele and mygalomorph spiders. Combined molecular–morphology species delimitation has shown great potential to delimit species boundaries in such ancient lineages. In the present study, molecular and morphological evidence were integrated to delimit species of the primitively segmented spider genus Songthela Ono, 2000. The cytochrome c oxidase subunit I gene (COI) was sequenced for 192 novel specimens belonging to 12 putative morphospecies. The evolutionary relationships within Songthela and the 12-morphospecies hypothesis were tested in two steps – species discovery and species validation – using four single-locus species delimitation approaches. All species delimitation analyses supported the 12-species hypothesis. Phylogenetic analyses yielded three major clades in Songthela, which are consistent with morphology. Accordingly, we assigned 19 known and 11 new species (S. aokoulong, sp. nov., S. bispina, sp. nov., S. dapo, sp. nov., S. huayanxi, sp. nov., S. lianhe, sp. nov., S. lingshang, sp. nov., S. multidentata, sp. nov., S. tianmen, sp. nov., S. unispina, sp. nov., S. xiujian, sp. nov., S. zizhu, sp. nov.) of Songthela to three species-groups: the bispina-group, the multidentata-group and the unispina-group. Another new species, S. zimugang, sp. nov., is not included in any species groups, but forms a sister lineage to the bispina- and unispina-groups. These results elucidate a high species diversity of Songthela in a small area and demonstrate that integrating morphology with COI-based species delimitation is fast and cost-effective in delimiting species boundaries. http://zoobank.org/urn:lsid:zoobank.org:pub:AF0F5B31-AFAF-4861-9844-445AE8678B67

APA, Harvard, Vancouver, ISO, and other styles

13

Lu, Zhiqiang, Yongshuai Sun, Ying Li, Yongzhi Yang, Gaini Wang, and Jianquan Liu. "Species delimitation and hybridization history of a hazel species complex." Annals of Botany 127, no. 7 (February 10, 2021): 875–86. http://dx.doi.org/10.1093/aob/mcab015.

Full text

Abstract:

Abstract Background and Aims Hybridization increases species adaptation and biodiversity but also obscures species boundaries. In this study, species delimitation and hybridization history were examined within one Chinese hazel species complex (Corylus chinensis–Corylus fargesii). Two species including four varieties have already been described for this complex, with overlapping distributions. Methods A total of 322 trees from 44 populations of these four varieties across their ranges were sampled for morphological and molecular analyses. Climatic datasets based on 108 geographical locations were used to evaluate their niche differentiations. Flowering phenology was also observed for two co-occurring species or varieties. Key Results Four statistically different phenotypic clusters were revealed, but these clusters were highly inconsistent with the traditional taxonomic groups. All the clusters showed statistically distinct niches, with complete or partial geographical isolation. Only two clusters displayed a distributional overlap, but they had distinct flowering phenologies at the site where they co-occurred. Population-level evidence based on the genotypes of ten simple sequence repeat loci supported four phenotypic clusters. In addition, one cluster was shown to have an admixed genetic composition derived from the other three clusters through repeated historical hybridizations. Conclusions Based on our new evidence, it is better to treat the four clusters identified here as four independent species. One of them was shown to have an admixed genetic composition derived from the other three through repeated historical hybridizations. This study highlights the importance of applying integrative and statistical methods to infer species delimitations and hybridization history. Such a protocol should be adopted widely for future taxonomic studies.

APA, Harvard, Vancouver, ISO, and other styles

14

Veith, Michael. "Molecular markers and species delimitation: examples from the European batrachofauna." Amphibia-Reptilia 17, no. 4 (1996): 303–14. http://dx.doi.org/10.1163/156853896x00027.

Full text

Abstract:

AbstractMolecular techniques have revolutionised zoological systematics since the beginning of the seventies. Within the last twenty years numerous new amphibian species have been described in Europe almost solely on the basis of molecular data. This paper focuses on the use of molecular character state and genetic distance data for the delimitation of species. Case studies of European anurans (Discoglossus, water frogs of the genus Rana) are discussed in the framework of concurring species concepts to illustrate problems of assigning species status to divergent populations on the basis of molecular data.

APA, Harvard, Vancouver, ISO, and other styles

15

Han, Wei, Lu Qiu, Jing Zhu, Zong-Qing Wang, and Yan-Li Che. "Exploring the diversity of Eupolyphaga Chopard, 1929 (Blattodea, Corydioidea): species delimitation based on morphology and molecular analysis." ZooKeys 1120 (September 5, 2022): 67–94. http://dx.doi.org/10.3897/zookeys.1120.87483.

Full text

Abstract:

Eupolyphaga Chopard, 1929 is a cockroach genus mainly endemic to China. In this study, the species diversity of this genus is further explored through morphology and molecular analysis. Four species are described new to science: Eupolyphaga miracidia Qiu, sp. nov., Eupolyphaga udenostyla Qiu, sp. nov., Eupolyphaga reducta Qiu, sp. nov., and Eupolyphaga simila Qiu, sp. nov. New knowledge on some known species is added, including new distribution records and characteristics of females. Forty-five COI sequences were newly sequenced and a molecular species delimitation analysis was performed using ABGD method. Eighteen molecular operational taxonomic units were obtained by ABGD analysis, which are nearly consistent with the results of morphological delimitation.

APA, Harvard, Vancouver, ISO, and other styles

16

Ślipiko, Monika, Kamil Myszczyński, Katarzyna Buczkowska, Alina Bączkiewicz, and Jakub Sawicki. "Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia." International Journal of Molecular Sciences 23, no. 24 (December 8, 2022): 15570. http://dx.doi.org/10.3390/ijms232415570.

Full text

Abstract:

Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be ‘the Holy Grail’; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.

APA, Harvard, Vancouver, ISO, and other styles

17

SHEIDAI, MASOUD, HANIYEH TEYMOORI, ZAHRA NOORMOHAMMADI, AHMAD-REZA MEHRABIAN, FAHIMEH KOOHDAR, and SOMAYEH GHASEMZADEH-BARAKI. "Species delimitation in the genus Tamarix: Morphological and molecular data." Phytotaxa 343, no. 2 (March 9, 2018): 101. http://dx.doi.org/10.11646/phytotaxa.343.2.1.

Full text

Abstract:

Tamarix (Tamaricaceae) is an ancient genus in Asia that contains about 54 to 90 species with unresolved taxonomy. Tamarix has major center of speciation in the Pakistan-Afghanistan-Iran-Turkmenistan-S-Kazakhstan-W-China area and in the eastern Mediterranean area. Tamarix species are highly plastic and tolerant to adversity being able to occupy different habitats, thus showing a wide range of ecological variations. Tamarix species have commercial value in the landscape and horticultural trade and are planted for erosion control and as wind breaks. In the genus Tamarix, many species are morphologically very similar probably due, in part, inter-specific hybridization. Tamarix species live in sympatry in Sistan and Baloochestan province of Iran and we have no report on the number of species and their genetic structure. Therefore, we performed morphometric study to delimit the species growing in these two provinces and also used combined ISSR (Inter simple sequence repeat) and RAPD (Random amplified polymorphic DNA) molecular markers to study their genetic structure. Morphological analyses separated plants of 6 studied species in different groups, indicating that morphological characters used can delimit Tamarix species. We also encountered some plants having intermediate morphological characters. AMOVA and Hickory test showed significant genetic differences of the studied species and Mantel test showed significant correlation between genetic distance and geographical distance. STRUCTURE analysis and population assignment test revealed some degree of genetic admixture among the studied species. Assignment tests showed that gene flow mainly occurred among the species that were growing in neighborhood regions. This genetic admixture may be the reason for intermediate morphological characters observed in some the plants.

APA, Harvard, Vancouver, ISO, and other styles

18

Takamura, Kenzi, Ryuhei Ueno, Natsuko Ito Kondo, and Kako Ohbayashi. "Pond chironomid communities revealed by molecular species delimitation reflect eutrophication." Ecology and Evolution 11, no. 9 (March 23, 2021): 4193–204. http://dx.doi.org/10.1002/ece3.7315.

Full text

APA, Harvard, Vancouver, ISO, and other styles

19

Yassin, Amir, Christiane Amédégnato, Corinne Cruaud, and Michel Veuille. "Molecular taxonomy and species delimitation in Andean Schistocerca (Orthoptera: Acrididae)." Molecular Phylogenetics and Evolution 53, no. 2 (November 2009): 404–11. http://dx.doi.org/10.1016/j.ympev.2009.06.012.

Full text

APA, Harvard, Vancouver, ISO, and other styles

20

Duminil, J., and M. Di Michele. "Plant species delimitation: A comparison of morphological and molecular markers." Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology 143, no. 3 (November 2009): 528–42. http://dx.doi.org/10.1080/11263500902722964.

Full text

APA, Harvard, Vancouver, ISO, and other styles

21

Zhao, Yan, Zhenzhen Yi, Alan Warren, and Weibo B. Song. "Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes (Alveolata, Ciliophora)." Proceedings of the Royal Society B: Biological Sciences 285, no. 1871 (January 24, 2018): 20172159. http://dx.doi.org/10.1098/rspb.2017.2159.

Full text

Abstract:

Recent advances in high-throughput sequencing and metabarcoding technologies are revolutionizing our understanding of the diversity and ecology of microbial eukaryotes (protists). The interpretation of protist diversity and the elucidation of their ecosystem function are, however, impeded by problems with species delimitation, especially as it applies to molecular taxonomy. Here, using the ciliate Euplotes as an example, we describe approaches for species delimitation based on integrative taxonomy by using evolutionary and ecological perspectives and selecting the most appropriate metabarcoding gene markers as proxies for species units. Our analyses show that: Euplotes ( sensu lato ) comprises six distinct clades, mainly as result of ecological speciation; the validity of the genera Euplotes ( sensu stricto ), Euplotoides , Euplotopsis and Moneuplotes are not supported; the vannus -type group, which includes species without distinct morphological differences, seems to be undergoing incipient speciation and contains cryptic species; the hypervariable V4 region of the small subunit rDNA and D1–D2 region of the large subunit rDNA are the promising candidates for general species delimitation in Euplotes .

APA, Harvard, Vancouver, ISO, and other styles

22

Aguado, María Teresa, María Capa, Domingo Lago-Barcia, João Gil, Fredrik Pleijel, and Arne Nygren. "Species delimitation in Amblyosyllis (Annelida, Syllidae)." PLOS ONE 14, no. 4 (April 10, 2019): e0214211. http://dx.doi.org/10.1371/journal.pone.0214211.

Full text

APA, Harvard, Vancouver, ISO, and other styles

23

Larson, Eric R., Magalie Castelin, Bronwyn W. Williams, Julian D. Olden, and Cathryn L. Abbott. "Phylogenetic species delimitation for crayfishes of the genusPacifastacus." PeerJ 4 (April 18, 2016): e1915. http://dx.doi.org/10.7717/peerj.1915.

Full text

Abstract:

Molecular genetic approaches are playing an increasing role in conservation science by identifying biodiversity that may not be evident by morphology-based taxonomy and systematics. So-called cryptic species are particularly prevalent in freshwater environments, where isolation of dispersal-limited species, such as crayfishes, within dendritic river networks often gives rise to high intra- and inter-specific genetic divergence. We apply here a multi-gene molecular approach to investigate relationships among extant species of the crayfish genusPacifastacus, representing the first comprehensive phylogenetic study of this taxonomic group. Importantly,Pacifastacusincludes both the widely invasive signal crayfishPacifastacus leniusculus,as well as several species of conservation concern like the Shasta crayfishPacifastacus fortis. Our analysis used 83 individuals sampled across the four extantPacifastacusspecies (omitting the extinctPacifastacus nigrescens), representing the known taxonomic diversity and geographic distributions within this genus as comprehensively as possible. We reconstructed phylogenetic trees from mitochondrial (16S, COI) and nuclear genes (GAPDH), both separately and using a combined or concatenated dataset, and performed several species delimitation analyses (PTP, ABGD, GMYC) on the COI phylogeny to propose Primary Species Hypotheses (PSHs) within the genus. All phylogenies recovered the genusPacifastacusas monophyletic, within which we identified a range of six to 21 PSHs; more abundant PSHs delimitations from GMYC and ABGD were always nested within PSHs delimited by the more conservative PTP method.Pacifastacus leniusculusincluded the majority of PSHs and was not monophyletic relative to the otherPacifastacusspecies considered. Several of these highly distinctP. leniusculusPSHs likely require urgent conservation attention. Our results identify research needs and conservation priorities forPacifastacuscrayfishes in western North America, and may inform better understanding and management ofP. leniusculusin regions where it is invasive, such as Europe and Japan.

APA, Harvard, Vancouver, ISO, and other styles

24

Nadler, Steven. "Species delimitation and nematode biodiversity: phylogenies rule." Nematology 4, no. 5 (2002): 615–25. http://dx.doi.org/10.1163/15685410260438908.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

25

Hu, Gui-Lin, Kai Gao, Ji-Shen Wang, Paul D. N. Hebert, and Bao-Zhen Hua. "Molecular phylogeny and species delimitation of the genus Dicerapanorpa (Mecoptera: Panorpidae)." Zoological Journal of the Linnean Society 187, no. 4 (October 21, 2019): 1173–95. http://dx.doi.org/10.1093/zoolinnean/zlz059.

Full text

Abstract:

Abstract Given that species is the fundamental unit in systematic biology, rigorous species delimitation is crucial for taxonomic studies, yet routine species delimitation remains an ongoing challenge in the taxonomic practice of insects. The two-horned scorpionfly Dicerapanorpa is a small genus in Panorpidae (Mecoptera) endemic to the Qinling-Bashan and Hengduan mountains, a biodiversity hotspot. However, species of Dicerapanorpa are difficult to delineate owing to marked intraspecific variation and interspecific similarity. Here, we investigate the diversity and species boundaries of Dicerapanorpa using an integrative approach based on DNA barcoding, morphological, geometric morphometric and molecular phylogenetic analyses. This integrative analyses confirmed the 13 described species of Dicerapanorpa and revealed three new species: Dicerapanorpa lativalva sp. nov., Dicerapanorpa hualongshana sp. nov. and Dicerapanorpa minshana sp. nov. Most molecular operational taxonomic units are in congruence with morphological clusters. Possible reasons for several discordances in Dicerapanorpa are tentatively discussed.

APA, Harvard, Vancouver, ISO, and other styles

26

Silva-do-Nascimento, Teresa Fernandes, Jordi Sánchez-Ribas, Tatiane M. P. Oliveira, Brian Patrick Bourke, Joseli Oliveira-Ferreira, Maria Goreti Rosa-Freitas, Ricardo Lourenço-de-Oliveira, et al. "Molecular Analysis Reveals a High Diversity of Anopheline Mosquitoes in Yanomami Lands and the Pantanal Region of Brazil." Genes 12, no. 12 (December 16, 2021): 1995. http://dx.doi.org/10.3390/genes12121995.

Full text

Abstract:

Identifying the species of the subfamily Anophelinae that are Plasmodium vectors is important to vector and malaria control. Despite the increase in cases, vector mosquitoes remain poorly known in Brazilian indigenous communities. This study explores Anophelinae mosquito diversity in the following areas: (1) a Yanomami reserve in the northwestern Amazon Brazil biome and (2) the Pantanal biome in southwestern Brazil. This is carried out by analyzing cytochrome c oxidase (COI) gene data using Refined Single Linkage (RESL), Assemble Species by Automatic Partitioning (ASAP), and tree-based multi-rate Poisson tree processes (mPTP) as species delimitation approaches. A total of 216 specimens collected from the Yanomami and Pantanal regions were sequenced and combined with 547 reference sequences for species delimitation analyses. The mPTP analysis for all sequences resulted in the delimitation of 45 species groups, while the ASAP analysis provided the partition of 48 groups. RESL analysis resulted in 63 operational taxonomic units (OTUs). This study expands our scant knowledge of anopheline species in the Yanomami and Pantanal regions. At least 18 species of Anophelinae mosquitoes were found in these study areas. Additional studies are now required to determine the species that transmit Plasmodium spp. in these regions.

APA, Harvard, Vancouver, ISO, and other styles

27

Agüero-Chapin, Guillermin, Yuliana Jiménez, Aminael Sánchez-Rodríguez, Reinaldo Molina-Ruiz, Oscar Vivanco, and Agostinho Antunes. "DISTATIS: A Promising Framework to Integrate Distance Matrices in Molecular Phylogenetics." Current Topics in Medicinal Chemistry 21, no. 7 (April 26, 2021): 599–611. http://dx.doi.org/10.2174/1568026621666210113164605.

Full text

Abstract:

Background: Molecular phylogenetic algorithms frequently disagree with the approaches considering reproductive compatibility and morphological criteria for species delimitation. The question stems if the resulting species boundaries from molecular, reproductive and/or morphological data are definitively not reconcilable; or if the existing phylogenetic methods are not sensitive enough to agree morphological and genetic variation in species delimitation. Objectives : We propose DISTATIS as an integrative framework to combine alignment-based (AB) and alignment-free (AF) distance matrices from ITS2 sequences/structures to shed light whether Gelasinospora and Neurospora are sister but independent genera. Methods: We aimed at addressing this standing issue by harmonizing genus-specific classification based on their ascospore morphology and ITS2 molecular data. To validate our proposal, three phylogenetic approaches: i) traditional alignment-based, ii) alignment-free and iii) novel distance integrative (DI)-based were comparatively evaluated on a set of Gelasinospora and Neurospora species. All considered species have been extensively characterized at both the morphological and reproductive levels and there are known incongruences between their ascospore morphology and molecular data that hampers genus-specific delimitation. Results: Traditional AB phylogenetic analyses fail at resolving the Gelasinospora and Neurospora genera into independent monophyletic clades following ascospore morphology criteria. In contrast, AF and DI approaches produced phylogenetic trees that could properly delimit the expected monophyletic clades. Conclusions: The DI approach outperformed the AF one in the sense that it could also divide the Neurospora species according to their reproduction mode.

APA, Harvard, Vancouver, ISO, and other styles

28

Ramirez, Jorge L., Luisa Simbine, Carla G. Marques, Eliana Zelada-Mázmela, Lorenzo E. Reyes-Flores, Adolfo S. López, Jaqueline Gusmão, Carolina Tavares, Pedro M. Galetti, and Patricia D. Freitas. "DNA Barcoding of Penaeidae (Decapoda; Crustacea): Non-Distance-Based Species Delimitation of the Most Economically Important Shrimp Family." Diversity 13, no. 10 (September 23, 2021): 460. http://dx.doi.org/10.3390/d13100460.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

29

Magoga, Giulia, Diego Fontaneto, and Matteo Montagna. "Factors affecting the efficiency of molecular species delimitation in a species‐rich insect family." Molecular Ecology Resources 21, no. 5 (March 6, 2021): 1475–89. http://dx.doi.org/10.1111/1755-0998.13352.

Full text

APA, Harvard, Vancouver, ISO, and other styles

30

Wade, E. J., T. Hertach, M. Gogala, T. Trilar, and C. Simon. "Molecular species delimitation methods recover most song-delimited cicada species in the EuropeanCicadetta montanacomplex." Journal of Evolutionary Biology 28, no. 12 (November 3, 2015): 2318–36. http://dx.doi.org/10.1111/jeb.12756.

Full text

APA, Harvard, Vancouver, ISO, and other styles

31

Martinsson, Svante, and Christer Erséus. "Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview." Diversity 13, no. 2 (January 20, 2021): 36. http://dx.doi.org/10.3390/d13020036.

Full text

Abstract:

Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.

APA, Harvard, Vancouver, ISO, and other styles

32

Ramirez, Jorge L., Cesar A. Santos, Carolina B. Machado, Alexandre K. Oliveira, Julio C. Garavello, Heraldo A. Britski, and Pedro M. Galetti. "Molecular phylogeny and species delimitation of the genus Schizodon (Characiformes, Anostomidae)." Molecular Phylogenetics and Evolution 153 (December 2020): 106959. http://dx.doi.org/10.1016/j.ympev.2020.106959.

Full text

APA, Harvard, Vancouver, ISO, and other styles

33

Lutz, Matthias, Markus Göker, Marcin Piatek, Martin Kemler, Dominik Begerow, and Franz Oberwinkler. "Anther smuts of Caryophyllaceae: Molecular characters indicate host-dependent species delimitation." Mycological Progress 4, no. 3 (August 2005): 225–38. http://dx.doi.org/10.1007/s11557-006-0126-4.

Full text

APA, Harvard, Vancouver, ISO, and other styles

34

Druzhinina, Irina S., Monika Komoń-Zelazowska, Adnan Ismaiel, Walter Jaklitsch, Temesgen Mullaw, Gary J. Samuels, and Christian P. Kubicek. "Molecular phylogeny and species delimitation in the section Longibrachiatum of Trichoderma." Fungal Genetics and Biology 49, no. 5 (May 2012): 358–68. http://dx.doi.org/10.1016/j.fgb.2012.02.004.

Full text

APA, Harvard, Vancouver, ISO, and other styles

35

HRIVNIAK, ĽUBOŠ, PAVEL SROKA, GENCER TÜRKMEN, ROMAN J. GODUNKO, and NİLGÜN KAZANCI. "A new Epeorus (Caucasiron) (Ephemeroptera: Heptageniidae) species from Turkey based on molecular and morphological evidence." Zootaxa 4550, no. 1 (January 22, 2019): 58. http://dx.doi.org/10.11646/zootaxa.4550.1.2.

Full text

Abstract:

Epeorus (Caucasiron) turcicus sp. nov. is described based on larvae from NE Turkey. The new species can be distinguished from other Caucasiron by a unique combination of several diagnostic characters: the presence of a rounded hypodermal medial femur spot, colouration of abdominal terga and sterna, narrow gill plate VII, fine hair-like setae on the surface of abdominal terga, and absence of postero-lateral projections on tergum X. In addition to morphological analysis, two single-locus analytical approaches are employed for delimiting the new species using COI sequences (Automatic Barcode Gap Discovery, ABGD; and General Mixed Yule Coalescent Model, GMYC). Both approaches unambiguously recognized E. (C.) turcicus sp. nov. as a distinct species. Our molecular dataset contains all Caucasiron species occurring in the Caucasus and the delimitation of individual species mostly follows the morphologically defined species. This study confirms the suitability of the GMYC approach for species delimitation within Caucasiron.

APA, Harvard, Vancouver, ISO, and other styles

36

Torrano-Silva, Beatriz N., Bruno R. Vieira, Rafael Riosmena-Rodríguez, and Mariana C. Oliveira. "Guidelines for DNA barcoding of coralline algae, focusing on Lithophylloideae (Corallinales) from Brazil." Botanica Marina 61, no. 2 (March 28, 2018): 127–40. http://dx.doi.org/10.1515/bot-2017-0040.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

37

Sheidai, Masoud, Melica Tabasi, Mohammad-Reza Mehrabian, Fahimeh Koohdar, Somayeh Ghasemzadeh-Baraki, and Zahra Noormohammadi. "Species delimitation and relationship in Crocus L. (Iridaceae)." Acta Botanica Croatica 77, no. 1 (April 1, 2018): 10–17. http://dx.doi.org/10.1515/botcro-2017-0015.

Full text

Abstract:

AbstractThe genusCrocusL. (Iridaceae) is monophyletic and contains about 100 species throughout the world.Crocusspecies have horticultural, medicinal and pharmacological importance. Saffron is the dried styles ofC. sativusand is one of the world’s most expensive spices by weight. Controversy exits about the taxonomy of the genus and the species relationship. Exploring genetic diversity and inter-specific cross-ability are important tasks for conservation of wild taxa and for breeding of cultivatedC. sativus. The present study was performed to study genetic variability and population structure in fiveCrocusL. species includingCrocus almehensisBrickell & Mathew,C. caspiusFischer & Meyer,C. speciosusMarschall von Biberstein,C. haussknechtiiBoissier, andC. sativusL. by inter simple sequence repeat (ISSR) molecular markers. We also used published internal transcribed spacer (ITS) sequences to study species relationship and compare the results with ISSR data. The results revealed a high degree of genetic variability both within and among the studied species. Neighbor joining (NJ) tree and network analysis revealed that ISSR markers are useful inCrocusspecies delimitation. Population fragmentation occurred inC. caspiusandC. sativus. Both ISSR and sequenced based analyses separatedC. sativusfrom the other studied species. Close genetic affinity ofC. sativusandC. pallisiiand inter-specific gene flow was supported by both data sets.

APA, Harvard, Vancouver, ISO, and other styles

38

Koohdar, Fahimeh, Neda Aram, and Masoud Sheidai. "Biosystematics, fingerprinting and DNA barcoding study of the genus Lallemantia based on SCoT and REMAP markers." Caryologia 74, no. 4 (March 8, 2022): 77–83. http://dx.doi.org/10.36253/caryologia-1163.

Full text

Abstract:

Lallemantia is a medicinally important plant in the world. Due to interspecific hybridization and horizontal gene transfer, spices relationship and delimitation on the genus Lallemantia is difficult based on different molecular markers. Therefore, selecting the appropriate marker can be important. Fingerprinting techniques continue to be used for genomic profiling for the characterization of germplasm and the establishment of the identity of varieties/hybrids/parental sources of aromatic and medicinal plants. For this, we need to produce detailed information on genetic diversity available in Lallemantia as well as investigate spices relationship and delimitation. Therefore, the present study was performed on Lallemantia species in Iran. We used the start codon targeted and retrotransposon-microsatellite amplified polymorphism molecular marker for our genetic investigation with the following aims: 1- To reveal the species delimitation and species relationship in Lallemantia, and 2- To investigate discriminating power of the start codon targeted and retrotransposon-microsatellite amplified polymorphism markers by Gst and NM analysis. The results obtained revealed that the start codon targeted marker is the best to show the relationships between species while the retrotransposon-microsatellite amplified polymorphism marker is the best for species delimitation. we found the loci with the high value of Gst (1.00) in start codon targeted and retrotransposon-microsatellite amplified polymorphism markers that can be used in barcoding and fingerprinting of L. royleana.

APA, Harvard, Vancouver, ISO, and other styles

39

Jurado-Rivera, José A., Francesco Zapelloni, Joan Pons, Carlos Juan, and Damià Jaume. "Morphological and molecular species boundaries in the Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda)." Contributions to Zoology 89, no. 4 (July 13, 2020): 353–72. http://dx.doi.org/10.1163/18759866-bja10004.

Full text

Abstract:

The Hyalella species diversity in the high-altitude water bodies of the Andean Altiplano is addressed using mitochondrial cox1 sequences and implementing different molecular species delimitation criteria. We have recorded the presence of five major genetic lineages in the Altiplano, of which one seems to be exclusive to Lake Titicaca and nearby areas, whereas the rest occur also in other regions of South America. Eleven out of 36 South American entities diagnosed by molecular delimitation criteria in our study are likely endemic to the Titicaca and neighbouring water bodies. We have detected a remarkable disagreement between morphology and genetic data in the Titicacan Hyalella, with occurrence of several cases of the same morpho-species corresponding to several Molecular Operational Taxonomic Units (MOTUs), some even distantly related, and other instances where a particular MOTU is shared by a morphologically heterogeneous array of species, including species with body smooth and others with body heavily armoured. Species diversification and incongruence between morphological and molecular boundaries within this species assemblage may be associated to the sharp changes in hydrological conditions experienced by the water bodies of the Altiplano in the past, which included dramatic fluctuations in water level and salinity of Lake Titicaca. Such environmental shifts could have triggered rapid morphological changes and ecological differentiation within the Hyalella assemblage, followed by phenotypic convergence among the diverse lineages. Factors such as phenotypic plasticity, incomplete lineage sorting or admixture between divergent lineages might lie also at the root of the morphological-genetic incongruence described herein.

APA, Harvard, Vancouver, ISO, and other styles

40

Zhang, JinMei, JianXiu Wang, Tao Xia, and ShiLiang Zhou. "DNA barcoding: species delimitation in tree peonies." Science in China Series C: Life Sciences 52, no. 6 (June 2009): 568–78. http://dx.doi.org/10.1007/s11427-009-0069-5.

Full text

APA, Harvard, Vancouver, ISO, and other styles

41

Scarpa, Fabio, Piero Cossu, Tiziana Lai, Daria Sanna, Marco Curini-Galletti, and Marco Casu. "Meiofaunal cryptic species challenge species delimitation: the case of the Monocelis lineata (Platyhelminthes: Proseriata) species complex." Contributions to Zoology 85, no. 2 (March 21, 2016): 123–45. http://dx.doi.org/10.1163/18759866-08502001.

Full text

Abstract:

Given the pending biodiversity crisis, species delimitation is a critically important task in conservation biology, but its efficacy based on single lines of evidence has been questioned as it may not accurately reflect species limits and relationships. Hence, the use of multiple lines of evidence has been portrayed as a means to overcome identification issues arising from gene/species tree discordance, morphological convergence or recent adaptive radiations. Here, the integrative taxonomic approach has been used to address the study of the Monocelis lineataspecies complex. The taxonomic resolution of the complex is challenging, as the species lacks sclerotised copulatory structures, which as a rule of thumb aid identification in Proseriata. Eighteen populations, which encompass most of the geographic range of the complex, were studied using morphology, karyology, crossbreeding experiments and molecular analysis. These different markers provided evidence of four (karyology) to eight (morphology) discrete entities, whereas crossings showed various degrees of intersterility among the tested populations. Molecular species delimitation revealed a different number of candidate species, spanning from five (ABGD and K/θ) to 11 (GMYC). Such incongruences reflect the multifaceted evolutionary history of M. lineata s.l.and hamper the full taxonomic resolution of the complex. However, two candidate species were consistently validated by all of the markers and are described as new species: Monocelis algicolanov. sp. and M. exquisitanov. sp. The latter species appear to have a restricted distribution, and the possibility that meiofaunal taxa may be of conservation concern is discussed.

APA, Harvard, Vancouver, ISO, and other styles

42

MEHRI, SHAHRAM, IMAN KOLBADI, and HASSAN SHIRAFKAN-AJIRLOU. "Species Delimitation In Rhabdosciadium (Apiaceae): Morphological and Molecular." Phytotaxa 437, no. 1 (March 23, 2020): 1–13. http://dx.doi.org/10.11646/phytotaxa.437.1.1.

Full text

Abstract:

Rhabdosciadium is a distinct and small Apiaceae genus represented by only 8 species worldwide, 5 of which are distributed in Turkey and 3 occur in Iran. They all are narrow endemic, rare mountain species. The genus is characterized by single-fruited umbellules, linear-cylindrical fruits, parennial, glabrous, and junciform habit, reduced cauline leaves, and fibrous collar at the base of the stem. Till present time, there has been no detailed information available on molecular phylogeny and genetic structure of these species in the country. Therefore, the present study was conducted with the aim to investigate species delimitation by both morphological and molecular data and to reveal genetic diversity and population structure in these three Rhabdosciadium species. For this study, 98 randomly collected plants from 15 geographical populations in Rhabdosciadium species were used. We encountered extensive within species genetic and morphological diversity. ISSR molecular markers could delimit the studied species. STRUCTURE analysis revealed the occurrence gene flow between these species. The Mantel test showed correlation between genetic distance and geographical distance of the populations studied. Phylogenetic tree was constructed based on ITS data set which separated out-groups from the studied species. Genetic affinity of the studied species have been discussed.

APA, Harvard, Vancouver, ISO, and other styles

43

Solovyeva, Evgeniya N., Evgeniy A. Dunayev, Roman A. Nazarov, Dmitriy A. Bondarenko, and Nikolay A. Poyarkov. "COI-Barcoding and Species Delimitation Assessment of Toad-Headed Agamas of the Genus Phrynocephalus (Agamidae, Squamata) Reveal Unrecognized Diversity in Central Eurasia." Diversity 15, no. 2 (January 21, 2023): 149. http://dx.doi.org/10.3390/d15020149.

Full text

Abstract:

We provide a diversity assessment of the agamid genus Phrynocephalus Kaup, 1825. We analyze COI mtDNA barcodes from 385 individuals sampled all over Phrynocephalus range. We apply the ABGD, ASAP, bGMYC, mlPTP and hsPTP species delimitation algorithms to analyze the COI gene fragment variation and assess the species diversity in Phrynocephalus. Nine species groups are revealed in Phrynocephalus in agreement with earlier studies on the phylogenetic relationships of the genus. We demonstrate that the present taxonomy likely underestimates the actual diversity of the genus. Alternative species delimitation algorithms provide a confusingly wide range of possible number of Phrynocephalus species—from 54 to 103 MOTUs (molecular operational taxonomic units). The ASAP species delimitation scheme recognizing 63 MOTUs likely most closely fits the currently recognized taxonomic framework of Phrynocephalus. We also report on 13 previously unknown Phrynocephalus lineages as unverified candidate species. We demonstrate that the ASAP and the ABGD algorithms likely most closely reflect the actual diversity of Phrynocephalus, while the mlPTP and hsPTP largely overestimate it. We argue that species delimitation in these lizards based exclusively on mtDNA markers is insufficient, and call for further integrative taxonomic studies joining the data from morphology, mtDNA and nuDNA markers to fully stabilize the taxonomy of Phrynocephalus lizards.

APA, Harvard, Vancouver, ISO, and other styles

44

Muñoz-Tobar, Sofía, and Michael Caterino. "Mountains as Islands: Species Delimitation and Evolutionary History of the Ant-Loving Beetle Genus Panabachia (Coleoptera, Staphylinidae) from the Northern Andes." Insects 11, no. 1 (January 20, 2020): 64. http://dx.doi.org/10.3390/insects11010064.

Full text

Abstract:

The ant-loving beetle genus Panabachia Park 1942 is a poorly studied beetle lineage from the new world tropics. We recently collected Panabachia from several previously unrecorded locations in the páramo biome of the high Ecuadorian Andes, with males exhibiting great morphological variation in the distribution of the foveae and depressions in the pronotum, as well as aspects of the male genitalia. Here, we employ phylogenetic and species delimitation methods with mitochondrial (COI) and nuclear protein-coding (wingless) gene sequences to examine the concordance of morphological characters and geography with hypothesized species boundaries. Three methods of species delimitation (bPTP, GMYC and Stacey) were used to estimate the number of species, and divergence times between putative species using molecular clock calibration. Phylogenetic analysis revealed two parallel radiations, and species delimitation analyses suggest there are between 17 and 22 putative species. Based on clade support and concordance across species delimitation methods we hypothesize 17 distinct clusters, with allopatric speciation consistent with most geographic patterns. Additionally, a widespread species appears to be present in northern páramo sites, and some sister species sympatry may indicate other diversification processes have operated on certain lineages of Panabachia. Divergence time estimates suggest that Panabachia originated in the Miocene, but most species analyzed diverged during the Pliocene and Pleistocene (5.3–0.11 Mya), contemporaneous with the evolution of páramo plant species.

APA, Harvard, Vancouver, ISO, and other styles

45

Chen, Weimiao, Majid Khayatnezhad, and Nima Sarhadi. "Gene flow and population structure in Allochrusa (caryophylloideae, caryophyllaceae) with the use of molecular markers." Genetika 53, no. 2 (2021): 799–812. http://dx.doi.org/10.2298/gensr2102799c.

Full text

Abstract:

Allochrusa Bunge is a genus of subfamily Caryophylloideae Rabeler & Bittrich contains about 8 species distributed in Turkey, Central Asia, Afghanistan, Caucasus, Transcaucasus and Iran. Three species of Allochrusa versicolor, A. bungei and A. persica occur in Iran show some degree of morphological overlaps that make the species delimitation difficult. Till present time, there has been no detailed information available on morphological and genetic structure of these species in the country. The aims of the present study are: 1) to find the diagnostic value of SCoT markers in delimitation of Allochrusa species, 2) to find the genetic structure of these taxa in Iran, and 3) to investigate the species inter-relationship. For this study, 97 randomly collected plants from 7 geographical populations in three Allochrusa species were used. We encountered extensive within species genetic and morphological diversity. SCoT molecular markers could delimit the studied species. AMOVA and STRUCTURE analysis revealed that the species of Allochrusa are genetically differentiated. The Mantel test showed correlation between genetic distance and geographical distance of the populations studied. Genetic affinity of the studied species has been discussed.

APA, Harvard, Vancouver, ISO, and other styles

46

Valdez-Mondragón, Alejandro, Claudia I. Navarro-Rodríguez, Karen P. Solís-Catalán, Mayra R. Cortez-Roldán, and Alma R. Juárez-Sánchez. "Under an integrative taxonomic approach: the description of a new species of the genus Loxosceles (Araneae, Sicariidae) from Mexico City." ZooKeys 892 (November 27, 2019): 93–133. http://dx.doi.org/10.3897/zookeys.892.39558.

Full text

Abstract:

A new species of the spider genus Loxosceles Heineken & Lowe, 1832, Loxosceles tenochtitlan Valdez-Mondragón & Navarro-Rodríguez, sp. nov., is described based on adult male and female specimens from the states of Mexico City, Estado de Mexico and Tlaxcala. Integrative taxonomy including traditional morphology, geometric and lineal morphology, and molecules (DNA barcodes of cytochrome c oxidase subunit 1 (CO1) and internal transcribed spacer 2 (ITS2)), were used as evidence to delimit the new species. Four methods were used for molecular analyses and species delimitation: 1) corrected p-distances under neighbor joining (NJ), 2) automatic barcode gap discovery (ABGD), 3) general mixed yule coalescent model (GMYC), and 4) poisson tree processes (bPTP). All molecular methods, traditional, geometric and lineal morphology were consistent in delimiting and recognizing the new species. Loxosceles tenochtitlansp. nov. is closely related to L. misteca based on molecular data. Although both species are morphologically similar, the average p-distance from CO1 data was 13.8% and 4.2% for ITS2 data. The molecular species delimitation methods recovered well-supported monophyletic clusters for samples of L. tenochtitlansp. nov. from Mexico City + Tlaxcala and for samples of L. misteca from Guerrero. Loxosceles tenochtitlansp. nov. is considered a unique species for three reasons: (1) it can be distinguished by morphological characters (genitalic and somatic); (2) the four different molecular species delimitation methods were congruent to separate both species; and (3) there is variation in leg I length of males between both species, with the males of L. misteca having longer legs than males of L. tenochtitlansp. nov., also morphometrically, the shape of tibiae of the palp between males of both species is different.

APA, Harvard, Vancouver, ISO, and other styles

47

Le Ru, Bruno P., Claire Capdevielle-Dulac, Emmanuel F. A. Toussaint, Desmond Conlong, Johnnie Van den Berg, Beatrice Pallangyo, George Ong'amo, et al. "Integrative taxonomy of Acrapex stem borers (Lepidoptera : Noctuidae : Apameini): combining morphology and Poisson Tree Process analyses." Invertebrate Systematics 28, no. 5 (2014): 451. http://dx.doi.org/10.1071/is13062.

Full text

Abstract:

Ten morphologically similar species of Acrapex from eastern and south-eastern Africa belonging to the A. stygiata and A. albivena groups are reviewed. Six species are described as new: A. brunneella, A. mitiwa, A. mpika, A. salmona, A. sporobola and A. yakoba. The Poaceae host plants of eight species are recorded; four species, A. mitiwa. A. subalbissima, A. syscia and A. yakoba, were found developing exclusively on Imperata cylindrica (L.) Beauv., (Andropogoneae); two species, A. sporobola and A. salmona, on I. cylindrica and Sporobolus macranthelus Chiov. (Zoysieae); and A. albivena on I. cylindrica, Miscanthus capensis (Nees) Andersson (Andropogoneae) and Cymbopogon sp. (Andropogoneae). Acrapex stygiata larvae developed on M. capensis and Cymbopogon sp. The host plants of A. brunneella and A. mpika remain unknown. We also conducted molecular phylogenetics and molecular species delimitation analyses on a comprehensive sample of 49 specimens belonging to nine of the studied species. Molecular phylogenetics and molecular species delimitation analyses provided additional evidence of the validity of the six newly described species but also suggested a level of hidden biodiversity for one of them.

APA, Harvard, Vancouver, ISO, and other styles

48

Becchimanzi, Andrea, Beata Zimowska, and Rosario Nicoletti. "Cryptic Diversity in Cladosporium cladosporioides Resulting from Sequence-Based Species Delimitation Analyses." Pathogens 10, no. 9 (September 10, 2021): 1167. http://dx.doi.org/10.3390/pathogens10091167.

Full text

Abstract:

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-α 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.

APA, Harvard, Vancouver, ISO, and other styles

49

Mateos, Eduardo, Ronald Sluys, Marta Riutort, and Marta Álvarez-Presas. "Species richness in the genus Microplana (Platyhelminthes, Tricladida, Microplaninae) in Europe: as yet no asymptote in sight." Invertebrate Systematics 31, no. 3 (2017): 269. http://dx.doi.org/10.1071/is16038.

Full text

Abstract:

This study forms a major step towards a comprehensive morphological and molecular analysis of the species diversity of European microplanid land planarians. It presents a molecular phylogenetic tree on the basis of information from the genes Cox1, 18S, 28S and elongation factor 1-α, and applies molecular and morphological species delimitation methodologies for Microplana specimens sampled over a wide geographic range within Europe. The study suggests that as yet there is no plateau or asymptote in the accumulation curve for European Microplana species, as our results facilitated an integrative delimitation of seven new species as well as the diagnosis of new populations of three already known species and one doubtful or problematic species. In some cases, the new records considerably enlarged the known range of a species. An integrative account is provided of each of these species. Molecular sequence information on newly collected land flatworms may quickly point the planarian systematist to taxa that need to be examined morphologically and thus may considerably reduce laborious and time-consuming histological analyses.

APA, Harvard, Vancouver, ISO, and other styles

50

Kornilios, P., D. Jablonski, R. A. Sadek, Y. Kumlutaş, K. Olgun, A. Avci, and C. Ilgaz. "Multilocus species-delimitation in the Xerotyphlops vermicularis (Reptilia: Typhlopidae) species complex." Molecular Phylogenetics and Evolution 152 (November 2020): 106922. http://dx.doi.org/10.1016/j.ympev.2020.106922.

Full text

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'Molecular species delimitation'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles