Using the putative asexual fungus Cenococcum geophilum as a model to test how species concepts influence recombination analyses using sequence data from multiple loci

2007 ◽  
Vol 52 (5-6) ◽  
pp. 191-201 ◽  
Author(s):  
Greg W. Douhan ◽  
Darren P. Martin ◽  
Dave M. Rizzo
Keyword(s):  
Sequence Data ◽  
Species Concepts ◽  
Cenococcum Geophilum ◽  
Multiple Loci

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.

Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)

Zootaxa ◽  
2020 ◽  
Vol 4772 (1) ◽  
pp. 89-110
Author(s):  
MATTHEW R. MOORE ◽  
STEFANI M. HARRISON ◽  
RONALD D. CAVE ◽  
MARC A. BRANHAM
Keyword(s):  
Species Complex ◽  
Gap Analysis ◽  
Sequence Data ◽  
Species Concepts ◽  
Neighbor Joining ◽  
The West ◽  
Research Attention ◽  
Operational Taxonomic Units ◽  
Floral Visitation ◽  
Morphological Species

The speciose genus Cyclocephala Dejean (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini) has attracted research attention due to their diversity, agroeconomic importance, and floral visitation habits. Uniquely among Cyclocephala species, C. mafaffa Burmeister and C. deceptor (Casey), two nearly identical species, are diagnosed by a pronotal character: beaded or not beaded basal pronotal margin. We evaluated these morphological species hypotheses with a phylogenetic analysis of 12S and COI, neighbor-joining analysis, and several single-locus species delimitation procedures (automatic barcode gap analysis and three Poisson tree processes analyses). Together, these analyses supported the species concepts for C. deceptor and C. mafaffa. Delimitation procedures supported several distinct molecular operational taxonomic units among these taxa. We consider the separation of C. deceptor and C. mafaffa to be valid. We conservatively synonymize the West Indian subspecies C. mafaffa grandis Burmeister under C. mafaffa and offer a discussion on subspecific concepts in Cyclocephalini. We designate the lectotype of Stigmalia deficiens Casey. Implications of this study for other geographically widespread cyclocephalines or species with variable pronotal morphology are discussed. 

scholarly journals Human CODIS STR Loci Profiling from HTS Data

2016 ◽  
Author(s):  
Darrell O. Ricke ◽  
Martha Petrovick ◽  
Johanna Bobrow ◽  
Tara Boettcher ◽  
Christina Zook ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Sequence Data ◽  
Read Length ◽  
Single Nucleotide ◽  
Str Loci ◽  
Multiple Loci ◽  
Protocol Development ◽  
High Throughput Dna Sequencing ◽  
Improving Accuracy ◽  
Identification Analysis

AbstractHuman DNA identification is currently performed by amplifying a small, defined set of short tandem repeat (STR) loci (e.g. CODIS) and analyzing the size of the alleles present at those loci by capillary electrophoresis. High-throughput DNA sequencing (HTS) could enable the simultaneous analysis of many additional STR and single nucleotide polymorphism (SNP) loci, improving accuracy and discrimination. However, it is necessary to demonstrate that HTS can generate accurate data on the CODIS loci to enable backwards compatibility with the FBI NDIS database. Sequencing can also detect novel polymorphisms within alleles that migrate with identical sizes by capillary electrophoresis, improving allele discrimination, and enhancing human identification analysis. All CODIS alleles from an individual can be amplified in a single, multiplex PCR reaction, and combined with additional barcoded samples prior to sequencing. A computational tool for allele identification from multiplexed sequence data has been developed. With longer-read-length platforms, 99.6% allele calling accuracy can be achieved. In the course of STR sequencing protocol development, 12 novel allele sequences have been identified for multiple loci. Sequencing STR loci combined with SNPs will enable new forensic applications.

DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach

2006 ◽  
Vol 84 (3) ◽  
pp. 335-341 ◽  
Author(s):  
S.G. Newmaster ◽  
A.J. Fazekas ◽  
S. Ragupathy
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Forensic Analysis ◽  
Plant Genome ◽  
Land Plants ◽  
Practical Applications ◽  
Species Discovery ◽  
Tiered Approach ◽  
Additional Layer ◽  
Multiple Loci

DNA barcoding based on the mitochondrial cytochrome c oxidase 1 (cox1) sequence is being employed for diverse groups of animals with demonstrated success in species identification and new species discovery. Applying barcoding systems to land plants will be a more challenging task as plant genome substitution rates are considerably lower than those observed in animal mitochondria, suggesting that a much greater amount of sequence data from multiple loci will be required to barcode plants. In the absence of an obvious well-characterized plant locus that meets all the necessary criteria, a key first step will be identifying candidate regions with the most potential. To meet the challenges with land plants, we are proposing the adoption of a tiered approach wherein highly variable loci are nested under a core barcoding gene. Analysis of over 10 000 rbcL sequences from GenBank demonstrate that this locus could serve well as the core region, with sufficient variation to discriminate among species in approximately 85% of congeneric pair-wise comparisons. Use of a secondary locus can be implemented when required and can vary from group to group if necessary. The implementation of a barcoding tool has multiple academic and practical applications. It will speed routine identifications and the detection of alien species, advance ecological and taxonomic inquiry, permit fast and accurate forensic analysis of plant fragments, and can function as an additional layer of quality control in the food industry.

Morphological and molecular data show an enlarged tropical Australian radiation in Synostemon (Phyllanthaceae, Phyllantheae) previously concealed by heteromorphic species concepts

2019 ◽  
Author(s):  
Ian R. H. Telford ◽  
Kanchana Pruesapan ◽  
Peter C. van Welzen ◽  
Jeremy J. Bruhl
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Molecular Data ◽  
Species Concepts ◽  
New Combinations ◽  
Morphological And Molecular Data ◽  
Nrits Sequence

Sauropus elachophyllus (F.Muell. ex Benth.) Airy Shaw and S. rigidulus (F.Muell. ex Müll.Arg.) Airy Shaw are revised under the reinstated genus Synostemon F.Muell. (Phyllanthaceae) using morphological and nrITS sequence data. Sauropus decrescentifolius J.T.Hunter & J.J.Bruhl and S. elachophyllus are shown to be conspecific as Synostemon elachophyllus (F.Muell. ex Benth.) I.Telford & Pruesapan and S. elachophyllus subsp. decrescentifolius (J.T.Hunter & J.J.Bruhl) I.Telford & Pruesapan, with Synostemon elachophyllus subsp. latior (Airy Shaw) I.Telford & Pruesapan (syn. Sauropus elachophyllus var. glaber Airy Shaw p.p.) raised in rank. The ‘Top End clade’ has morphological synapomorphies of fused staminal filaments and connectives, and linear, longitudinal anthers. Four new species are named: Synostemon cowiei I.Telford & J.J.Bruhl, S. inaequisepalus I.Telford & J.J.Bruhl, S. kakadu I.Telford & J.J.Bruhl and S. nitmiluk I.Telford & J.J.Bruhl and new combinations are provided: S. crassifolius (Müll.Arg.) I.Telford & Pruesapan, S. ditassoides (Müll.Arg.) I.Telford & Pruesapan, S. dunlopii (J.T.Hunter & J.J.Bruhl) I.Telford & Pruesapan, S. filicinus (J.T.Hunter & J.J.Bruhl) I.Telford & Pruesapan, S. gracilis (J.T.Hunter & J.J.Bruhl) I.Telford & Pruesapan, S. rigidulus (F.Muell. ex Müll.Arg.) I.Telford & Pruesapan, and S. stenocladus (S.Moore) I.Telford & Pruesapan, with S. pinifolius (J.T.Hunter & J.J.Bruhl) I.Telford & Pruesapan also raised in rank.

scholarly journals Heuristic optimization for global species clustering of DNA sequence data from multiple loci

2013 ◽  
pp. n/a-n/a
Author(s):  
Douglas Chesters ◽  
Fang Yu ◽  
Huan-Xi Cao ◽  
Qing-Yan Dai ◽  
Qing-Tao Wu ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Heuristic Optimization ◽  
Dna Sequence Data ◽  
Multiple Loci

scholarly journals A novel workflow to improve multi-locus genotyping of wildlife species: an experimental set-up with a known model system

2019 ◽  
Author(s):  
Mark A.F. Gillingham ◽  
B. Karina Montero ◽  
Kerstin Wihelm ◽  
Kara Grudzus ◽  
Simone Sommer ◽  
...  
Keyword(s):  
Sequence Data ◽  
Model Organism ◽  
Model Systems ◽  
Model Organisms ◽  
Amplification Efficiency ◽  
Amplification Bias ◽  
Link Type ◽  
Multiple Loci ◽  
Number Variation ◽  
Set Up

ABSTRACTGenotyping novel complex multigene systems is particularly challenging in non-model organisms. Target primers frequently amplify simultaneously multiple loci leading to high PCR and sequencing artefacts such as chimeras and allele amplification bias. Most next-generation sequencing genotyping pipelines have been validated in non-model systems whereby the real genotype is unknown and the generation of artefacts may be highly repeatable. Further hindering accurate genotyping, the relationship between artefacts and copy number variation (CNV) within a PCR remains poorly described. Here we investigate the latter by experimentally combining multiple known major histocompatibility complex (MHC) haplotypes of a model organism (chicken, Gallus gallus, 43 artificial genotypes with 2-13 alleles per amplicon). In addition to well defined “optimal” primers, we simulated a non-model species situation by designing “naive” primers, with sequence data from closely related Galliform species. We applied a novel open-source genotyping pipeline (ACACIA) to the data, and compared its performance with another, previously published, pipeline. ACACIA yielded very high allele calling accuracy (>98%). Non-chimeric artefacts increased linearly with increasing CNV but chimeric artefacts leveled when amplifying more than 4-6 alleles. As expected, we found heterogeneous amplification efficiency of allelic variants when co-amplifying multiple loci. Using our validated ACACIA pipeline and the example data of this study, we discuss in detail the pitfalls researchers should avoid in order to reliably genotype complex multigene systems. ACACIA and the datasets used in this study are publicly available at GitLab and FigShare (https://gitlab.com/psc_santos/ACACIAandhttps://figshare.com/projects/ACACIA/66485).

scholarly journals The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

2021 ◽  
Author(s):  
Teun Boekhout ◽  
M. Catherine Aime ◽  
Dominik Begerow ◽  
Toni Gabaldón ◽  
Joseph Heitman ◽  
...  
Keyword(s):  
Species Concept ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Biological Species ◽  
Species Concepts ◽  
Biological Species Concept ◽  
Sequencing Technology ◽  
Morphological Aspects ◽  
Growth Profiles ◽  
Genome Information

AbstractHere we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.

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