scholarly journals The challenges and potential utility of phenotypic specimen-level phylogeny based on maximum parsimony

2018 ◽  
Vol 109 (1-2) ◽  
pp. 301-323 ◽  
Author(s):  
Emanuel TSCHOPP ◽  
Paul UPCHURCH
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Parsimony ◽  
Large Scale ◽  
Intraspecific Variability ◽  
Species Level ◽  
A Posteriori ◽  
Operational Taxonomic Units ◽  
Vertebrate Palaeontology ◽  
Tree Topologies ◽  
Parsimony Criterion

ABSTRACTSpecimen-level phylogenetic approaches are widely used in molecular biology for taxonomic and systematic purposes. However, they have been largely ignored in analyses based on morphological traits, where phylogeneticists mostly resort to species-level analyses. Recently, a number of specimen-level studies have been published in vertebrate palaeontology. These studies indicate that specimen-level phylogeny may be a very useful tool for systematic reassessments at low taxonomic levels. Herein, we review the challenges when working with individual organisms as operational taxonomic units in a palaeontological context, and propose guidelines of how best to perform a specimen-level phylogenetic analysis using the maximum parsimony criterion. Given that no single methodology appears to be perfectly suited to resolve relationships among individuals, and that different taxa probably require different approaches to assess their systematics, we advocate the use of a number of methodologies. In particular, we recommend the inclusion of as many specimens and characters as feasible, and the analysis of relationships using an extended implied weighting approach with different downweighting functions. Resulting polytomies should be explored using a posteriori pruning of unstable specimens, and conflicting tree topologies between different iterations of the analysis should be evaluated by a combination of support values such as jackknifing and symmetric resampling. Species delimitation should be consistent among the ingroup and based on a reproducible approach. Although time-consuming and methodologically challenging, specimen-level phylogenetic analysis is a highly useful tool to assess intraspecific variability and provide the basis for a more informed and accurate creation of species-level operational taxonomic units in large-scale systematic studies. It also has the potential to inform us about past speciation processes, morphological trait evolution, and their potential intrinsic and extrinsic drivers in pre-eminent detail.

scholarly journals Mini-barcodes are equally useful for species identification and more suitable for large-scale species discovery in Metazoa than full-length barcodes

2019 ◽  
Author(s):  
Darren Yeo ◽  
Amrita Srivathsan ◽  
Rudolf Meier
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Species Level ◽  
Full Length ◽  
New Techniques ◽  
Species Discovery ◽  
Operational Taxonomic Units ◽  
The Mean ◽  
Window Approach ◽  
Moderate Length

AbstractNew techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared to full-length barcodes. This is here tested based on 20 empirical datasets covering ca. 30,000 specimens and 5,500 species, as well as six clade-specific datasets from GenBank covering ca. 98,000 specimens for over 20,000 species. All specimens in these datasets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (3 windows: 100-bp, 200-bp, 300-bp) and by excising nine mini-barcodes with established primers (length: 94 – 407-bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular Operational Taxonomic Units (mOTUs) that were obtained using three different species delimitation techniques (PTP, ABGD, objective clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length (>200-bp). Only very short mini-barcodes (<200-bp) perform poorly, especially when they are located near the 5’ end of the Folmer region. The mean congruence between morphospecies and mOTUs is ca. 75% for barcodes >200-bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes.

Genetic algorithm for large-scale maximum parsimony phylogenetic analysis of proteins

2005 ◽  
Vol 1725 (1) ◽  
pp. 19-29 ◽  
Author(s):  
Tobias Hill ◽  
Andor Lundgren ◽  
Robert Fredriksson ◽  
Helgi B. Schiöth
Keyword(s):  
Genetic Algorithm ◽  
Phylogenetic Analysis ◽  
Maximum Parsimony ◽  
Large Scale

scholarly journals Longer is Not Always Better: Optimizing Barcode Length for Large-Scale Species Discovery and Identification

2020 ◽  
Vol 69 (5) ◽  
pp. 999-1015 ◽  
Author(s):  
Darren Yeo ◽  
Amrita Srivathsan ◽  
Rudolf Meier
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Species Level ◽  
Full Length ◽  
Data Sets ◽  
New Techniques ◽  
Species Discovery ◽  
Operational Taxonomic Units ◽  
Window Approach ◽  
Prime End

Abstract New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable, and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared with full-length barcodes. This is here tested based on 20 empirical data sets covering ca. 30,000 specimens (5500 species) and six clade-specific data sets from GenBank covering ca. 98,000 specimens ($&gt;$20,000 species). All specimens in these data sets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (three windows: 100 bp, 200 bp, and 300 bp) and by excising nine mini-barcodes with established primers (length: 94–407 bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular operational taxonomic units (mOTUs) that were obtained using three different species delimitation techniques (Poisson Tree Process, Automatic Barcode Gap Discovery, and Objective Clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length ($&gt;$200 bp). Only very short mini-barcodes (&lt;200 bp) perform poorly, especially when they are located near the 5$^\prime$ end of the Folmer region. The mean congruence between morphospecies and mOTUs was ca. 75% for barcodes $&gt;$200 bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes. [DNA barcoding; metabarcoding; mini-barcodes; species discovery.]

scholarly journals Identification of Indian Spiders through DNA barcoding: Cryptic species and species complex

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kaomud Tyagi ◽  
Vikas Kumar ◽  
Shantanu Kundu ◽  
Avas Pakrashi ◽  
Priya Prasad ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Genetic Distances ◽  
Pairwise Distance ◽  
Global Database ◽  
Species Discovery ◽  
Operational Taxonomic Units ◽  
Tree Topologies ◽  
Multiple Species

Abstract Spiders are mega diverse arthropods and play an important role in the ecosystem. Identification of this group is challenging due to their cryptic behavior, sexual dimorphism, and unavailability of taxonomic keys for juveniles. To overcome these obstacles, DNA barcoding plays a pivotal role in spider identification throughout the globe. This study is the first large scale attempt on DNA barcoding of spiders from India with 101 morphospecies of 72 genera under 21 families, including five endemic species and holotypes of three species. A total of 489 barcodes was generated and analyzed, among them 85 novel barcodes of 22 morphospecies were contributed to the global database. The estimated delimitation threshold of the Indian spiders was 2.6% to 3.7% K2P corrected pairwise distance. The multiple species delimitation methods (BIN, ABGD, GMYC and PTP) revealed a total of 107 molecular operational taxonomic units (MOTUs) for 101 morphospecies. We detected more than one MOTU in 11 morphospecies with discrepancies in genetic distances and tree topologies. Cryptic diversity was detected in Pardosa pusiola, Cyclosa spirifera, and Heteropoda venatoria. The intraspecies distances which were as large as our proposed delimitation threshold were observed in Pardosa sumatrana, Thiania bhamoensis, and Cheiracanthium triviale. Further, shallow genetic distances were detected in Cyrtophora cicatrosa, Hersilia savignyi, Argiope versicolor, Phintella vittata, and Oxyopes birmanicus. Two morphologically distinguished species (Plexippus paykulli and Plexippus petersi) showed intra-individual variation within their DNA barcode data. Additionally, we reinstate the original combination for Linyphia sikkimensis based on both morphology and DNA barcoding. These data show that DNA barcoding is a valuable tool for specimen identification and species discovery of Indian spiders.

Species-level phylogenetic analysis of pterocephaliids (Trilobita, Cambrian) from the Great Basin, western USA

2011 ◽  
Vol 85 (6) ◽  
pp. 1128-1153 ◽  
Author(s):  
Melanie J. Hopkins
Keyword(s):  
Phylogenetic Analysis ◽  
Great Basin ◽  
Species Level ◽  
Character State ◽  
State Transformation ◽  
Late Cambrian ◽  
The Family ◽  
Composite Section ◽  
Tree Topologies ◽  
Direct Ancestor

Considerable systematic work devoted to late Cambrian trilobites includes very little species-level phylogenetic analysis. This paper presents the phylogenetic analysis of 36 species representing eight genera assigned to the Family Pterocephaliidae that occur in the Great Basin of the western United States during the Steptoean stage (Furongian). Continuous characters are treated in four different ways: discretization using finite mixture coding, discretization using gap-weighting, “as such” using ranges of values as implemented in the phylogeny program TNT, and exclusion altogether. Results indicate that even the inclusion of only a few continuous characters dramatically increases the resolution of nodes. Despite the different treatments of continuous characters, major features of the trees are shared across all results. The subfamily Pterocephaliinae is restricted to genera which possess a concave anterior border. Relative stratigraphic placement was estimated using a composite section built in CONOP and used to scale the tree topologies and to assess stratigraphic consistency. Although previously hypothesized multispecies evolutionary series are not supported by the results, tree topology, stratigraphic distribution, and optimized character state transformation support the interpretation of several sister taxa as direct ancestor-descendent pairs.

scholarly journals General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways

Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 336
Author(s):  
Boštjan Murovec ◽  
Leon Deutsch ◽  
Blaž Stres
Keyword(s):  
16S Rrna ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Enzymatic Reactions ◽  
Operational Taxonomic Units ◽  
Biochemical Pathways ◽  
Meaningful Information ◽  
Novel Biomarkers ◽  
Reproducible Analysis ◽  
Microbiome Profiling

General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.

scholarly journals Influence of temperature on the larval development of the edible crab, Cancer pagurus

2009 ◽  
Vol 89 (4) ◽  
pp. 753-759 ◽  
Author(s):  
Monika Weiss ◽  
Sven Thatje ◽  
Olaf Heilmayer ◽  
Klaus Anger ◽  
Thomas Brey ◽  
...  
Keyword(s):  
Larval Development ◽  
Body Mass ◽  
Large Scale ◽  
Citrate Synthase ◽  
C:N Ratio ◽  
Intraspecific Variability ◽  
Larval Body ◽  
Influence Of Temperature ◽  
Cancer Pagurus ◽  
Influence Of Temperature On

The influence of temperature on larval survival and development was studied in the edible crab, Cancer pagurus, from a population off the island of Helgoland, North Sea. In rearing experiments conducted at six different temperatures (6°, 10°, 14°, 15°, 18° and 24°C), zoeal development was only completed at 14° and 15°C. Instar duration of the Zoea I was negatively correlated with temperature. A model relating larval body mass to temperature and developmental time suggests that successful larval development is possible within a narrow temperature range (14° ± 3°C) only. This temperature optimum coincides with the highest citrate synthase activity found at 14°C. A comparison for intraspecific variability among freshly hatched zoeae from different females (CW 13–17 cm, N = 8) revealed that both body mass and elemental composition varied significantly. Initial larval dry weight ranged from 12.1 to 17.9 μg/individual, the carbon content from 4.6 to 5.8 μg/individual, nitrogen from 1.1 to 1.3 μg/individual, and the C:N ratio from 4.1 to 4.4. A narrow larval temperature tolerance range of C. pagurus as well as the indication of intraspecific variability in female energy allocation into eggs may indicate a potential vulnerability of this species to climate change. Large-scale studies on the ecological and physiological resilience potential of this commercially fished predator are needed.

Phylogeny accurately predicts behaviour in Indian Ocean Clitaetra spiders (Araneae:Nephilidae)

2009 ◽  
Vol 23 (3) ◽  
pp. 193 ◽  
Author(s):  
Matjaž Kuntner ◽  
Ingi Agnarsson
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
Indian Ocean ◽  
Species Level ◽  
Web Architecture ◽  
Evolutionarily Conserved ◽  
The Family ◽  
Behavioural Biology

Phylogenies are underutilised, powerful predictors of traits in unstudied species. We tested phylogenetic predictions of web-related behaviour in Clitaetra Simon, 1889, an Afro-Indian spider genus of the family Nephilidae. Clitaetra is phylogenetically sister to all other nephilids and thus important for understanding ancestral traits. Behavioural information on Clitaetra has been limited to only C. irenae Kuntner, 2006 from South Africa which constructs ladder webs. A resolved species-level phylogeny unambiguously optimised Clitaetra behavioural biology and predicted web traits in five unstudied species and a uniform intrageneric nephilid web biology. We tested these predictions by studying the ecology and web biology of C. perroti Simon, 1894 on Madagascar and C. episinoides Simon, 1889 on Mayotte. We confirm predicted arboricolous web architecture in these species. The expected ontogenetic allometric transition from orbs in juveniles to elongate ladder webs in adults was statistically significant in C. perroti, whereas marginally not significant in C. episinoides. We demonstrate the persistence of the temporary spiral in finished Clitaetra webs. A morphological and behavioural phylogenetic analysis resulted in unchanged topology and persisting unambiguous behavioural synapomorphies. Our results support the homology of Clitaetra hub reinforcement with the nephilid hub-cup. In Clitaetra, behaviour was highly predictable and remained consistent with new observations. Our results confirm that nephilid web biology is evolutionarily conserved within genera.

Phylogenetic analysis of the subfamily Hylodinae (Anura, Leptodactylidae) based on morphological characters

2005 ◽  
Vol 26 (2) ◽  
pp. 139-147 ◽  
Author(s):  
Francisca do Val ◽  
Paulo Nuin
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
The Other ◽  
The Family

AbstractThe systematics and phylogenetic relationships of the family Leptodactylidae are controversial as is the intrafamilial phylogeny of the leptodactylids. Here we analyze the relationships of the leptodactylid subfamily Hylodinae. This subfamily has been considered to be monophyletic and composed of three genera, Hylodes, Crossodactylus and Megaelosia. In the present study 49 characters were used, based on different studies on Leptodactylidae phylogeny. Maximum parsimony methods with unweighted and successively weighted characters were used to estimate the phylogeny of the Hylodinae. Upon analysis, the data provided further evidence of the monophyletic status of the three genera, with Megaelosia being the basal genus and the other two genera being sister taxa. The analysis with successive weighting results in a more resolved topology of the species subgroups of the genus Hylodes and separates this genus from Crossodactylus and confirms that the hylodines are monophyletic.

Intraspecific variability of morphological characters in the species-rich deep-sea genus Acantholaimus Allgén, 1933 (Nematoda: Chromadoridae)

Nematology ◽  
2016 ◽  
Vol 18 (4) ◽  
pp. 455-473 ◽  
Author(s):  
Dmitry M. Miljutin ◽  
Maria A. Miljutina
Keyword(s):  
Deep Sea ◽  
Intraspecific Variability ◽  
Morphological Characters ◽  
Molecular Data ◽  
Species Discrimination ◽  
Species Differentiation ◽  
Lateral Field ◽  
Operational Taxonomic Units ◽  
General Arrangement ◽  
Taxonomic Approach

Acantholaimusis a species-rich genus of deep-sea nematodes, often with dozens of species found at the same locality but each represented by single or few individuals. Species discrimination by morphological characters in this genus is therefore often difficult due to transitional forms that may be referred to several species because of lack of data on intraspecific variability. The aim of this study was to evaluate the intraspecific variability of morphological characters that are most often used inAcantholaimustaxonomy, in order to distinguish those which are most informative for species differentiation. A reverse taxonomic approach was applied for initial species discrimination. Two loci, one each from small and large subunits of rRNA, were sequenced for 59Acantholaimusspecimens from two deep-sea locations. Twenty-seven Molecular Operational Taxonomic Units (MOTU) were identified, of which 12 were represented by more than one individual. These were then analysed for intraspecific variability in morphological characters. Some of the examined characters showed high intraspecific variability; specifically: length of cephalic setae; distance from anterior end to amphid; shape of anterior setae; position and arrangement of cervical setae. In the absence of genetic data, these characters should be used with caution for differential diagnoses or species discrimination. Other characters were more conservative within the same MOTU: body proportions; length of outer labial setae; amphidial diam.; appearance of lateral field; general arrangement of cervical setae; and shape of tail. These characters may be successfully used for species discrimination in the absence of molecular data.

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