The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics

2014 ◽  
Vol 27 (6) ◽  
pp. 1078-1092 ◽  
Author(s):  
A. Watanabe ◽  
D. E. Slice
Keyword(s):  
Geometric Morphometrics ◽  
Phylogenetic Inference ◽  
Cranial Ontogeny

Classifying camel breeds using geometric morphometrics: A case study in Kuwait

2019 ◽  
Vol 230 ◽  
pp. 103824
Author(s):  
Bader H. Alhajeri ◽  
Randa Alaqeely ◽  
Hasan Alhaddad
Keyword(s):  
Geometric Morphometrics

scholarly journals A Comparison of Traditional and Geometric Morphometric Techniques for the Study of Basicranial Morphology in Horses: A Case Study of the Araucanian Horse from Colombia

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 118
Author(s):  
Pere Miquel Parés-Casanova ◽  
Arcesio Salamanca-Carreño ◽  
René Alejandro Crosby-Granados ◽  
Jannet Bentez-Molano
Keyword(s):  
Geometric Morphometrics ◽  
Domestic Animal ◽  
New Techniques ◽  
Geometric Morphometric ◽  
Animal Populations ◽  
Morphometric Methods ◽  
Mature Group ◽  
Geometric Morphometric Analysis ◽  
Shape And Size

Skull size and shape have been widely used to study domestic animal populations and breeds. Although several techniques have been proposed to quantify cranial form, few attempts have been made to compare the results obtained by different techniques. While linear morphometrics has traditionally been used in breed characterization, recent advances in geometric morphometrics have created new techniques for specifically quantifying shape and size. The objective of this study was to compare two morphometric methods for their ability to describe external morphology. For this purpose, 20 skull specimens of adult male Araucanian horses were examined. Two age categories were established (the “mature group”, M3 not fully erupted to moderately worn, n = 7; and the “senile group”, M3 totally erupted and highly worn, n = 13). Both methods showed that there were statistical differences between generations, but discrimination rates were different between methods with the geometric morphometric analysis obtaining a rate of 97.5%. Although linear morphometrics was found to be compatible with geometric morphometrics, the latter was better able to discriminate the two groups and it also provides more information on shape.

scholarly journals A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Thomas H. A. Ederveen ◽  
Jos P. H. Smits ◽  
Karima Hajo ◽  
Saskia van Schalkwijk ◽  
Tessa A. Kouwenhoven ◽  
...  
Keyword(s):  
Phylogenetic Inference ◽  
Species Level ◽  
Single Locus ◽  
Bioinformatics Pipeline ◽  
Discriminative Ability ◽  
Staphylococcus Capitis ◽  
Complex Microbial Community ◽  
Reference Genomes

AbstractWe present TaxPhlAn, a new method and bioinformatics pipeline for design and analysis of single-locus sequence typing (SLST) markers to type and profile bacteria beyond the species-level in a complex microbial community background. TaxPhlAn can be applied to any group of phylogenetically-related bacteria, provided reference genomes are available. As TaxPhlAn requires the SLST targets identified to fit the phylogenetic pattern as determined through comprehensive evolutionary reconstruction of input genomes, TaxPhlAn allows for the identification and phylogenetic inference of new biodiversity. Here, we present a clinically relevant case study of high-resolution Staphylococcus profiling on skin of atopic dermatitis (AD) patients. We demonstrate that SLST enables profiling of cutaneous Staphylococcus members at (sub)species level and provides higher resolution than current 16S-based techniques. With the higher discriminative ability provided by our approach, we further show that the presence of Staphylococcus capitis on the skin together with Staphylococcus aureus associates with AD disease.

scholarly journals Deciphering the Taxonomic Delimitation of Ottelia acuminata (Hydrocharitaceae) Using Complete Plastomes as Super-Barcodes

2021 ◽  
Vol 12 ◽  
Author(s):  
Yunheng Ji ◽  
Jin Yang ◽  
Jacob B. Landis ◽  
Shuying Wang ◽  
Zhenyan Yang ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Management Practices ◽  
Conservation Management ◽  
Species Conservation ◽  
Phylogenetic Inference ◽  
Independent Sequence ◽  
Varietal Identification ◽  
Effective Conservation ◽  
Conservation And Management

Accurate species delimitation and identification, which is a challenging task in traditional morphology-based taxonomy, is crucial to species conservation. Ottelia acuminata (Hydrocharitaceae) is a severely threatened submerged macrophyte endemic to southwestern China. The taxonomy of O. acuminata, which has long been in dispute, remains unresolved, impeding effective conservation and management practices. Here, we aim to address the long-standing issues concerning species boundary and intraspecific subdivision of O. acuminata using complete plastome sequences as super-barcodes. The taxonomic delimitation of O. acuminata was explored using phylogenetic inference and two independent sequence-based species delimitation schemes: automatic barcode gap discovery (ABGD) and multi-rate Poisson tree processes (mPTP). The reciprocally reinforcing results support the reduction of the closely related congeneric species, O. balansae and O. guanyangensis, as two conspecific varieties of O. acuminata. Within the newly defined O. acuminata, accurate varietal identification can be achieved using plastome super-barcodes. These findings will help inform future decisions regarding conservation, management and restoration of O. acuminata. This case study suggests that the use of plastome super-barcodes can provide a solution for species delimitation and identification in taxonomically difficult plant taxa, thus providing great potential to lessen the challenges of inventorying biodiversity, as well as biologically monitoring and assessing threatened species.

Size matters: the effects of ontogenetic disparity on the phylogeny of Trematopidae (Amphibia: Temnospondyli)

2020 ◽  
Vol 190 (1) ◽  
pp. 79-113
Author(s):  
Bryan M Gee
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Phylogenetic Inference ◽  
Type Specimens ◽  
Directional Bias ◽  
Skull Length ◽  
Size Disparity ◽  
Tree Topologies

Abstract Trematopids are a clade of terrestrial Permo-Carboniferous temnospondyl amphibians. The intrarelationships of this clade are poorly known. This is largely attributable to a substantial disparity in size between type specimens, which range from the small-bodied lectotype of Mattauschia laticeps (< 4 cm skull length) to the large-bodied holotype of Acheloma cumminsi (> 15 cm skull length). Inferred correlation of size disparity with ontogenetic disparity has led previous workers either to omit taxa in phylogenetic analyses or to forgo an analysis altogether. Here, I take a specimen-level approach and multiple subsampling permutations to explore the phylogeny of the Trematopidae as a case study for assessing the effects of ontogenetic disparity on phylogenetic reconstruction in temnospondyls. The various analyses provide evidence that ontogenetic disparity confounds the phylogenetic inference of trematopids but without a directional bias. Tree topologies of most permutations are poorly resolved and weakly supported, reflecting character conflict that results from the inability of the analyses to differentiate retained plesiomorphies from juvenile features. These findings urge caution in the interpretation of phylogenetic analyses for which ontogenetic disparity exists, but is unaccounted for, and provide a strong impetus for more directed exploration of the interplay of ontogeny and phylogeny across Temnospondyli.

scholarly journals Taxonomic identification using virtual palaeontology and geometric morphometrics: a case study of Jurassic nerineoidean gastropods

Palaeontology ◽  
2020 ◽  
Author(s):  
Yael Leshno Afriat ◽  
Yael Edelman‐Furstenberg ◽  
Rivka Rabinovich ◽  
Jonathan A. Todd ◽  
Hila May
Keyword(s):  
Geometric Morphometrics ◽  
Taxonomic Identification
Sign in / Sign up

Export Citation Format

Share Document