scholarly journals Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)

2020 ◽  
Author(s):  
Jean-Yves Rasplus ◽  
Lillian Jennifer Rodriguez ◽  
Laure Sauné ◽  
Yang-Qiong Peng ◽  
Anthony Bain ◽  
...  
Keyword(s):  
Gc Content ◽  
Indirect Evidence ◽  
Principal Component ◽  
Morphological Plasticity ◽  
Morphological Characters ◽  
Evolutionary Rates ◽  
Morphological Data ◽  
Morphological Evidence ◽  
Ancestral State ◽  
Fig Trees

ABSTRACTDespite their ecological and evolutionary importance as key components of tropical ecosystems, the phylogeny of fig trees is still unresolved. We use restriction-site-associated DNA (RAD) sequencing (ca 420kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus representing all known subgenera and sections and five outgroups. We compare morphological and molecular results to highlight discrepancies and reveal possible inference bias. We analyse marker and taxon properties that may bias molecular inferences, with existing softwares and a new approach based on iterative principal component analysis to reduce variance between clusters of samples. For the first time, with both molecular and morphological data, we recover a monophyletic subgenus Urostigma and a clade with all gynodioecious fig trees. However, our analyses show that it is not possible to homogenize evolutionary rates and GC content for all taxa prior to phylogenetic inference and that four competing positions for the root of the molecular tree are possible. The placement of the long-branched section Pharmacosycea as sister to all other fig trees is not supported by morphological data and considered as a result of a long branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides the genus Ficus into monoecious versus gynodioecious species appears most likely. Active pollination is inferred as the ancestral state for all topologies, ambiguity remains for ancestral breeding system including for the favored topology, and it appears most likely that the ancestor of fig trees was a freestanding tree. Increasing sampling may improve results and would be at least as relevant as maximizing the number of sequenced regions given the strong heterogeneity in evolutionary rates, and to a lesser extent, base composition among species. Despite morphological plasticity and frequent homoplasy of multiple characters, we advocate giving a central role to morphology in our understanding of the evolution of Ficus, especially as it can help detect insidious systematic errors that tend to become more pronounced with larger molecular data sets.

scholarly journals Morphological and genetic diversity of Senecio vulgaris L. (Asteraceae) in Iran

2021 ◽  
Vol 80 (2) ◽  
Author(s):  
Mostafa Ebadi ◽  
Rosa Eftekharian
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Morphological Characters ◽  
Mantel Test ◽  
Morphological Data ◽  
Principal Coordinates Analysis ◽  
Cauline Leaf ◽  
Senecio Vulgaris ◽  
Molecular Features ◽  
Principal Coordinates

Senecio vulgaris L., an annual herb belonging to the Asteraceae, is widely distributed in different regions of the world. There is no information on the intraspecific variations of the morphological and molecular features of this species. In the present investigation, we studied the morphological and genetic diversity of 81 accessions of S. vulgaris collected from 10 geographical populations. Eleven inter simple sequence repeat (ISSR) primers were used for the examination of genetic variations among the populations. Analysis of molecular variance (AMOVA) and GST analyses revealed significant differences among the investigated populations. A significant correlation between genetic distance and geographical distance was revealed by the Mantel test. However, reticulation analysis indicated the occurrence of gene flow among most of the populations studied. Principal component analysis (PCA) plot showed that the number of capitula, length of the cauline leaf and plant height were the most variable morphological characters. Principal coordinates analysis (PCoA) plot revealed two groups of populations, according to molecular and morphological data. The results suggested the existence of possible intraspecific taxonomic ranks within this species.

scholarly journals A Systematic Analysis of the Alpine Saxifrage Complex (Saxifragaceae) in the Canadian Arctic Islands Using Morphology and Chloroplast DNA Data

2004 ◽  
Vol 118 (3) ◽  
pp. 326 ◽  
Author(s):  
Caroline Healy ◽  
Lynn J. Gillespie
Keyword(s):  
Morphological Variability ◽  
Canadian Arctic ◽  
Principal Component ◽  
Distinct Species ◽  
Morphological Characters ◽  
Sympatric Species ◽  
Sensu Stricto ◽  
Morphological Data ◽  
Systematic Analysis ◽  
Site Analysis

The Saxifraga nivalis complex displays significant ecological, morphological and cytological variation. Most European studies suggest that the S. nivalis complex comprises two distinct species: Saxifraga nivalis sensu stricto and Saxifraga tenuis. However, the presence of intermediate morphotypes, inconsistencies in chromosomal counts and variability in morphological keys and descriptions have led to different taxonomic interpretations of the complex in North America. This study investigated the systematics of Canadian Arctic Island members of this complex from 157 specimens using 23 morphological characters. Principal component analysis of the morphological data revealed two adjacent clusters, corresponding to the two taxa and consistent with a close morphological similarity and the presence of hybrids. A preliminary restriction site analysis of five non-coding regions of the chloroplast genome, trnH-trnK, trnT-trnF, trnF-trnV, trnV-rbcL and rbcL-ORF106, was conducted using 21 restriction endonucleases. This analysis indicated a length difference between the trnT-trnF region of S. nivalis and that of S. tenuis, but no difference in restriction sites for any of the assayed regions. These results confirm that in the Canadian Arctic, the S. nivalis complex consists of two closely related, largely sympatric species, with notable morphological variability, and possible hybrids.

scholarly journals Genetic Variability and Diversity Analysis in Pod and Seed Characters of Some Neglected and Underutilized Legumes (NULs)

2019 ◽  
pp. 1-8
Author(s):  
J. O. Agbolade ◽  
T. P. Olakunle ◽  
K. M. Popoola ◽  
J. A. Idowu ◽  
A. I. Isiaka ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Principal Component ◽  
Morphological Characters ◽  
Morphological Data ◽  
Diversity Analysis ◽  
International Institute ◽  
Mean Values ◽  
The Mean ◽  
Pod Length ◽  
100 Seed Weight

In response to the paucity of information challenge on the neglected and underutilized legumes, this paper explored pods and seeds morphological data of the twenty-four accessions of these crops with a view to establishing the occurrence of genetic variability and diversity analysis among the studied taxa. Twenty-four accessions of neglected and underutilized legumes (NULs) obtained from International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria were assessed for genetic variability and diversity analysis through Pod and seed morphological characters. Each accession was planted into plot of 5 ridges of 5 meter long, spaced 1 meter apart and replicated three times at the teaching and research farm of the Federal University Oye Ekiti, Ekiti State, Nigeria. Descriptive statistics was employed to evaluate differences in the mean values of the accessions while discriminatory traits among accessions were identified by Principal Component Analysis (PCA). Similarities among the studied plants were assessed by cluster analysis. The first two principal component axes explained 72% of the total variation. Pod length, pod width and 100-seed weight were traits that contributed most of the variations in the legume accessions. There was a display of intra-species similarities and inter-specific genetic diversity among the studied accessions.

Complementary description of Panonychus caricae Hatzinikolis, 1984, with the resurrection of the genus Sasanychus Ehara, 1978 (Acari, Prostigmata, Tetranychidae)

Zootaxa ◽  
2020 ◽  
Vol 4881 (3) ◽  
pp. 515-531
Author(s):  
TEA ARABULI ◽  
TOMOKO MATSUDA ◽  
MOHAMED W. NEGM ◽  
TETSUO GOTOH
Keyword(s):  
Panonychus Ulmi ◽  
Morphological Data ◽  
Coi Gene ◽  
Morphological Evidence ◽  
Closely Related Species ◽  
World Species ◽  
Maximum Likelihood Tree ◽  
The World ◽  
Morphological Differences ◽  
Fig Trees

A complementary description of Panonychus caricae Hatzinikolis, 1984, is presented based on the morphology of adult female and male individuals collected from fig trees (Ficus sp., Moraceae) in Greece. Morphological differences between Panonychus caricae and two closely related species, Panonychus ulmi (Koch, 1836) and Panonychus hadzhibejliae (Reck, 1947), are discussed. Panonychus caricae can be separated from two other Panonychus species using the length of the female dorsal setae in combination with the ratio between the length of female dorsal opisthosomal setae f2 and h1, and the ratio between the length of dorsal setae sc1 and h1. A phylogenetic maximum likelihood tree was constructed based on the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA (mtDNA) from 10 species of the subgenus Panonychus s.str. (including the re-described species P. caricae) and the only two species of the subgenus Sasanychus. The phylogenetic tree indicates that these 12 species are clearly separated from each other. The two subgenera, Panonychus s.str. and Sasanychus, comprise strongly supported monophyletic clades with 98% bootstrap values. The convergence of molecular and morphological data (dorsal setae set on tubercles or not, number of tactile setae on tibiae I and II, and patterns of the dorsocentral striae) suggests that Sasanychus should not be classified under the genus Panonychus. Consequently, molecular and morphological evidence supports the resurrection of the genus Sasanychus, which contains two species, S. akitanus (Ehara) and S. pusillus Ehara & Gotoh, as distinct from Panonychus. A key to the world species of Panonychus and Sasanychus is also provided.

Taxonomic revision of Carex chungii (Cyperaceae; sect. Mitratae) and allied species

Phytotaxa ◽  
2017 ◽  
Vol 317 (1) ◽  
pp. 29
Author(s):  
XIAO-FENG JIN
Keyword(s):  
Principal Component Analysis ◽  
Entire Range ◽  
Principal Component ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Literature Survey ◽  
The Other ◽  
Morphological Data ◽  
Herbarium Specimens ◽  
Specific Rank

In this paper, Carex chungii and other five names at species rank, plus one variety and one form, all from of C. sect. Mitratae, were revised. They constitute a group of morphologically very similar taxa, difficult to tell apart. Our study was based on literature survey, fieldwork, herbarium specimens, statistical analysis of morphological characters and SEM observations of achenes and perigynia. Analysis of morphological data of 94 individuals from eleven populations using principal component analysis (PCA) revealed five clusters, which we consequently considered to correspond to five species. The achenes of Carex genkaiensis were strikingly different from all the other species regarding achene apex contracted into a 0.2–0.5 mm long neck-like appendage (vs. into a discoid-annulate style-base), as well as its perigynium indumentum (pubescent vs. sparsely pubescent). Carex anhuiensis, C. xuanchengensis and C. truncatirostris f. erostris are all synonymized to C. truncatirostris. The previously recognized Carex kamagariensis from Japan is synonymized to C. chungii. Carex chungii var. rigida is recognized as specific rank and the new name C. nanpingensis is proposed. Our study is the first effort to address the taxonomy of this complicate group as a whole in its entire range.

scholarly journals Distribution, variation, and relationship of Curcuma soloensis Valeton in Java, Indonesia based on morphological characters

2020 ◽  
Vol 21 (8) ◽  
Author(s):  
MUHAMAD JALIL ◽  
AZIZ PURWANTORO ◽  
BUDI SETIADI DARYONO ◽  
Purnomo PURNOMO
Keyword(s):  
Leaf Blade ◽  
Solomon Islands ◽  
Curcuma Longa ◽  
Leaf Shape ◽  
Principal Component ◽  
Morphological Characters ◽  
Morphological Data ◽  
Flesh Color ◽  
Central Java ◽  
Relationship Of

Abstract. Jalil M, Purwantoro A, Daryono BS, Purnomo. 2020. Distribution, variation, and relationship of Curcuma soloensis Valeton in Java, Indonesia based on morphological characters. Biodiversitas 21: 3867-3877. Curcuma soloensis Valeton (locally called temu genyeh) was a plant originating from Solomon Islands and was synonymous with Curcuma longa L. This plant was often considered to be turmeric (Curcuma longa Linn.) or temulawak (Curcuma zanthorrhiza Roxb.), because the rhizome is almost the same color. The purpose of this study was to determine the distribution, variation, and relationship of C. soloensis in Java, Indonesia. Retrieval of data with exploratory roaming methods in 12 districts/cities in Java Island as a center for planting medicinal plants. Morphological character observations were made on habit, rhizome, roots, tubers, leaves, pseudo-stems, and flowers. Morphological data were analyzed by descriptive and numerical methods. Analysis of grouping with Gower Coefficients because it uses 45 binary and multistate data. Principal Component Analysis (PCA) was performed to determine the role of each character in the grouping. Cluster analysis and PCA graphics were assisted with MVSP 3.1 software. The results of the study were obtained from 25 accessions of C. soloensis in East Java (Trenggalek, Pacitan, Ponorogo), Central Java (Wonogiri, Karanganyar, Magelang, Semarang), Yogyakarta (Yogyakarta City, Bantul, Gunungkidul), and West Java (Ciamis and Tasikmalaya). The variation of C. soloensis lies in habit, stem color, leaf shape, rhizome shape, rhizome flesh color, and tuber shape. The highest abundance percentage is in Pajangan, Tirtomoyo, and Tawangmangu. The dendrogram divides 32 OTUs into two clusters on the phenon line 0.617, namely cluster A (C. zanthorrhiza) and cluster B (C. soloensis and C. longa). PCA results showed that the characters that had the most role in grouping were leaf blade color, leaf blade length, rhizome shape, root color, rhizome taste, outer and inner rhizome flesh color.

scholarly journals Diversity of Sambucus nigra pollen within Slovakia in selected morphological characters by SEM study

2020 ◽  
Vol 28 (4) ◽  
pp. 399-404
Author(s):  
V. Horčinová Sedláčková ◽  
O. Grygorieva ◽  
I. Gurnenko ◽  
O. Vergun
Keyword(s):  
Principal Component Analysis ◽  
Morphological Characteristics ◽  
Pollen Grains ◽  
Principal Component ◽  
Component Analysis ◽  
Morphological Data ◽  
Morphological Evidence ◽  
Sambucus Nigra ◽  
Important Indicator ◽  
Exine Ornamentation

This study analyzed pollen morphology and characteristics of 20 Sambucus nigra L. genotypes from populations of various ecotypes and geographical localities from the territory of Slovakia. We used principal component analysis to explore variability in pollen grain size (polar and equatorial diameter), shape, aperture type, and exine ornamentation by scanning electron microscopy. The combination of these morphological characteristics and ultrastructure allows us to determine the differences or similarities between the same and various species and genotypes, which may be a useful tool for systematics with significant diagnostic value. The findings confirmed small differences among the genotypes in measured traits with polar and equatorial diameters in the range from 22.30 to 26.64 μm and from 12.81 to 14.45 μm, respectively. Shape index (P/E ratio) depending on elongation or roundness of pollen grains varied from 1.66 to 2.02. Hierarchical cluster analysis (HCA) and principal component analysis (PCA) of morphological data helped to compare evaluated morphometric parameters and identified three closely related groups. It was noted that the diversity of surface sculpturing of pollen grains in combination with their shape and size enables us to use a complex of fine morphologic signs for S. nigra pollen identification. Pollen data combined with other morphological evidence (e.g., floral characters) have more recently become an important indicator of which genotypes may be the best representatives of species.

scholarly journals Taxonomic revision of the genus Elmomorphus Sharp, 1888 I. Japanese and Korean species (Coleoptera: Dryopidae)

2021 ◽  
Vol 758 ◽  
Author(s):  
Ján Kodada ◽  
Dávid Selnekovič ◽  
Manfred A. Jäch ◽  
Katarína Goffová ◽  
Peter Vďačný
Keyword(s):  
Mitochondrial Gene ◽  
Principal Component ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Evidence ◽  
Morphometric Variation ◽  
Morphometric Characters ◽  
Gene Coding ◽  
Interspecific Divergence

The species of Elmomorphus Sharp, 1888 occurring in Japan and Korea are redescribed and illustrated: E. brevicornis Sharp, 1888 (Japan, Korea) and E. amamiensis Nomura, 1959 (Japan). The standard barcoding fragment of the mitochondrial gene coding for cytochrome c oxidase subunit I (COI) was sequenced and used together with morphological characters to delimit the taxonomic boundaries of the two species. To assess their morphometric variation, eight morphometric characters were measured and statistically evaluated using principal component analysis. The two species of Elmomorphus formed distinct and well-separated clusters in the COI tree. Their interspecific divergence is very high, ranging from 22.7 to 23.9%. On the other hand, morphometric characters, including those previously presumed to be diagnostic, overlap and per se do not allow unambiguous species identification. Reliable morphological distinguishing characters are described for males and females. Molecular data along with the morphological evidence strongly confirm the species status of E. amamiensis. An identification key to the Japanese and Korean species is provided.

scholarly journals Integrative taxonomy of the new millipede genus Coxobolellus, gen. nov. (Diplopoda : Spirobolida : Pseudospirobolellidae), with descriptions of ten new species

2020 ◽  
Author(s):  
Piyatida Pimvichai ◽  
Henrik Enghoff ◽  
Somsak Panha ◽  
Thierry Backeljau
Keyword(s):  
New Species ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Sequence Divergence ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
Morphological Data ◽  
Morphological Evidence ◽  
Morphological Differences

Pseudospirobolellidae is a poorly known family of spirobolidan millipedes with only two genera and five described species. Yet, the descriptive taxonomy and molecular systematics of this group have been largely neglected. Therefore, the present work presents an integrative taxonomic study of new pseudospirobolellid taxa in Thailand. To this end, two mitochondrial gene fragments (COI and 16S rRNA) combined with morphological characters were used to define the genus Coxobolellus, gen. nov. with 10 new species, viz. C. albiceps, sp. nov., C. compactogonus, sp. nov., C. fuscus, sp. nov., C. nodosus, sp. nov., C. serratus, sp. nov., C. simplex, sp. nov., C. tenebris, sp. nov., C. tigris, sp. nov., C. transversalis, sp. nov. and C. valvatus, sp. nov. The interspecific COI sequence divergences among the new species ranged from 6 to 15%. The intergeneric COI sequence divergence between species of Coxobolellus, gen. nov., Benoitolus birgitae and Pseudospirobolellus sp. ranged from 20 to 23%. Three major morphological differences separate Coxobolellus, gen. nov. from Benoitolus and Pseudospirobolellus, namely (1) the protruding process on the 3rd (and 4th) coxae on male legs, (2) the posterior gonopod telopodite divided into two parts, and (3) a conspicuous opening pore at the mesal margin at the end of the coxal part of the posterior gonopod. Thus, the new genus is well supported by both mtDNA and morphological evidence, while the delimitation of the 10 new species is supported by the congruence between mtDNA and morphological data. Yet, with respect to the relationships of Benoitolus birgitae, morphological data suggest a similarity with Coxobolellus, gen. nov. and Pseudospirobolellus, whereas mtDNA data place this species in the Pachybolidae. Further phylogenetic analyses are needed to explore this apparent incongruence and test the monophyly of Pseudospirobolellidae.

Morphological and molecular characterisation of Panagrellus spp. (Cephalobina: Panagrolaimidae): taxonomic status and phylogenetic relationships

Nematology ◽  
2006 ◽  
Vol 8 (6) ◽  
pp. 921-938 ◽  
Author(s):  
S. Patricia Stock ◽  
Steven Nadler
Keyword(s):  
Sequence Data ◽  
Principal Component ◽  
Taxonomic Status ◽  
Single Species ◽  
Morphological Characters ◽  
Morphological Data ◽  
Lsu Rdna ◽  
Type Specimens ◽  
Worldwide Distribution ◽  
Tree Topologies

AbstractThe genus Panagrellus currently comprises 12 known species. These nematodes have a worldwide distribution and have been found in a variety of habitats such as slime flux, thermal springs, insect frass and spoiled cider. Diagnosis of Panagrellus species is rather problematic since few morphological features can be used to discriminate between species and the original publications do not indicate the number of specimens measured and lack standard descriptions of variance. In this study we review the taxonomic status of several species from this genus combining classical morphological data and molecular sequences. Eleven live isolates and fixed material from currently available type specimens representing six Panagrellus species were included. Morphological analysis included the examination of qualitative and quantitative characters of males and females. The taxonomic utility of morphometric data was evaluated by means of multivariate statistics (principal component and canonical discriminant analyses). Phylogenetic inference was based on analysis of nucleotide sequences from the LSU rDNA gene and morphological characters. Parsimony tree topologies inferred from nucleotide datasets strongly supported monophyly of the P. dubius isolates, but not the P. redivivus isolates. Phylogenetic interpretation of these rDNA sequence data suggests that both the P. redivivus and P. dubius isolates each include more than a single species. Only two of the 15 morphological characters evaluated were variable within the ingroup taxa. A long spicule bifurcation length maps on the combined evidence trees as a putative synapmorphy for P. dubius, whereas male D% was homoplastic within isolates of that species. The diagnosis of the genus Panagrellus is emended.

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