Phylogenetic analysis of the Australian Salicornioideae (Chenopodiaceae) based on morphology and nuclear DNA

2005 ◽  
Vol 18 (1) ◽  
pp. 89 ◽  
Author(s):  
K. A. Shepherd ◽  
T. D. Macfarlane ◽  
M. Waycott
Keyword(s):  
Morphological Analysis ◽  
Nuclear Dna ◽  
Population Level ◽  
Bootstrap Support ◽  
Closely Related Species ◽  
Molecular Analyses ◽  
Strong Bootstrap Support ◽  
Tribal Classification ◽  
Molecular Characters

The Salicornioideae Kostel. are distinctive among the Chenopodiaceae Venet.. However, their phylogenetic relationships are poorly understood. Analyses of morphological and molecular characters were undertaken to evaluate relationships within the subfamily and to test the monophyly of the endemic Australian genera Halosarcia Paul G. Wilson, Pachycornia Hook.f., Sclerostegia Paul G. Wilson, Tecticornia Hook.f. and Tegicornia Paul G. Wilson. Kalidium Moq. and Halopeplis Bunge ex Ung.-Sternb. of the tribe Halopeplideae were used as outgroup representatives in the morphological analysis and resolved sister to the tribe Salicornieae. Allenrolfea Kuntze; Halocnemum Bieb. and Heterostachys Meyer formed an early branching group sister to a moderately supported clade comprised of the remaining Salicornieae. Only terminal groups of closely related species received significant bootstrap support in this analysis. In contrast, the current tribal classification of the Salicornioideae was not supported in the molecular analysis as Allenrolfea occidentalis Kuntz (tribe Salicornieae) positioned sister to Kalidium foliatum Moq. (tribe Halopeplideae) and the remaining Salicornieae. Three major clades received strong bootstrap support: Microcnemum+Arthrocnemum, Sarcocornia+Salicornia, and the endemic Australian genera. None of the endemic Australian genera was individually supported as monophyletic in either the morphological or the molecular analyses. Subspecies complexes, polyploids and hybrids may contribute to the lack of resolution and apparently high levels of homoplasy in the morphological analysis. A greater understanding of population level processes is required to begin to resolve the phylogeny of this complex group.

scholarly journals Recovery of Chloroplast Genomes from Medieval Millet Grains Excavated from the Areni-1 Cave in Southern Armenia

2021 ◽  
Author(s):  
Stephen M. Richards ◽  
Leiting Li ◽  
James Breen ◽  
Nelli Hovhannisyan ◽  
Oscar Estrada ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Demographic History ◽  
Northern China ◽  
Haplotype Network ◽  
Bootstrap Support ◽  
Hybridization Capture ◽  
Chloroplast Genomes ◽  
Broomcorn Millet ◽  
Strong Bootstrap Support ◽  
The Rich

Abstract Broomcorn millet (Panicum miliaceum L.) was domesticated in northern China at least 7,000 years ago and was subsequentially adopted as a cereal in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, a region that has an important history in crop domestication. The rich botanical material found at Areni-1 includes grains identified by morphology as broomcorn millet that were 14C dated to the medieval era (873 ± 36 CE and 1118 ± 35 CE). To retrace the demographic history of these broomcorn millet samples, we used ancient DNA extraction and hybridization capture enrichment to sequence and assemble three chloroplast genomes from the Areni-1 grains and then compared these sequences to 50 modern chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity and little inference on broomcorn demography could be made. However, in a phylogeny the chloroplast genomes separated into two clades with strong bootstrap support, similar to what has been reported for nuclear DNA from broomcorn millet. In a haplotype network, the chloroplast genomes of two accessions of wild (undomesticated) broomcorn millet contained a relatively large number of variants, 11 SNPs. These SNPs were not present in the domesticated varieties, suggesting these wild accessions may not be directly related to the lineages that underwent domestication or that broomcorn millet may have undergone a domestication bottleneck resulting in lost diversity in the chloroplast genome. These results demonstrate that broomcorn millet from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.

scholarly journals Comparative Morphological, Ultrastructural, and Molecular Studies of Four Cicadinae Species Using Exuvial Legs

Insects ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 199 ◽  
Author(s):  
Jun-Ho Song ◽  
Wook Jin Kim ◽  
Ji-Min Cha ◽  
Sungyu Yang ◽  
Goya Choi ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Morphological Analysis ◽  
Surface Pattern ◽  
Bootstrap Support ◽  
Diagnostic Features ◽  
Closely Related Species ◽  
Monophyletic Cluster ◽  
High Bootstrap ◽  
Methodological Approaches ◽  
Leg Morphology

Previous studies have suggested that exuviae can be used for the identification of cicada species, but the precise characteristics that differ among species have not been determined. Thus, we performed the first comparative analyses of the leg morphology, ultrastructure, and mitochondrial DNA sequences of exuviae of four dominant cicada species in Korea, Hyalessa maculaticollis (Motschulsky, 1866), Meimuna opalifera (Walker, 1850), Platypleura kaempferi (Fabricius, 1794) and Cryptotympana atrata (Fabricius, 1775), the source of Cicadidae Periostracum, a well-known traditional medicine. A morphological analysis revealed that the profemur length, femoral tooth angle, and distance between the intermediate and last tooth of the femoral comb are useful characteristics for identification. We also evaluated the usefulness of the size, degree of reflex, and number of spines on the mid-legs and hind legs as diagnostic features. An ultrastructural study showed that Meimuna opalifera has a unique surface pattern on the legs. The sequences obtained using exuviae were identical to previously obtained sequences for adult tissues. Moreover, in a phylogenetic analysis using CO1 sequences, each species formed a monophyletic cluster with high bootstrap support. Accordingly, multiple methodological approaches using exuviae might provide highly reliable identification tools. The integrative data provide useful characteristics for the exuviae-based identification of closely related species and for further taxonomic and systematic studies of Cicadinae.

New subtribe Pachitinae (Orchideae) of Orchidaceae: Evidence from morphological and molecular analyses

Phytotaxa ◽  
2017 ◽  
Vol 329 (2) ◽  
pp. 114
Author(s):  
GUI-ZHEN CHEN ◽  
JIE HUANG ◽  
GUO-QIANG ZHANG ◽  
LIANG MA ◽  
SHI-PIN CHEN
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Molecular Analyses ◽  
Taxonomic Treatment

The subtribal delimitation and relationships of Orchideae remain unresolved. In the present study, the phylogenetic relationships among all subtribes of Orchideae were reconstructed, utilizing five plastid and two nuclear DNA sequences (rbcL, trnS-trnG, matK, trnL-F, psbA-trnH, Xdh and ITS) from 178 taxa of Orchideae. The combined results show that most clades are successively sister to the grade of clades representing antecedently accepted subtribes, but Pachites and Huttonaea do not belong to the previous classification of Disinae. In contrast, these two genera represent two additional isolated lineages. On this basis, a new subtribe, Pachitinae, is tentatively proposed to accommodate this taxon. Also, the subtribe Huttonaeinae Schltr. was recovered (1926: 568). In addition to the taxonomic treatment of this subtribe, the delimitation of many related subtribes in Orchideae is discussed.

Morphological Evolution in the Mulberry Family (Moraceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 530-552 ◽  
Author(s):  
Wendy L. Clement ◽  
George D. Weiblen
Keyword(s):  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Nuclear Dna ◽  
Morphological Evolution ◽  
Molecular Data ◽  
Breeding Systems ◽  
Pollination Syndromes ◽  
Character Matrix ◽  
Tribal Classification

The mulberry family Moraceae comprises 37 genera and approximately 1,100 species distributed throughout tropical and temperate regions worldwide. Moraceae exhibit a complex array of inflorescence architectures, breeding systems, and pollination syndromes, which forms the basis of traditional taxonomic classification. However, morphologically based classification conflicts with evolutionary relationships proposed by molecular phylogenetics. In this study we assembled a morphological character matrix for analysis separately and in combination with existing molecular data. We evaluated 81 vegetative, reproductive, and wood anatomical characters for 94 species representing nearly all Moraceae genera. Using parsimony and Bayesian methods, these characters were evaluated with respect to ndhF chloroplast and 26S nuclear DNA sequences. Topological comparisons tested whether opposing classification schemes are more or less supported by the data. Results did not support any classification of Moraceae based on morphology. We present a revised tribal classification and describe a new tribe, Maclureae, revise the membership of tribe Castilleae and describe two subtribes, Castillineae and Antiaropsineae, and reinstate the genera Malaisia (including Malaisia scandens) and Sloetia (including Sloetia elongata). Lastly we discuss the evolution of inflorescence architecture in relation to other floral features.

Defining new dung beetle tribes to resolve discrepancies between phylogeny and tribal classification in the subfamily Scarabaeinae (Coleoptera: Scarabaeidae)

Zootaxa ◽  
2019 ◽  
Vol 4608 (1) ◽  
pp. 131 ◽  
Author(s):  
ADRIAN L.V. DAVIS ◽  
CHRISTIAN M. DESCHODT ◽  
CLARKE H. SCHOLTZ
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Analytical Methods ◽  
Dung Beetle ◽  
Morphological Characters ◽  
Bootstrap Support ◽  
Strong Bootstrap Support ◽  
History Of ◽  
Tribal Classification ◽  
Partial Revision

The monophyletic, dung beetle subfamily, Scarabaeinae, has a long history of subdivision into tribes and subtribes represented by groups of genera unified by designated characters. Various tribal names have been proposed although only 11 or 12 were considered valid in recent reviews. Three of these 12 tribes have now been invalidated due to extensive polyphyly indicated by both morphological and molecular phylogenies. Although partial revision of tribal classification was proposed in the most recent global molecular phylogeny of the subfamily, this was primarily limited to redefinition of membership or provision of support for pre-existing tribes. Complete revision was not attempted as the phylogeny examined interrelationships between only ~52% of the valid described genera. It was also hampered by inconsistencies in topology using different analytical methods, weakened by limited bootstrap support for many basal nodes, as well predicting several phylogenetic relationships that seemed anomalous with regards to biogeographical hypotheses. Nevertheless, using this phylogeny, we propose further revision of tribal classification in a clade of primarily African genera included within a group defined as “basal Scarabaeinae”. Using three different methods, the sister lineages of this clade were consistently recovered, mostly with strong bootstrap support for their molecular relatedness. Therefore, we provide a number of defining morphological characters to support their proposed designation as three new tribes: Byrrhidiini, Endroedyolini and Odontolomini. We also discuss approaches to a full tribal revision as well as the implications for historical biogeography of the Scarabaeinae. 

Geographic variation, phylogeny and systematic status of Gracilinanus microtarsus (Mammalia: Didelphimorphia: Didelphidae)

Zootaxa ◽  
2011 ◽  
Vol 2761 (1) ◽  
pp. 1 ◽  
Author(s):  
SIMONE LÓSS ◽  
LEONORA PIRES COSTA ◽  
YURI L. R. LEITE
Keyword(s):  
Molecular Phylogeny ◽  
Geographic Variation ◽  
Morphological Characters ◽  
Morphological Data ◽  
Southern Brazil ◽  
Morphological Classification ◽  
Molecular Analyses ◽  
Paraphyletic Group ◽  
Molecular Characters

The gracile mouse opossum Gracilinanus microtarsus occurs mainly along the Atlantic forest of eastern and southern Brazil. Earlier studies revealed high levels of genetic divergence among samples across its range. Here, we analyzed the congruence of geographic variation between molecular and morphological characters to evaluate whether the populations that have been segregated by molecular divergence represent more than one species, as previously suggested. We examined 195 specimens of G. microtarsus, 94 of G. agilis, and 12 of Cryptonanus sp., and inferred a phylogeny based on 25 discrete morphological characters. We compared this result with a phylogeny based on partial cytochrome b sequences of 27 specimens. The monophyly of the genus, and of both G. microtarsus and G. agilis were corroborated by morphological and molecular analyses. The molecular phylogeny recovered three clades, and the morphological data indicated three distinct lineages, which also segregated in morphometric space, indicating the possibility of occurrence of three cryptic species within what is currently identified as G. microtarsus. However, morphological and molecular phylogenies were not completely congruent, and the morphological classification of the specimens included in the molecular analysis resulted in a paraphyletic group in the molecular phylogeny. Hence, our results suggest that G. microtarsus represents one species, diagnosable by morphological and molecular characters, showing strong morphological and molecular variation throughout its distributional range.

scholarly journals The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Growth Hormones ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

scholarly journals The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ying-ying Ye ◽  
Jing Miao ◽  
Ya-hong Guo ◽  
Li Gong ◽  
Li-hua Jiang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Phylogenetic Studies ◽  
Gc Skew ◽  
Strong Bootstrap Support

AbstractThe complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

scholarly journals Hip Fracture Types in Canadian Men and Women Change Differently with Age: A Population-Level Analysis

2016 ◽  
Vol 9 ◽  
pp. CMAMD.S38531 ◽  
Author(s):  
Richard G. Crilly ◽  
Marita Kloseck ◽  
Selam Mequanint
Keyword(s):  
Hip Fracture ◽  
Relative Proportion ◽  
Local Population ◽  
Population Level ◽  
Community Dwelling ◽  
Administrative Database ◽  
Fracture Type ◽  
Discharge Abstract Database ◽  
Fracture Types

Background We have previously reported a gender difference in the occurrence of hip fracture type with age in our local population. In the current report, we have explored this phenomenon in a Canadian population using five years of data from a national administrative database. We have compared community-dwelling and institutionalized individuals to determine if frailty is important and has a differential effect on the type of hip fracture experienced. Methods Hospitalization records from 2005 to 2009, in which the most responsible diagnosis, that is the diagnosis causing the admission to hospital, was a hip fracture, were obtained from the Discharge Abstract Database of the Canadian Institute for Health Information. Hip fracture type was identified using the Canadian Classification of Health Interventions and the International Classification of Diseases 10th Revision, Canada (ICD-10-CA). Hip fracture proportions were calculated for the study period and stratified by age group and sex. Results The relative proportion of intertrochanteric fractures in women rose from 35% in the youngest group (55–59 years) to 51% in the oldest group (84+ years; P < 0.0001). In men, the proportions remain relatively stable (47% and 44%, respectively). Community and institutionalized patients showed the same pattern. Conclusions The change in the proportion of the two hip fracture types that occur in women but not men may point to differences in the etiology and consequently the approaches to prevention for the two fracture types. Level of frailty did not seem to be important.

Salicornia cuscoensis (Amaranthaceae/Chenopodiaceae), a new species from Peru (South America)

Phytotaxa ◽  
2017 ◽  
Vol 319 (3) ◽  
pp. 254 ◽  
Author(s):  
M. ÁNGELES ALONSO ◽  
MANUEL B. CRESPO ◽  
HELMUT FREITAG
Keyword(s):  
New Species ◽  
South America ◽  
Morphological Characters ◽  
Tierra Del Fuego ◽  
South American ◽  
Habitat Distribution ◽  
Closely Related Species ◽  
Molecular Analyses ◽  
Southern Patagonia ◽  
A New Species

The name Salicornia cuscoensis given to a plant from high Andean saltmarshes near Cusco [Cuzco] and Ayacucho, Peru (South America) is validated by a diagnosis and description. The main morphological characters that separate S. cuscoensis from other closely related species are creeping habit, delicate branches, inflorescence of short and thin spikes, and seed indumentum. The new species clearly differs from other perennial Salicornia taxa growing in high Andean saltmarshes such as S. pulvinata and S. andina. The former forms small compact cushions producing very short, few-flowered inflorescences. The latter shows woody stems and forms larger rounded carpets. Morphologically, S. cuscoensis is also similar to S. magellanica, a species growing along the seashore in southern Patagonia and Tierra del Fuego, but the latter has shorter and wider inflorescences and larger seeds with a different type and arrangement of indumentum. Molecular analyses also supported the separation of S. cuscoensis. Data on habitat, distribution and phylogenetic relationships are presented for the new species and its relatives, and an identification key is given for the South American taxa of the genus Salicornia.

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