scholarly journals Phylogenetic signal of orbicules at family level: Rubiaceae as case study

Taxon ◽  
2011 ◽  
Vol 60 (3) ◽  
pp. 742-757 ◽  
Author(s):  
Brecht Verstraete ◽  
Inge Groeninckx ◽  
Erik Smets ◽  
Suzy Huysmans
Keyword(s):  
Phylogenetic Signal ◽  
Family Level

scholarly journals Pułapka współuzależnienia w rodzinie z problemem alkoholowym

2016 ◽  
pp. 141-159
Author(s):  
Katarzyna Błaszczuk
Keyword(s):  
Adult Life ◽  
Family Intervention ◽  
Her Family ◽  
Daily Routines ◽  
Drinking Problem ◽  
Significant Damage ◽  
The Family ◽  
Lack Of Control ◽  
Family Level

A family faced with alcohol de­pendence of its member most often does not take any action to solve the problem. This is mainly due to the lack of knowl­edge about co ­dependency of all people living under one roof with the addict. The spouse/partner as well as children of the addicted individual feel shame as they are blamed by the person abusing alcohol for the situation, and that hin­ders or cripples any attempts to solve the problem. Times of drinking and associat­ed fighting, aggression and violence are interspersed with “honeymoon ­like pe­riods”, so family members are convinced that one day the addiction will end and “things will somehow turn out right”. It is not only the drinking person but also his/her closest relatives who deny there is a problem if the fact is pointed out and confirmed by anyone outside the family. Despite the suffering and damage caused by the lack of the drinking person’s con­cern for his/her family as well as his/her absence and disengagement from the daily routines, the spouse/partner and the children put on “masks” and claim there is no problem. The greatest trag­edy of children living in a family with a drinking problem is the fact that, with­out being aware of it, they continue to play the same roles in their adult life, as ACA. An addicted person may de­cide to stop drinking only if they admit full responsibility for the effects of their own lack of control over drinking which leads to significant damage on a person­al and family level, exposing everyone to suffering and harm. Of great impor­tance in motivating an alcoholic to re­main sober is a short family intervention during a meeting in a group of people significant for the addict. The essence of co ­dependency may be explained using a case study showing the attempts made by a wife trying to justify behaviours of her husband who abuses alcohol.

The anatomy of an unstable node: a Levantine relict precipitates phylogenomic dissolution of higher-level relationships of the armoured harvestmen (Arachnida: Opiliones: Laniatores)

2019 ◽  
Author(s):  
Shlomi Aharon ◽  
Jesus A. Ballesteros ◽  
Audrey R. Crawford ◽  
Keyton Friske ◽  
Guilherme Gainett ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Signal ◽  
Future Studies ◽  
Phylogenetic Placement ◽  
Unstable Node ◽  
The Family ◽  
Family Level ◽  
The Matrix ◽  
Tree Topologies ◽  
Unstable Position

After tumultuous revisions to the family-level systematics of Laniatores (the armored harvestmen), the basally branching family Phalangodidae presently bears a disjunct and irregular distribution, attributed to the fragmentation of Pangea. One of the curious lineages assigned to Phalangodidae is the monotypic Israeli genus Haasus, the only Laniatores species that occurs in Israel, and whose presence in the Levant has been inferred to result from biogeographic connectivity with Eurasia. Recent surveys of Israeli caves have also yielded a new troglobitic morphospecies of Haasus. Here, we describe this new species as Haasus naasane sp. nov. So as to test the biogeographic affinity of Haasus, we sequenced DNA from both species and RNA from Haasus naasane sp. nov., to assess their phylogenetic placement. Our results showed that the new species is clearly closely related to Haasus judaeus, but Haasus itself is unambiguously nested within the largely Afrotropical family Pyramidopidae. In addition, the Japanese ‘phalangodid’ Proscotolemon sauteri was recovered as nested within the Southeast Asian family Petrobunidae. Phylogenomic placement of Haasus naasane sp. nov. in a 1550-locus matrix indicates that Pyramidopidae has an unstable position in the tree of Laniatores, with alternative partitioning of the matrix recovering high nodal support for mutually exclusive tree topologies. Exploration of phylogenetic signal showed the cause of this instability to be a considerable conflict between partitions, suggesting that the basal phylogeny of Laniatores may not yet be stable to addition of taxa. We transfer Haasus to Pyramidopidae (new familial assignment). Additionally, we transfer Proscotolemon to the family Petrobunidae (new familial assignment). Future studies on basal Laniatores phylogeny should emphasise the investigation of small-bodied and obscure groups that superficially resemble Phalangodidae.

Estimating effects of global warming from past range changes for cold demanding refugial taxa: A case study on South-west Anatolian species Poecilimon birandi

Biologia ◽  
2012 ◽  
Vol 67 (6) ◽  
Author(s):  
Sarp Kaya ◽  
İslam Gündüz ◽  
Battal Çiplak
Keyword(s):  
Global Warming ◽  
Phylogenetic Signal ◽  
Marker Gene ◽  
Haplotype Diversity ◽  
Cold Climate ◽  
Dispersal Ability ◽  
The West ◽  
South West ◽  
Significant Genetic Structure

AbstractAlthough changes in biodiversity and in ecosystems are surely caused by a range of interacting drivers, such as natural or human-induced factors, one of the important drivers having major impacts on climate and biodiversity and leading to range changes and fragmentation is global warming. Defining past range changes/fragmentations during interglacial periods may provide tools to understand possible impacts of global warming on present biodiversity. To test this assumption we studied a marker gene in the bush-cricket Poecilimon birandi, a species confined to South-west Anatolia that demands a cold climate. Haplotypes of P. birandi constituted three main phylogroups,West, East and Demre. All haplotypes are unique to the respective phylogroup. An AMOVA suggested considerable divergence at all hierarchical levels. Though there is a strong isolation between phylogroups, the East and West groups harbour considerable haplotype diversity. Most of the demographic analyses suggest stable historical populations for the West and East phylogroups, but a coalescent-based demographic analysis indicates a bottleneck for the West phylogroup. The main conclusions are; (i) P. birandi contains considerable phylogenetic signal in 16S rDNA, (ii) there were at least three contemporaneous radiations, which might have originated from isolated refugial populations during Pleistocene, (iii) within a refugium, range changes induced by climatic shifts may be only vertical through an altitudinal gradient, (iv) significant genetic structure can arise in a small heterogeneous area, if the species requires particular habitats and has weak dispersal ability, (v) climatic shifts may cause fragmentation or extinction of populations, but can also lead to divergence of populations suffering from fragmentation, and (vi) altitudinal heterogeneity plays a buffering role, allowing for survival of the refugial biodiversity.

scholarly journals PHYLOGENETIC SIGNAL OF SUBSETS OF MORPHOLOGICAL CHARACTERS: A CASE STUDY IN THE GENUS ERYTHEMIS (ANISOPTERA: LIBELLULIDAE)

Caldasia ◽  
2014 ◽  
Vol 36 (1) ◽  
pp. 85-106 ◽  
Author(s):  
Fredy Palacino-Rodríguez ◽  
Enrique González-Soriano ◽  
Carlos Eduardo Sarmiento
Keyword(s):  
Phylogenetic Signal ◽  
Morphological Characters

scholarly journals Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina

2017 ◽  
Vol 4 (10) ◽  
pp. 171095 ◽  
Author(s):  
Joshua M. Hallas ◽  
Anton Chichvarkhin ◽  
Terrence M. Gosliner
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Signal ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Variable Regions ◽  
Multiple Sequence Alignments ◽  
Mathematical Algorithm ◽  
Construction Methods ◽  
Phylogenetic Informativeness ◽  
Family Level

Molecular estimates of phylogenetic relationships rely heavily on multiple sequence alignment construction. There has been little consensus, however, on how to properly address issues pertaining to the alignment of variable regions. Here, we construct alignments from four commonly sequenced molecular markers (16S, 18S, 28S and cytochrome c oxidase subunit I) for the Nudibranchia using three different methodologies: (i) strict mathematical algorithm; (ii) exclusion of variable or divergent regions and (iii) manually curated, and examine how different alignment construction methods can affect phylogenetic signal and phylogenetic estimates for the suborder Doridina. Phylogenetic informativeness (PI) profiles suggest that the molecular markers tested lack the power to resolve relationships at the base of the Doridina, while being more robust at family-level classifications. This supports the lack of consistent resolution between the 19 families within the Doridina across all three alignments. Most of the 19 families were recovered as monophyletic, and instances of non-monophyletic families were consistently recovered between analyses. We conclude that the alignment of variable regions has some effect on phylogenetic estimates of the Doridina, but these effects can vary depending on the size and scope of the phylogenetic query and PI of molecular markers.

Phylogenetic signal in matK vs. trnK: A case study in early diverging eudicots (angiosperms)

2008 ◽  
Vol 48 (3) ◽  
pp. 1120-1130 ◽  
Author(s):  
Khidir W. Hilu ◽  
Chelsea Black ◽  
Diaga Diouf ◽  
J. Gordon Burleigh
Keyword(s):  
Phylogenetic Signal ◽  
Early Diverging Eudicots

scholarly journals Evaluating evolutionary pressures and phylogenetic signal in earthworms: a case study - the number of typhlosole lamellae in Hormogastridae (Annelida, Oligochaeta)

2016 ◽  
Vol 178 (1) ◽  
pp. 4-14 ◽  
Author(s):  
Daniel F. Marchán ◽  
Marta Novo ◽  
Rosa Fernández ◽  
Irene de Sosa ◽  
Dolores Trigo ◽  
...  
Keyword(s):  
Phylogenetic Signal

scholarly journals Automatic Image Classification Using Neural Networks Increases Accuracy for Allergenic Pollen Monitoring

2020 ◽  
Author(s):  
Marcel Polling ◽  
Chen Li ◽  
Lu Cao ◽  
Fons Verbeek ◽  
Letty de Weger ◽  
...  
Keyword(s):  
Airborne Pollen ◽  
Pollen Grains ◽  
Allergenic Pollen ◽  
Herbarium Specimens ◽  
Pollen Monitoring ◽  
Pollen Concentrations ◽  
Family Level ◽  
Source Of Information ◽  
Urticaceae Pollen

Abstract Monitoring of airborne pollen concentrations provides an important source of information for the globally increasing number of hay fever patients. Airborne pollen are traditionally counted under the microscope, but with the latest developments in image recognition methods, automating this process has become feasible. A challenge that persists, however, is that many pollen grains cannot be distinguished beyond the genus or family level using a microscope. Here, we assess the use of a Convolutional Neural Network (CNN) to increase taxonomic accuracy for airborne pollen. As a case study we use the nettle family (Urticaceae), which contains two main genera (Urtica and Parietaria) common in European landscapes which pollen cannot be separated by trained specialists. While pollen from Urtica species have very low allergenic relevance, those from several species of Parietaria are severely allergenic. We collect pollen from both fresh as well as from herbarium specimens and use these to train the CNN model VGG16. The model shows that Urticaceae pollen can be distinguished with 98.3% accuracy. We then apply our model on Urticaceae pollen collected from aerobiological samples and show that the genera can be confidently distinguished, despite the more challenging input images that are often overlain by debris. Our method can also be applied to other pollen families in the future and will thus help to make allergenic pollen monitoring more specific.

scholarly journals Driven progressive evolution of genome sequence complexity in Cyanobacteria

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Andrés Moya ◽  
José L. Oliver ◽  
Miguel Verdú ◽  
Luis Delaye ◽  
Vicente Arnau ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Ridge Regression ◽  
Phylogenetic Signal ◽  
Controversial Issue ◽  
Sequence Complexity ◽  
Environmental Interactions ◽  
Genome Level ◽  
Biological Functionality ◽  
Standard Tests

Abstract Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species’ biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven—the minimum, ancestor–descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.

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