scholarly journals An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life

2020 ◽  
Vol 38 (1) ◽  
pp. 108-127 ◽  
Author(s):  
Heiner Kuhl ◽  
Carolina Frankl-Vilches ◽  
Antje Bakker ◽  
Gerald Mayr ◽  
Gerhard Nikolaus ◽  
...  
Keyword(s):  
Tree Of Life ◽  
Vocal Production ◽  
Binding Motifs ◽  
Coding Sequences ◽  
Early Diversification ◽  
Sister Clade ◽  
Family Level ◽  
Long Time ◽  
Transcription Factor Binding Motifs ◽  
Avian Family

Abstract Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life

Phoronida

2017 ◽  
Author(s):  
Judith Fuchs
Keyword(s):  
Life Cycle ◽  
Small Group ◽  
Larval Stage ◽  
Intertidal Zone ◽  
Marine Invertebrates ◽  
Tree Of Life ◽  
General Morphology ◽  
Family Level ◽  
Planktonic Larval Stage

This chapter describes the taxonomy of Phoronida, a small group of exclusively marine invertebrates found in most of the world's oceans from the intertidal zone to about 400 metres depth. Phoronids are meroplanktonic with a planktonic larval stage usually less than 2 mm in length and a benthic adult whose length ranges from a few cm up to 50 cm. The chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Anellida: Holoplanktonic Polychaeta

2017 ◽  
Author(s):  
Claudia Castellani ◽  
Robert Camp
Keyword(s):  
Life Cycle ◽  
Marine Environment ◽  
Tree Of Life ◽  
General Morphology ◽  
Family Level

This chapter describes the taxonomy of Polychaeta, an almost exclusively marine group of organisms belonging to the phylum Annelida. With over 10,000 species described worldwide, they represent one of the most abundant animal taxa in the marine environment. The chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Crustacea: Euphausiacea

2017 ◽  
Author(s):  
Alistair J. Lindley
Keyword(s):  
Life Cycle ◽  
Tree Of Life ◽  
General Morphology ◽  
Family Level

This chapter describes the taxonomy of Euphausiacea, exclusively marine holoplanktonic crustaceans commonly known as krill. Although not highly diverse, with only two families and ~ 86 species worldwide, they are often a major component of the biomass of the plankton and micronekton of the world's oceans. This chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Crustacea: Lophogastrida and Mysida

2017 ◽  
Author(s):  
Claudia Castellani ◽  
Maiju Lehtiniemi ◽  
Kenneth Meland
Keyword(s):  
Life Cycle ◽  
Ballast Water ◽  
Water Systems ◽  
Tree Of Life ◽  
Brood Pouch ◽  
General Morphology ◽  
Family Level ◽  
Adaptive Nature

This chapter describes the taxonomy of Lophogastrida and Mysida, small shrimp-like crustaceans commonly known as ‘opossum shrimps’ because of the ventral brood pouch in the female. Because of their highly adaptive nature, they have progressively invaded new areas via new connections of water systems and through ballast water. The chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Crustacea: Ostracoda

2017 ◽  
Author(s):  
Martin V. Angel ◽  
Anthony W.G. John
Keyword(s):  
Life Cycle ◽  
Tree Of Life ◽  
General Morphology ◽  
Family Level ◽  
Oceanic Species

This chapter describes the taxonomy of Ostracoda, small bivalved crustaceans ranging in size from 0.2 to > 30 mm. The majority are benthic and belong to the subclass Podocopa. The chapter focuses on the holoplanktonic oceanic species. It covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Protozooplankton: Foraminifera

2017 ◽  
Author(s):  
Rowena Stern ◽  
Claire Taylor ◽  
Saeed Sadri
Keyword(s):  
Life Cycle ◽  
Marine Organisms ◽  
Tree Of Life ◽  
Family Level

This chapter describes the taxonomy of foraminifera. Foraminifera are one of the most common shelled marine organisms and date back to the Cambrian era where they are responsible for the colour of the sediment on some shorelines. The chapter covers their life cycle, ecology and distribution, and generalized morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Protozooplankton: Ciliates

2017 ◽  
Author(s):  
Alex Kraberg ◽  
Rowena Stern ◽  
Michaela Strüder-Kypke
Keyword(s):  
Life Cycle ◽  
Nutrient Cycling ◽  
Food Web ◽  
Tree Of Life ◽  
Family Level ◽  
Freshwater Habitats

This chapter describes the taxonomy of ciliates. Ciliates can be found in almost every environment; the majority of species, however, are aquatic and occur in marine, brackish, and freshwater habitats. They play a major role in nutrient cycling in the food web; some are also capable of photosynthesis through acquisition of chloroplasts from their prey. The chapter covers their life cycle, generalized morphology, and ecology and distribution. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

Chordata: Fish eggs and larvae

2017 ◽  
Author(s):  
Peter Munk ◽  
Jørgen G. Nielsen
Keyword(s):  
Life Cycle ◽  
Tree Of Life ◽  
Fish Eggs ◽  
General Morphology ◽  
Family Level ◽  
Eggs And Larvae ◽  
Fish Eggs And Larvae

This chapter describes the taxonomy of fish eggs and larvae. Most fish eggs and larvae are planktonic, and are commonly found in plankton net tows. Collectively these fish stages are referred to as ichthyoplankton. The chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.

scholarly journals Exploring functionally annotated transcriptional consensus regulatory elements with CONREL

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Davide Dalfovo ◽  
Samuel Valentini ◽  
Alessandro Romanel
Keyword(s):  
Cell Lines ◽  
Web Application ◽  
Regulatory Networks ◽  
Regulatory Elements ◽  
Levels Of Abstraction ◽  
Binding Motifs ◽  
Extensive Collection ◽  
Transcription Factor Binding Motifs ◽  
Gene Regulatory ◽  
Genomic Regions

Abstract Understanding the interaction between human genome regulatory elements and transcription factors is fundamental to elucidate the structure of gene regulatory networks. Here we present CONREL, a web application that allows for the exploration of functionally annotated transcriptional ‘consensus’ regulatory elements at different levels of abstraction. CONREL provides an extensive collection of consensus promoters, enhancers and active enhancers for 198 cell-lines across 38 tissue types, which are also combined to provide global consensuses. In addition, 1000 Genomes Project genotype data and the ‘total binding affinity’ of thousands of transcription factor binding motifs at genomic regulatory elements is fully combined and exploited to characterize and annotate functional properties of our collection. Comparison with other available resources highlights the strengths and advantages of CONREL. CONREL can be used to explore genomic loci, specific genes or genomic regions of interest across different cell lines and tissue types. The resource is freely available at https://bcglab.cibio.unitn.it/conrel.

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