Comparative genomics and evolution of avian specialized traits

2021 ◽  
Vol 23 ◽  
Author(s):  
Lei Wu ◽  
Xiaolu Jiao ◽  
Dezhi Zhang ◽  
Yalin Cheng ◽  
Gang Song ◽  
...  
Keyword(s):  
Size Variation ◽  
Genomic Data ◽  
Gene Interaction ◽  
Regulatory Elements ◽  
High Elevation ◽  
Small Scale ◽  
Comparative Genomic ◽  
Evolutionary Mechanisms ◽  
Origin And Evolution ◽  
Genomic Structural Variation

Abstract: Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage coloration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioral, and developmental biology data.

scholarly journals Lithospheric mantle refertilization by DMM-derived melts beneath the Cameroon Volcanic Line—a case study of the Befang xenolith suite (Oku Volcanic Group, Cameroon)

2021 ◽  
Vol 176 (5) ◽  
Author(s):  
Sylvin S. T. Tedonkenfack ◽  
Jacek Puziewicz ◽  
Sonja Aulbach ◽  
Theodoros Ntaflos ◽  
Mary-Alix Kaczmarek ◽  
...  
Keyword(s):  
Lithospheric Mantle ◽  
Size Variation ◽  
African Plate ◽  
Cameroon Volcanic Line ◽  
Origin And Evolution ◽  
Volcanic Group ◽  
Cenozoic Volcanism ◽  
Composition Of Minerals ◽  
Ree Patterns

AbstractThe origin and evolution of subcontinental lithospheric mantle (SCLM) are important issues of Earth’s chemical and physical evolution. Here, we report detailed textural and chemical analyses on a mantle xenolith suite from Befang (Oku Volcanic Group, Cameroon Volcanic Line), which represents a major tectono-magmatic structure of the African plate. The samples are sourced from spinel-facies mantle and are dominated by lherzolites. Their texture is cataclastic to porphyroclastic, and foliation defined by grain-size variation and alignment of spinel occurs in part of peridotites. Spinel is interstitial and has amoeboidal shape. Clinopyroxene REE patterns are similar to those of Depleted MORB Mantle (DMM) except LREEs, which vary from depleted to enriched. The A-type olivine fabric occurs in the subset of one harzburgite and 7 lherzolites studied by EBSD. Orthopyroxene shows deformation consistent with olivine. The fabric of LREE-enriched clinopyroxene is equivalent to those of orthopyroxene and olivine, whereas spinel and LREE-depleted clinopyroxene are oriented independently of host rock fabric. The textural, chemical and thermobarometric constraints indicate that the Befang mantle section was refertilised by MORB-like melt at pressures of 1.0–1.4 GPa and temperatures slightly above 1200–1275 °C. The olivine-orthopyroxene framework and LREE-enriched clinopyroxene preserve the protolith fabric. In contrast, the LREE-depleted clinopyroxene, showing discordant deformation relative to the olivine-orthopyroxene protolith framework, and amoeboidal spinel crystallized from the infiltrating melt. The major element and REEs composition of minerals forming the Befang peridotites indicate subsequent reequilibration at temperatures 930–1000 °C. This was followed by the formation of websterite veins in the lithospheric mantle, which can be linked to Cenozoic volcanism in the Cameroon Volcanic Line that also brought the xenoliths to the surface. This study therefore supports the origin of fertile SCLM via refertilization rather than by extraction of small melt fractions, and further emphasizes the involvement of depleted melts in this process.

scholarly journals The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations

2019 ◽  
Author(s):  
Mosè Manni ◽  
Felipe A. Simao ◽  
Hugh M. Robertson ◽  
Marco A. Gabaglio ◽  
Robert M. Waterhouse ◽  
...  
Keyword(s):  
Draft Genome ◽  
Gene Families ◽  
Sister Group ◽  
Sensu Stricto ◽  
Comparative Genomic ◽  
Gene Repertoire ◽  
Animal Group ◽  
Origin And Evolution ◽  
Genomic Analyses ◽  
Metabolism Gene

AbstractThe dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion which might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential.The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

scholarly journals Facies Evaluation and Depositional Environments of Carbonates of the Bagh Group, Dhar District, Madhya Pradesh, India

2021 ◽  
Vol 38 (1) ◽  
pp. 33-40
Author(s):  
Sreejita Chatterjee ◽  
Dhiren Kumar Ruidas
Keyword(s):  
Grain Size ◽  
Large Scale ◽  
Energy Condition ◽  
Size Variation ◽  
High Energy ◽  
Depositional Environments ◽  
Small Scale ◽  
Peninsular India ◽  
Sedimentary Structures ◽  
Nodular Limestone

A significant event of marine transgression took place in Central India during Late Turonian-Coniacian. Fossiliferous marine succession of Bagh Group is one of the few carbonate successions exposed in peninsular India which was in focus of the current study for understanding this event. The signatures of this event were identified in the carbonate succession. The carbonates of Bagh Group are composed of two formations: the lower part is represented by Nodular limestone Formation which is overlain by Bryozoan limestone Formation at the top. On the basis of grain size variation and sedimentary structures, the Nodular limestone is divisible into three facies: facies ‘A’, facies ‘B’ and facies ‘C’. A hardground exists between facies B and facies C. Lack of sedimentary structures and high mud content indicates low energy depositional setting for the Nodular limestone Formation. Similarly, Bryozoan limestone Formation is divisible into five facies: facies ‘D’, facies ‘E’, facies ‘F’, facies ‘G’ and facies ‘H’ based on grain size variation and sedimentary structures. All of these five facies are fossiliferous. Glauconites are present within facies ‘G’ and have two modes of occurrence - as infilling within Bryozoan limestone and as altered feldspar. Presence of both small- and large-scale cross-stratification in Bryozoan limestone with lesser mud content are indicative of high energy shallow marine conditions. Large-scale cross-stratifications are possibly representing tidal bars while the small scale cross stratifications are formed in inter bar setting. Presence of reactivation surfaces within facies ‘E’ also supports their tidal origin. Increase in depositional energy condition is also evident from dominated by packstone facies.

scholarly journals Pancreatic cancer-derived organoids – a disease modeling tool to predict drug response

2020 ◽  
Vol 8 (5) ◽  
pp. 594-606 ◽  
Author(s):  
Pierre-Olivier Frappart ◽  
Karolin Walter ◽  
Johann Gout ◽  
Alica K Beutel ◽  
Mareen Morawe ◽  
...  
Keyword(s):  
Drug Testing ◽  
Disease Modeling ◽  
Individualized Medicine ◽  
Expression Patterns ◽  
Culture Conditions ◽  
Ductal Adenocarcinoma ◽  
Small Scale ◽  
Comparative Genomic

Background Organotypic cultures derived from pancreatic ductal adenocarcinoma (PDAC) termed pancreatic ductal cancer organoids (PDOs) recapitulate the primary cancer and can be derived from primary or metastatic biopsies. Although isolation and culture of patient-derived pancreatic organoids were established several years ago, pros and cons for individualized medicine have not been comprehensively investigated to date. Methods We conducted a feasibility study, systematically comparing head-to-head patient-derived xenograft tumor (PDX) and PDX-derived organoids by rigorous immunohistochemical and molecular characterization. Subsequently, a drug testing platform was set up and validated in vivo. Patient-derived organoids were investigated as well. Results First, PDOs faithfully recapitulated the morphology and marker protein expression patterns of the PDXs. Second, quantitative proteomes from the PDX as well as from corresponding organoid cultures showed high concordance. Third, genomic alterations, as assessed by array-based comparative genomic hybridization, revealed similar results in both groups. Fourth, we established a small-scale pharmacotyping platform adjusted to operate in parallel considering potential obstacles such as culture conditions, timing, drug dosing, and interpretation of the results. In vitro predictions were successfully validated in an in vivo xenograft trial. Translational proof-of-concept is exemplified in a patient with PDAC receiving palliative chemotherapy. Conclusion Small-scale drug screening in organoids appears to be a feasible, robust and easy-to-handle disease modeling method to allow response predictions in parallel to daily clinical routine. Therefore, our fast and cost-efficient assay is a reasonable approach in a predictive clinical setting.

The consequences of Canadian Cordillera thermal regime in recent tectonics and elevation: a reviewThis article is one of a series of papers published in this Special Issue on the theme Lithoprobe — parameters, processes, and the evolution of a continent.Geological Survey of Canada Contribution 20090195.

2010 ◽  
Vol 47 (5) ◽  
pp. 621-632 ◽  
Author(s):  
R. D. Hyndman
Keyword(s):  
Thermal Regime ◽  
Upper Mantle ◽  
High Surface ◽  
Plate Boundary ◽  
High Elevation ◽  
Mantle Xenoliths ◽  
Tectonic Activity ◽  
Small Scale ◽  
Canadian Cordillera ◽  
Crust And Upper Mantle

The crust and upper mantle thermal regime of the Canadian Cordillera and its tectonic consequences were an important part of the Cordillera Lithoprobe program and related studies. This article provides a review, first of the thermal constraints, and then of consequences in high surface elevation and current tectonics. Cordillera and adjacent craton temperatures are well constrained by geothermal heat flow, mantle tomography velocities, upper mantle xenoliths, and the effective elastic thickness, Te. Cordillera temperatures are very high and laterally uniform, explained by small scale convection beneath a thin lithosphere, 800–900 °C at the Moho, contrasted to 400–500 °C for the craton. The high temperatures provide an explanation for why the Cordillera has high elevation in spite of a generally thin crust, ∼33 km, in contrast to low elevation and thicker crust, 40–45 km, for the craton. The Cordillera is supported ∼1600 m by lithosphere thermal expansion. In the Cordillera only the upper crust has significant strength; Te ∼ 15 km, in contrast to over 60 km for the craton. The Cordillera is tectonically active because the lithosphere is sufficiently weak to be deformed by plate boundary and gravitational forces; the craton is too strong. The Canadian Cordillera results have led to new understandings of processes in backarcs globally. High backarc temperatures and weak lithospheres explain the tectonic activity over long geological times of mobile belts that make up about 20% of continents. They also have led to a new understanding of collision orogenic heat in terms of incorporation of already hot backarcs.

scholarly journals Origin and evolution of developmental enhancers in the mammalian neocortex

2016 ◽  
Vol 113 (19) ◽  
pp. E2617-E2626 ◽  
Author(s):  
Deena Emera ◽  
Jun Yin ◽  
Steven K. Reilly ◽  
Jake Gockley ◽  
James P. Noonan
Keyword(s):  
De Novo ◽  
Regulatory Elements ◽  
Evolutionary Constraint ◽  
Regulatory Sequences ◽  
En Bloc ◽  
Origin And Evolution ◽  
Stem Lineage ◽  
Coexpressed Genes ◽  
Human And Mouse ◽  
Insight Into

Morphological innovations such as the mammalian neocortex may involve the evolution of novel regulatory sequences. However, de novo birth of regulatory elements active during morphogenesis has not been extensively studied in mammals. Here, we use H3K27ac-defined regulatory elements active during human and mouse corticogenesis to identify enhancers that were likely active in the ancient mammalian forebrain. We infer the phylogenetic origins of these enhancers and find that ∼20% arose in the mammalian stem lineage, coincident with the emergence of the neocortex. Implementing a permutation strategy that controls for the nonrandom variation in the ages of background genomic sequences, we find that mammal-specific enhancers are overrepresented near genes involved in cell migration, cell signaling, and axon guidance. Mammal-specific enhancers are also overrepresented in modules of coexpressed genes in the cortex that are associated with these pathways, notably ephrin and semaphorin signaling. Our results also provide insight into the mechanisms of regulatory innovation in mammals. We find that most neocortical enhancers did not originate by en bloc exaptation of transposons. Young neocortical enhancers exhibit smaller H3K27ac footprints and weaker evolutionary constraint in eutherian mammals than older neocortical enhancers. Based on these observations, we present a model of the enhancer life cycle in which neocortical enhancers initially emerge from genomic background as short, weakly constrained “proto-enhancers.” Many proto-enhancers are likely lost, but some may serve as nucleation points for complex enhancers to evolve.

scholarly journals Comparative genomic analysis of the proteasome β5t subunit gene: implications for the origin and evolution of thymoproteasomes

2011 ◽  
Vol 64 (1) ◽  
pp. 49-58 ◽  
Author(s):  
Yoichi Sutoh ◽  
Mizuho Kondo ◽  
Yuko Ohta ◽  
Tatsuya Ota ◽  
Utano Tomaru ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Subunit Gene ◽  
Origin And Evolution

scholarly journals Standing genetic variation in a tissue-specific enhancer underlies selfing-syndrome evolution inCapsella

2016 ◽  
Vol 113 (48) ◽  
pp. 13911-13916 ◽  
Author(s):  
Adrien Sicard ◽  
Christian Kappel ◽  
Young Wha Lee ◽  
Natalia Joanna Woźniak ◽  
Cindy Marona ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Mating System ◽  
Allelic Variation ◽  
Size Variation ◽  
Regulatory Elements ◽  
Flower Size ◽  
Evolutionary Transitions ◽  
Tissue Specific ◽  
Organ Specific ◽  
Petal Size

Mating system shifts recurrently drive specific changes in organ dimensions. The shift in mating system from out-breeding to selfing is one of the most frequent evolutionary transitions in flowering plants and is often associated with an organ-specific reduction in flower size. However, the evolutionary paths along which polygenic traits, such as size, evolve are poorly understood. In particular, it is unclear how natural selection can specifically modulate the size of one organ despite the pleiotropic action of most known growth regulators. Here, we demonstrate that allelic variation in the intron of a general growth regulator contributed to the specific reduction of petal size after the transition to selfing in the genusCapsella. Variation within this intron affects an organ-specific enhancer that regulates the level of STERILE APETALA (SAP) protein in the developing petals. The resulting decrease inSAPactivity leads to a shortening of the cell proliferation period and reduced number of petal cells. The absence of private polymorphisms at the causal region in the selfing species suggests that the small-petal allele was captured from standing genetic variation in the ancestral out-crossing population. Petal-size variation in the current out-crossing population indicates that several small-effect mutations have contributed to reduce petal-size. These data demonstrate how tissue-specific regulatory elements in pleiotropic genes contribute to organ-specific evolution. In addition, they provide a plausible evolutionary explanation for the rapid evolution of flower size after the out-breeding-to-selfing transition based on additive effects of segregating alleles.

Inferring a Tumor Progression Model for Neuroblastoma From Genomic Data

2005 ◽  
Vol 23 (29) ◽  
pp. 7322-7331 ◽  
Author(s):  
Sven Bilke ◽  
Qing-Rong Chen ◽  
Frank Westerman ◽  
Manfred Schwab ◽  
Daniel Catchpoole ◽  
...  
Keyword(s):  
Tumor Progression ◽  
Cancer Biology ◽  
Clinical Evidence ◽  
Genomic Data ◽  
Comparative Genomic ◽  
Molecular Evidence ◽  
Cancer Evolution ◽  
Progression Model ◽  
Tumor Progression Model ◽  
Core Idea

Purpose The knowledge of the key genomic events that are causal to cancer development and progression not only is invaluable for our understanding of cancer biology but also may have a direct clinical impact. The task of deciphering a model of tumor progression by requiring that it explains (or at least does not contradict) known clinical and molecular evidence can be very demanding, particularly for cancers with complex patterns of clinical and molecular evidence. Materials and Methods We formalize the process of model inference and show how a progression model for neuroblastoma (NB) can be inferred from genomic data. The core idea of our method is to translate the model of clonal cancer evolution to mathematical testable rules of inheritance. Seventy-eight NB samples in stages 1, 4S, and 4 were analyzed with array-based comparative genomic hybridization. Results The pattern of recurrent genomic alterations in NB is strongly stage dependent and it is possible to identify traces of tumor progression in this type of data. Conclusion A tumor progression model for neuroblastoma is inferred, which is in agreement with clinical evidence, explains part of the heterogeneity of the clinical behavior observed for NB, and is compatible with existing empirical models of NB progression.

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