scholarly journals Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits

2020 ◽  
Author(s):  
Ting-Ru Mao ◽  
Ye-Wei Liu ◽  
Madhava Meegaskumbura ◽  
Jian Yang ◽  
Gajaba Ellepola ◽  
...  
Keyword(s):  
Body Size ◽  
Morphological Evolution ◽  
Principal Component ◽  
Morphological Diversity ◽  
Fold Increase ◽  
Model System ◽  
Model Organisms ◽  
Related Condition ◽  
Geometric Morphometric ◽  
Eye Size

ABSTRACTEpitomized by the well-studied Astyanax mexicanus, cavefishes provide important model organisms to understand adaptations in response to divergent natural selection. However, the spectacular Sinocyclocheilus diversification of China, the most diverse cavefish clade in the world harboring nearly 75 species, demonstrate evolutionary convergence for many traits, yet remain poorly understood in terms of their morphological evolution. Here, using a broad sample of 49 species representative of this diversification, we analyze patterns of Sinocylocheilus evolution in a phylogenetic context. We categorized species into morphs based on eye-related condition: Blind, Micro-eyed (small-eyed), and Normal-eyed and we also considered three habitat types (Troglodytic – cave-restricted; Troglophilic – cave-associated; Surface – outside of caves). Geometric morphometric analyses show Normal-eyed morphs with fusiform shapes being segregated from Blind/Micro-eyed (Eye-regressed) morphs with deeper bodies along the first principal component (“PC”) axis. The second PC axis accounts for shape complexity related to the presence of horns. Ancestral character reconstructions of morphs suggest at least three independent origins of Blind morphs, each with different levels of modification in relation to the typical morphology of ancestral Normal-eyed morphs. Interestingly, only some Blind or Micro-eyed morphs bear horns and they are restricted to a single clade (Clade B) and arising from a Troglodytic ancestral species. Our geophylogeny shows an east-to-west diversification spanning the Pliocene and the Pleistocene, with Troglodytic species dominating karstic subterranean habitats of the plains whereas predominantly Surface species inhabit streams and pools in hills to the west (perhaps due to the scarcity of caves). Integration of morphology, phylogeny and geography suggests Sinocyclocheilus are pre-adapted for cave dwelling. Analyses of evolutionary rates suggest that lineages leading to Blind morphs were characterized by significant rate shifts, such as a slowdown in body size evolution and a 3.3 to 12.5 fold increase in the evolutionary rate of eye regression. Furthermore, body size and eye size have undergone reversals, but horns have not, a trait that seem to require substantial evolutionary time to form. These results, compared to the Astyanax model system, indicate Sinocyclocheilus fishes demonstrate extraordinary morphological diversity and variation, offering an invaluable model system to explore evolutionary novelty.

scholarly journals Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ting-Ru Mao ◽  
Ye-Wei Liu ◽  
Madhava Meegaskumbura ◽  
Jian Yang ◽  
Gajaba Ellepola ◽  
...  
Keyword(s):  
Body Size ◽  
Morphological Evolution ◽  
Principal Component ◽  
Fold Increase ◽  
The Body ◽  
Molecular Dating ◽  
Model Systems ◽  
Habitat Types ◽  
Related Condition ◽  
Environmental Pressures

Abstract Background Natural model systems are indispensable for exploring adaptations in response to environmental pressures. Sinocyclocheilus of China, the most diverse cavefish clade in the world (75 species), provide unique opportunities to understand recurrent evolution of stereotypic traits (such as eye loss and sensory expansion) in the context of a deep and diverse phylogenetic group. However, they remain poorly understood in terms of their morphological evolution. Therefore, we explore key patterns of morphological evolution, habitat utilization and geographic distribution in these fishes. Results We constructed phylogenies and categorized 49 species based on eye-related condition (Blind, Micro-eyed, and Normal-eyed), habitat types (Troglobitic—cave-restricted; Troglophilic—cave-associated; Surface—outside caves) and existence of horns. Geometric-morphometric analyses show Normal-eyed morphs with fusiform shapes segregating from Blind/Micro-eyed deeper bodied morphs along the first principal-component axis; second axis accounts for shape complexity related to horns. The body shapes showed a significant association with eye-related condition and horn, but not habitat types. Ancestral reconstructions suggest at least three independent origins of Blind morphs, each with different levels of modification in relation to their ancestral Normal-eyed morphs; Sinocyclocheilus are also pre-adapted for cave dwelling. Our geophylogeny shows an east-to-west diversification spanning Pliocene and Pleistocene, with early-diversifying Troglobitic species dominating subterranean habitats of karstic plains whereas predominantly Surface forms inhabit hills to the west. Evolutionary rates analyses suggest that lineages leading to Blind morphs were characterized by significant rate shifts, such as a slowdown in body size evolution and a 5–20 fold increase in rate of eye regression, possibly explained by limited resource availability. Body size and eye size have undergone reversals, but not horns, a trait entailing considerable time to form. Conclusions Sinocyclocheilus occupied cave habitats in response to drying associated with aridification of China during late Miocene and the Pliocene. The prominent cave-adaptations (eye-regression, horn-evolution) occur in clades associated with the extensive subterranean cave system in Guangxi and Guizhou provinces. Integration of morphology, phylogeny, rate analyses, molecular-dating and distribution show not only several remarkable patterns of evolution, but also interesting exceptions to these patterns signifying the diversification of Sinocyclocheilus as an invaluable model system to explore evolutionary novelty.

scholarly journals Variation in pleiotropic hub gene expression is associated with interspecific differences in head shape and eye size in Drosophila

2021 ◽  
Author(s):  
Elisa Buchberger ◽  
Anıl Bilen ◽  
Sanem Ayaz ◽  
David Salamanca ◽  
Cristina Matas de las Heras ◽  
...  
Keyword(s):  
Natural Variation ◽  
Compound Eye ◽  
Genetic Manipulation ◽  
Morphological Evolution ◽  
Morphological Diversity ◽  
Network Evolution ◽  
Head Shape ◽  
Eye Size ◽  
Recurrent Mutations ◽  
Repeated Evolution

Abstract Revealing the mechanisms underlying the breath-taking morphological diversity observed in nature is a major challenge in Biology. It has been established that recurrent mutations in hotspot genes cause the repeated evolution of morphological traits, such as body pigmentation or the gain and loss of structures. To date, however, it remains elusive whether hotspot genes contribute to natural variation in the size and shape of organs. Since natural variation in head morphology is pervasive in Drosophila, we studied the molecular and developmental basis of differences in compound eye size and head shape in two closely related Drosophila species. We show differences in the progression of retinal differentiation between species and we applied comparative transcriptomics and chromatin accessibility data to identify the GATA transcription factor Pannier (Pnr) as central factor associated with these differences. Although the genetic manipulation of Pnr affected multiple aspects of dorsal head development, the effect of natural variation is restricted to a subset of the phenotypic space. We present data suggesting that this developmental constraint is caused by the co-evolution of expression of pnr and its co-factor u-shaped (ush). We propose that natural variation in expression or function of highly connected developmental regulators with pleiotropic functions is a major driver for morphological evolution and we discuss implications on gene regulatory network evolution. In comparison to previous findings, our data strongly suggests that evolutionary hotspots are not the only contributors to the repeated evolution of eye size and head shape in Drosophila.

scholarly journals Ontogenetic and static allometry in the skull and cranial units of nine-banded armadillos (Cingulata: Dasypodidae: Dasypus novemcinctus)

2020 ◽  
Vol 131 (3) ◽  
pp. 673-698
Author(s):  
Kévin Le Verger ◽  
Lionel Hautier ◽  
Jérémie Bardin ◽  
Sylvain Gerber ◽  
Frédéric Delsuc ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Morphological Evolution ◽  
Morphological Diversity ◽  
Shape Variation ◽  
Dasypus Novemcinctus ◽  
Global Pattern ◽  
Geometric Morphometric ◽  
Multi Scale ◽  
Infraorbital Canal ◽  
Row Reduction

Abstract A large part of extant and past mammalian morphological diversity is related to variation in size through allometric effects. Previous studies suggested that craniofacial allometry is the dominant pattern underlying mammalian skull shape variation, but cranial allometries were rarely characterized within cranial units such as individual bones. Here, we used 3D geometric morphometric methods to study allometric patterns of the whole skull (global) and of cranial units (local) in a postnatal developmental series of nine-banded armadillos (Dasypus novemcinctus ssp.). Analyses were conducted at the ontogenetic and static levels, and for successive developmental stages. Our results support craniofacial allometry as the global pattern along with more local allometric trends, such as the relative posterior elongation of the infraorbital canal, the tooth row reduction on the maxillary, and the marked development of nuchal crests on the supraoccipital with increasing skull size. Our study also reports allometric proportions of shape variation varying substantially among cranial units and across ontogenetic stages. The multi-scale approach advocated here allowed unveiling previously unnoticed allometric variations, indicating an untapped complexity of cranial allometric patterns to further explain mammalian morphological evolution.

scholarly journals Grill Workers Exposure to Polycyclic Aromatic Hydrocarbons: Levels and Excretion Profiles of the Urinary Biomarkers

2020 ◽  
Vol 18 (1) ◽  
pp. 230
Author(s):  
Marta Oliveira ◽  
Sílvia Capelas ◽  
Cristina Delerue-Matos ◽  
Simone Morais
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
High Performance ◽  
Principal Component ◽  
Fold Increase ◽  
Urinary Biomarkers ◽  
Analysis Model ◽  
Exposed Workers ◽  
Polycyclic Aromatic ◽  
The Impact

Grilling activities release large amounts of hazardous pollutants, but information on restaurant grill workers’ exposure to polycyclic aromatic hydrocarbons (PAHs) is almost inexistent. This study assessed the impact of grilling emissions on total workers’ exposure to PAHs by evaluating the concentrations of six urinary biomarkers of exposure (OHPAHs): naphthalene, acenaphthene, fluorene, phenanthrene, pyrene, and benzo(a)pyrene. Individual levels and excretion profiles of urinary OHPAHs were determined during working and nonworking periods. Urinary OHPAHs were quantified by high-performance liquid-chromatography with fluorescence detection. Levels of total OHPAHs (∑OHPAHs) were significantly increased (about nine times; p ≤ 0.001) during working comparatively with nonworking days. Urinary 1-hydroxynaphthalene + 1-hydroxyacenapthene and 2-hydroxyfluorene presented the highest increments (ca. 23- and 6-fold increase, respectively), followed by 1-hydroxyphenanthrene (ca. 2.3 times) and 1-hydroxypyrene (ca. 1.8 times). Additionally, 1-hydroxypyrene levels were higher than the benchmark, 0.5 µmol/mol creatinine, in 5% of exposed workers. Moreover, 3-hydroxybenzo(a)pyrene, biomarker of exposure to carcinogenic PAHs, was detected in 13% of exposed workers. Individual excretion profiles showed a cumulative increase in ∑OHPAHs during consecutive working days. A principal component analysis model partially discriminated workers’ exposure during working and nonworking periods showing the impact of grilling activities. Urinary OHPAHs were increased in grill workers during working days.

scholarly journals Effect of Time and Legume Type on Germination-Induced Proteolysis of Lentils and Faba Beans

Proceedings ◽  
2020 ◽  
Vol 70 (1) ◽  
pp. 4
Author(s):  
Sara Bautista-Expósito ◽  
Elena Peñas ◽  
Albert Vanderberg ◽  
Juana Frias ◽  
Cristina Martínez-Villaluenga
Keyword(s):  
Amino Acids ◽  
Protease Activity ◽  
Protein Quality ◽  
Principal Component ◽  
Fold Increase ◽  
Protein Digestibility ◽  
Essential Amino Acids ◽  
Seedling Development ◽  
Positive Effects ◽  
Faba Beans

Legumes are alternative protein sources that have been successfully used to develop diverse meatless foods. Although these plant-based products have a lower impact on the environment than equivalent animal-based products, they have lower protein digestibility. Germination could be a useful bioprocess to enhance protein digestibility in legumes, although its effect at different times of seedling development has been little studied in lentils and faba beans. This work investigated the effect of germination time (4 and 6 days after full seed imbibition) on the proteins of three types of Canadian lentils (“gray zero tannin”, G; “caviar black”, B; and “red dehulled”, D) and faba beans (“zero vicin/convicin”, F). Germination increased total nitrogen (4–14% increase) and total levels of some amino acids: Asp in all the sprouts studied; Ser, Pro, Ala, Cys, His and Lys in G; and Met and Tyr in B. A concurrent degradation of the 7S and 11S globulin subunits, the accumulation of peptides below 20 kDa and free essential and non-essential amino acids (4- to 6-fold increase) were observed after germination in all the legumes studied. These effects were attributable to the increased protease activity observed after sprouting. Trypsin inhibitory activity was lower in legume sprouts, except for D, where a small increase was detected. Time, legume type and their interaction showed significant effects on the parameters studied. Germination effects were generally more remarkable at longer stages of seedling development. Among the legumes studied, D showed a differential behavior characterized by a faster protein degradation and release of small peptides, probably due to its higher protease activity as indicated by principal component analysis. These results evidence the positive effects of germination on the protein digestibility of different lentil types and faba beans. The protein quality of plant-based foods could be improved through the selection of legume species with higher germination-induced proteolytic rates and optimized germination times.

scholarly journals Research on Plants for the Understanding of Diseases of Nuclear and Mitochondrial Origin

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Claudia P. Spampinato ◽  
Diego F. Gomez-Casati
Keyword(s):  
Current Knowledge ◽  
Model System ◽  
Human Diseases ◽  
Model Organisms ◽  
Human Cell Lines ◽  
Molecular Defects ◽  
Human Genes ◽  
Clinical Disorders ◽  
Mitochondrial Origin ◽  
Experimental Findings

Different model organisms, such asEscherichia coli,Saccharomyces cerevisiae,Caenorhabditis elegans,Drosophila melanogaster, mouse, cultured human cell lines, among others, were used to study the mechanisms of several human diseases. Since human genes and proteins have been structurally and functionally conserved in plant organisms, the use of plants, especiallyArabidopsis thaliana, as a model system to relate molecular defects to clinical disorders has recently increased. Here, we briefly review our current knowledge of human diseases of nuclear and mitochondrial origin and summarize the experimental findings of plant homologs implicated in each process.

Nest temperature´s influence on morphology of Dermochelys coriacea hatchlings incubated in hatcheries in Oaxaca, Mexico

2021 ◽  
Author(s):  
Jesús García-Grajales ◽  
Juan Francisco Meraz ◽  
José Luis Arcos García ◽  
Eustacio Ramírez Méndez
Keyword(s):  
Incubation Temperature ◽  
Carapace Width ◽  
Principal Component ◽  
Dermochelys Coriacea ◽  
Egg Mass ◽  
Natural Environments ◽  
Data Logger ◽  
Geometric Morphometric ◽  
Low Weight ◽  
Incubation Temperatures

The influence of nest incubation temperatures on the carapace shape and morphological traits of Dermochelys coriacea (Vandelli 1761) hatchlings incubated in two hatcheries of Oaxaca, Mexico was evaluated. This study was carried out from October 2016 through May 2017. On each beach, there are community groups consisting of volunteers without association with universities, that protect and relocate the nests to increase hatching success. In each translocated nest, a data logger was placed in the centre of the egg mass. Hatchlings were collected as they emerged from each nest. The carapaces of the hatchlings were photographed and subjected to geometric morphometric analysis; later, hatchlings were weighed and their bodies were measured. The mean temperature of 12 nests in each hatchery were recorded, with no significant differences between hatcheries. The principal component analysis (PCA) revealed an overlapping of the carapace shape under different duration of temperature. Temperature had a significant influence on hatchling morphology. Higher mean incubation temperatures produced hatchlings with low weight, smaller appendage; narrower carapace width and shorter flippers length. Lower mean incubation temperatures produced hatchlings that had greater weight, greater appendage width, wider carapace width and longer flipper length. Results indicate that the D. coriacea hatchlings incubated in hatcheries demonstrate morphology that varies in relation to nest incubation temperature in a similar way to hatchlings produced in natural environments.

scholarly journals The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Nature Plants ◽  
2016 ◽  
Vol 2 (11) ◽  
Author(s):  
Xiangchao Gan ◽  
Angela Hay ◽  
Michiel Kwantes ◽  
Georg Haberer ◽  
Asis Hallab ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Human Genetics ◽  
Morphological Evolution ◽  
Morphological Diversity ◽  
Close Relative ◽  
Gene Duplications ◽  
Tandem Gene Duplication ◽  
Genome Wide ◽  
Differential Gene

Abstract Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

scholarly journals Skull morphometric characters in parrots (Psittaciformes)

2020 ◽  
Vol 28 (1) ◽  
pp. 104-120
Author(s):  
Tibor Pecsics ◽  
Miklós Laczi ◽  
Gergely Nagy ◽  
Tamás Kondor ◽  
Tibor Csörgő
Keyword(s):  
Ventral View ◽  
Relative Size ◽  
Relative Length ◽  
Principal Component ◽  
Relative Width ◽  
Geometric Morphometric ◽  
Morphometric Characters ◽  
Lacrimal Bone ◽  
The Tropics ◽  
Avian Group

AbstractParrots (Psittaciformes) are a unique and diverse avian group and vary tremendously in size, shape, and colour. Mainly distributed throughout the tropics and subtropics, most species of parrots are largely or exclusively arboreal with several exceptions. The species also differ in diet and habitat, which led to different musculoskeletal adaptations of the skull. However, parrots have conspicuous generalized external features; in this recent study, we tried to increase our knowledge of the cranial shape and foraging habits. A geometric morphometric approach was used to analyse two-dimensional cranial landmarks. We used principal component (PC) analyses on measurements that may be related to diet. The PCs described the relative height of the cranium, the relative length and curvature of the beak, differences in the orientation and curvature of the lacrimal bone and the upper margin of orbits, variation in the size and position of the palatine bone and the relative width of the cranium, and variation in the relative size of the neurocranium compared to the viscerocranium. The dietary categories overlap in the morphospace but the analysis in lateral and ventral view resulted in significant differences.

scholarly journals Macroscopy and Microscopy Study of Scopraia dulcis L.

2018 ◽  
Vol 23 (1) ◽  
pp. 56
Author(s):  
Djoko Santosa ◽  
Subagus Wahyuono ◽  
Sugeng Riyanto ◽  
SM Widyastuti
Keyword(s):  
Glandular Trichomes ◽  
Principal Component ◽  
Morphological Diversity ◽  
Microscopy Study ◽  
Sampling Location ◽  
Scoparia Dulcis ◽  
Region Selection ◽  
Microscopy Analysis ◽  
Palisade Cells ◽  
Selection Of

A morphological diversity analysis of Scoparia dulcis by macroscopy and microscopy has been conducted. The aim of this research is to determine the morphological and anatomical character of S. dulcis which grow in Opak watershed, Special Region of Yogyakarta. Samples were taken from Sleman (Cangkringan, Ngemplak Kalasan, and Prambanan) and Bantul (Imogiri and Pundong) region. Selection of sampling location is based on altitude difference. The samples are the third leaf order from the tip of the stem. They were measured in length and width. Microscopy analysis was performed by observing the number of glandular trichomes, palisade cells in the epidermis and stomata in the upper and lower epidermis. The data obtained were analyzed using principal component analysis (PCA). The results show that based on morphological and anatomical assessment, there were found 3 clusters of S. dulcis, i.e. Cangkringan-Ngemplak-Prambanan, Kalasan, and Imogiri-Pundong cluster.

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