scholarly journals Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae

2020 ◽  
Vol 37 (8) ◽  
pp. 2341-2356 ◽  
Author(s):  
Laura Ávila Robledillo ◽  
Pavel Neumann ◽  
Andrea Koblížková ◽  
Petr Novák ◽  
Iva Vrbová ◽  
...  

Abstract Satellite repeats are major sequence constituents of centromeres in many plant and animal species. Within a species, a single family of satellite sequences typically occupies centromeres of all chromosomes and is absent from other parts of the genome. Due to their common origin, sequence similarities exist among the centromere-specific satellites in related species. Here, we report a remarkably different pattern of centromere evolution in the plant tribe Fabeae, which includes genera Pisum, Lathyrus, Vicia, and Lens. By immunoprecipitation of centromeric chromatin with CENH3 antibodies, we identified and characterized a large and diverse set of 64 families of centromeric satellites in 14 species. These families differed in their nucleotide sequence, monomer length (33–2,979 bp), and abundance in individual species. Most families were species-specific, and most species possessed multiple (2–12) satellites in their centromeres. Some of the repeats that were shared by several species exhibited promiscuous patterns of centromere association, being located within CENH3 chromatin in some species, but apart from the centromeres in others. Moreover, FISH experiments revealed that the same family could assume centromeric and noncentromeric positions even within a single species. Taken together, these findings suggest that Fabeae centromeres are not shaped by the coevolution of a single centromeric satellite with its interacting CENH3 proteins, as proposed by the centromere drive model. This conclusion is also supported by the absence of pervasive adaptive evolution of CENH3 sequences retrieved from Fabeae species.

2020 ◽  
Author(s):  
Patricia Kaye Tahura Dumandan

Understanding the mechanisms driving biodiversity patterns amidst an era of global environmental change is the core of modern ecological research. The magnitude of biodiversity losses associated with anthropogenic activities has prompted resource managers and ecologists alike to identify strategies to address conservation issues. Broadly, two types of approaches are employed to answer ecological research questions: 1) single-species and 2) ecosystem-based approach. Single-species approaches are often useful to elucidate mechanisms driving population trajectories of individual species. On the other hand, ecosystem-based approaches can help in identifying general patterns that may be useful for multi-species management. Here, I used both approaches in assessing broad-scale patterns and mechanisms driving count trends of migrating raptors recorded at Hawk Mountain Sanctuary (HMS), Pennsylvania. In the first chapter, I used a hierarchical breakpoint model to identify the assemblage-wide and species-specific timing of the shifts in count trends. Then I evaluated if changes in trend directionality of counts were linked to species’ traits (body size, population size, migratory behavior, tolerance to human presence, DDT (dichlorodiphenyltrichlorethane) susceptibility, habitat or dietary specialization). I found that an assemblage-wide shift in counts occurred around 1974, and this timing was common among 14 of the 16 species in the assemblage. Moreover, I found that habitat specialization appeared to explain the synchronous positive and negative count trends of multiple species. Other traits that I evaluated were not consistently associated with either types of trends. The temporal shift in trends in 1974 emphasized the relative importance of DDT, an organochlorine known to have adversely influenced several wildlife species and was banned in the US around the 1970s, in driving population dynamics of raptor species. However, because the counts of species susceptible to DDT were highly variable after 1974, this may suggest that a suite of additional factors, acting together, affected the recovery of species from DDT-associated declines. Additionally, the potential role of habitat specialization in count trends may suggest important linkages between habitat use and demography. In the second chapter, I used a generalized linear mixed-effects model to assess the relationships between changes in the count totals and total proportional cover of major land-use types in nine states located in the northeastern US (Connecticut, Maine, Massachusetts, New Hampshire, New Jersey, New York, Pennsylvania, Rhode Island, Vermont). The hierarchical modelling approach that I used allowed me to identify average and species-specific responses to the proportional cover of forested and urban area. These land-use variables were not associated with overall raptor counts. However, species-specific responses were variable and significant. I found that counts of Northern Goshawk, American Kestrel, Rough-legged Hawk, Sharp-shinned Hawk, and Red-tailed Hawk were positively associated with forest cover. On the other hand, Turkey and Black Vultures, Bald Eagle, and Peregrine Falcon were positively associated with urban cover. Moreover, Red-shouldered Hawk, Broad-winged Hawk, and Northern Harrier were not significantly associated with forest cover but were negatively associated with urban cover. Merlin and Cooper’s Hawk exhibited similar non-significant associations to forest but positive associations with urban cover. Finally, Golden Eagle and Osprey were not significantly associated with either land-use variables. These results provided insights on the potential influence of land-use changes on the demography of migrating raptors. Thus, these findings may be useful in improving our predictions of the population trajectories of these species in future landscape scenarios. These results illustrate the utility of evaluating species-level and assemblage-wide patterns in long-term count data. In this case, it allowed me to identify general patterns in counts of migrating raptors and gain detailed insights on the responses of individual species to land-use changes. In doing so, I was able to better understand the potential drivers of their ecological dynamics. By integrating information from these two approaches, we can expect to obtain a better understanding of natural systems and consequently, increase the probability of successful conservation outcomes.


eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Amanda Kowalczyk ◽  
Raghavendran Partha ◽  
Nathan L Clark ◽  
Maria Chikina

Although lifespan in mammals varies over 100-fold, the precise evolutionary mechanisms underlying variation in longevity remain unknown. Species-specific genetic changes have been observed in long-lived species including the naked mole-rat, bats, and the bowhead whale, but these adaptations do not generalize to other mammals. We present a novel method to identify associations between rates of protein evolution and continuous phenotypes across the entire mammalian phylogeny. Unlike previous analyses that focused on individual species, we treat absolute and relative longevity as quantitative traits and demonstrate that these lifespan traits affect the evolutionary constraint on hundreds of genes. Specifically, we find that genes related to cell cycle, DNA repair, cell death, the IGF1 pathway, and immunity are under increased evolutionary constraint in large and long-lived mammals. For mammals exceptionally long-lived for their body size, we find increased constraint in inflammation, DNA repair, and NFKB-related pathways. Strikingly, these pathways have considerable overlap with those that have been previously reported to have potentially adaptive changes in single-species studies, and thus would be expected to show decreased constraint in our analysis. This unexpected finding of increased constraint in many longevity-associated pathways underscores the power of our quantitative approach to detect patterns that generalize across the mammalian phylogeny.


Weber, in his classical memoir entitled “De aure et auditu Hominis et Animalium, Pars i., De aure Animalium aquatilium,” published in 1820, was the first to show that in certain families of Physostomous Teleostei, viz., the Siluridæ and Cyprinidæ, there exists a peculiar connection between the auditory organ and the air-bladder, by means of a chain of movably interconnected ossicles. To these two families, and to three others, viz., the Characinidæ, Gymnotidæ, and Gymnarchidæ, in which this singular mechanism was subsequently discovered, Sagemehl (33) applied the collective name of Ostariophyseæ ( oσταρiov , ossicle; ϕvσŋ air-bladder), for the reason that the possession of this highly specialized mechanism implied community of descent. Since the publication of Weber’s memoir, various contributions to this subject have been made, but deal for the most part either with special features, or with individual species, or with a very limited number of species in particular families. In no single family of Ostariophyseæ has any attempt at present been made to institute a systematic and comparative examination of any considerable number of genera, and, at the same time, to deal with the various modifications which pertain to the air-bladder, auditory organ, and skeleton as correlated and mutually dependent factors. With regard to papers on such special points as the nature of the “complex” vertebra and the homologies of the Weberian ossicles, reference may be made to the contributions of Baudelot (1), Grassi (17), and Nusbaum (29), and to a recently published and valuable paper by Sörensen (37), which treats of certain skeletal modifications, not only in the Ostariophyseæ in general but in other Teleostei. Of papers dealing with other special points, the contributions of Hasse (19) and Nusbaum ( loc. cit. ) to the anatomy of the auditory organ must also be mentioned. Of individual families, the Siluridæ have received but little attention. Sagemehl’s paper deals mainly with the air-bladder of the Characinidæ. The papers of Grassi, Baudelot, and Nusbaum relate almost exclusively to the Cyprinidæ. The valuable observations of Sörensen, while more extensive as regards the families included within the range of his investigations, are nevertheless restricted to certain special features, and, apart from the development of ossifications in its walls, have but scanty reference to the air-bladder, or to the Weberian ossicles, or to the auditory organ in the relatively few Siluridæ described by him. Weber ( loc. cit. ) himself only described the air-bladder and the ossicles which bear his name in a single species ( Silurus glanis ). Johannes Müller, in his various contributions to the Berlin Academy during the years 1843-45, added somewhat to our knowledge of these structures, and notably by his discovery of the “elastic-spring” apparatus, but Müller’s attention was mainly directed to the grosser features in the anatomy of the air-bladder, to the entire exclusion of all but the slightest reference to the important skeletal modifications which are associated with the peculiar structure of that organ in the Siluridæ, or to the auditory ossicles. Reissner (32) has given a fairly complete account of the singular bone-encapsuled air-bladder of Rhinelepis , but among the most valuable of recent contributions to this branch of vertebrate morphology are the papers by Professor Ramsay Wright relating to the aberrant Siluroid Hypophthalmus (44), and to the more normal North American species Amiurus catus (42, 43), to which reference will subsequently be made. In this connexion reference may also be made to the numerous scattered references to the air-bladder of the Indian Siluridæ contained in the papers of the late Dr. Francis Day (9, 10), which, although often too brief, in several instances at any rate are valuable as throwing some light on the degenerate condition of that organ in certain rare abnormal forms. It is remarkable that this important family of Fishes has so little occupied the attention of morphologists, especially when we take into consideration the interesting modifications which its various members have undergone, and the fact that in this family the air-bladder and “auditory” ossicles are subject to greater variations, and are more highly specialized than in any other group of Ostariophyseæ. Probably the main reason why the Siluridæ have been so much neglected is due to the fact that they are principally tropical in habitat, or live in remote and inaccessible districts. Investigators at home are consequently dependent upon the exertions of collectors, who, as a rule, do not pay much attention to Fishes, and the relatively few species which do find their way to Europe are required for museum specimens. Fortunately for us we had the opportunity of purchasing the third series of the Siluroids collected by that eminent ichthyologist, the late Dr. Bleeker, who had amassed a magnificent collection of East Indian Fishes, amongst which the Siluridse were well represented. Subsequently we added to our collection what other specimens we were able to procure, especially African and South American species.


1993 ◽  
Vol 23 (4) ◽  
pp. 591-597 ◽  
Author(s):  
Jiing-Shyang Hseu ◽  
Joseph Buongiorno

The softwood lumber that Canada exports to the United States is a heterogeneous mix of spruce, fir, red cedar, pine, hemlock, and other species. The purpose of this study was to determine to what extent each species is a distinct economic good by using a characteristic demand equation. The theory consisted of a cost-minimizing aggregate U.S. demand for imports and of share equations for each species. Partial adjustment was introduced to accommodate out-of-equilibrium observations. The results showed that the demand for each species, except fir, was elastic with respect to the price of that species, with elasticities that differed substantially by species. Cross-price elasticities between individual species were generally small. It is shown how the effect of a price change of any single species consists of two parts: a market-expansion effect that is the same for all species and a substitution effect that is species specific.


2021 ◽  
Vol 12 (10) ◽  
Author(s):  
Carine Racca ◽  
Sébastien Britton ◽  
Sabrine Hédouin ◽  
Claire Francastel ◽  
Patrick Calsou ◽  
...  

AbstractCentromeres are defined by chromatin containing the histone H3 variant CENP-A assembled onto repetitive α-satellite sequences, which are actively transcribed throughout the cell cycle. Centromeres play an essential role in chromosome inheritance and genome stability through coordinating kinetochores assembly during mitosis. Structural and functional alterations of the centromeres cause aneuploidy and chromosome aberrations which can induce cell death. In human cells, the tumor suppressor BRCA1 associates with centromeric chromatin in the absence of exogenous damage. While we previously reported that BRCA1 contributes to proper centromere homeostasis, the mechanism underlying its centromeric function and recruitment was not fully understood. Here, we show that BRCA1 association with centromeric chromatin depends on the presence of R-loops, which are non-canonical three-stranded structures harboring a DNA:RNA hybrid and are frequently formed during transcription. Subsequently, BRCA1 counteracts the accumulation of R-loops at centromeric α-satellite repeats. Strikingly, BRCA1-deficient cells show impaired localization of CENP-A, higher transcription of centromeric RNA, increased breakage at centromeres and formation of acentric micronuclei, all these features being R-loop-dependent. Finally, BRCA1 depletion reveals a Rad52-dependent hyper-recombination process between centromeric satellite repeats, associated with centromere instability and missegregation. Altogether, our findings provide molecular insights into the key function of BRCA1 in maintaining centromere stability and identity.


2021 ◽  
Vol 8 ◽  
Author(s):  
Jaco C. de Smit ◽  
Muriel Z. M. Brückner ◽  
Katherine I. Mesdag ◽  
Maarten G. Kleinhans ◽  
Tjeerd J. Bouma

Abundant research has shown that macrobenthic species are able to increase sediment erodibility through bioturbation. So far, however, this has been at the level of individual species. Consequently, we lack understanding on how such species effects act on the level of bioturbator communities. We assessed the isolated and combined effects of three behaviorally contrasting macrobenthic species, i.e., Corophium volutator, Hediste diversicolor, and Limecola balthica, at varying densities on the critical bed shear stress for sediment resuspension (τcr). Overall, the effect of a single species on sediment erodibility could be described by a power function, indicating a relatively large effect of small bioturbator densities which diminishes toward higher individual density. In contrast to previous studies, our results could not be generalized between species using total metabolic rate, indicating that metabolic rate may be only suitable to integrate bioturbation effects within and between closely related species; highly contrasting species require consideration of species-specific bioturbation strategies. Experiments at the benthic community level revealed that the ability of a benthic community to reduce τcr is mainly determined by the species that has the largest individual effect in reducing τcr, as opposed to the species that is dominant in terms of metabolic rate. Hence, to predict and accurately model the net effect of bioturbator communities on the evolution of tidal flats and estuaries, identification of the key bioturbating species with largest effects on τcr and their spatial distribution is imperative. Metabolic laws may be used to describe their actual activity.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arangasamy Yazhini ◽  
Narayanaswamy Srinivasan ◽  
Sankaran Sandhya

AbstractAfrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing < 30% sequence identity with their homologues. Rigorous sequence searches and complementary approaches were employed to annotate 156 uncharacterized protein sequences and 28 species-specific proteins. For 122 proteins we predicted potential functional roles, 43 of which we associated with protein- and nucleic-acid binding roles. Further, we analysed domain content and variations in their combinations within Afrotheria and identified 141 unique functional domain architectures, highlighting proteins with potential for specialized functions. Finally, we discuss the potential relevance of highly represented protein families such as MAGE-B2, olfactory receptor and ribosomal proteins in L. africana and E. edwardii, respectively. Taken together, our study reports the first comparative study of the Afrotherian proteomes and highlights salient molecular features.


2005 ◽  
Vol 68 (6) ◽  
pp. 1217-1221 ◽  
Author(s):  
PAVEL KRCMAR ◽  
EVA RENCOVA

A sensitive and rapid method for the quantitative detection of bovine-, ovine-, swine-, and chicken-specific mitochondrial DNA sequences based on real-time PCR has been developed. The specificity of the primers and probes for real-time PCR has been tested using DNA samples of other vertebrate species that may also be present in rendered products. The quantitative detection was performed with dual-labeled probes (TaqMan) using absolute quantification with external standards of single species meat-and-bone meals. This method facilitates the detection of 0.01% of the target species–derived material in concentrate feed mixtures and fish meals.


2016 ◽  
Vol 371 (1694) ◽  
pp. 20150269 ◽  
Author(s):  
Santiago Soliveres ◽  
Peter Manning ◽  
Daniel Prati ◽  
Martin M. Gossner ◽  
Fabian Alt ◽  
...  

Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity–multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities.


Author(s):  
Huaijiang He ◽  
Chunyu Zhang ◽  
Fengguo Du ◽  
Xiuhai Zhao ◽  
Song Yang ◽  
...  

Understory plants are important components of forest ecosystem productivity and diversity. Compared to biomass models of overstory canopy trees, few are available for understory saplings and shrubs and therefore their roles in estimation of forest carbon pools are often ignored. In this study, we harvested 24 understory species including 4 saplings, 9 tree-like shrubs and 11 typical shrubs in coniferous and broadleaved mixed forest in northeastern China and developed the best fit allometric equations of above- and below-ground and total biomass by species-specific or multispecies using morphological measurements of basal diameter, height and crown area as independent variables. The result showed that single basal diameter, height or crown area had good explanatory power for both species-specific and multispecies (p&lt;0.001). The best-fit models included only basal diameter in sapling and tree-like shrubs, and combinations of crown area, height, and basal diameter in typical shrubs. The logarithmic model was most desired among the 4 model forms of linear, quadratic, multiple linear and logarithmic, for species-specific and multispecies. The models we developed should help the estimation of forest ecosystem carbon stocks, especially for belowground component, and provide tools for quantification of individual species biomass of understory plants.


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