scholarly journals The Mobilome of Reptiles: Evolution, Structure, and Function

2019 ◽  
Vol 157 (1-2) ◽  
pp. 21-33 ◽  
Author(s):  
Stéphane Boissinot ◽  
Yann Bourgeois ◽  
Joseph D. Manthey ◽  
Robert P. Ruggiero

Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

1977 ◽  
Vol 168 (1) ◽  
pp. 1-8 ◽  
Author(s):  
J C Ramsey ◽  
W J Steele

Free loosely bound and tightly bound polyribosomes were separated from rat liver homogenate by salt extraction followed by differential centrifugation, and several of their structural and functional properties were compared to resolve the existence of loosely bound polyribosomes and verify the specificity of the separation. The free and loosely bound polyribosomes have similar sedimentation profiles and polyribosome contents, their subunit proteins have similar electrophoretic patterns and their products of protein synthesis in vitro show a close correspondence in size and amounts synthesized. In contrast, the tightly bound polyribosomes have different properties from those of the free and loosely bound polyribosomes; their average size is significantly smaller; their polyribosome content is higher; their 60 S-subunit proteins lack two components and contain four or more components not found elsewhere; their products of protein synthesis in vitro differ in size and amounts synthesized. These observations show that rat liver membranes entrap a large fraction of the free polyribosomes at low salt concentrations and that these polyribosomes are similar to those of the free-polyribosome fraction and are different from those of the tightly bound polyribosome fraction in size, structure and function.


2019 ◽  
Vol 11 (8) ◽  
pp. 2162-2177 ◽  
Author(s):  
David A Ray ◽  
Jenna R Grimshaw ◽  
Michaela K Halsey ◽  
Jennifer M Korstian ◽  
Austin B Osmanski ◽  
...  

Abstract Transposable elements (TEs) play major roles in the evolution of genome structure and function. However, because of their repetitive nature, they are difficult to annotate and discovering the specific roles they may play in a lineage can be a daunting task. Heliconiine butterflies are models for the study of multiple evolutionary processes including phenotype evolution and hybridization. We attempted to determine how TEs may play a role in the diversification of genomes within this clade by performing a detailed examination of TE content and accumulation in 19 species whose genomes were recently sequenced. We found that TE content has diverged substantially and rapidly in the time since several subclades shared a common ancestor with each lineage harboring a unique TE repertoire. Several novel SINE lineages have been established that are restricted to a subset of species. Furthermore, the previously described SINE, Metulj, appears to have gone extinct in two subclades while expanding to significant numbers in others. This diversity in TE content and activity has the potential to impact how heliconiine butterflies continue to evolve and diverge.


2001 ◽  
Vol 1 ◽  
pp. 119-132 ◽  
Author(s):  
Karl E. Havens

This paper critically evaluates some complex methods that have been used to characterize the structure and function of freshwater plankton communities. The focus is on methods related to plankton size structure and carbon transfer. The specific methods reviewed are 1) size spectrum analysis, 2) size-fractionated phytoplankton productivity, 3) size-fractionated zooplankton grazing, 4) plankton ecological transfer efficiency, and 5) grazer effects on phytoplankton community structure. Taken together, these methods can provide information on community ecological properties that are directly related to practical issues including water quality and fisheries productivity. However, caution is warranted since application without a complete understanding of assumptions and context of the manipulations could lead to erroneous conclusions. As an example, experimental studies involving the addition or removal of zooplankton, especially when coupled with nutrient addition treatments, could provide information on the degree of consumer vs. resource control of phytoplankton. Resource managers subsequently could use this information in developing effective measures for controlling nuisance algal biomass. However, the experiments must be done critically and with sufficient safeguards and other measurements to ensure that treatments (e.g., zooplankton exclosure by screening of water) actually are successful and do not introduce other changes in the community (e.g., removal of large algae). In all of the methods described here, the investigator must take care when generalizing results and, in particular, carry out a sufficient number of replications to encompass both the major seasonal and spatial variation that occurs in the ecosystem.


1987 ◽  
Vol 6 (2) ◽  
pp. 287-294 ◽  
Author(s):  
Zsuzsanna Schwarz-Sommer ◽  
Nancy Shepherd ◽  
Eckhard Tacke ◽  
Alfons Gierl ◽  
Wolfgang Rohde ◽  
...  

ACS Nano ◽  
2012 ◽  
Vol 6 (2) ◽  
pp. 1625-1636 ◽  
Author(s):  
Ryan Coppage ◽  
Joseph M. Slocik ◽  
Beverly D. Briggs ◽  
Anatoly I. Frenkel ◽  
Rajesh R. Naik ◽  
...  

2019 ◽  
Author(s):  
David A Ray ◽  
Jenna R Grimshaw ◽  
Michaela K Halsey ◽  
Jennifer M Korstian ◽  
Austin B Osmanski ◽  
...  

AbstractTransposable elements (TEs) play major roles in the evolution of genome structure and function. However, because of their repetitive nature, they are difficult to annotate and discovering the specific roles they may play in a lineage can be a daunting task. Heliconiine butterflies are models for the study of multiple evolutionary processes including phenotype evolution and hybridization. We attempted to determine how TEs may play a role in the diversification of genomes within this clade by performing a detailed examination of TE content and accumulation in 19 species whose genomes were recently sequenced. We found that TE content has diverged substantially and rapidly in the time since several subclades shared a common ancestor with each lineage harboring a unique TE repertoire. Several novel SINE lineages have been established that are restricted to a subset of species. Furthermore, the previously described SINE, Metulj, appears to have gone extinct in two subclades while expanding to significant numbers in others. Finally, a burst of TE origination corresponds temporally to a burst of speciation in the clade, potentially providing support to hypotheses that TEs are drivers of genotypic and phenotypic diversification. This diversity in TE content and activity has the potential to impact how heliconiine butterflies continue to evolve and diverge.


2014 ◽  
Vol 38 (9) ◽  
pp. 741-750 ◽  
Author(s):  
Chris Hoi Houng Chan ◽  
Ina Laura Pieper ◽  
Scott Fleming ◽  
Yasmin Friedmann ◽  
Graham Foster ◽  
...  

2018 ◽  
Vol 97 (2) ◽  
pp. 578-591 ◽  
Author(s):  
B.U. Metzler-Zebeli ◽  
E. Magowan ◽  
M. Hollmann ◽  
M.E.E. Ball ◽  
A. Molnár ◽  
...  

2020 ◽  
Author(s):  
Soniya Devi Yambem ◽  
Sonam Chorol ◽  
Manjari Jain

AbstractAnimal vocal communication ranges from simple to complex based on repertoire size, structure, and composition of calls and the information encoded in them. According to the social complexity hypothesis, communication complexity tends to increase with an increase in social complexity. While several studies on mammalian systems exist supporting this, evidence from avian systems is comparatively limited. Towards this, we present evidence for complex acoustic communication in a cooperatively breeding passerine, Jungle Babbler, based on three aspects of complexity: an extensive repertoire of acoustically-distinct calls, within-call structural complexity and the diverse behavioural contexts in which these calls are used. Jungle Babblers were found to possess a structurally and functionally diverse vocal repertoire comprising 15 different calls. Detailed acoustic analyses of multisyllabic calls revealed that these calls are composed of different notes. Further, despite a large number of notes present in the repertoire, the number of calls were limited to 15. This implies that there may be underlying rules that determine call composition to give rise to functional calls to which receivers respond. We also found that these calls were produced in a variety of affiliative and agonistic contexts and were employed towards coordination of diverse social behaviours including group movement, foraging, brood care, aggression and vigilance. Yet, 7 out of 15 vocalizations were produced in the context of vigilance. This disproportionate investment of vocalizations towards co-ordinated acoustic vigilance is characteristic of many cooperatively breeding birds. Our study extends support for the social complexity hypothesis and also lays the foundation for future investigations on combinatorial and syntactical rules underlying call structure and function in bird vocalizations.Significance statementStudies on vocal complexity in birds have focussed mainly on repertoire size, structure and function. However, fine temporal and spectral features of elements that constitute a call/song are rarely examined to evaluate vocal complexity. We examined complex communication in a cooperatively breeding social passerine, Jungle Babbler for which we assessed repertoire size, function, acoustic features of calls and of their constituent elements. Jungle Babblers were found to possess a structurally and functionally diverse vocal repertoire comprising of 15 calls, 46% of which were in the context of vigilance, thereby extending support to the social complexity hypothesis. We also found that several calls were composed of multiple, acoustically distinct notes. These findings will be foundational in understanding the interrelations between sociality and communicative complexity and underlying combinatorial rules that determine call structure and function.


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