Evolution of Functional Genes in Cetaceans Driven by Natural Selection on a Phylogenetic and Population Level

2012 ◽  
Vol 40 (3) ◽  
pp. 341-354 ◽  
Author(s):  
Andre E. Moura ◽  
Ada Natoli ◽  
Emer Rogan ◽  
A. Rus Hoelzel
Author(s):  
Mohan Matthen

Physicalism appears to undermine the autonomy of ‘special sciences’ such as biology, and to leave little room for proprietary biological laws or causation. Mendel’s ‘Laws’ are so-called because they are fundamental to the subject-area, but since they describe causal processes that are wholly physical in nature, they seem to reduce to physical laws, given certain propositions about the composition of DNA. The same goes for other principles of the biological sciences. This argument has been challenged by Hilary Putnam, on the grounds that good explanations, for instance in mathematical terms, could range more widely than any given physical realization. Putnam argues that mathematics could thus have an autonomous role in science despite physicalism. Putnam’s insight has been applied to classical genetics by Philip Kitcher. A gene is a unit of inheritance that passes unchanged from parent to offspring according to certain rules. It is these rules that are essential to understanding inheritance, not details of interaction in the DNA substrate. Putnam and Kitcher here employ a notion similar to Aristotle’s ‘formal causes’ – functional and structural determinants of biological characteristics that are somewhat independent of material constitution. There are other conceptions of laws to be found in philosophy of science. Some think that they are propositions with the capacity to impart axiomatic structure to what is known about a domain. The principle of natural selection plays this role in biology, though it is a priori. Again, some think that laws are necessary truths: on cladistic systems of classification, the proposition that the common raven is a bird is arguably a law under this understanding. The nature of causal patterns in natural selection has been a matter of some discussion recently. The view that individual-level causes are sufficient to explain selection-outcomes is tempting to the reductionist, but distorts the explanatory aims of evolutionary theory. Clearly, evolutionary theory requires population-level causes. On the other hand, it has been questioned whether natural selection itself should be understood as a ‘force’ acting on a population, somewhat in the same manner as gravitation acts on a body. Statistical views of natural selection seek alternatives to this way of understanding selection. Finally, what are biological entities? Some ontologies admit no priority among collections of atoms – the argument is that an organism, for instance, is nothing more than such a collection. Many biologists, however, treat of composite entities as internally organized complex systems. On this view, cells, organisms, populations, and ecosystems have privileged ontological status.


2007 ◽  
Vol 30 (4) ◽  
pp. 371-371
Author(s):  
Liane Gabora

AbstractThe argument that heritable epigenetic change plays a distinct role in evolution would be strengthened through recognition that it is what bootstrapped the origin and early evolution of life, and that, like behavioral and symbolic change, it is non-Darwinian. The mathematics of natural selection, a population-level process, is limited to replication with negligible individual-level change that uses a self-assembly code.


1991 ◽  
Vol 332 (1262) ◽  
pp. 91-102 ◽  

The study of allocation of resources offers the possibility of understanding the pressures of natural selection on reproductive functions. In allocation studies, theoretical predictions are generated and the assumptions as well as the predictions can be tested in the field. Here, we review some of the theoretical models, and discuss how much biological reality can be included in them, and what factors have been left out. We also review the empirical data that have been generated as tests of this body of theory. There are many problems associated with estimating reproductive resources, and also with testing how allocation of these resources affects reproductive and other components of fitness, and we assess how important these may be in allowing empirical results to be interpreted. Finally, we discuss the relevance of resource allocation patterns to the evolution of unisexual flowers, both at the level of individual plants (monoecy, andro- and gynomonoecy) and at the population level (dioecy).


2018 ◽  
Author(s):  
Lysanne Snijders ◽  
Ralf H. J. M. Kurvers ◽  
Stefan Krause ◽  
Indar W. Ramnarine ◽  
Jens Krause

AbstractIndividual foraging is under strong natural selection. Yet, whether individuals differ consistently in their foraging success across environments, and which individual and population-level traits might drive such differences, is largely unknown. We addressed this question in a field experiment, conducting over 1,100 foraging trials with nine subpopulations of guppies, Poecilia reticulata, translocating them across environments in the wild. A-priori, we determined the individual social phenotypes. We show that individuals consistently differed in reaching food, but not control, patches across environments. Social individuals reached more food patches than less social ones and males reached more food patches than females. Overall, individuals were, however, more likely to join females at patches than males, which explains why individuals in subpopulations with relatively more females reached, on average, more food patches. Our results provide rare evidence for individual differences in foraging success across environments, driven by individual and population level (sex ratio) traits.


Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 296-303 ◽  
Author(s):  
Alan R. Templeton ◽  
Hope Hollocher ◽  
Susan Lawler ◽  
J. Spencer Johnston

Natural populations of Drosophila mercatorum are variable for the number of X-linked 28S ribosomal genes bearing a 5-kilobase insert. A separate polymorphic X-linked gene controls whether 28S repeats bearing the insert are preferentially underreplicated during the formation of polytene tissue. Female flies having at least a third of their 28S genes bearing the insert and lacking the ability to preferentially underreplicate inserted repeats display the abnormal abdomen syndrome. The syndrome is characterized by retention of juvenile abdominal cuticle into the adult, a slowdown in larval developmental time, and an increase in early female fecundity. The life history traits are expressed in nature and provide a basis for strong natural selection. The abnormal abdomen syndrome should be favored whenever the adult age structure is skewed towards young individuals, and field studies confirm this prediction. The closely related species, Drosophila hydei, also bears these inserts and appears to be subject to similar selection. However, D. mercatorum responds to this selection primarily through the allelic variation that controls preferential underreplication, whereas D. hydei responds primarily through adjustment of the proportion of inserted 28S genes. This is interpreted to mean that the evolution of a multigene family arises from the interaction of population-level and DNA-level processes.Key words: ribosomal DNA, natural selection, concerted evolution, life history, multigene families, Drosophila mercatorum, Drosophila hydei.


2020 ◽  
Author(s):  
Marcelo Otero ◽  
Silvina Sarno ◽  
Sofía Acebedo ◽  
Javier Alberto Ramirez

<p>Evolution of metabolism is a longstanding yet unresolved question, and several hypotheses were proposed to address this complex process from a Darwinian point of view. Modern statistical bioinformatic approaches targeted to the comparative analysis of genomes are being used to detect signatures of natural selection at the gene and population level, as an attempt to understand the origin of primordial metabolism and its expansion. These studies, however, are still mainly centered on genes and the proteins they encode, somehow neglecting the small organic chemicals that support life processes. In this work, we selected steroids as an ancient family of metabolites widely distributed in all eukaryotes and applied unsupervised machine learning techniques to reveal the traits that natural selection has imprinted on molecular properties throughout the evolutionary process. Our results clearly show that sterols, the primal steroids that first appeared, have more conserved properties and that, from then on, more complex compounds with increasingly diverse properties have emerged, suggesting that chemical diversification parallels the expansion of biological complexity. In a wider context, these findings highlight the worth of chemoinformatic approaches to a better understanding the evolution of metabolism.</p>


2018 ◽  
Vol 373 (1747) ◽  
pp. 20170106 ◽  
Author(s):  
Jona Kayser ◽  
Carl F. Schreck ◽  
QinQin Yu ◽  
Matti Gralka ◽  
Oskar Hallatschek

Evolutionary dynamics are controlled by a number of driving forces, such as natural selection, random genetic drift and dispersal. In this perspective article, we aim to emphasize that these forces act at the population level, and that it is a challenge to understand how they emerge from the stochastic and deterministic behaviour of individual cells. Even the most basic steric interactions between neighbouring cells can couple evolutionary outcomes of otherwise unrelated individuals, thereby weakening natural selection and enhancing random genetic drift. Using microbial examples of varying degrees of complexity, we demonstrate how strongly cell–cell interactions influence evolutionary dynamics, especially in pattern-forming systems. As pattern formation itself is subject to evolution, we propose to study the feedback between pattern formation and evolutionary dynamics, which could be key to predicting and potentially steering evolutionary processes. Such an effort requires extending the systems biology approach from the cellular to the population scale. This article is part of the theme issue ‘Self-organization in cell biology’.


2021 ◽  
Author(s):  
Marcelo Otero ◽  
Silvina Sarno ◽  
Sofía Acebedo ◽  
Javier Alberto Ramirez

<p>Evolution of metabolism is a longstanding yet unresolved question, and several hypotheses were proposed to address this complex process from a Darwinian point of view. Modern statistical bioinformatic approaches targeted to the comparative analysis of genomes are being used to detect signatures of natural selection at the gene and population level, as an attempt to understand the origin of primordial metabolism and its expansion. These studies, however, are still mainly centered on genes and the proteins they encode, somehow neglecting the small organic chemicals that support life processes. In this work, we selected steroids as an ancient family of metabolites widely distributed in all eukaryotes and applied unsupervised machine learning techniques to reveal the traits that natural selection has imprinted on molecular properties throughout the evolutionary process. Our results clearly show that sterols, the primal steroids that first appeared, have more conserved properties and that, from then on, more complex compounds with increasingly diverse properties have emerged, suggesting that chemical diversification parallels the expansion of biological complexity. In a wider context, these findings highlight the worth of chemoinformatic approaches to a better understanding the evolution of metabolism.</p>


Author(s):  
Douglas Allchin

In our culture no one needs a biology class to learn about “survival of the fittest.” Yet one might need instruction to unlearn the misconceptions engendered by the analogy’s potent imagery. In popular perspectives, this single phrase conjures images of humans—however civilized—as brutish organisms vying for jobs, status, and power. Maybe they also compete for prime mates. The language of “survival” resonates with “survivor” contests on television: “Outwit. Outplay. Outlast.” Mention of the “fittest” implies that physical “fitness” and athletic prowess are ideals. At the same time, the extremeness of reference to only the “fittest” implies that a human’s fate seems to be life versus death, fit versus unfit, winning versus losing. In all, cooperation and coexistence give way to warfare, conflict, and backstabbing gossip: “society, red in tooth and claw,” to adapt Tennyson’s phrase. Mostly, life reduces to competition. Cutthroat competition. Through just one expression, all these interpretations seem to have a biological basis. None of them are scientifically justified. “Survival of the fittest” is not a neutral phrase, idly describing natural selection. Instead, through unintended metaphors the language fosters major misconceptions. One might hope to remedy these many confusions. But how? “Survival of the fittest” seems to describe both organic evolution and human culture. So first, one must carefully distinguish the processes of each, functioning at different levels (essay 6). Second, one needs to understand how ideology can be unduly naturalized (or improperly inscribed in “nature”). The phrase was never purely descriptive. It expressed cultural values (essay 7). Even with both these pitfalls resolved, however, problems may persist because of the very language itself. The connotations of the phrase seem inescapable. Here, I consider the misconceptions latent in each individual term: “survival” and “fit”—as well as the “-est” suffix. That may help us craft a more fitting analogy or catchphrase to describe natural selection. Consider first the implications of the word “survival.” What matters to evolution is differences in survival rate at a population level. Differential survival leads to differential reproduction, the essence of natural selection.


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