Tuesday, October 11, 2016

Macroevolution - Terms and Linkages

A few years ago, I had taken a class called Macroevolution. During the class we read several seminal papers on the subject and discussed the implications of these topics. At the end of the class, we set up on the white board some of the principle topics in macroevolution. The discussion involved how the topics were linked and specifically what they could be/were linked to. The class ended with a bunch of evolutionary topics that were heavily interacting and influencing each other. 

I though this was fascinating and I ended up taking pictures of the board after we had finished the class. Below is a cleaned up version of that work session with the appropriate terminology defined and/or discussed below. Keep in mind that the interactions depicted in the diagram are not all of the possible interactions, they are just the most prevalent ones that we happened upon during our discussion. 

Macroevolutionary concepts. Click for a larger version.

 The descriptions and definitions below are taken or paraphrased directly from the source literature as cited.

Adaptation – Any change in the structure or functioning of successive generations of a population that makes it better suited to its environment. (Oxford Dictionary of Biology)

Burden - Evolutionary constraints caused by functional interdependency and maintained by internal selection or in other words hierarchically nested interdependence of characters within the organism (Schoch, 2010). Basically these are genes that are hard wired into the genome and passed down through generations that are really difficult, if not impossible, to get rid of. For instance, almost all tetrapods have four limbs since the first tetrapod.

Constructional Morphology – Phylogenetic, functional, and morphogenic constraints and their dynamic relationship which help to explain a variety of evolutionary phenomena such as sub-optimal structures, convergence, parallel evolution, channeled evolutionary pathways, and the geometrical patterns that characterize organic structure (Reif et al, 1985).

Deep Homology – the sharing of the genetic regulatory apparatus that is used to build morphologically and phylogenetically disparate animal features. Homology, as classically defined, refers to a historical continuity in which morphological features in related species are similar in pattern or form because they evolved from a corresponding structure in a common ancestor. Deep homology also implies a historical continuity, but in this case the continuity may not be so evident in particular morphologies; it lies in the complex regulatory circuitry inherited from a common ancestor (Shubin et al, 2009).

Developmental Constraint – The theory that during development the systems within an individual organism will develop a limited and discrete subset of phenotypes, regardless of the environmental variance or experimental manipulation. In other words, regularities and trends observed in phylogeny are a reflection of a conserved set of pattern-generating rules. These internal rules of development define the realm of possible variation and place limits on the process of adaptation (Alberch, 1989).

Disparity (Morphological Disparity) – The total amount of the dissimilarities among all and any kinds of biological groups of organisms (Pavlinov, 2011).

Diversity (Taxonomic Diversity, Biodiversity) – The existence of a wide variety of species (species diversity) or other taxa of plants, animals, and microorganisms in a natural community or habitat, or of communities within a particular environment (ecological diversity), or of genetic variation within a species (genetic diversity). The maintenance of a high level of biodiversity is important for the stability of ecosystems (Oxford Dictionary of Biology).

Exaptation – A morphological or physiological character that predisposes an organism to adapt to a changed environment or lifestyle. (Oxford Dictionary of Biology)

Extinction Rate – The number of extinctions during a given period of time.

Gradualism (Phyletic Gradualism) - It holds that new species arise from the slow and steady transformation of entire populations. Under its influence we seek unbroken fossil series linking two forms by insensible gradation as the only complete mirror of Darwinian processes; we ascribe all breaks to imperfections in the record (Eldredge and Gould, 1972).

GRNs (Gene Regulatory Network) – GRNs are large networks that determine the course of animal development. These networks consist largely of the functional linkages among regulatory genes that produce transcription factors and their target cis-regulatory modules in other regulatory genes, together with genes that express spatially important signaling components. They have a modular structure, consisting of assemblies of multigenic subcircuits of various forms. Each such subcircuit performs a distinct regulatory function in the process of development. GRNs have been attributed to being the reason why there is little change in the phylum and superphylum-level body plans since the Early Cambrian (Davidson and Erwin, 2006).

Mass Extinctions – The extinction of a large number of species within a relatively short interval of the geological time scale. (Oxford Dictionary of Biology)

Natural Selection – The process that, according to Darwinism, brings about the evolution of new species of animals and plants. Darwin noted that the size of any population tends to remain constant despite the fact that more offspring are produced than are needed to maintain it. He also saw that variations existed between individuals of the population and concluded that disease, competition, and other forces acting on the population eliminated those individuals less well adapted to their environment. The survivors would pass on any heritable advantageous characteristics to their offspring and in time the composition of the population would change in adaptation to a changing environment. Over a long period of time this process could give rise to organisms so different from the original population that new species are formed. (Oxford Dictionary of Biology)

Punctuated Equilibrium – An evolution hypothesis that states in evolutionary history the development of new species occurs very rapidly in short bursts (lasting typically less than 100,000 years), which are separated by long periods in which little evolutionary change occurs (Oxford Dictionary of Science).

Red Queen Hypothesis – An evolutionary theory that describes how the coevolution of competing species creates a dynamic equilibrium, in which the probability of extinction remains fairly constant over time. Hence, evolution is seen neither as ‘progressive’ – with a species’ chances of survival improving over time – nor as ‘escalatory’ – with increasing vulnerability to extinction over time. Instead, as one species evolves improvements that make it more competitive, its competitors experience selection pressures that force them to evolve in order to keep pace with it. Ones that lag too far behind will become extinct (Oxford Dictionary of Biology).

Rock Record – The availability of the information on the fossil record, which is correlated with the availability of rocks during a particular time period. The absence or presence of rocks, which have the possibility of containing a set of fossils could have an influence on how scientists perceive the evolution of a particular group (evolutionary rate, extinction rate, diversity, etc.) (Barrett et al., 2009).

Signor-Lipps Effect – This effect is where for most organisms, it is unlikely that the true last occurrence of an extinct species or family will be recorded. Therefore, almost all observed time ranges are truncated. This causes a "smearing" of the record of an extinction event backward in time (Raup, 1986). In other words, a fundamental problem with using biostratigraphic last occurrences to infer patterns of extinction is that, barring reworking, last occurrences nearly always underestimate time of extinction. Signor and Lipps (1982) showed that a random distribution of errors at biostratigraphic range end-points can produce apparent gradual decline preceding a sudden extinction boundary (Meldahl, 1990).

Species Selection – Selection is one of two process of origination and persistence of clades that has been proposed. Selection encompasses those interactions between heritable, emergent character variation and the environment that cause differences in rates of birth or death among varying individuals (Vrba and Gould, 1986). Species selection requires that species be units of selection, and thus there must be properties of the species, rather than the sum of the properties of individuals, upon which selection can act (Erwin, 2000).

Species Sorting – Sorting is one of two process of origination and persistence of clades that has been proposed. In Darwinian Theory, evolutionary change is the product of sorting (differential birth and death among varying organisms within a population). Sorting is a simple description of differential representation; it contains, in itself, no statement about causes. As its core, Darwinism provides a theory for the causes of sorting- natural selection acting upon organisms in the “struggle for existence.” However, other processes (genetic drift, for example) produce sorting as well (Vrba and Gould, 1986).

Stasis – An evolutionary theory where there is zero rate of evolution and no extinction of speciation; evolutionary change occurs only in response to changes in the physical environment (Stenseth and Smith, 1984).

2008, in Hine, R. S., ed., Oxford Dictionary of Biology: Oxford, Oxford University Press.
2010, in Daintith, J., and Martin, E., eds., Oxford Dictionary of Science: Oxford, Oxford University Press.
Alberch, P., 1989, The logic of monsters: Evidence for internal constraint in development and evolution: Geobios, v. 22, no. Supplement 2, p. 21-57.
Barrett, P. M., McGowan, A. J., and Page, V., 2009, Dinosaur diversity and the rock record: Proceedings of the Royal Society of London. Series B: Biological Sciences, v. 10.1098/rspb.2009.0352, p. 1-8.
Davidson, E. H., and Erwin, D. H., 2006, Gene Regulatory Networks and the Evolution of Animal Body Plans: Science, v. 311, no. 5762, p. 796-800.
Eldredge, N., and Gould, S. J., 1972, Punctuated equilibria: An alternative to phylogenetic gradualism, in Schopf, T. J. M., ed., Models in Paleobiology: San Francisco, Freeman, Copper and Company, p. 82-115.
Erwin, D. H., 2000, Macroevolution is more than repeated rounds of microevolution: Evolution & Development, v. 2, no. 2, p. 78-84.
Meldahl, K. H., 1990, Sampling, species abundance, and the stratigraphic signature, of mass extinction: A test using Holocene tidal flat molluscs: Geology, v. 18, no. 9, p. 890-893.
Pavlinov, I. Y., 2011, Morphological Disparity: An Attempt to Widen and to Formalize the Concept, INTECH Open Access Publisher.
Raup, D. M., 1986, Biological extinction in earth history: Science, v. 231, no. 4745, p. 1528-1533.
Reif, W.-E., Thomas, R. D. K., and Fischer, M. S., 1985, Constructional morphology: The analysis of constraints in evolution dedicated to A. Seilacher in honour of his 60. birthday: Acta Biotheoretica, v. 34, no. 2, p. 233-248.
Schoch, R. R., 2010, Riedl's burden and the body plan: selection, constraint, and deep time: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, v. 314B, no. 1, p. 1-10.
Shubin, N., Tabin, C., and Carroll, S., 2009, Deep homology and the origins of evolutionary novelty: Nature, v. 457, no. 7231, p. 818-823.
Signor, P. W., III, and Lipps, J. H., 1982, Sampling bias, gradual extinction patterns and catastrophes in the fossil record Geological Society of America Special Paper, v. 190, p. 291-296.
Stenseth, N. C., and Smith, J. M., 1984, Coevolution in Ecosystems: Red Queen Evolution or Stasis?: Evolution, v. 38, no. 4, p. 870-880.
Vrba, E. S., and Gould, S. J., 1986, The Hierarchical Expansion of Sorting and Selection: Sorting and Selection Cannot Be Equated: Paleobiology, v. 12, no. 2, p. 217-228.