BioNotes.Org

ML, vim, biology, math, and more

Patterns and Processes of Vertebrate Evolution

Chapter 1: Current Problems in Evolutionary Theory

September 15, 2020

  • “Although Darwin’s theory sought to deal with evolution over all time scales, almost all of his evidence was drawn from the modern biota.” (p. 2)
    • Darwin “argued that both the patterns and processes of evolution were identical over vastly different timescales [aka whether across a dozen generations or over hundreds of millions of generations].”
    • Darwin’s used his famous diagram (reproduced on Carroll p. 3) to convey his hypothesis that “evolution both at the levels of populations and species and over the vast expanse of geological time is characterized by gradual and continuous change.” (p. 2)
    • This page reproduces both Darwin’s notebook sketch from 1837 and the offically published version in 1859.
  • But, “the patterns established from the fossil record of the major groups of vascular plants, vertebrates, and nonvertebrate metazoans are conspicuously different.” (p. 2)
    • “There are relatively few major lineages, all of which are very distinct from one another.”
    • “Gaps between the lineages indicate that adaptive space is not fully occupied.”
    • “Instead of showing gradual and continuous change through time, the major lineages appear suddenly in the fossil record, already exhibiting many of the features by which their modern representatives are recognized.
  • “It must be assumed that evolution occurs much more rapidly between groups than within groups. For most of their evolutionary history, fundamental aspects of their anatomy and way of life for these lineages do not change significantly. Very few intermediates between groups are known from the fossil record.” (p. 4)
  • “Progressive increase in the knowlege of the fossil record over the past hundred years emphasizes how wrong Darwin was in extrapolating the pattern of long-term evolution from that observed within populations and species.” (p. 8)

Evidence from invetebrate fossil record (p. 4)

  • [By the lower Cambrian >510mya], “the earliest known members of all the major [nonvertebrate metazoans] had already achieved the basic body plan of their descendants.”
  • “Few fossils are yet known of plausible intermediates between the invertebrate phyla.”

Evidence from placental mammals (p. 4)

  • “Among the vertebrates, the radiation of placental mammals shows a similar pattern.”
  • “Scattered, fragmentary remains of primitive placental mammals are known as early as the lower Cretaceous ( ~135mya), but their fossils only become common in the late Cretaceous or early Cenozoic (~65mya).”
  • “By the beginning of the Eocene (~57mya), all the major groups living today, as well as many extinct orders, had differentiated.”
  • “Critical characteristics… have remained essentially constant during the subsequent 57 million years separating them from the living fauna.”
  • See Figure 1.3 on p. 6, drawn from Gingerich, 1977 in Chapter 15 (p. 469-500) of Patterns of Evolution, as Illustrated by the Fossil Record, Vol. 5 edited by A. Hallam

Evidence from vascular plants (p.4-7)

  • “The pattern of large-scale evolution of vascular plants is similar.”
  • “A relatively small number of major groups appear suddenly in the fossil record and then persist with little fundamental change for hundreds of millions of years.”
  • “By the end of the Devonian (~360mya), many of the major subdivisions of vascular plants living today can be recognized on the basis of distinctive reproductive structures.” (p. 6)
  • “The basic patterns (regarding how sporangia attach in the Lycopsida, Pteropsida, and Sphenopsida) have been maintained for more than 350 million years.”
  • “Few, if any, intermediates are known between these patterns.” (p. 7)

Large-scale evolutionary phenomona (p. 9-11)

  • Here are some aspects of evolution that are only clear over large spans of time, distinct from selection at the level of populations or individual species:
    1. The origin of major new structures
    2. The extremely irregular occupation of adaptive space as opposed to the nearly continuous spectrum of evolutionary change postulated by Darwin
    3. The apparently much greater rates of evolution during the origin of groups as compared to that seen during their subsequent duration
    4. The cause and nature of major radiations
    5. The cause and significance of mass extinction
  • “The contrast between the patterns seen in populations / living species versus in the fossil record has led to the study of microevolution versus macroevolution.” (p. 10) One of the main goals of this book is to examine how well Darwinian microevolutionary natural selection can be applied to macroevolution.

Obstacles to the unification of short- and long-term evolutionary processes (p. 11 - 14)

  • “Although organisms living today are but a continuation of an evolutionary sequence begun 3.5 billion years ago, the information that can be gained from the study of living forms differs radically from that which can be learned by studying their fossil remains.”
  • “Studies of living populations have inherent temporal limitations…no speciation events among vertebrates have been documented during the whole of [recorded] human history.” The impressive and fast radation of cichlid fish species in the lakes of West Africa but still too quickly for humans to directly observe. For example, the largest lake is Lake Victoria which has 500 species of cichlids which must have evolved in the last 15,000 years because Victoria was almost dry before then.
  • Unfortunately, the study of fossils presents its own challenges when one is trying to characterize evolutionary phenomena in deep time.
    • “Fossils provide no direct evidence of the nature of mutations or mutation rates involved in the evolution of novel structures or physiological patterns, nor means to measure selection coefficients.”
    • “Moreover, only a fraction of the characters that can be studied in living populations are preserved in fossils, which are almost always limited to bony or calcareous structures.”
    • The most spectacular recent advance in the study of extinct organism has been the capacity to recover DNA from fossils….unfortunately, the conditions necessary for the preservation of DNA appear so limiting that one can expect to be able to sample only a few organisms within the vastness of geological time.” (p. 13)
  • Because of the different subject matter studied, research on micro- and macroevolutionary phenomena are typically published in different scientific journals…More recently founded journals try to bridge the gap, including Paleobiology, Historical Biology, and Evolutionary Biology.”
  • Another serious barrier to developing a unified theory of evolution encompassing data from both living and fossil populations is the fact that very few scientists have devoted equal attention to problems over these different time spans.”
  • Some of the few scientists who have bridged the gap include: G. G. Simpson “who brought paleontology into the modern synthesis in the 1950s and Bjorn Kurtén who pioneered efforts to study the rates of evolution in extinct populations.” (p. 13)
  • In Morphological Change in Quartenary Mammals of North America (1993), Martin and Barnosky summarize the work of Bell, Baumgartner, and Olson (1985). Bell et al. provide a “vital factual link between patterns and processes that can be studied directly in living species but can only be assumed to have occured in most fossil sequences.” (p. 13)
  • “Paleontology has contributed more than any other discipline to demonstrating the historical fact of evolution–but vertebrate palentologists did not generally accept the theory of natural selection until well into the twentieth century.” (p. 14)
  • “The most conspicuous challenge to Darwinian selection theory in the past forty years is the theory of punctuated equilibrium.
    • Punctuated equlibrium as originally proposed focuses on individual species but its consequences apply to large-scale and long-term evolutionary patterns and proceses.
    • Punctuated equlibrium and the debates surrounding it have forced biologists “to examine currently available data more objectively, to search for more information, especially the careful collection and study of fossils from relatively recent strata in an effort to bridge the gap between micro- and macroevolutionary phenomena.”
  • “This book differs from earlier attempts to bridge the micro-macro divide by focusing on a single major taxon: the vertebrates.”

Vertebrates as a model to study evolution

  • Challenges of using non-metazoan fossil record to bridge gap between micro-macro.
  • Meanwhile, studying all metazoans together present their own challenges.
    • “The many phyla of multicellular animals have fundamentally different body plans and ways of life that make it very difficult to compare specific patterns of evolution between them. Beginning with Simpson (1944), comparisons have repeatedly been made between the rates of evolution between clams and mammals, but it is difficult to establish quantitative measures that can be applied to both groups (Stanley, 1975).”
    • Most importantly, “the most significant periods in the evolution [of the many metozoan phyla, including] their origins and early stages of differentiation are extremely poorly documented in the fossil record (Lipps and Signor, 1992). (p. 15)
    • Advantages of studying vertebrates as a model group for understanding long-term evolution:
      1. They are unquestionably a monophyletic group
      2. Nearly all vertebrates “exhibit a single pattern of reproduction, involving recombination of gametes from two sexes.”
      3. Nearly all vertebrates are free-living…[with the exceptions of semi-colonial behavior naked mole rates, parasitism through sexual physical attachment between males and females among some deep sea fish, and lampreys].”
  • “The basic consistency of anatomy, developmental processes, and reproductive mode among vertebrates act as a control in what can be considered an experimental system. Within this system, one may examine the effects of variable such as, changing environments, different taxonomic affinities on the rates and patterns of evolution over different time scales.” (p. 15)
  • Despite their useful consistency (in terms of similar body plan and modes of reproduction), vertebrates simultaneously exhibit a huge diversity.
    • As of the mid-1990s, 45,000 species have been identified with many more to be named among oceanic fish and possibly other groups. (Minelli, 1993) The only more speciose metazoan taxon is arthropods with “countless millions of insect” species.
    • In terms of scale, vertebrates range from fish and amphibians weighing a few grams to the largest whales.
    • Vertebrates are some of the best-studied organisms on the planet.
    • Because humans are vertebrates, we have special insight into how vertebrates live.
  • Another great reason to study vertebrates is their unparalleled fossil record. (Carroll, 1987) (p. 16)
    • “In contrast to other metazoan groups, the origin of the fossilizable skeleton occurred early in their radiation, so that most major events in their history are well documented.”
    • There a good number of fossils in all the major groups.
    • The main part of the body that fossilizes is the vertebrate skeleton which connects with many structures and functions of a body.
    • Even some behavior can be studied from vertebrate fossils in the form of fossilized versions of footprints, burrows, excrement, nests, eggs, etc.

Consideration of other major taxa

  • Arthropods, foraminifera, diatoms, vascular plants, angiosperms, etc. all have major value but have their own obstacles to understanding long-term evolution. (p. 16)
  • “In short, no group shows a greater potential for the study of its evolutionary history than does the vertebrates.” (p. 18)

Chapter 2: Theories of evolution at the level of populations and species

September 27-29, 2020

Introduction

  • Perhaps Darwin emphasized gradualism partly as a counter-weight against his contemporaries who believed in saltationist “big jumps” in phenotype within a single generation. And in a different intellectual milieu, Darwin might have spoken less of gradualism. (p. 19-20)
  • Darwin believed that “small, isolated populations might have the greatest potential for rapid change b/c natural selection would act most effectively on a small [geographic] area with limited environmental variability…” (p. 20)
  • But Darwin also suggested that a large population across a large geographic area might have the greater variation needed to ensure larger change and longer-term survival (on a group level).
  • Perhaps “the optimal model for rapid and long-term evolution would be a large area subject to repeated break up and coalescence of environments and populations.”
    • “The entire species could contribute to the variability available…[while] repeated isolation would contribute to locally more effective natural selection.”
    • Darwin “specifically noted that partially isolated populations might evolve more rapidly because of limited interbreeding with other populations that were subject to different selective pressures.”
  • Darwin then made a suggestion that is similar to that made by “species selection” hypothesis advanced by paleobiologist Steven M. Stanley at Johns Hopkins and University of Hawaii. See Stanley’s 1975 paper and his 1979 book Macroevolution: Patterns and Processes.
    • In other words, Darwin “argued that many populations might last for brief periods of time but that only the most divergent would be most likely to survive, since natural selection would tend to eliminate intermediate forms.” (p. 20)
    • However, “Darwin was not dogmatic on this point.”
  • Darwin implied in his chart that there are many unvarying species (aka those that, post-speciation, do not exhibit phyletic evolution). Furthermore, he suggests that “such unvarying species, despite their numerical predominance [in his chart], were extremely vulnerable to extinction.”

What are species? Biological vs. morphological species (p. 21)

  • In 1982’s The Growth of Biological Thought, Ernst Mayr describes how there “was a lot of controversy about the objective nature of species” in the period after acceptance of Darwinian natural selection. (p. 21)
  • Today, paleontologists still face a major challenge with objectively differentiating species in “evolving lineages”.
  • In contrast, biologists studying modern populations find it relatively easy to differentiate between different populations.
    • It turns out that, per studies like the ones cited by Diamond in Horrible Plant Species (Nature, 1992), the breadth of species identified are readily distinguished by Mayr’s biological species concept at least for the Metazoa and Plantae kingdoms. For these two taxons, we rarely find “hybrids or intermediates” which cannot be cleanly categorized into distinct species. (p. 21)
  • Official biological species concept from Mayr, 1963: *Species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups.” (p. 21)

Phyletic evolution vs. speciation (p. 21)

  • Any evolutionary change within a lineage is called anagenesis which is the same as phyletic evolution. Phyletic evolution is the progressive accumulation of change within a single lineage.
  • In contrast, cladogenesis refers to a multiplication of lineages, aka speciation.
  • According to Mayr (1963) and Simpson (1953), “speciation per se is not necessarily accompanied by significant morphological change.”

Discussion of types of speciation (p. 21-24)

  • “While [the anagenetic process of] phyletic evolution results from natural selection and is directly associated with adaptation within a lineage, the initial stage of speciation [aka cladogenesis] is typically imposed on the species by external forces that not reflect specific aspects of the adaptation of the parental species.” (p. 21)
  • Sympatric versus allopatric populations
  • Character displacement
  • Three types of speciation:
  • See also ring species (Carroll, p. 53)

Inadequacies of the fossil record (p. 24-25)

  • On the one hand, the 1861 discovery of Archaeopteryx was hugely important in establishing a potential link between birds and reptiles. However, it was separated by 10s of millions of years from either lineage. Archeaopteryx “…contributed no information as to the patterns and processes of evolution at the species level [because] it was isolated by tens of millions of years and enormous gaps in morphology from its nearest possible relatives.” (p. 25)
  • As another example, “the horse genera known at the time of Darwin were separated from one another by tens of millions of years.”
  • Darwin pleaded the fragmentary nature of the fossil record and admitted that “he who rejects these views on the nature of the geological record, will rightly reject my whole theory.” (Origin of Species, p. 342)
  • “Despite more than a hundred years of intensive collecting efforts…the fossil record still does not yield the picture of infinitely numerous transitional links that [Darwin] expected.” Instead, paleontologists have found a quite different pattern.

History of Stratigraphy (p. 25-27)

  • “Although fossil vertebrates and the remains of leaves and woody structures of plants have been studied primarily in reference to their biological nature, most paleontologists who study the remains of microorganisms, nonvertebrate metazoans, and plant spores and pollen are mainly concerned with the use of fossils for characterizing particular geological horizons.” (p. 25-26)
  • “Extensive use of fossils as stratigraphic indicators in the nearly 150 years since the publication of The Origin of Species shows that a great many fossil species either have long timespans (hundreds of feet of strata aka tens of millions of years) or are restricted to a single horizon.”
  • “Few well-studied examples from the record of fossil invertebrates show a pattern of evolution such as that predicted by Darwin.”
    • Darwin suggested that lineages that are constant aka do not undergo phyletic change (anagenetic change) would tend be short-lived b/c they indicate lack of adaptability, esp. when competing with more adaptable species.
    • In contrast, we see various lineages that seem unchanged for millions of years in the fossil record.

Eldredge and Gould and Punctuated Equilibrium (p. 27-33)

  • Eldgridge and Gould coined the term phyletic gradualism to contrast with punctuated equilibrium. (p. 31) Important note: the new coinage phyletic gradualism should not be confused with the traditional term phyletic evolution (which is contrasted with speciation).
  • Eldredge and Gould set up a strawman version of Neo-Darwinism aka The Modern Synthesis. Of the 4 tenets they list on Carroll p. 32, only the first would be agreed upon by Darwin, G.G. Simpson, and other Neo-Darwinists: “New species arise by the transformation of an ancestral population into its modified descendants.” (p. 32)
  • Tenets 2-4 listed by E&G are not what Simpson et al. would agree to:
    • Tenet 2: “The transformation is even and slow.” Strawman of uniformity across time!
    • Tenet 3: “The transformation involves large numbers, usually the entire ancestral population.” Strawman of uniformity across population.
    • Tenet 4: “The transformation over all or a large part of the ancestral species’ geographical range.” Strawman of uniformity across physical space.

Quotes from Gould and Eldredge 1977

From the abstract for Punctuated Equilibria: The Tempo and Mode of Evolution Reconsidered

We believe that punctuational change dominates the history of life: evolution is concentrated in very rapid events of speciation (geologically instantaneous, even if tolerably continuous in ecological time). Most species, during their geological history, either do not change in any appreciable way, or else they fluctuate mildly in morphology, with no apparent direction. Phyletic gradualism is very rare and too slow, in any case, to produce the major events of evolution. Evolutionary trends are not the product of slow, directional transforma- tion within lineages; they represent the differential success of certain species within a clade- speciation may be random with respect to the direction of a trend (Wright’s rule).

As an a priori bias, phyletic gradualism has precluded any fair assessment of evolutionary tempos and modes. It could not be refuted by empirical catalogues constructed in its light because it excluded contrary information as the artificial result of an imperfect fossil record. With the model of punctuated equilibria, an unbiased distribution of evolutionary tempos can be established by treating stasis as data and by recording the pattern of change for all species in an assemblage. This distribution of tempos can lead to strong inferences about modes. If, as we predict, the punctuational tempo is prevalent, then speciation-not phyletic evolution-must be the dominant mode of evolution.

We argue that virtually none of the examples brought forward to refute our model can stand as support for phyletic gradualism; many are so weak and ambiguous that they only reflect the persistent bias for gradualism still deeply embedded in paleontological thought. Of the few stronger cases, we concentrate on Gingerich’s data for Hyopsodus and argue that it provides an excellent example of species selection under our model. We then review the data of several studies that have supported our model since we published it five years ago. The record of human evolution seems to provide a particularly good example: no gradualism has been detected within any hominid taxon, and many are long-rangirig; the trend to larger brains arises from differential success of essentially static taxa. The data of molecular genetics support our assumption that large genetic changes often accompany the process of speciation.

Phyletic gradualism was an a priori assertion from the start-it was never “seen” in the rocks; it expressed the cultural and political biases of 19th century liberalism. Huxley advised Darwin to eschew it as an “unnecessary difficulty.” We think that it has now become an empirical fallacy. A punctuational view of change may have wide validity at all levels of evolutionary processes. At the very least, it deserves consideration as an alternate way of interpreting the history of life.

Conclusion to Chapter Two (p. 33)

  • “The most striking claim made by Gould and Eldredge is that natural selection is not a significant force in controlling the pattern or rate of evolution at the level of species. Thus, they deny the primary tenet of evolutionary theory as proposed by Darwin.”
  • “Can [Gould and Eldredge’s thesis] be maintained in view of the evidence provided by modern studies of living populations?”

Chapter 3: Evolution in modern populations

Contrasting approaches by Darwin, Dobzhansky, Mayr, and Gould & Eldredge (p. 34)

  • 10/10/2020
  • Although Darwin drew his evidence primarily from living populations, he applied his theory of evolution by natural selection to the whole history of life, on geologic timescales.
  • In contrast, Gould and Eldredge draw most of their evidence for punctuated equilibrium from the fossil record and apply it to living populations. This is somewhat counter to their assertion that they were inspired by the mid-20th century work in living ecosystems by Dobzhansky and Mayr.

Five propositions of Darwinsim

  • Four major premises for Darwin’s theory of natural selection (p. 34):
    1. All populations exhibit some degree of natural variation.
    2. A significant fraction of that variation is inherited from generation to generation.
    3. Environmental resources are limited such that only a small fraction of the individuals in each generation successfully produce offspring in the next generation.
    4. Traits that favor the survival of individuals in one generation will be preferentially perpetuated in the next generation.
  • The above four premises are overwhelmingly supported by converging lines of evidence from “anatomy, protein polymorphism, genetics, and the demography of living populations.” (p. 34)
  • There is also implicitly a 5th proposition: “Progressive changes traits from generation to generation will result in long-term evolutionary change.” (p. 35)
    • This fifth proposition is where Eldredge and Gould (henceforth, E&G) disagree with Mayr, Dobzhansky, Wright and the other authors of the modern synthesis.
    • E&G claim that over the vast majority of a species’ duration, there is little progressive change; what genetic changes occur drift back and forth in a random manner.
    • “Evolutionary change resulting from natural selection [is] considered capable of tracking minor, short-term environmental variations, frequently in an oscillatory manner, but having little long-term signficance.”

Examples (p. 35)

  • “Darwin’s best examples of large scale morphological change within known species were primarily limited to [domesticated] plants and animals. In these cases, historical records going back several thousand years documented morphological changes as great as those that separate well-established species. “
    • However, the artificial selection exerted by humans on domesticated organisms is significantly stronger than that expected in the natural world.
    • “No examples are known of changes of this magnitude in natural populations within such a limited time [aka thousands of years, on the scale of human written language].”
  • Classic examples of change of allele frequencies in living populations
  • In 1986, John Endler’s Natural Selection in the Wild tabulated many studies of living populations. However, most of these studies “are of short duration and long-term oscillation or random change around a common mean cannot be precluded.”