November 25, 2009 Bioe 109 Fall 2009 Lecture 25 Development and evolution. - let s finish off Monday s lecture. The end-permian extinction

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1 November 25, 2009 Bioe 109 Fall 2009 Lecture 25 Development and evolution - let s finish off Monday s lecture The end-permian extinction - some consider the end-permian extinction to one of the four most significant events in the history of life - on par with the origin of life, the evolution of the eukaryotic cell, and the Cambrian explosion. - it was the closest the multicellular life on earth ever came to total annihilation. - the end-permian extinction resulted in the loss of 52% of all families and 96% of all species. - it was the only mass extinction that affected insects - 8 of 27 existing orders vanished of the existing 27 families of reptiles and 6 of 9 amphibian families were also wiped out. - over 70% of all marine invertebrate genera were extinguished including all the reef-building corals. - what caused this great extinction? - one important factor was the formation of the supercontinent of Pangaea. - this represents the only period on earth in which all the land masses were combined into a single continent. - the formation of Pangaea did not cause the extinctions directly because it existed for tens of millions of years before and after the cataclysm. - what else was going on? 1. sea level changes. - sea level fell dramatically at the end of the Permian. - as little as 10% of the shallow continental seas remained covered. - although important, this cannot account for the large extinction itself - sea level has fallen dramatically during recent ice ages and has had little effect on species loss. 2. ocean chemistry. - today oceans are well oxygenated in shallow water, continental shelf regions and deep water habitats as well. - at the end of the Permian, however, the deep water environs turned anoxic. - evidence for the anoxic deep water comes from the abundant presence of pyrite (FeS 2 ). - pyrite is a product of sulphur-reducing bacteria that are anaerobic. - how did this happen? - one hypothesis is that the formation of Pangaea disrupted the existing pattern of oceanic circulation. - this lead to widespread stagnation. - the evidence suggests that not only were deep waters anoxic but they also contained high concentrations of CO 2. - in other words, the ocean bottoms may have become like bog water.

2 - an overturn is hypothesized to have occurred when cool surface water sank and lifted the stagnant deep sea water up to the surface. - when this spread over the continental shelf areas, it would have had a deadly effect. - is there evidence to support this scenario? - yes, from the appearance of compounds like uranous fluoride in shallow continental areas that are only deposited under anoxic conditions. 3. increased volcanic activity - at the end of the Permian, huge areas of Siberia were covered in magma from flowing volcanoes - these are called the Siberian flood basalts. - these basalts are 400 to 3,000 m thick and cover 1.5 million km 2 of northeast Asia. - they were formed over a period of roughly 600,000 years. - this is the largest outpouring of magma ever seen on earth. - this volcanic activity would have had dramatic effects on world climate. - at the end of the Permian there is first evidence for a dramatic cooling trend. - large glaciers were present in parts of Asia and Australia. - the combined effects of sea level changes, anoxic overturn, and rapid climatic change has been called the world-gone-to-hell hypothesis. - these events occurred very quickly - in less than one million years. Catastrophic mass extinction. - the K-T mass extinction is, perhaps, our best example of catastrophic mass extinction caused by meteor impact. - this theory has been championed by Louis Alvarez and his colleagues at Berkeley. - the initial evidence used by Alvarez was the discovery in Italy in 1978 of a thin layer of the compound iridium at the K-T boundary. - iridium is a rare element on earth (restricted mainly to the planet s core) but is rather common in extraterrestrial bodies. - the presence of an iridium enriched layer at the K-T boundary has now been described at over 100 sites throughout the world, including cores taken from ocean drilling. - the source of this iridium was postulated to be a meteorite about 10 km in diameter that hit the earth at a speed of 10 km/s. - the precise location of the impact crater was located in 1993 in just off the north coast of the Yucatan peninsula in Mexico. - it measures some 300 km in diameter and is called the Chicxulub crater. - what would have been the impact of this huge object hitting the earth? - first, it would have released large amounts of debris into the atmosphere. - the ocean floor where this impact occurred is formed of large beds of anhydrite (CaSO 4 ). - vaporization of anhydrite and sea water would have produced a large amount of atmospheric water and SO 2. - the molecules would react to produce sulphuric acid and cause acid rain. - sulphur dioxide is also a good scatterer of solar radiation in the visible spectrum - this would have lead to global cooling.

3 - this global cooling would have been strongly enhanced by the dust also released. - the impact would also have created widespread fire - there is considerable evidence for this from the presence of ash and soot at the KT boundary. - it would also have triggered massive earthquakes, perhaps as large as magnitude 13 on the Richter scale, and set off volcanoes around the world. - widespread volcanism would have released large amounts of ash and sulphur dioxide that would contribute to global cooling. - it would also release CO 2 and other greenhouse gases that would contribute to a longer term global warming. - finally, the impact would have created a large tidal wave, estimated as large as 4 km high! - in sum, between acid rain, widespread fires, intense cooling, extensive darkness causing a failure of primary productivity, and an enormous tidal wave, there was no shortage of killing mechanisms. Who survives mass extinctions? 1. widespread/generalist species outsurvive endemic/specialized species. - this is generally true for both marine and terrestrial taxa. - it is interesting to note that the size of a species geographic range is an emergent property that is not a direct target of selection (i.e., species are selected to have large geographic ranges). 2. temperate marine species outsurvive tropical species. - this is sometimes the nowhere-else-to-go hypothesis. - since mass extinctions commonly involve periods of global cooling, tropical species habitats may disappear completely! - temperate species are capable of shifting their distributions south to track their preferred temperatures. 3. small-bodied species outsurvive large-bodied species. - there are many related factors involved here. - large species tend to have smaller population sizes and slower rates of reproduction. - they are thus more prone to local extinction than smaller species. Periodicity of mass extinctions - in the early 1980 s Raup and Sepkowski documented a very intriguing pattern exhibited by mass extinctions. - they demonstrated a periodicity of the spacing of extinction peaks of roughly 26.2 my. - there are two missing extinctions at cycles 5 and 7 which correspond to points in the mid Cretaceous and early Jurassic. - what can produce this cycle and why is not 100% consistent? - no cycles are known on earth, or within our solar system, that can account for this periodicity it is too long. - this implicates forces beyond our solar system.

4 - more recently, Rhode and Muller (2005) documented an even more compelling 62-million-year cycle from Sepkowski s data set on 18,000 marine genera over the past 500 million years. - their cycle was most convincingly demonstrated on short-lived genera (i.e., those that lived less than 45 million years). - although the short-lived genera represent only about 44% of the diversity present at any one time, they were responsible for 86% of the variation in amplitude of the 62-million-year cycle. - what can produce these cycles? - one explanation is that it reflects a periodicity of increased probabilities of large meteorite impacts with the earth. - these impacts would throw up large amounts of dust into the atmosphere and cause collapses of marine and terrestrial food chains. - there is some corroborative evidence for this interpretation by the dating of large impact craters on the earth s surface. - what can be the ultimate forcing agent? 1. transit of the solar system through the spiral arms of the milky way galaxy? - no, this would produce a cycle of 50 my. 2. vertical oscillation of the solar system about the vertical plane of the galaxy? - no, this would produce a cycle of 33 my. 3. precession of a tenth planet? - passage of this planet through the solar system may cause meteor showers. - recently, there have been a number of planet-like bodies discovered beyond Pluto (not a planet anymore!) most notably the dwarf planet Eris. - Eris has an orbit of about 557 years. - it is unclear if the orbits of dwarf planets can cause increases in meteor impacts with a periodicity of 26.2 my or 62 my. 4. a binary star? - the sun may have a binary companion dubbed the death star Nemesis. - the rotation of this star would again cause periods of intense meteor showers. - unlikely - not yet discovered! AN IMPORTANT QUESTION: If there is a true 26.2 my cycle, where are we currently in this cycle? ANSWER: About half way through! - another 13.5 my to go. Development and Evolution - despite its central importance to evolutionary biology, developmental biology has not been incorporated into evolutionary theory until very recently. - this lack of integration can be blamed on both camps. - throughout the modern synthesis, evolutionary biologists were largely unable, or unwilling, to incorporate development into the growing body of evolutionary theory.

5 - similarly, many developmental biologists simply did not attempt to relate their studies to evolutionary theory. - today, evolutionary biologists and developmental biologists are finally making progress in understanding the role of development in evolution (in an area now called Evo-Devo ). - some old questions related to evolution and development include: 1. Can developmental processes lead to discontinuous new phenotypes and have such phenotypes been major contributors to evolution? 2. Do developmental processes bias or constrain the direction of evolution? 3. How do developmental processes evolve? Heterochrony - heterochrony means different time. - it is the name given to a very important evolutionary phenomenon - a change in the timing or the rate of developmental events. - observations of changes of ontological developments in relation to phylogeny are old concepts in biology. - this was reflected in Haeckel s famous biogenetic law formulated in 1866 that ontogeny recapitulates phylogeny. - Haeckel believed that ancestral adult forms are retained in the embryological stages of their descendants. - during development, an organism was supposed to climb its own evolutionary tree. - the existence of fish-like characters (like gill slits) in the embryos of mammals was taken as evidence for this process. - Haeckel realized that exceptions to his biogenetic law existed and in 1875 coined the term heterochrony to deal with these problems. - heterochrony can take two basic forms. - if the rate of shape change is increased, or its period extended, the descendant passes beyond the morphological condition of the ancestor. - this shift leading to overdevelopment is called peramorphosis. - the opposite of this, a reduction in the rate of change, or a contraction of the period of operation, results in the descendant passing through a reduction in growth stages and thus retaining a juvenile stage of the ancestor. - this underdevelopment is called paedomorphosis. - the terminology here gets rather complicated - both paedomorphosis and peramorphosis can be split into three categories depending on the mechanism of heterochrony. - changes can occur in the rate, onset time, or offset time of the developmental process. - this leads to six different heterochronic mechanisms:

6 Paedomorphosis Peramorphosis rate slower faster (neoteny) onset time later earlier offset time earlier later (progenesis) (hypermorphosis) - for example, neoteny refers to paedomorphosis brought about by a slower rate of development resulting in the retention of juvenile characters. - although these changes are conceptually straightforward, it is often difficult to distinguish them in practice. - for example, the shortened jaw and bulbous cranium of humans resembles the juvenile state in chimpanzees. - thus, these features have traditionally been thought to represent neoteny. - however, some biologists now think that the enlarged cranium is formed by a prolonged period of brain growth (hypermorphosis) without any comparable growth of the jaw. - a classic example of neoteny involves the axolotl, a member of the tiger salamander complex. - in normal tiger salamanders, the terrestrial adult loses the external gills and tail fin of the aquatic larval stage. - the axolotl and other neotenic forms grow and reproduce at the same adult size but remain aquatic and retain external gills and a tail fin. - some populations of axolotls are facultative neotenic, capable of metamorphosis if their aquatic habitat dries up. - others are obligately neotenic and cannot advance past this stage. - the mechanism underlying the evolution of neoteny in this group involves the hormone thyroxin. - experiments in some species of axolotls have shown that injection of thyroxine induces metamorphosis suggesting that neoteny is caused by the failure of the hypothalamus to release TSH (thyroid stimulating hormone). - progenesis is also common in many species of dwarf salamanders. - for example, in the tropical American genus Thorius (in the family Plethodontidae) some species mature at about 14 mm. - these species have many characters found in the juvenile stages of other salamanders suggesting that their development has been abbreviated. - in fact, many of the bones of the skull are poorly ossified and remain partly, or completely, cartilaginous. - peramorphosis is extremely common in many groups. - any situation in which a character is exaggerated in a species relative to its close relatives is suggests peramorphosis. - gigantism is usually thought to represent an example of hypermorphosis.

7 - after the colonization of islands, gigantism is very common in groups such as lizards, birds, and rodents. - in contrast, island dwarfism is common in large mammals (e.g., dwarf elephants on Mediterranean Islands) What is the evolutionary significance of heterochrony? 1. large changes in phenotypes may be easily accomplished - in many cases, mutations at one or several genetic loci may be involved. 2. likely important in speciation - reproductive isolation is achieved easily between gene pools differing in heterochronic mutations. 3. may release lineages from phylogenetic constraints - in paedomorphosis, the descendant no longer passes through the same developmental stages as the ancestor. - this can free the species from the constraint imposed by that structure. - paedomorphosis can, however, only affect existing structures. Developmental genetics and evolution - I introduced Hox/HOM genes last class when I discussed the Cambrian explosion. - today, I will discuss the role that these genes play in developmental and some of the implications of these patterns for evolution. - Hox genes were first discovered in Drosophila. - they were identified by the discovery of so-called homeotic mutations that involved gross alterations in phenotype. - for example, the Hox gene antennapedia (Antp) was identified from a mutation that converted a Drosophila antennae into a leg. - the bithorax mutation produced a four-winged fly resembling a dragonfly (the halteres are absent). - these were immediately recognized as a very special class of genes - the vast majority of mutations fail to do anything so dramatic. - homeotic genes have been found in all major animal phyla. - they share a number of common characteristics: 1. Organized in multi-gene complexes - this indicates that the Hox gene families have been elaborated by gene duplication events. - every different major group analyzed has a unique pattern of elaboration or loss of some genes. 2. All contain a highly-conserved 180 bp homeobox domain - the homeodomain (also called the homeobox ) represents a DNA binding motif. - its high degree of evolutionary conservation suggests that this structure is critical for binding to regulatory elements. 3. Exhibit spatial and temporal colinearity

8 - spatial colinearity means that there is a perfect correlation between the 3-5 order of the homeotic genes on a chromosome and their anterior to posterior location of gene products in the embryo. - genes at the 3 end of the complex are always expressed in the head. - those at the 5 end are always expressed in the posterior regions of the developing embryo. - temporal colinearity means that Hox genes expressed in order of their position in the cluster. - genes at the 3 end are also expressed earlier in development and at higher concentrations than those at the 5 end. - homeotic genes are thus the key regulatory genes that control the timing and degree of expression of other genes. - they are the master switches that control the fate of cells by specifying where they are in time and space (i.e., location). - for example, the Hox gene ultrabithorax (Ubx) in Drosophila is believed to regulate the expression of somewhere between 85 and 170 genes. Homeotic genes and the evolution of body plans - the Hox genes first discovered in Drosophila were thought to control the segmentation patterns in insects. - this was disproved by their discovery in other major animal groups like arthropods and annelids. - it was then proposed that Hox genes were intimately associated with segmentation that is such an important characteristic of the Cambrian explosion. - this was also shown to be incorrect by their discovery in green plants, fungi, and other unsegmented animals (like jellyfish). - this finding means that Hox genes evolved well before the Cambrian explosion and must do something much more basic than specifying anterior-posterior cell fates. - the phylogenetic history of the Hox genes has been the target of a number of studies. - these studies have shown that there appear to be 3-5 genes that are ancestral to others in the complex. - these are: 1. labial (lb) 2. proboscipedia (pb) 3. Deformed (dfd) 4. Antennapedia (Antp) 5. Abdominal-B (Abd-B) - other loci have descended from these genes by gene duplication events. - mapping these genes onto phylogenies of the major animal phyla have shown that Abd-B is associated with the evolution of bilateral animals (annelids, crustaceans, tetrapods). - the entire Hox cluster has been duplicated many times in various vertebrate lineages. - most Hox clusters possess 9-11 loci. - four Hox clusters are found in mice and other mammals (called Hoxa through Hoxd) - the total number of Hox genes in mice is there are three ways that Hox genes can influence morphological evolution:

9 1. Changes in total number - increasing the number of Hox/HOM loci is believed to have set the stage for increased differentiation of body parts. Species No. of Hox genes snails, slugs 3-6 arthropods 9 tubeworms 10 mice 39 zebrafish 42 - the increased number of Hox genes has undoubtedly allowed the evolution of more complex body plans. 2. Changes in spatial expression - changes in the spatial expression of Hox loci likely underlies much morphological evolution. - the textbook describes the changes that have taken place in the spatial expression of Hox genes in different arthropod groups. - it is through modifying the spatial expression, rather than changing the total number of genes, that underlies much of the diversification of arthropod body plans. - however, modification of the protein products of Hox genes (like the alanine region of Ubx) have likely contributed to morphological changes as well. 3. Changes in gene interactions - changes in the interactions between Hox/HOM loci and their downstream targets probably underlies all morphological evolution. - in other words, the spatial expression of a Hox gene may be similar between two species but different suites of genes come under their control. - this principle is illustrated by the ectopic expression of eyes. - the term ectopic refers to the expression of a gene in tissues where it is not normally expressed. - in Drosophila, the Pax6/eyeless mutation (ey) causes partial or complete absence of compound eyes. - in mice, the small eye mutation (Sey) causes failure of the development of the eye. - the sequences of the proteins encoded by these two loci are 94% identical. - Halder et al. (1995) were able in Drosophila to obtain ectopic expression of the eyeless gene - in other words, they were able to express this gene in tissues where it is not normally activated. - by doing so, they were able to induce the development of eyes in various parts of the fly s body such as its legs, wings, or antennae. - the ey gene thus acts as a master switch that turns on all the genes responsible for making a compound eye. - Halder et al. (1995) estimated that there might be about 2,000-2,500 genes involved. - Halder et al. (1995) were also able to obtain ectopic expression of the mouse Sey gene in Drosophila. - surprisingly, the mouse homologue was able to induce development of the compound eyes in different tissues too.

10 - the downstream targets of this Hox gene are likely to be entirely different (think of the differences between a vertebrate and an insect eye). - we thus infer that the ancestral function of this gene has remained intact - to control the development of photoreceptor cells. - the evolutionary pathways of insect and vertebrate eyes have diverged considerably since this time (when the gene probably regulated the expression of simple aggregations of light-sensitive cells) but they are regulated by a common element.