OMNAMO BIOLOGY CONCEPTS

Monday, 16 September 2013

Biogeography

BIOGEOGRAPHY

We have referred to pattern and process throughout different sections of this course. These concepts are central to the study of biogeography which, in turn, incorporates many of the topics in evolutionary biology. Biogeography often leads us to infer process from pattern.
Biogeography is the study of the distributions of organisms in space and time. It can be studied with a focus on ecological factors that shape the distribution of organisms, or with a focus on the historical factors that have shaped the current distributions. Certain regions of the world have "Mediterranean climates" where ocean current and wind patterns hit the west coast of N and S continents (Medit. region, California coast, Chile coast, SW Africa coast). Similar climate has lead toconvergent , but unrelated (by definition) types of plants. To make sense of these types of ecological patterns we require a phylogenetic (historical) perspective: we need to focus on monophyletic groups.
The importance of a geographic scale was certainly appreciated by Darwin: the Galapagos finches were morphologically distinct and geographically distinct and there must be a connection. Moreover, the general view that speciation is a central phenomenon in evolution, and that most speciation is allopatric speciation assumes that geography plays a central role: some geographic feature divides a species range in two or more parts and over time speciation is achieved (details in later lectures).
These sorts of observations were made by early biogeographers who recognized certain types of distributions of organisms. Some species are restricted to a certain region and are referred to as endemic species. Endemism needs to be defined with relation to the taxonomic group: all life forms we know are endemic to the planet earth; the genus Geospiza (Darwin's finches) are restricted to the Galapagos islands; Geospiza fortis is endemic to specific islands; the spotted owl is endemic to the old-growth forests of the pacific northwest. Cosmopolitan species have a world wide distribution. They may be restricted to specific habitats, but occur on most continents.
In addition to endemism, another important pattern that needed to be explained were examples of disjunct distributions where clearly related species (or even the same species) are found in different areas. Marsupials are found in Australia and South America. Ratite birds (Ostrich, Emu&Cassowary, Rhea) are found in Africa, Australia and South America, respectively.
Alfred Russell Wallace noticed that different regions of the world had congruent patterns of endemic species and he drew up six biogeographic realms (see fig. 18.2, pg. 510; nearctic, neotropical, holarctic, ethiopian, oriental and australian). Wallace worked primarily in Malaysian region and had noticed a clear break between Australian fauna and the fauna on the islands to the northwest. This break has come to be known as Wallace's line (also a line between the Australian and the Asian biogeographic zones). These patterns described long before continental drift was an issue.
Different biogeographic areas can be quantified for levels of similarity in their biota (biota=general term for flora+fauna, includes microbes). N₁ = number of species (or other taxonomic unit) in one region, N₂ = number in another region (N₁ < N₂) and C = number of same species. Index of Similarity = C/N₁. For Australia: New Guinea, I.S. = 0.93 (93%), while Australia: Philippines, I.S. = 0.50 (50%). See table 18.1, pg 511. This provides a simple quantification of Wallace's Line.
How do we account for these patterns? Early biogeographers tended to invoke dispersal (prior to knowledge about continental drift). Potential problems: ad hoc, could pull dispersal out of a hat whenever you needed to explain a peculiar distribution. Leads to many wild scenarios of "gravid females" (pregnant, or inseminated females carrying eggs) making there way to distant regions. Muddyfooted duck carrying propagules in its feet; land bridges invoked connecting disjunct regions. Criticized by many as unscientific: cannot falsify the dispersal hypothesis because it is something we'll never know for sure, thus is of no explanatory power.
Nevertheless, all these types of events probably have occurred at some point. The Bering land bridge is well documented as an avenue of dispersal; the Opossum (a marsupial) in North America clearly dispersed here from South America via the Isthmus of Panama (see below); oceanic islands have life on them and it must have gotten there by dispersal. Several modes of dispersal can be described: Corridors between two regions on the same land mass, Filter bridges as selective connections between two areas, Sweepstakes as rare chance events (e.g. muddyfooted duck).
Dispersal hypotheses often associated with arguments about centers of origin: those regions with the greatest species (or higher rank) diversity. Greater diversity should be due to presence in that region longer (more time for speciation), hence should be the region where the group originated and from which dispersal events took place. Assumes that extant diversity has not moved from origin of diversity. Possible, but not guaranteed for all taxa.
Alternative to Centers of Origin and subsequent Dispersal as a way to explain the current distribution of species is vicariance where some barrier to genetic exchange causes the separation of the related taxa. With the acceptance of continental drift, vicariance biogeography became a discipline in which one could test hypotheses (see below). See models in fig. 18.6, 18.8 and 18.9, pgs. 518-521.
As with most dichotomies in science: often need to invoke Both vicariance and dispersal to account for distributions (not always in the same instance). Example: Galapagos finches had to have dispersed to the archipelago from the mainland and in so doing imposed a vicariance event on themselves. South American land bridge when sea levels dropped in the Pliocene the isthmus of Panama rose and served as an avenue of dispersal for terrestrial mammals (the "Great American Interchange" where unique N.American mammals dispersed to S. America and unique S. Amer. mammals moved north, 3 mil. years ago; see fig. 18.14, tables, 18.2, 18.3, pgs. 528-529), but served as a vicariance event for marine life that was distributed in the region. Lead to the formation of Geminate species (species pairs on either side of the isthmus who are each other's closest relative and were probably one species before the sea level dropped).
Pleistocene refugia nicely illustrate how vicariance and dispersal may need to be invoked to explain current distributions. Glacial ice sheet forced species to new distributions (vicariance event), after glacial retreat, the separated forms dispersed to previous regions (or wider distribution). Relative roles of dispersal and vicariance in determining species distributions can vary widely with a given species dispersal abilities (see fig. 18.3, 18.4 pg. 514-515). Essential to realize that dispersal has two components: the ability to move and the ability to become established. These two properties may not be "optimized" in the same organism.
Continental Drift as source of vicariance events. Evidence for continental drift provided by disjunct fossil specimens: Mesosaurus in South America and Africa. Illustrates the space and time component of biogeography since the strata reflect the same time (old) but are widely separated in space. Continents must have moved. (Fig. 18.5, pg. 517).
Major stages of the split-up of continents: Pangaea formed in Permian (> 250 MyBP) and began to break up in the Triassic (200 MyBP). Laurasia andGondwana separated at the Tethys seaway (135 MyBP). Tropical corals, sea grasses and mangroves are related in Americas and old world tropics reflecting earlier Tethyan distribution. Gondwana began to break up about 80 MyBP and the major continents were separated by late Cretaceous (65 MyBP). India smashed into Asia crating the Himalayas. As the continents separated vicariance events abounded and the fauna of various continents became increasingly Provincialized. The South American mammals had many unique forms with respect to the North American Fauna. Marsupials in Australian zone are distinct form of mammal.
Testing biogeographic hypotheses with cladistic analysis. Brundin's midges (fig. 18.7, 18.8, pg. 519-520) a classic in vicariance biogeography. Sibley and Ahlquist's Ratites and the Gondwana breakup. Testing hypotheses about the sequence of vicariance events with cladograms from several species. Validity of biogeographic hypothesis can be supported by congruence of independent cladograms from unrelated species (see Cracraft, 1983, American Scientist vol. 71: pg273). By considering the relationships of organisms and their geographic distributions, the most parsimonious combination of the species cladograms can lead to an hypothesis of vicariance events, a so-called area cladogram which presents the sequence of splitting events.
Using cladistic methods, one can test biogeographic hypotheses by asking whether area cladograms for other, unrelated taxa are congruent. If different taxa all have similar area cladograms (i.e., are "congruent"), then the sequence of vicariance events is supported. If one taxon is represented in a region where none of the other taxa are found, then one might be forced to invoke dispersal to account for the disjunct distribution. The strength of this approach is that hypotheses are testable and one need not resort to ad hoc explanations that should be taken on faith. Biogeography can be practiced in a scientific manner despite its historical nature.

Conservation Genetics

CONSERVATION GENETICS

Conservation biology is a rapidly growing discipline of cology and evolutionary biology. In many ways the issues surrounding the conservation of endangered or threatened species have rejuvenated aspects of population genetics and systematics that were often viewed as "academic." Indeed, may aspects of conservation biology can be view as "applied" ecology and evolutionary biology.
We will consider two different approaches to conservation genetics: 1) population genetic issues relating to the maintenance of genetic variability, and 2) systematics issues relating to the description of biodiversity and the recognition of evolutionary "units" for preservation.
Due to the rapid destruction of habitat there are many species that are going extinct. One estimate is in the neighborhood of 100 species per day! Habitat destruction is generally attributable to human impact, but the causes of extinction are varied: environmental variability, natural catastrophes, demographic variability (stochasticity), genetic stochasticity, etc. Faced with this problem, biologist set out to determine a Minimum Viable Population Size (MVP): a population size that ensure the persistence of a species for specified period of time. One description is a 99% chance of persistence of 1000 years.
Theoretical population genetics simulations have lead to some predictions. There should be a positive relation between population carrying capacity (population size the (local) environment can sustain) and the average time to population extinction. Moreover, extinction times are exponentially distributed so a large proportion of populations will go extinct in a period of time less than the mean time to extinction.

The implication from these simulation results is that Larger Populations are Better: it will take longer for a larger population to go extinct, and larger populations will lower the extinction curve. If environmental stochasticity is added to these models, theory suggests that MVP should be 500 - 1000. If demographic stochasticity (randomly fluctuating birth and death rates, i.e., random population growth rates), MVP needs to be sustained at higher values (1000 - 5000). If this system is placed in the context of an interwoven ecosystem, the MVP should probably be higher.
MVP and Genetic variation Population genetic theory indicates that inbreeding depression will be likely with an effective population size of N_e < 50. To avoid the possibility of inbreeding, a lower limit of MVP = 500. These numbers may seem like obscure conclusions from a series of complex Populus simulations, but they are the working numbers for policy issues : N = 50 defines the critical list; N = 500 defines the endangered list.
The values for MVP and "critical" versus "endangered" lists stem from some basic issues relating to effective population size. N_erefers to the effective number of breeders in the population, and can be affected greatly by variance in reproductive success A focus here is the ratio of effective size to census size N_e/N ratio. Observations from field and laboratory experiments indicate that N_e/N ratios are about 0.25 (range = 0.05 to 1.0). This means that either some individuals are breeding and others are not, or that some individuals have different degrees reproductive success that others. It is possible that a substantial proportion of the population does reproduce, but that a small number of individuals produce most of offspring reducing the genetic pool from which alleles are drawn. This reduces the N_e/N ratio and hence brings the population closer to the demographic danger zone.
With a N_e/N ratio of 0.25, the census size should be 4 times higher than the simple numbers predicted by "critical" and "endangered" estimates. Now add population size fluctuations: bottlenecks in census size affect N_emore severely. Recall: = (1/N_e) = (1/t)

(1/N_e)
The net effect of these factors is that MVP should be 5X to 10X N_e.
Given a finite amount of space for a nature preserve, do you establish a Single Large or Several Small (SLOSS) system. The answer depends on the likely causes of extinction in the particular system of concern. If the species is subject to demographic fluctuations, it would be better to maintain one large system, since the plot above suggests that extinction is more likely in small populations. In systems of species where environmental stochasticity is a general problem , the Several Small approach is probably better: many sub-reserves will reduce the chances of losing the entire system.
The SLOSS debate is closely related to the dynamics of Metapopulations. The maintenance of genetic diversity can be enhanced by structuring in a metapopulation system. Alleles that might be lost in one deme can be fixed in another, and the average of the metapopulation system may maintain more heterozygosity than a simple population of similar total population size. The solution to this is not general since metapopulation systems may have varying degrees of migration between demes (at some level of migration, metapopulations become 'systems of subpopulations' since in the strict sense the demes of a metapopulation experience little gene flow.)
Metapopulations can also contribute to the purging of deleterious recessive alleles. With some level of inbreeding in demes, deleterious recessives will be selected against. With limited amounts of gene flow, the system can effectively purge these alleles that might not be expressed in a large random mating population. One approach is to have semi- isolated subpopulations with corridors for dispersal.

There is no one solution to all these problems. The answers depend on 1) the species and ecosystem in question, 2) the demographic issues (constant or variable) and 3) the existing levels of genetic variation.
Many issues in conservation genetics have been centered around Zoo Biology. Most zoos maintain rare or endangered species and are involved in captive breeding programs with such species. Again, a central issue is the maintenance of genetic variation. A number of recent studies have addressed the captive breeding protocol to determine how mating systems affect the maintenance of genetic variation.
Using Drosophila, several studies have shown that populations maintained with equal founder size (EFS) retain more genetic variation that populations maintained by random mating. EFS approaches equalize the number of founders that contribute to the "captive" population each generation. Similarly, equal founder representation (EFR) studies retain slightly more genetic variation than randomly mating populations. EFR populations are maintained with a controlled pedigree where the parentage of each contributing female and male is known. These types of studies use allozyme electrophoresis to study directly the levels of heterozygosity in experimental (EFS, EFR) and randomly mating control populations over time. In addition, fitness studies can be performed by competing experimental flies against tester stocks to determine if a higher fitness is maintained. The conclusion from these studies is that controlled mating schemes can make a difference in retailing genetic variation and attaining higher levels of fitness. The next step is how do you translate these findings into captive breeding of Panda Bears??
Phylogenetic approaches to conservation biology have received a lot of attention. This follows directly from the general concern about Biodiversity. To properly appreciate and understand biodiversity, we must have a sense of phylogenetic structure of the taxa involved. This applies to broad levels of organization (soil bacteria, plants, animals) as well as to smaller taxonomic units (populations within species). Molecular systematic approaches have been of great use since many new techniques can be applied without harming wild individuals, and can even be applied to museum skins for historical comparisons. In the context of the Endangered Species Act several important issues come up: What is the phylogenetic relationship of the endangered species? How much and what type of genetic variation (gene trees)? What do we preserve? What IS a species? Any genetically distinct entity has evolutionary potential.
Two case studies: The Dusky seaside sparrow: The species declined in the 1960's; by 1980 only 6 birds remained that were all male. A captive breeding program was initiated and captive Scott's seaside sparrow was chosen as the females. When the last male Dusky died Avise & Nelson analyzed its mitochondrial DNA (mtDNA) and found that the Dusky and Scott's seaside sparrows were members of different clades on the phylogeny of these sparrows. The implication is that more detailed phylogenetic knowledge of the endangered species would have lead to different management decisions in handling this captive breeding program (choosing a different species to mate to the Dusky)
The red wolf was placed into a captive breeding program in 1974. By 1975 it was extinct in the wild. Early data suggested that red wolves hybridized with coyotes. Since coyote populations do well in human-disturbed habitats, hybridization may have affected the survival of the red wolf. Wayne & Jenks studied the mitochondrial DNA from captive red wolves and from 77 animals collected from the wild during the capture program. They also used the polymerase chain reaction (PCR) to sequence mitochondrial DNA from museum skins ("ancient DNA techniques") collected before hybridization between red wolves and coyotes is thought to have begun. They found that red wolves have either a gray wolf or a coyote mtDNA, indicating that the red wolf "species" is entirely a hybrid. Other researchers disagree about the species "status" of the red wolf. Nevertheless, this raises the question: What should we protect? If the species isn't really a clear entity phylogenetically, does it deserve a conservation/captive breeding effort? Wayne & Jenks argue that their data should not be used to advocate the discontinuation of the conservation effort of the red wolf.
These examples illustrate why the recognition of Evolutionarily Significant Units (ESU) is an issue of great concern in conservation genetics. ESUs are defined various ways, but they are recognized as populations with independent evolutionary histories. Fixed allelic differences or strong phylogenetic support such as multiplesynapomorphies distinguishing one population from another are good grounds for the recognition of distinct ESUs. Hence, a full understanding of how to do molecular systematics is very important in molecular conservation genetics.
It should be emphasized that mitochondrial DNA markers are maternally inherited and may not reflect the true evolutionary history of the entire populations. Hence it is advisable to have additional nuclear markers for ESU recognition such as allozymes, RAPDs or microsatellites. RAPDs are Randomly Amplified Polymorphic DNA. This method uses the polymerase chain reaction to amplify random regions of the genome with short random 10-base primers. Microsatellites are regions of the genome that vary in the number of tandemly repeated sequences. The repeats are short (2-4 base pair repeat unit), but there may be many of them in a row. Individuals differ in the number of repeat units they have and this difference can be determined by gel electrophoresis.
Another relevant level of concern is a Management Unit (MU). These are defined as populations that have different frequencies of alleles, but do not necessarily show fixed differences between populations. Hence several MUs may exist within an ESU. The figures below illustrate the difference. The general lesson is that molecular approaches to conservation biology are potentially highly informative since many overt phenotypic characteristics cannot reveal important differences that distinguish populations. Since conserving endangered species is inherently a "genetic" endeavor, to the extent that we recognize species as discrete reservoirs of historically unique genetic material, the molecular approaches are very useful.

Coevolution

COEVOLUTION

First some definitions: coevolution is a change in the genetic composition of one species (or group) in response to a genetic change in another. More generally, the idea of some reciprocal evolutionary change in interacting species is a strict definition of coevolution.
At first glance (or thought), it might seem that everything is involved in coevolution. This assumption might stem from the fact that virtually all organisms interact with other organisms and presumably influence their evolution in some way. But this assumption depends entirely on ones definition of the term Coevolution.
The term is usually attributed to Ehrlich and Raven's study of butterflies on plants (1964) but the term was used by others prior to 1964 and the idea was very present in the Origin of Species. Ehrlich and Raven documented the association between species of butterflies and their host plants noting that plants' secondary compounds (noxious compounds produced by the plant) determined the usage of certain plants by butterflies. The implication was that the diversity of plants and their "poisonous" secondary compounds contributed to the generation of diversity of butterfly species.
Here we have a very general observation of one group of organisms having an influence on another group of organisms. Is this coevolution? Some would argue that it is not good evidence for coevolution because the reciprocal changes have not been documented clearly. Like the issue of defining an adaptation, we should not invoke coevolution without reasonable evidence that the traits in each species were a result of or evolved from the interaction between the two species.
Lets consider plants and insects: there is little evidence to determine whether plants' secondary compounds arose for the purpose of preventing herbivores from eating plant tissue. Certain plants may have produced certain compounds as waste products and herbivores attacked those plants that they could digest. Parasites and hosts: when a parasite invades a host, it will successfully invade those hosts whose defense traits it can circumvent because of the abilities it caries at that time. Thus presence of a parasite on a host does not constitute evidence for coevolution. These criticisms are quite distinct from the opportunity for coevolution once a parasite has established itself on a host.
The main point is that any old interaction, symbiosis, mutualism, etc. is not synonymous with coevolution. In one sense there has definitely been "evolution together" but whether this fits our strict definition of coevolution needs to be determined by careful 1) observation, 2) experimentation and 3) phylogenetic analysis.
The classic analogy is the coevolutionary arms race: a plant has chemical defenses, an insect evolves the biochemistry to detoxify these compounds, the plant in turn evolves new defenses that the insect in turn "needs" to further detoxify. At present the evidence for these types of reciprocal adaptations is limited, but the suggestive evidence of plant animal interactions is widespread. An important point is the relative timing of the evolution of the various traits that appear to be part of the coevolution. If the presumed reciprocally induced, sequential traits actually evolved in the plant (host) before the insect (parasite) became associated with it, we should not call it coevolution. See different example figs. 22.6-22.7, pgs. 621-622 + text.
There are a variety of different modes of coevolution. In some cases coevolution is quite specific such as those between two cellular functions. The endosymbiont theory proposes that current day mitochondria and chloroplasts were once free-living unicellular individuals. These cells entered the cytoplasm of other cells, an example of the general phenomenon of endosymbiosis. Current-day mitochondrial and chloroplast genomes are much smaller than the genome sizes of their presumed free-living ancestors. Some of this reduction in genome size is due to the transfer of genes from organelle genomes to the nuclear genome. Thus, being in the cellular environment has influenced the evolution of organelle genomes. There is evidence that the faster rate of evolution of animal mitochondrial DNA has accelerated the rate of evolution of some of the nuclear genes that function in the mitochondria. Thus there is some evidence for reciprocal phenomena
Other modes of coevolution involve competitive interaction between two specific species. The Plethodon salamander study is a good example: two species are competing: in the Great Smoky mountains the two species compete strongly as evidenced by the fact that each species will increase population size if the other is removed. Here there is a clear reciprocal interaction between the two populations (species), each affecting the other.
[The role of competition between species, the coevolutionary responses to this competition and the consequences for the evolution of communities is illustrated in the Anolis lizard fauna of the Caribbean. There is coevolution because the competitive interactions between resident and invading species of Anolis involve reciprocal responses in the evolution of body size. These affect the structure of the lizard community as evidenced by the general pattern of there being a single species of lizard on each island.]
Character displacement also provides and example of a pattern we might interpret as the result of coevolution. Mud snails show pattern of character displacement in sympatry due presumably to competition for food items (don't confuse this with reinforcement; the selective agent here is not reduced hybrid fitness). We might call this co evolution because both species show a shift when compared to allopatric samples of each species (mean of both ~ 3.2 in allopatry vs. ~ 4.0 and ~ 2.8 in sympatry). If only one species exhibited character displacement and you were a really picky evolutionist you might not be convinced of a reciprocal response.
Another strong case is the Ant - Acacia mutualism. Here specific traits in each species appear to have evolved in response to the interaction. The ant (Pseudomyrmex species) depends on the Acacia plant for food and housing; acacia depends on ant for protection from potential herbivores (species that eat plant tissue). Specific characters of the plant appear to have evolved for the maintenance of this mutualism: 1) swollen, ~ hollow thorns (= ant home), 2) extra-floral nectaries (source of nectar outside the flower [i.e., the usual location] providing ants with food), 3) leaflet tips = Beltian bodies (= 99% of solid food for larval/adult ants). Specific characters in the ant that have evolved for the maintenance of this mutualism: 1) defense against herbivores 2) removal of fungal spores from Beltian body break-point (prevents fungal pathogens from invading plant tissues). The main point is that there are traits in both the ant and the acacia that are traits not normally found in close relatives of each that are not involved in similar mutualisms: mutualistic traits have evolved for the interaction in reciprocal fashion. See another example : fig. 22.1 & table 22.1, pg. 611.
Coevolution may be considered among broad groups of taxa, so called diffuse coevolution (such as the general coevolution between plants and insects [assuming it is real]). A nice idea, but in fact the real action must be going on between pairs of species from each group. It is true that the Pierid butterflies (family Pieridae) are associated with the plant family Cruciferae, so there may be something general about each taxon that allows the coevolution to proceed. But the true reciprocal events must be mediated at the host species-insect species level.
Mimicry presents a context were coevolutionary phenomena should be evident. Generally, we would expect that Mullerian mimicry would be more likely to exhibitreciprocal evolutionary patterns since both species involved are unpalatable and therefore have an opportunity to affect the evolution of each other's color patters. This does not mean that Batesian mimicry (one unpalatable model) will not involve coevolutionary phenomena, but the evolution of warning coloration is certainly going to be more asymmetrical since the palatable species will show a greater response to the state of the model than will the model show to the evolving state of the mimic.
The Mullerian mimics Heliconius erato and H. melpomene. illustrate both the frequency dependent nature of mimicry and the fact that each can influence the evolution of the other. One would expect that the more abundant species would be the model in a mullerian system, since it is what the selective agent (predation) is cueing on. In general H. erato is the more abundant of the two species and H. melpomene mimics the wing patterns of H. erato. In one area of overlap of the two species, H. melpomene is the more abundant and H. erato assumes the hindwing band pattern of H. melpomene (see figure below). Thus depending on local conditions, both species are influencing the adaptive responses of the other and thus fits strict definition of coevolution.
A crucial component of coevolution is phylogenetic analysis. If the cladograms of the host and the cladograms of the parasite are congruent (e.g., figs. 22.2 - 22.3, pg. 612-613) this certainly suggests coevolutionary phenomena. But again, be careful and think about it: cospeciation is just "association by descent". Have there been reciprocal phenomena?; maybe just the speciation of the host induced the speciation of the parasite and there was not parasite induced speciation of the host. One needs to know the evolutionary history before we can make firm statements about "co"evolution.

Molecular Systematics

MOLECULAR SYSTEMATICS

Molecular biology has revolutionized the field of systematics. DNA evolves by mutations being incorporated in the DNA and fixed in populations. This will lead todivergence of DNA sequences in different species. Although diverged, we can refer to two DNA sequences as homologous (just as we would for any morphological trait such as forelimbs). Nicely demonstrates descent with modification as a definition of evolution. For this reason, DNA should be an excellent tool for inferring phylogenies: large number of homologous characters that should be (??) less subject to convergent evolution than other characters that might lead to a confusion of grade and clade.
To estimate phylogenies we first must estimate how much sequence divergence there has been between the various taxa we want to study. Several methods: direct sequencing. Elegant molecular methods available, a lot of work but provides lots of data. Each nucleotide position is a character and the actual nucleotide that is present at that site is the character state.
A character can be phylogenetically informative when nucleotide changes are shared by two or more taxa. A character can be phylogenetically uninformativewhen all nucleotides are the same among taxa, or when only a single taxon has a different nucleotide.

		I			U				I
A	C	T	C	G	A	C	T	A	G	A	T
A	C	T	C	G	T	C	T	A	G	A	T
A	C	A	C	G	T	C	T	A	G	A	T
A	C	A	C	G	T	C	T	A	C	A	T
A	C	A	C	G	T	C	T	A	C	A	T

A less direct method of determining sequence divergence is by restriction enzyme mapping. These are enzymes that recognize specific sequences in the DNA and cut the DNA strands. Depending on the location of restriction recognition sites in the DNA, DNA fragments of various lengths will be generated by the restriction enzyme digest resulting in a restriction fragment pattern. One can also determine where various restriction enzymes cut a given piece of DNA and draw up arestriction map of the stretch of DNA. The extent to which two restriction maps (or restriction fragment patterns) are similar serves as an estimator of sequence similarity (or difference). Restriction enzymes will recognize only a fraction of the entire DNA sequence, so one will not know all the differences between two stretches of DNA. The data serve as an estimate and because it usually involved less work can be done on many individuals.
DNA-DNA hybridization is another indirect way of obtaining estimates of DNA sequence divergence between two taxa. DNA strands are melted apart at high temperature and allowed to "reanneal" in the presence of the DNA of another species. One species' DNA has been labeled with a radioactive nucleotide. This formheteroduplex DNA. The heteroduplex DNA is gradually heated and the amount of single stranded DNA that has "melted" apart is determined by the amount of radioactive label that is counted in each fraction collected from the various temperature steps. Very similar DNA will melt at a high temperature and heteroduplexes between diverged DNAs will melt at a lower temperature. Sequence divergence is proportional to melting temperature. See fig. 17.19, pg. 497.
Phenetic approaches: DNA hybridization, sequence divergence from sequencing, restriction patterns or restriction maps. In each case the data would be in the form of a single number indication the similarity or difference between the DNAs of each pair of species in the study.
Cladistic approaches: direct sequencing, restriction maps and restriction fragments (fragments less desirable). In each case one would look for shared derived character states (nucleotide, restriction recognition site) among taxa. With restriction sites shared loss is unreliable as a uniting character because the nucleotide change could have occurred anywhere in the recognition sequence. Like refrigerator/pizza/invertebrate example.
Molecular approaches to systematics for us to think about the rates of molecular evolution. If DNA or proteins evolved at a constant rate in all species, then one could use estimates of sequence divergence to build very reliable phylogenies. If there was a molecular clock we could determine the "true phylogeny". Fact is, there is no one molecular clock.
Different proteins and DNA sequences evolve at different rates. Why? Different functional constraints. Different proteins do different things and some can do their structural or functional job with any of several different amino acids at many of the positions (fibrinopeptides). Other proteins will not function properly with "any" amino acid changes (histones: two amino acid differences between peas and cows!). Intron sequences less constrained than coding exon sequences, and hence introns tend to diverge faster than exons. Synonymous sites evolve faster than non-synonymous sites, again due to different functional constraints (i.e., some form of selection against "incorrect" sequences). Nuclear DNA tends to evolve slower than mitochondrial DNA (in vertebrates). Unit evolutionary period: time required to observe a given unit of divergence. A 1% divergence of vertebrate mitochondrial DNA takes about 250,000 to 500,000 years.
What gene do I use??: Depends on the taxa you are studying and the amount of divergence among them. Histones good for "macrosystematics", fibrinopeptides, mtDNA good for "microsystematics" or population level phylogenies. See fig. 17.15, pg. 489.
Note problems with tree building from data: unequal rates and convergence.
As if the choice of gene/protein were not a problem. What if different lineages evolve at different rates? Test for this with the relative rate test. Compare the paths from two different taxa to a third taxon. If the paths are the same: taxa are evolving at the same rate; if not: different rates. Extreme rate fluctuations are a problem; slight ones are not as they would not lead to regrouping taxa (depending on how "slight" is defined)
Convergence over long stretches of DNA is unlikely, although it has been reported for lysozyme. Another kind of "convergence" can occur due to the limited number of character states in DNA. Back mutations: e.g. A changes to T, T changes to C and C changes back to A. Could occur in one step or many. Maximal random divergence: 25% similarity
Nonetheless molecular tools have allowed major leaps in our understanding of biological diversity: Bacterial evolution: three kingdoms, not five; Endosymbiont hypothesis, essentially proven; AIDS virus: rapid evolution is good for the virus, bad for us.

Phylogenetic Inference

PHYLOGENETIC INFERENCE

The crucial issue in systematics is that there is a history of the organisms we wish to classify, but we don't know that history. We must infer the sequence of branches or evolutionary transformations that have taken place. There is a true phylogeny which we may never know, our task is to collect and analyze data to provide the best estimate of the true phylogeny.
We will work some examples that illustrate the difficulty of this task. Phenetics: classification based on overall similarity. See fig. 14.4, pg. 378. Matrix of shared character states. Those taxa with the most number of similar character states are deemed more similar.
Distance (or similarity) matrix derived from morphological measurements, genetic distance measures, etc. Each cell in the matrix is a value indicating the degree of difference (or similarity) between the two taxa. These can be clustered by UPGMA (unweighted pair group methods with averages). The two most similar (least distant) taxa are joined to form a group (e.g., taxa 1 & 2); the length of each branch is half the distance value between the two taxa. The next most similar taxon (3) is joined to the tree and the distance is calculated as the average of the distance from taxon 1 to taxon 3 and taxon 2 to taxon 3. At each such step in building a tree, the number of taxa in the matrix is reduced by one and new distance values are calculated as the average distance from each member of the group just formed to each taxon outside that group. This process of adding the most similar new taxon to a group is continued until all taxa are joined.
The tree produced is a Phenogram and is one way to infer relationships. Why might this tree not reflect phylogeny (true ancestor descendant relationships)? 1)Variable evolutionary rates: faster evolving taxon will be more different from all others and appear as an "outgroup" 2) Homoplasy (convergence) will tend to make character states similar between unrelated taxa and the UPGMA approach will join them.
Cladistics: classification reflects sequence of branching events, not degree of difference/similarity. See figures 17.6 and 17.7, pages 471-472. Classification is onshared derived characters (synapomorphies). Note that relationships are never based on the absence of characters (e.g., "Invertebrates" makes sense to us, but refrigerators and pizzas are "invertebrates" because they don't have back bones, but they clearly are not related to animals. For that matter, plants are invertebrates!). Tree produced is a Cladogram and is a hypothesis of relationship. A taxon can evolve at a different rate, but it will tend to accumulateautapomorphies which will not be shared with any other taxa and thus will affect the branch pattern less (but variable rate can lead to incorrect cladograms). How about Homoplasies? They will affect the hypothesis since those characters showing convergences (or parallelisms) will contradict data from other characters.
This brings us to the topic of Parsimony: in constructing cladograms we seek that branching pattern which requires the fewest number of evolutionary steps. Example of marine mammals (chosen since we know that it is an example of a convergence). It is more parsimonious to evolve fins twice and all the characters that hold mammals together once, than it is to evolve fins once and all the characters that ally whales with other mammals twice. We tolerate fins as Homoplasies(=analogies) since it is much more parsimonious than calling all the mammalian characters homoplasies. See fig. 17.13, pg. 485 and work through it.
Parsimony is central to the cladistic method and can be used for both studying the Polarity (direction of evolution in a transformation series) of characters and the confidence of hypotheses of relationships. Example: Drosophila chromosome banding patterns (e.g., chromosomal inversions, figs. 17.16 and 17.17, pg. 491, 494). Each species has a distinct pattern of bands in their salivary gland chromosomes. The sequence of bands appears to have been inverted for certain sections of the chromosome during evolution. One can determine a network of likely evolutionary steps from one species to another. Big problem: can start anywhere in the network. Need to establish where the network begins, i.e. where to Root the tree?
Choose an Outgroup: A taxon (or taxa) that are known to lie outside that group in question and are thus believed to be ancestral to the ingroup. Requiresindependent information. Once properly selected the determination of polarity falls out logically based on parsimony. the identification of an outgroup can help identify Character reversals = reversal in a trend of character change. An example is winglessness in insects: insects evolved from a wingless myriapod ancestor, but there are groups derived (i.e., more recently evolved) insects that have no wings (fleas). Wings have been lost in fleas and represent a character reversal. The use of an outgroup is extremely important in phylogenetic inference as it allows you to determine the "polarity" or direction of evolution as illustrated with insect wings. Once a reliable phylogenetic tree has been produced based on a data set of characters properly rooted with an outgroup, one can use the polarity provided by the outgroup to analyze the patterns of character evolution in general (how many times does a character originate during evolution?). See fig. 17.9, pg. 476.
Another means of determining the direction of evolution in a transformation series is by studying the development of the related taxa. Not as easy as "Ontogeny recapitulates phylogeny" once claimed because different developmental stages can be lost either early and/or late in development making difficult in some cases. In general, however, development can provide resolving power in studies of transformation series (fig. 17.11, pg. 478).
Compatibility methods: go with the tree that is supported by the largest number of characters. Said another way: the most likely tree is that which is supported by the greatest number of independent characters (the largest "clique" of characters) in which there are no homoplasies.

Schools of Systematics

SCHOOLS OF SYSTEMATICS

First of three lectures on Systematics. We are following a natural progression from the variation and dynamics of genes within populations, to divergence of populations and speciation to systematics = the scientific study of the kinds and diversity of organisms and their relationships.
A systematic or phylogenetic perspective on diversity of life itself follows logically from the fact that there is a phylogenetic tree that relates all organisms: from one generation to the next there is a pedigree that relates the parents to offspring. Within a population at any one time there is a complex pedigree or network of the ancestry of genes that describes who received what genes from whom. Among populations of a species there is a tree indicating which populations diverged from others and the sequence of branching events of population separation. At the species level, there is another tree of relationships that describes the sequence of branching events that led to the formation of descendant from ancestral species. Thus, just as a kind of population thinking is required to appreciate the evolutionary significance of variation among individuals, a kind of tree thinking is required to appreciate the evolutionary significance of the history of ancestor-descendant relationships that unites all levels of organization: genes, individuals, populations, species, higher taxa.
What are the goals of modern systematics? 1. Differentiate individual organisms and establish the basic units: species 2. to arrange these units in a logical hierarchy that permits easy and simple recognition in the basis of similarity = classification 3. to keep the details of 1 and 2 separate = nomenclature 4. determine the evolutionary (ancestor-descendant) relationships between all levels of the hierarchy =phylogeny.
Identification is not classification. Identification is to place an individual into an already existing classification scheme. Classification is to assemble groups into larger groups. There are conflicting goals of systematics: static classification of organisms into pigeon holes for easy reference; but this should reflect a dynamichistory of common descent = phylogeny. A systematic solution to the problem of diversity incorporates both of these goals, but this result is not always easily obtained.
Terminology: Taxon (taxa) = a group of organisms of any taxonomic rank that is sufficiently distinct to be worthy of being assigned to a definite category.Category= rank or level in hierarchic classification. Taxa = robin, thrushes, songbirds, birds, vertebrates, animals
Categories = species, family, suborder, class, subphylum, kingdom
How do you classify? Historically: Downward classification by logical division. Analogous to "20 questions". In Aristotle's time things were either animals or plants. One could start by asking oneself: is this an animal or a plant? Does this have feathers or not? and so on down until it was properly placed in its category.
Linnaeus believed in the reality of the genus. He used downward classification through his Linnaean hierarchy (kingdom, phylum, class, order, family, genus, species [recall: King Philip Came Over From Germany Speaking]) to reach the genus and then make the final division into the appropriate species. This approach lead to the Binomial nomenclature: Genus + species: Homo sapiens, etc.
This methodology gave way to Upward classification by empirical grouping. It became apparent that the groupings of Linnaeus were not Natural. The bottom of a downward classification process often lead to groupings where members had clearly the wrong affinity.
Darwin's discovery forced the thinking towards Descent from a common ancestor. It became apparent that these were the Natural groups that had been sought. What ultimately is the basis for upward classification? Characters. Can take varied forms: morphology, chemistry, behavior, ecology, physiology all could provide good characters.
Characters have character states: we all have hair, but our hair is different color; we all have eyes but our eyes are different color. Character states may vary together in Character complexes, or they may vary independently = Mosaic evolution of characters. Skin, eye and hair color all vary together in humans. Is this three characters or one (pigmentation)? Morphological and molecular characters may not evolve together, in a mosaic fashion (reading in section next week). Different characters may suggest different patterns of relationships (see fig. 14.3, pg. 377), again an example of mosaic evolution.
Homologous characters = characters sharing a common genetic and developmental history. Ancestor and descendant are linked by intermediate forms having the same character. These characters are the basis of determining a true phylogeny
Analogous characters = homoplasious characters: two characters not sharing a common genetic and developmental history and usually attained by adaptation to a similar ecological or functional challenge. Bats and Birds forelimbs and wings: they are homologous as forelimbs, but analogous as wings (a simple but crucialdistinction).
Analogous characters are attained by convergent evolution where descendants resemble each other more than they do their respective ancestors. Ichthyosaur, Fish, Porpoise; desert plants. Parallel evolution e.g. marsupials (M) and placentals (P). Ancestors are viewed as different but related. Point is: two possible evolutionary trees could be drawn:
(P,M) (P,M) (P,M) (P,M) or (M,M,M,M) (P,P,P,P)

If the characters that a set of organisms have could be either analogous or homologous characters, the systematist is faced with several problems: 1) attempting to identify which are which, and 2) deciding whether (or how) to perform character weighting. Excluding characters is an extreme form of weighting (weight = 0). Placentals have a placenta, marsupials a pouch where the immature young finish their development. These are major characters, should they carry more weight in our assignment of relationship. If we looked for other characters in the animals we could probably find many that would link the dog-dog, squirrel-squirrel, cat-cat, anteater-anteater, etc. Since characters are the data we will use to do systematics other questions arise: 1) should we use single or many characters?, 2) what are legitimate characters (morphology, ecology, etc.)? 3) how do we weight those that are chosen?
Analogous/homologous problem revolves around the distinction of the similarity of characters with adaptive or genetic bases. This leads to the distinction betweengrade and clade. Grade = level of adaptation; organisms of similar grade due to similar adaptations due to convergence (e.g., the "dog" grade or the "anteater" grade that goes across marsupial/placental distinction). Clade = a group descended from one common ancestor; a genetic lineage (e.g., the placental clade vs. the marsupial clade).
There are different schools of systematics: different schools place different emphasis on the goals of systematics. Some will emphasize classification over phylogeny (grade over clade); another emphasizes phylogeny over classification (clade over grade).
Phenetics (Numerical taxonomy) classification based on overall similarity of organisms. Treat all characters of equal weight and amass as many character as you can. Enter the characters into a computer that runs an algorithm that gives you a number reflecting the degree of similarity between different taxa. Assumes: homologous and analogous characters will be in there together, but rate of character change is roughly proportional to evolutionary distance and the homologous characters will carry the day. Results plotted in a Phenogram showing evolutionary relationships. See fig. 14.1, pg. 373, 14.4, pg. 378.
Cladistics (Phylogenetic systematics) Clade is everything. Define a hierarchical series of dichotomous branching events reflecting ancestor-descendant relationships. Seeks to identify monophyletic groups that, by definition, are derived from a single common ancestor. Defines these groups as taxa sharing derived characters (synapomorphies). Assumes that speciation is dichotomous producing two sister taxa and that the ancestral taxon disappears at the speciation event. See handout for examples and terminology; see fig. 14.1, 14.2, 14.6, pg. 373, 376, 382.
Evolutionary systematics uses homologous characters but will commonly weight characters differently depending on the "importance" of the character. A good evolutionary systematist is one who "knows" the group and can thus decide which characters to weight more heavily. Criticized as being highly subjective and not scientific because decisions are not testable hypotheses, but statements of faith about the importance of the characters. Acknowledges grade as relevant to the study: crocodiles and birds are different classes to evolutionary systematists, but sister taxa to cladists.
Which approach do we use? Ideally a classification should be objective in that the criteria use to classify are not subject to the whim of the person doing the classifying. Objectivity is important if classification is to be a scientific endeavor: someone else ought to be able to step in and repeat your "experiment" in classification. Moreover a classification should be natural and not artificial so that if a set of characters were used to assign relationships, these relationships should also be apparent in other characters not used in the analysis. There are natural groups that have been generated during the history of life and systematists should attempt to discover these groups. In recent years cladistics has become the dominant school of systematics as it meets these two criteria well. However, phenetics is still very active and character weighting is still being used. Note that natural groups might generate many more hierarchical levels than the classical Linnaean hierarchy (see fig. 14.8, 14.9, pg. 386-387).
Terminology (See fig. 14.6, pg. 382 and note the different terms used for synapomorphy, symplesiomorphy and that analogy = homoplasy).
Monophyletic - referring to a group of taxa descended from a single common ancestor (e. g. angiosperms or seed plants)
Apomorphic - a derived character (seeds in angiosperms and gymnosperms relative to ferns)
Plesiomorphic - an ancestral character (stomata in angiosperms and gymnosperms)
note: apo and plesiomorphic are relative terms: vascular tissue is apomorphic to the monophyletic group above the bryophytes, but plesiomorphic to the angiosperms)
Syn - shared Aut - "self", unique to a group
synapomorphies are shared derived characters and are what define monophyletic groups because the members of that group have the character because they are descended from a common ancestor (seeds in angiosperms and gymnosperms)
symplesiomorphies are shared ancestral characters (chlorophyll in the angiosperms and gymnosperms)
autapomorphies are derived characters unique to one group (flowers in angiosperms)
autplesiomorphies can't exist, by definition
Paraphyletic group includes some but not all of the descendants of a common ancestor. Incomplete grouping based on symplesiomorphies (e.g. the non-natural group of ferns and gymnosperms based on the presence of chlorophyll and stomata; angios have these but are not in the group)
Polarity distinguishes between the plesiomorphous and apomorphous state of a character by comparison to an outgroup (a taxon know to lie outside the hierarchy of the groups being considered, e.g., the outgroup algae determines the polarity of the evolution of seeds and secondary growth with respect to the other taxa)
Sister taxa are the two lineages that descend from a common ancestor following a splitting event; can be considered at any level of hierarchy in a cladogram

Cases of Speciation

CASE HISTORIES OF SPECIATION I&II

Some of the best examples of speciation are examples of diversification on archipelagos. These provide clear contexts of allopatry and hence provide the extrinsicbarrier to gene exchange from the source (usually mainland) population.
The most famous are the Galapagos Islands. The islands are young (some ~ 1 million years), have a volcanic origin providing an opportunity for new arrivals to "radiate" into open niches and the islands are quite distant from the mainland. This isolation and context of primary succession (e.g., development of a flora and fauna on a "clean slate") will allow for a random element in community composition. Irrespective of genetic consequences of the founding event, subsequent evolution of species quite likely will be under dramatically different selective regime than those in the source population.
Darwin's Finches. Morphological and genetic studies indicate that they are derived from single ancestral finch, i.e., are monophyletic. There has been dramatic specialization in ecological roles, each species having distinct morphologies and associated food items (beak size and shape associated with seed size, grub feeding, tool use, etc.). Classic examples of different distributions of beak depths: difference between means is greater between species when they occur on the same island than when they occur alone on different islands (see figure below).
Often cited as a clear indication that competition played a role in the adaptive radiation of the finches. There are obvious alternative hypotheses to explain these patterns: populations on different island differ by these amounts as a consequence of drift; different islands have different plants, insects (food items in general) thus the differences are a result of food, not competitors). As P.R. Grant concludes in Ecology and Evolution of Darwin's Finches, Princeton Univ. Press, 1985, patterns of differentiation and speciation are a combined effect of adaptation to different flora/food and adaptive responses to competitors. The issue of different plants/food on different islands just shifts the question to another trophic level: how did the different islands come to be different in these species.
Another evolutionary paradigm: the Hawaiian islands. Again the islands are young (< 5 million years old), have a volcanic origin and an interesting one: convection currents in the earth's mantle generate a "hot spot" where volcanic activity occurs above. The pacific plate moves northwest over this spot so the islands' geographical location is related to their age (Kauai in the north west is ~ 5 million years old; Hawaii [the big island] in the southeast is ~ 500,000 years old and still active).
Hawaiian Drosophila show remarkable patterns of colonization and speciation. At least 700 species of Drosophilids on Hawaiian islands. Not just typical little fruit flies either: large body size, dramatic "picture wing" species, some with "hammer-head" shaped heads. Banding patterns of polytene chromosomes allows phylogeny reconstruction: these and other data show that patterns of colonization are from older to younger islands (flies on Hawaii are derived from ancestors on Maui). Most species are found only on one island (high levels of endemism; more later in Biogeography). This implies that most new colonization events have lead to speciation events! This observation lead Hampton Carson to propose the founder-flush model of speciation.
African cichlid fishes are another remarkable case of "explosive speciation" (the Hawaiian Drosophila of the fish world). Geology and geography again plays an important role. African rift lakes: great fresh-water lakes in east Africa. Formed recently: < 1 million years old. Lake Victoria colonized by one (??) founder 200,000 years ago(??) now has ~ 200 species of fish!. Recent study (Meyer et al. 1990, Nature vol. 347, pg. 550 and see pg. 512) used mitochondrial DNA to show that the species in the lake are indeed monophyletic and that there is very little sequence divergence between species: confirms short time span. But there has been remarkable evolution of morphological, ecological and behavioral variation in these fish: algae grazers, snail crushers, plankton feeders, paedophages (clamp onto the mouth of a fish brooding her young in her mouth and force her to spit out here young into the mouth of the attacker), one fish (in Lake Malawi) plucks the eyes out of other fish as food. All this diversity in 200,000 years with very little genetic differentiation.
Another set of important examples of speciation are those that are believed to have speciated as a result of isolation in Pleistocene refugia. Glacial advances and retreats during the Pleistocene epoch acted as vicariance events in areas where glaciers were present (Wisconsin ice sheet). Dramatic evidence of this is in the North American bird fauna and the clear faunal break between the east and west, e.g., wood warblers; Peterson's field guides have an Eastern and Western edition).
Climatic changes associated with the glacial advances and retreats altered habitats in the tropics resulting in "islands" of habitat that fluctuated in size and geographic location, leading to fragmentation of distributions and contribution to speciation. Believed to one explanation for patterns of speciation in the Amazon. Also a possible explanation for the Larus ring species complex: genus Larus (seagulls) fragmented in Siberia during the Pleistocene. Diverged populations of Larus argentatus (herring gull) colonized eastern Siberia, across the Bering straits, across North America, Iceland and back to Northern Europe becoming increasingly diverged at each step. Hybrid zones exist between successive populations but the ends of the ring are reproductively isolated implying that speciation has gone to completion (an example of geographic speciation)
There have been some controversial examples of sympatric speciation documented in the literature. The apple maggot fly (Rhagoletis pomonela) mates and lays eggs on a specific host, originally Hawthorn. In 1864 Rhagoletis was found on apple trees that had been introduced to regions where hawthorn grew. In early 1960'sRhagoletis was found on cherry. This host race formation has been argued as an incipient stage of sympatric speciation. Advantage of this model is that the temporal framework is reasonably well documented and the species in question is an agricultural pest so it is likely that it will receive further study and the issue can be settled.
Model invoking a survival locus (S) and a host selection locus (H) with each with new mutant alleles that shift survival and selection to the new host (e.g., apple from Hawthorn).
Allochronic speciation was proposed as a model where species differentiated in time. Crickets of the genus Gryllus were taken as an example because species with virtually identical songs and morphology had evolved as spring adults versus fall adults (overwinter as juveniles or eggs, respectively). The model may apply but this particular example was shot down by phylogenetic analysis which showed that the two "allochronic species" (Gryllus veletis and Gryllus pennsylvanicus are actually distantly related in the genus (see figures).