Speciation PDF

1 Unit V Speciation and isolating mechanisms, Molecular evolution I. Speciation It is the formation of new and distinct species in the course of evolution. Speciation involves the splitting of a single evolutionary lineage into two or more genetically independ...

1 Unit V Speciation and isolating mechanisms, Molecular evolution I. Speciation It is the formation of new and distinct species in the course of evolution. Speciation involves the splitting of a single evolutionary lineage into two or more genetically independent lineages. Speciation is a process within evolution that leads to the formation of new, distinct species that are reproductively isolated from one another. Anagenesis, or ‘phyletic evolution’, occurs when evolution acts to create new species, which are distinct from their ancestors, along a single lineage, through gradual changes in physical or genetic traits. In this instance, there is no split in the phylogenetic tree. Conversely, ‘speciation’ or cladogenesis arises from a splitting event, where a parent species is split into two distinct species, often as the result of geographic isolation or another driving force involving the separation of populations. The reproductive isolation that is integral to the process of speciation occurs due to reproductive barriers, which are formed as a consequence of genetic, behavioural or physical differences arising between the new species. These are either pre-zygotic (pre- mating) mechanisms, for example, differences in courtship rituals, non-compatible genitalia, or gametes, which are unable to fertilize between species. Alternatively, they are post- zygotic (post-mating), for example zygote mortality or the production of sterile offspring. Reproductive isolation leads to reinforcement of the distinction between species through natural selection and sexual selection.  2 In eukaryotic species—that is, those whose cells possess a clearly defined nucleus—two important processes occur during speciation: the splitting up of one gene pool into two or more separated gene pools (genetic separation) and the diversification of an array of observable physical characteristics (phenotypic differentiation) in a population. There are many hypotheses about how speciation starts, and they differ mainly in the role of geographic isolation and the origin of reproductive isolation (the prevention of two populations or more from interbreeding with one another). Types of Speciation There are five types of speciation: allopatric, peripatric, parapatric, and sympatric and artificial. 1. Allopatric Speciation Allopatric speciation occurs when members of a population become geographically isolated from one another, to the extent that genetic exchange, through mating, is prevented or interfered with. This may be a result of geographical changes, such as the formation of a mountain by a volcano, island formation, habitat separation by glaciers and rivers, or habitat fragmentation caused by human activity. Alternatively, species members may emigrate, resulting in population separation by dispersal; this is commonly known as vicariance. The separated populations then undergo divergence in genotypic or phenotypic traits as a result of different selective pressures acting upon populations. This leads natural selection to cause genetic drift as mutations arise within populations. Over time, the separate populations may develop morphologically distinct features due to adaption to their new environment. The features may become so distinctively different that reproductive isolation occurs, preventing the inbreeding of populations and thus forming new species. If the populations become sufficiently different that they are classified as new species, but not distinct enough for reproductive isolation to occur, the species may come back into contact and mate, producing hybrids. The extent of the effect that geographic barriers may have on a population often depends on the dispersal ability of the organism; for example, the new formation of a river in a landscape would create an impassable barrier for small terrestrial mammals, insects and reptiles. However, birds and larger mammals would likely disperse across the river with ease. An elegant example of allopatric speciation, which first inspired Charles Darwin to develop the theory of evolution and natural selection, is the divergent populations of finches inhabiting  3 the Galapagos Islands, and known as ‘Darwin’s finches’. Darwin noticed that each of the Galapagos Islands hosted a population of finches, which although relatively similar in morphology (compared with other bird species), exhibited slight differences in features such as body size, colour and beak length or shape. He noted that there were different food sources available for the birds on each of the different islands, and came to the conclusion that the differences in beak shape were an adaption toward acquiring the particular food source. Fourteen species of Galapagos finches that evolved from a common ancestor. The different shapes of their bills, suited to different diets and habitats, show the process of adaptive radiation. 2. Sympatric Speciation A controversial alternative to allopatric speciation is sympatric speciation, in which reproductive isolation occurs within a single population without geographic isolation. In general, when populations are physically separated, some reproductive isolation arises. How genetic divergence can happen within a population of individuals that are continually interacting with one another is usually difficult to explain. Examples of sympatric speciation are often disputed because they must show convincing evidence of species descending from the same ancestral species, the reproductive isolation of the group, and of allopatry not causing the speciation. Nevertheless, sympatric speciation has been shown to have occurred in apple maggot flies (Rhagoletis pomonella), a parasitic insect that laid its eggs in the fruit of wild hawthorns (Crataegus) until one subset of the population began to lay its eggs in the fruit of domesticated apple trees (Malus domestica) that grew in the same area. That small group of apple maggot flies selected a different host species from the rest of its kind, and its offspring became accustomed to domesticated apples and later laid their own eggs in them, thereby cementing the shift in host.  4 Sympatric selection might also result from a combination of sexual selection and ecological factors. Studies of African cichlid fishes in Lake Nyasa and other lakes in the East African Rift System record so-called species flocks (individuals of the same species that “flock” together in one large assemblage) that have arisen in ecologically uniform lakes. Such a condition substantially reduces the chances of allopatry being the cause of speciation, and it may result in groups of females within a population developing a strong affinity for males with different extreme phenotypic traits, such as scale markings and limbs that differ in size from average individuals. Cichlid fish (family Cichlidae). Dlimnothrissa Other studies suggest that sympatry among cichlid fishes also occurs in rivers feeding the East African Rift System lakes, as well as in Nicaragua’s crater lakes. 3. Parapatric Speciation Parapatric speciation is an extremely rare case of speciation that occurs when a population is continuously distributed within a geographic area without any specific barriers to gene flow. Nonetheless, the population does not mate randomly within the population, but rather individuals mate more commonly with their closest geographic neighbours, resulting in uneven gene flow. Non-random mating may increase the rate of dimorphism within populations, in which varied morphological forms of the same species are displayed. The result of parapatric  5 speciation is one or more distinct sub-populations (known as ‘sister species’), which have small, continuous overlaps in their biogeographic range and are genotypically dimorphic. 4. Peripatric Speciation Peripatric speciation is a form of allopatric speciation that occurs when populations that have become isolated have very few individuals. Through this process, the population goes through a genetic bottleneck. Within the small sub-population, organisms which are able to survive within the new environment may carry genes that were rare within the main population but that cause a slight variation to behaviour or morphology. Through repeated matings, the frequency of these, once rare, genes increase within the small population. This is known as the ‘founder effect’. Over time, the characteristic that was determined by the gene becomes fixed within the population, leading to an isolated species that is evolutionarily distinct from the main population.  6 5. Artificial Speciation Artificial speciation is the form of speciation that can be achieved by the input of human influence. By separating populations, and thereby preventing breeding, or by intentionally breeding individuals with desired morphological or genotypic traits, humans can create new, distinct species. This is also known as ‘artificial selection’; most modern domesticated animals and plants have undergone artificial selection. Although evolution of our modern crops and livestock has taken thousands of years, it is possible to visualize the process of artificial selection in species that have short life cycles. Artificial selection has been demonstrated most effectively in species of Fruit Fly (Drosophila melanogaster). Experiments in which flies are placed into environments which contain different resources or habitats show the changes that occur when the flies adapt to each environment. After several generations, the flies are removed from the experimental zone and are allowed to cohabitate, although the populations are unable to mate due to the reproductive isolation process that occurred while in isolation. II. Isolation It is a driving force behind evolution because the changes that build up in different populations over time is what causes the evolution of new species. When two populations are isolated by enough mechanisms, they can be considered different species. This process is called speciation. What Causes Isolation? There is a wide range of factors that can isolate species from one another. Isolating mechanisms, in the end, cause speciation by preventing two species from mating with one another. Speciation occurs when two species can no longer mate and produce a viable offspring.  7 Isolating mechanisms come in two main types: separation due to geographic isolation and separation which occurs in the same location. Geographically separated species are more common. For example, a single shrimp population used to live where Panama now resides. After the formation of the land bridge that separates the Caribbean Sea and the North Pacific Ocean, different species of shrimp descended from the original shrimp species as each adapted to its unique environment. Isolating mechanisms The reproductive characteristics which prevent species from fusing. Isolating mechanisms are particularly important in the biological species concept, in which species of sexual organisms are defined by reproductive isolation, i.e. a lack of gene mixture. The term isolating mechanisms was introduced by T Dobzhansky in the 1930s, and has been popularized in a number of books by E Mayr. Both authors originally proposed that isolating mechanisms were group traits beneficial at the level of the species. Types of Isolating Mechanisms Basically, if a sperm cell and an egg cell are able to fuse, fertilize, and result in a living offspring, the parents are of the same species. Isolation is what keeps species separated. This can include things like their geographic location, their mating seasons, their behaviours, and the biochemical properties of their reproductive process. These factors are called pre-zygotic isolation mechanisms because they happen before an organism is born. Two broad kinds of isolating mechanisms between species are typically distinguished, together with a number of sub-types (modified from Mayr 1970). 1) Pre-mating isolating mechanisms Factors which cause species to mate with their own kind (assortative mating). a) Temporal isolation. Individuals of different species do not mate because they are active at different times of day or in different seasons. b) Ecological isolation. Individuals mate in their preferred habitat, and therefore do not meet individuals of other species with different ecological preferences. c) Behavioral isolation. Potential mates meet, but choose members of their own species. d) Mechanical isolation. Copulation is attempted, but transfer of sperm does not take place. 2) Post-mating isolating mechanisms Genomic incompatibility, hybrid in viability or sterility. a) Gametic incompatibility. Sperm transfer takes place, but egg is not fertilized. b) Zygotic mortality. Egg is fertilized, but zygote does not develop. c) Hybrid inviability. Hybrid embryo forms, but of reduced viability. d) Hybrid sterility. Hybrid is viable, but resulting adult is sterile. e) Hybrid breakdown. First generation (F1) hybrids are viable and fertile, but further hybrid generations (F2 and backcrosses) may be in viable or sterile.  8 Isolating mechanisms are types of isolation, like behavioural and geographic, that can lead to the formation of new species. One species becoming two is called speciation. So basically, mechanisms of isolation can lead to speciation. Isolation happens when part of a population becomes separated and stops breeding with the other part. After a long enough time being separated, the two populations might not be able to produce offspring with each other, called reproductive isolation. At this point, both parts of the populations evolve towards being two completely separate species. III. Molecular Evolution Changes in the base pair sequences in DNA or RNA molecules and changes in amino acid sequences and their molecular configuration in different proteins, from generation to generation are known as molecular evolution. It is possible to measure differences between these molecules obtained from different organisms (such as humans, apes, monkeys, prosimians etc.) on a unit scale of amino acids or nucleotides and demonstrate their relationships. As the molecular sequences are heritable, their variations produce molecular records that have been transferred from generation to generation during evolution. A triplet made of three pairs of nucleotides is called a codon. A codon will change if one of the three bases changes and it may or may not end up in a change in the amino acid synthesized by it. Majority of these changes are small and inconsequential but accumulate over long periods to bring about large alterations in the gene frequencies in populations. Two kinds of such changes are possible.  9 1. Silent site substitution These are such changes in DNA sequences which do not result in any change in amino acid synthesis and hence composition of proteins is not changed. They are usually changes in the last base pair of the codon. For example, in mRNA strand GCA codes for alanine and if adenine is replaced by guanine, the resulting GCG will still code for the same amino acid alanine. Silent site substitutions do not bring about any phenotypic changes. 2. Replacement substitution They are changes in the bases of codons that result in synthesis of new amino acids and are capable of altering the structure of proteins that are controlled by them and thus changing the phenotype. Silent site substitutions have much higher rate of change as compared to the replacement substitutions, since the former do not produce changes that can be exposed to natural selection but the latter do. For the same reason genes which are less vital to the cell can undergo rapid changes by replacement substitution without showing harmful effects. Pseudogenes, which are duplicated sequences of bases and do not code for proteins and hence are not exposed to natural selection, are known to undergo higher rate of evolutionary changes. Sequencing amino acids: Comparing amino acid sequences in a protein in different species by using biochemical techniques is one of the most popular methods to determine phylogeny. For example, in haemoglobin two pairs of alpha and beta sequences of polypeptide chains form a tetramer that can be distinguished by different amino acid sequences in different species. In vertebrates, different types of globin chains appeared during evolution and in each species they followed their own evolutionary path by changes in the amino acid sequences. They are all variations of a single globin ancestor that is controlled by similar globin genes which are believed to have originated by gene duplication of the original type. Neutral Theory of Molecular Evolution The neutral theory of molecular evolution describes how the differences between and within species came to be. The theory asserts that the majority of genetic variations within a species are neutral, meaning that do not positively or negatively impact the organism. It also suggests that the differences between and within species have evolved by neutral mechanisms, rather than Darwin’s natural selection.  10 Molecular evolution concerns how gene sequences change over time. The accumulation of changes in gene sequences constitutes evolution, which can lead to different characteristics and subsequently give rise to different species. Change in DNA sequences is commonly brought on by mutations. Mutations can be inherited, but are also occurring during cell replication. When a mutation arises that is advantageous to the individual, certain advantages in life and reproduction may ensue. Advantageous mutations, therefore, have a selective advantage, where they can be selected for and spread throughout the population. Deleterious mutations, on the other hand, are more likely to be removed from the population. Mutations can also be neutral or nearly neutral, where they do not cause significant changes in functioning to the organism. Basis of the neutral theory of molecular evolution The neutral theory of molecular evolution was first proposed by Motoo Kimura in 1968, and independently by Jack King and Thomas Jukes in 1969. At the time, studies on genetic sequences were showing that the previous idea which postulated that most of the differences between species were caused by selection on advantageous mutations was actually not true. The neutral theory instead proposed that the majority of molecular changes, such as in DNA sequence, are caused by random processes acting on selectively neutral mutants, meaning they inferred no advantage or disadvantage. By using complex calculations, Kimura showed that the rate of evolution cannot be explained by positive or negative selection because it is too high and that many mutations must instead be neutral. Neutral mutations become widespread by a process called random genetic drift, in which a mutation spreads throughout the population due to chance alone. While the neutral theory diminishes the role of classic Darwinian selection, in which evolution is due primarily to beneficial alleles, the concept is actually not anti-Darwinian. The theories share several aspects, such as the recognition that positive natural selection underlies adaptation to the environment, and that new mutations in regions with important functions are usually deleterious, which is why they are removed and do not contribute to variation between or within species. The point of disagreement is how large a role advantageous and neutral mutations play in differences between and within species. Motoo Kimura (1986) proposed that a vast majority of base substitutions that are preserved in a population are neutral with regards to natural selection. Positive substitutions are so rare that they are inconsequential in molecular evolution, while negative changes are quickly eliminated by natural selection. Natural selection seems to favour neutral changes which determine the overall rate of sequential evolution. For instance, pseudogenes have the highest substitution rate among the genes but the changes are completely neutral with regard to selection.  11 The theory was tested by J. McDonald and M. Kreitman (1991) by comparing base sequences of alcohol dehydrogenase gene of Drosophila melanogaster, D. simulans and D. yakuba. Kimura’s theory not only contradicts classical Darwinism but also does not explain fixation of various types of alleles in different sizes of population. The theory holds that the rate of fixation of neutral mutations does not depend on population size but the genes are fixed or eliminated by genetic drift. The impact of the neutral theory The neutral theory provided a much-desired null hypothesis to test empirical genetic data against. To show that a sequence is being selected upon, one needs to be able to reject the null hypothesis that the sequence is evolving neutrally. The neutral theory has been used as a basis for many statistical tests which investigate genetic variance. DNA sequence data grew in use during the late 20th century, and many of the discoveries from these sequencing experiments supported the predictions of the neutral theory. For example, it was found that changes in protein sequences were more likely to be conservative (i.e. less likely to affect protein function) than radical, and that pseudogenes (“dead” genes which do not have a function) evolve at a high rate. Both of these findings were seen as support for the idea that divergence between species is due to neutral evolution in less functionally important regions. In other words, if most mutations were adaptive, more changes in important genetic regions than would be expected. The neutral theory provides theoretical framework for testing and predicting molecular evolution in the absence of positive selection. Molecular evolution address two broad range of questions: 1. Use DNA to study the evolution of organisms, e.g. population structure, geographic variation and phylogeny 2. Use different organisms to study the evolution process of DNA. Recent controversy surrounding the neutral theory The neutral theory was questioned when initially published, but evidence seemed to mount in support of the theory. Some aspects of the neutral theory are now generally accepted, such as that neutral mutations exist, that large parts of many eukaryotic genomes are non- functional, and that neutral variation is widespread. However, in 2018, a paper strongly contending the neutral theory was published and stirred up debate. This new paper, by Andrew Kern and Matthew Hahn, criticized the grounds on which the neutral theory was founded and the evidence produced since, and claimed that the idea that neutral mechanisms ultimately cause within and between species differences should be dismissed. The debate that followed discussed the roles of positive and negative selection in genetic variation. Kern and Hahn encouraged that scientists “firmly reject its universality”. Despite this, the neutral theory appears to be still mostly accepted. Rather, modifications to terminology, and the assumption that differences in single nucleotides are selectively neutral can be misleading in certain cases.