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Species and Speciation I. Species Concepts II. Recognizing Species III. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates 4. Mechanical isolation - genitalia don't fit 5. Gametic Isolation - gametes transfered but sperm can't fertilize egg B. Post-Zygotic Isolation 1. Patterns: 2. Mechanisms: - epistatic incompatibilities AAbb x aaBB AaBb – A and B don’t work together QTL mapping Locus 1 Hms1 1g1g Locus 2 Hms2 M. guttatus 2g2g X 1n1n 1g1n M. nasutus F1 2n2n 2g2n F2: All ok except if: 1g,1g, 2n2n Male sterility Epistatic incompatibility Species and Speciation I. Species Concepts II. Recognizing Species III. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates 4. Mechanical isolation - genitalia don't fit 5. Gametic Isolation - gametes transfered but sperm can't fertilize egg B. Post-Zygotic Isolation 1. Patterns: 2. Mechanisms: - epistatic incompatibilities - inversion incompatibilities Inversion (changes the order of genes on a chromosome) The only functional gametes are those that DID NOT cross over – and preserve the parental combination of alleles Inversions in different populations of D. pseudoobscura (Dobzhansky& Sturtevant 1938) Visualized inversion complexes in giant chromosomes of salivary glands of hybrids, where homologous chromosomes replicate 100’s of times and pair up Relative frequencies (percentages) of five chromosomal inversions in D. pseudoobscura in different geographic regions. 1. Distribution suggests these inversions may be preserving co-adapted gene complexes; ST high at warm temperature. 2. Experiment confirmed that the ST arrangement was selected for at warmer temperatures. Species and Speciation I. Species Concepts II. Recognizing Species A. Morphology B. Genetic Analysis C. Hybrid Analyses - Create hybrids and examine their fertility. Infertility may be due to: - Epistatic interactions between loci derived from different parents. Maybe species one has A1A1B1B1 and species 2 has A2A2B2B2, and maybe A1 and B1 don't work together. If one is a sex linked gene, then sterility might be sex-specific. - Hybrids that receive different inversion chromosomes may have lower fitness because crossing over produces aneuploid gametes - with chromosomes that lack centromeres and are lost from the cell line. - Hybrids receiving chromosomes from parents with different reciprocal translocations may not have neat homologous sets. Species and Speciation I. Species Concepts II. Recognizing Species III. Making Species - Reproductive Isolation IV. Speciation Speciation Speciation is not a goal, or an adaptive product of selection. It is simply a potential consequence of genetic changes that occurred for other reasons (selection, drift, mutation, etc.). Speciation I. Modes: Speciation I. Modes: A. Allopatric: Divergence in geographically separate populations - Vicariance - range divided by new geographic feature A B C Almost all most recent divergence events date to 3my, and separate species on either side of the isthmus Speciation I. Modes: A. Allopatric: Divergence in geographically separate populations - Vicariance - range divided by new geographic feature - Peripatric - divergence of a small migrant population A B Abert’s Squirrel Kaibab Squirrel Crossed grand canyon to the north during Ice Age and isolated. Speciation I. Modes: A. Allopatric: Divergence in geographically separate populations - Vicariance - range divided by new geographic feature - Peripatric - divergence of a small migrant population B. Parapatric - neighboring populations diverge, even with gene flow Speciation I. Modes: A. Allopatric: Divergence in geographically separate populations - Vicariance - range divided by new geographic feature - Peripatric - divergence of a small migrant population B. Parapatric - neighboring populations diverge, even with gene flow B. Parapatric - neighboring populations diverge, even with gene flow Hybrid Backcross?? Hybrid Speciation I. Modes: A. Allopatric: Divergence in geographically separate populations - Vicariance - range divided by new geographic feature - Peripatric - divergence of a small migrant population B. Parapatric - neighboring populations diverge, even with gene flow C. Sympatric: Divergence within a single population C. Sympatric: Divergence within a single population Maynard Smith (1966) - hypothesized this was possible if there was disruptive selection within a population - perhaps as a specialist herbivore/parasite colonized and adapted to a new host. C. Sympatric: Divergence within a single population Maynard Smith (1966) - hypothesized this was possible if there was disruptive selection within a population - perhaps as a specialist herbivore/parasite colonized and adapted to a new host. Example: Hawthorn/Apple Maggot Fly (Rhagoletis pomonella) Hawthorn maggot fly is a native species that breeds on Hawthorn (Crataegus sp.) C. Sympatric: Divergence within a single population Maynard Smith (1966) - hypothesized this was possible if there was disruptive selection within a population - perhaps as a specialist herbivore/parasite colonized and adapted to a new host. Example: Hawthorn/Apple Maggot Fly (Rhagoletis pomonella) Europeans brought apples to North America. They are in the same plant family (Rosaceae) as Hawthorn. C. Sympatric: Divergence within a single population Maynard Smith (1966) - hypothesized this was possible if there was disruptive selection within a population - perhaps as a specialist herbivore/parasite colonized and adapted to a new host. Example: Hawthorn/Apple Maggot Fly (Rhagoletis pomonella) Europeans brought apples to North America. They are in the same plant family (Rosaceae) as Hawthorn. In 1864, apple growers noticed infestation by Apple Maggot flies...which were actually just "hawthorn flies"... C. Sympatric: Divergence within a single population Maynard Smith (1966) - hypothesized this was possible if there was disruptive selection within a population - perhaps as a specialist herbivore/parasite colonized and adapted to a new host. Example: Hawthorn/Apple Maggot Fly (Rhagoletis pomonella) races breed on their own host plant, and have adapted to the different seasons of fruit ripening. Only a 4-6% hybridization rate. Temporal, not geographic, isolation. C. Sympatric: Divergence within a single population But can a generalist speciate sympatrically? Tauber and Tauber. 1977a and 1977b. Science. Two species of green lacewings - generalist insect predators Chrysopa downesi has one generation in early spring C. carnea breeds and has three generations in summer C. Sympatric: Divergence within a single population But can a generalist speciate sympatrically? Tauber and Tauber. 1977a and 1977b. Science. Two species of green lacewings - generalist insect predators Chrysopa downesi has one generation in early spring, then diapause C. carnea breeds has three generations in summer, no diapause The differences are due to responses to photoperiod C. downesi stops reproducing and goes into diapause under long day length (summer), whereas C. carnea reproduces under long day length. C. Sympatric: Divergence within a single population But can a generalist speciate sympatrically? Tauber and Tauber. 1977a. Science 197:592. The species are completely interfertile in the lab: Did reciprocal matings: C. downesi x C. carea Reared F1 offspring under long day length (16L:8D). Found all F1 did not enter diapause (C. carnea photoperiod response is dominant). C. Sympatric: Divergence within a single population But can a generalist speciate sympatrically? Tauber and Tauber. 1977a. Science 197:592. Did F1 x F1 cross: Found 7% (~1/16) of F2 exhibited diapause at 16L:8D. This is consistent with a model of 2 independently assorting autosomal genes with complete dominance at each and an additive effect. AABB x aabb F1 all A-B- phenotype F2 A-B- = 9/16 A-bb = 3/16 C. carnea photoperiod aaB- = 3/16 aabb = 1/16.... ~ 7% C. downesi photoperiod C. Sympatric: Divergence within a single population But can a generalist speciate sympatrically? Tauber and Tauber. 1977a. Science 197:592. F1 x C. downesi backcross had 3:1 ratio, as expected of model. AaBb x aabb AaBb = .25 Aabb = .25 C. carnea photoperiod aaBb = .25 aabb = .25 C. downesi photoperiod C. Sympatric: Divergence within a single population But can a generalist speciate sympatrically? Tauber and Tauber. 1977b. Science 197:1298. How did this temporal separation get established? C. downesi is dark green and prefers hemlock forests C. carnea is light green and prefers fields and meadows Difference governed by a single locus where dark is incompletely dominant. C. Sympatric: Divergence within a single population But can a generalist speciate sympatrically? Tauber and Tauber. 1977b. Science 197:1298. How did this temporal separation get established? C. downesi is dark green and prefers hemlock forests C. carnea is light green and prefers fields and meadows Difference governed by a single locus where dark is incompletely dominant. Hypothesize that selection for different morphs in different habitats created the stable dimorphism, reinforced by inbreeding within the habitats. intermediate heterozygote C. Sympatric: Divergence within a single population But can a generalist speciate sympatrically? Tauber and Tauber. 1977b. Science 197:1298. How did this temporal separation get established? C. downesi is dark green and prefers hemlock forests C. carnea is light green and prefers fields and meadows Difference governed by a single locus where dark is incompletely dominant. Hypothesize that selection for different morphs in different habitats created the stable dimorphism, reinforced by inbreeding within the habitats. Selection then favored early breeding in C. downesi, as that is when insects feeding on conifers are most abundant. Speciation I. Modes II. Mechanisms Speciation I. Modes II. Mechanisms A. Progressive Genomic Incompatibility Tilley et al. 1990. PNAS. Desmognathus ochrophaeus in western NC 1. correlation between geographic distance and genetic distance Tilley et al. 1990. PNAS. Desmognathus ochrophaeus in western NC 2. Placed sympatric and allopatric males and females (reciprocal mating design) together for an evening and examined the cloaca of female in the morning for presence of sperm packet. Calculated "Coefficient of Isolation": (sum of % of sympatric matings) - (sum of % of allopatric matings) 2 = total isolation by sexual selection 0 = no differentiation by sexual selection Speciation I. Modes II. Mechanisms A. Progressive Genomic Incompatibility B. Hybrid Incompatibility - Dobzhansky and Müller (1930's) Pairs of genes that work together diverge in different populations; epistatic combinations broken down in hybrids. Speciation I. Modes II. Mechanisms A. Progressive Genomic Incompatibility B. Hybrid Incompatibility - Dobzhansky and Müller (1930's) Pairs of genes that work together diverge in different populations A1A1B2B2 works A1A1B1B1 lethal A1 A2A2B2B2 works B1 A2A2B1B1 works Speciation I. Modes II. Mechanisms A. Progressive Genomic Incompatibility B. Hybrid Incompatibility C. Differential Selection C. Differential Selection - Assumed to be primary, but few studies documenting that reproductive isolation of phenotypes correlates with fitness differential in different environments. Rundle et al. (2000). Science 287:306. C. Differential Selection - Assumed to be primary, but few studies documenting that reproductive isolation of phenotypes correlates with fitness differential in different environments. Rundle et al. (2000). Science 287:306. Sticklebacks colonizing lakes...PHYLOGENY: limnetic benthic limnetic benthic limnetic benthic C. Differential Selection - Assumed to be primary, but few studies documenting that reproductive isolation of phenotypes correlates with fitness differential in different environments. Rundle et al. (2000). Science 287:306. Mate selection correlates with ecotype, not with genetic relatedness.... example of parallel evolution, too. Speciation I. Modes II. Mechanisms A. Progressive Genomic Incompatibility B. Hybrid Incompatibility C. Differential Selection D. Hybridization D. Hybridization - When hybridization occurs, it show increase gene flow between populations. How are hybrids stabilized as a reproductively isolated group? - adaptation to an extreme habitat Gompert et al. 2006. Science 314: 1923. - adaptation to an extreme habitat Gompert et al. 2006. Science 314: 1923. Two species of small western butterflies have overlapping ranges. - adaptation to an extreme habitat Gompert et al. 2006. Science 314: 1923. Two cluster Three cluster Probabilities of assigning individuals from these populations to a particular dendrogram "cluster" - adaptation to an extreme habitat Gompert et al. 2006. Science 314: 1923. Two cluster Three cluster Probabilities of assigning individuals from these populations to a particular dendrogram "cluster" Are the alpine populations simply in hybrid zone, or are they ‘reproductively isolated’? - adaptation to an extreme habitat Gompert et al. 2006. Science 314: 1923. Two cluster Three cluster Probabilities of assigning individuals from these populations to a particular dendrogram "cluster" Are the alpine populations simply in hybrid zone, or are they reproductively isolated? They are fixed for several alleles, suggesting no gene flow. - adaptation to an extreme habitat Gompert et al. 2006. Science 314: 1923. Two cluster Three cluster Probabilities of assigning individuals from these populations to a particular dendrogram "cluster" Are the alpine populations simply in hybrid zone, or are they reproductively isolated? They are fixed for several alleles, suggesting no gene flow. - Also used coalescence to estimate time since a common ancestor within each 'species". The alpine populations had a more recent history (400,000 yrs) than either of the others (1.2-1.9 my) - adaptation to an extreme habitat Gompert et al. 2006. Science 314: 1923. - What maintains this genetic uniqueness? - adaptation to an extreme habitat Gompert et al. 2006. Science 314: 1923. - What maintains this genetic uniqueness? Fidelity to Host Plant - adaptation to an extreme habitat Gompert et al. 2006. Science 314: 1923. - What maintains this genetic uniqueness? Fidelity to Host Plant Also, their eggs don't stick to the leaf; they drop off into litter. This may be adaptive, as winds blow leaves a long way from original plant at high elevations. The host plant is a perennial, so dropping into the leaf litter keeps it close to host plant. Other species, even if they used the plant, would have eggs dispersed from the host plant. That's bad for butterflies, 'cuz caterpillars don't disperse too far... D. Hybridization - When hybridization occurs, it show increase gene flow between populations. How are hybrids stabilized as a reproductively isolated group? - adaptation to extreme habitat - sexual selection - sexual selection Mavarez et al. 2006. Nature 441:868 X BACKCROSS BACKCROSS Backcrossing (and recombination) creates genotypes in which a few different genes from one species are placed in the genetic background of the other = introgression. Selection or drift can work on these variants. Mating probabilities in no-choice experiments: strong Positive Assortative Mating female Male H. mel H. heur H. cyn H. mel 1.00 0.07 0.18 H. heur 0.10 1.00 0.44 H. cyn 0.12 0.02 1.00 Mate Pairing in Tetrads: strong Positive Assortative Mating Implications of Hybridization and Introgression - Hybridization combines whole genomes in the F1. - Backcrossing creates genotypes with varying %’s of genetic contributions from both species – at the gene, gene region, chromosome scales. - Adaptive combinations remain. - Neutral combinations remain. H. Anomalus is a hybrid species. Some regions of the genome show a mixing of genes (introgression) – these are areas of homology with same gene order (red). Other areas, like region T, show 0% introgression, because gene order is different and hybrids getting recombinant types in this region were inviable. 16 of 26 areas where there is no introgression are associated with pollen sterility (QTL). (C) The distribution across markers of the proportion of H. petiolaris alleles seen in experimental hybrids. There were three generations of crossing within the hybrid population, followed by two generations of backcrossing to H. annuus. Therefore, in the absence of selection, one expects 1/8 of the genes to derive from H. petiolaris, with a distribution concentrated in the 1– 25% class. In regions of genome with the same gene order in H. petiolaris and H. annuus (red ), most markers fail to introgress, but some introgress more than expected. In regions of genome that differ in gene order as a result of chromosome rearrangements, there is almost no introgression (blue). (D) Patterns of introgression along the genomes are similar between experimental hybrids and the natural hybrid species, H. anomalus. Three of the 17 H. anomalus chromosomes are shown. The letters to the left (R, S, T, Q) indicate homology of these chromosomes to regions of the parental genomes. (The leftmost chromosome is rearranged, and combines linkage blocks R and S.) Arrows to the right indicate the genetic markers. The shading indicates the likelihood that the regions derived from H. annuus (blue) or H. petiolaris (yellow). (A, Courtesy USDA; B, redrawn from Rogers et al. 1982; C, data from Table 1 in Rieseberg et al. 1995a; D, redrawn from Fig. 3 in Rieseberg and Noyes 1998.) Implications of Hybridization and Introgression - Hybridization combines whole genomes in the F1 - Backcrossing creates genotypes with varying %’s of genetic contributions from both species – at the gene, gene region, chromosome scales - Adaptive combinations remain. - Neutral combinations remain. - Selection eliminates combinations that don’t work. So, genes or regions that remain different after introgression remain ‘species specific’. - Indeed, maybe it is only these gene/regions that give the species a unique genetic identity. These are regions that probably influence reproductive isolating mechanisms, too. Harrison and Larsen 2014 Speciation I. Modes II. Mechanisms A. Progressive Genomic Incompatibility B. Hybrid Incompatibility C. Differential Selection D. Hybridization E. Polyploidy E. Polyploidy Autopolyploidy = within one species Mitotic Error and Selfing: “bud” “all flower cells” “gametes” “zygote” E. Polyploidy Autopolyploidy May be able to reproduce (clonally or parthenogenically) 3n Meiotic Error, Parthenogenesis: normal 2n 1n 3n 2n parents error 2n “gametes” “zygote” “organism” E. Polyploidy Autopolyploidy May be able to reproduce (clonally or parthenogenically) 3n Meiotic Error, Backcross: normal 2n 1n 4n 3n 2n parents error 2n “gametes” “zygote” “organism” E. Polyploidy Autopolyploidy May be able to reproduce (clonally or parthenogenically) 3n Meiotic Error, Mating, Genome Doubling: normal 2n 1n 4n 3n 2n error 2n “doubling” 4n parents “gametes” “zygote” “organism” E. Polyploidy Allopolyploidy = different species Spartina Spartina alternifolia, native to US, was found in southern England in late1800's. There is a European species Spartina maritima. Early in the 20th century a sterile hybrid was found and was called Spartina townsendii This went through a process of diploidization (increased ploidy) and became a new sexually reproducing species known as Spartina anglica S. maritima sterile hybrid S. anglica S. alterniflora Spartina alterniflora from NA colonized Europe X Spartina maritima native to Europe Sterile hybrid – Spartina x townsendii Allopolyploidy – 1890’s Spartina anglica – an allopolyploid and a worldwide invasive outcompeting native species E. Polyploidy Allopolyploidy “Genome Doubling”, with subsequent gene silencing, deletions, and “diploidization” 2n 4n 2n Speciation I. Modes II. Mechanisms III. Rates III. Rates Mark Pagel,* Chris Venditti, Andrew Meade .2006. Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level . Science 314:119. A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.