bs148h 18 September 2007 Read: Text pgs , ch 25 & 26

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1 bs148h 18 September 2007 Read: Text pgs , ch 25 & 26 geology & fossils Linnean systematics vs phylogenetic cladistics five kingdoms three domains tree of life homologous vs analogous (convergent) parts orthologous vs paralogous DNA sequences retrotransposons: strange paralogs out groups & synapomorphies (shared derived characters) mono- para- & polyphyletic groups (goodbye reptiles, watch out dogs!) some aspects of human phylogeny The old Five Kingdoms Linnean systematics is an hierarchical classification scheme. (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species) It preceded evolutionary theory and is based on phenetics - observed phenotypic similarities {ex: morphospecies }. Darwin wrote in The Origin of Species that "our classifications will come to be, as far as they can be so made, genealogies." We are still in the midst of the an effort to reconcile the existing taxonomy w/ modern phylogenetic cladistics: an attempt to develop classification (taxonomy) consistent with evolutionary history - decent w/ modification The new Three Domains... keep in mind that phylogenetic trees are hypotheses that fit the best available data.

2 "The affinities of all the beings of the same class have sometimes been represented by a great tree... Charles Darwin, 1859 Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence In addition to fossil organisms, phylogenetic history can be inferred from certain morphological and molecular similarities among living organisms.... similarities due to shared ancestry are called homologies.... the similarity in the number & arrangement of bones in the forelimbs of mammals is due to their descent from a common ancestor with the same bone structure;... genes or other DNA sequences are homologous if the nature of their similarity suggests that they are descended from the sequences carried by a common ancestor. Figure 25.6 Aligning segments of DNA. Systematists use computer software to find and realign similar sequences along DNA segments from two species. A potential red herring in constructing a phylogeny is similarity due to convergent evolution - called analogy - rather than to shared ancestry (homology). Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages. Convergent evolution in mechanical design of lamnid sharks and tunas. Donley, JM Nature 429,61-65 Consider wings vs forelimbs of bats & birds. Bird and bat wings are analogous - they have separate evolutionary origins, but are superficially similar because they evolved to serve the same function.... though bird and bat wings are analogous as wings, as forelimbs they are homologous. Birds & bats did not inherit wings from a common ancestor, but they did inherit forelimbs from a common ancestor with forelimbs. Homologous sequences are orthologous if they were separated by a speciation event. 99% of the genes of humans & mice orthologous, 50% of our genes are orthologous with those of yeast. Homologous sequences are paralogous if they were separated by a gene duplication event so they are found in more than one copy in the same genome. The genes encoding myoglobin & hemoglobin are ancient paralogs. {many human hormones are paralogs} Humans have huge families of more than 1,000 paralogous olfactory receptor genes. {many are degenerate pseudogenes } Homologous sequences. Orthologs and Paralogs are two types of homologous sequences. Orthology describes genes in different species that derive from a common ancestor. Orthologous genes may or may not have the same function. Paralogy describes homologous genes within a single species that diverged by gene duplication.

3 Orthologous & paralogous retroelements Retroelements and the human genome... N Bannert & R Kurth 2004 PNAS 101: Retroelements constitute a large portion of our genomes {~45%!!!}. One class of these elements, the human endogenous retroviruses (HERVs( HERVs), is comprised of remnants of ancient exogenous retroviruses that have gained access to the germ line.... HERV-derived transcripts and proteins have been detected in healthy and diseased human tissues, and HERV-K, the youngest, most conserved family, is able to form virus-like particles. Although it is generally accepted that the integration of retroelements can cause significant harm by disrupting or disregulating essential genes, the role of HERV expression in... diseases remains controversial.... HERV proteins might even serve the needs of the host and are therefore under positive selection. HERV-K: an orthologous gene in chimpanzees, bonobos & gorillas A HERV-K K provirus in chimpanzees, bonobos and gorillas, but not humans Barbulescu et al Current Biology 11: Evidence from DNA sequencing studies strongly indicated that humans and chimpanzees are more closely related to each other than either is to gorillas. However, precise details of the lineage leading to humans from those leading to the African great apes have remained uncertain. The unique insertion sites of endogenous retroviruses, like those of other transposable genetic elements, should be useful for resolving phylogenetic relationships among closely related species. We identified a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome. Humans contain an intact preintegration site at this locus. These observations provide very strong evidence that,... chimpanzees, bonobos, and gorillas are more closely related to each other than they are to humans.... demonstrate the utility of using HERV-K to trace human evolution. Retrotransposons are a weird form of Paralogous genes. L1 RETROTRANSPOSONS Shape the Mammalian Genome Haig H. Kazazian Jr Science 289, Genomic mobile elements called retrotransposons make up about 40% of the mammalian genome.... these small pieces of DNA are duplicated by a "copy and paste" mechanism they are transcribed into RNA, reverse-transcribed into DNA, and the complementary DNA is then inserted back into the genome at a new site. {by reverse transcriptase coded by L1,} Although retrotransposons have been viewed as selfish DNAs that provide no benefit to their host cell, we now know that over evolutionary time they have increased the diversity of the genome through a variety of mechanisms Estimating the retrotransposition rate of human Alu elements Cordaux et al. GENE 373: MAY About 30% of the human genome is comprised of Alu and (L1) retrotransposons..., and their insertions have caused a number of human genetic disorders... Here, we... estimate the retrotransposition rate (RR) of Alu elements in humans.... yielded RR on the order of one new Alu insertion every ~20 births... After systematists have separated homologous from analogous similarities, they must sort through the homologies to distinguish between shared primitive and shared derived characters. acters. For example, all mammals share the homologous character of a backbone. However, the presence of a backbone does not distinguish mammals from other vertebrates because nonmammalian vertebrates such as fishes and reptiles also have backbones. The backbone is a homologous structure that predates the branching of the mammalian clade from the other vertebrates; it is a shared primitive character, shared beyond the taxon we are trying to define. In contrast, hair, a character shared by all mammals but not found in nonmammalian vertebrates, is a shared derived character, {synapomorphy!!!} an evolutionary novelty unique to a particular clade in this case, the mammalian clade. Systematists use outgroup comparison to differentiate between shared derived characters and shared primitive characters.

4 Patterns of shared characteristics can be depicted in a diagram called a cladogram. If the shared characteristics are due to common ancestry (homologous), then the cladogram forms the basis of a phylogenetic tree. Within the tree, a clade (from the Greek klados, branch) is defined as a group of species that includes an ancestral species and all its s descendants. The cat family represents a clade within a larger clade that also includes the dog family. But not all groupings of organisms qualify as clades. A valid clade is monophyletic (meaning single tribe ), signifying that it consists of the ancestor species and all its descendants. A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants. A polyphyletic grouping is several species that lack a common ancestor. a CLADE is a : most recent common ancestor and all its descendants : not all descendants of most recent common ancestor in recent years many taxonomists have begun to insist that taxa should be monophyletic, The reptiles would be paraphyletic, since they exclude birds. The group Reptiles does not form a clade, so this is not a valid phylogenetic name : does not include of most recent common ancestor & all descendants However, if birds are included, Reptilia is a valid phylogenetic name. Multiple and Ancient Origins of the Domestic Dog Vilà et al. Science 276, , 13 June Several methods of phylogenetic analysis... supported a grouping of dog haplotypes into four distinct clades. Are domestic dogs monophyletic? As available data about DNA sequences increase the difficulty of building the phylogenetic tree that best describes evolutionary history also grows. What if you are analyzing data for 50 species? There are different ways to arrange 50 species into a tree! Systematists can never be sure of finding the true phylogeny, but they can narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood. {mathematical methods to search for the simplest plausible phylogeny}

5 Biogeography and evolution of the genus Homo Finlayson C Trends Ecol & Evol. 20 (8): AUG 2005 Multiregional evolution (d) proposes that present-day populations worldwide are the descendants of in situ evolution after an initial dispersal of Homo erectus from Africa during the Lower Pleistocene. {~650 kybp} {then gene flow homogenizes H. erectus & H. neanderthalensis H. sapiens} Modern human origins: progress and prospects. Stringer, C. Phil. Trans. R. Soc. Lond. B 357, (2002) Article The alternative, Out-of of-africa 2 {the 2 nd wave replacement hyp (a)}, proposes that all present-day populations are descended from a recent common ancestor that lived in East Africa ~ years ago, the population of which replaced all regional populations. {H. sapiens comes out of Africa & exterminates H. neanderthalensis} The weight of the evidence is now in favour of Out-of of-africa 2, Neanderthals and the modern human colonization of Europe. Mellars P. Nature Nov 25;432(7016): Related Articles, The fate of the Neanderthal populations of Europe and western Asia has gripped the popular and scientific imaginations for the past century. Following at least 200,000 years of successful adaptation to the glacial climates of northwestern Eurasia, they disappeared abruptly between 30,000 and 40,000 years ago, to be replaced by populations all but identical to modern humans. The most significant contributions to these issues over the past decade have come from detailed studies of the DNA structure of present-day human populations in different areas of the world, combined with the gradually accumulating recovery of residual traces of 'ancient' DNA extracted from a number of Neanderthal and early anatomically modern human remains. Molecular analysis of Neanderthal DNA from the northern Caucasus Ovchinnikov et al Nature 404, The expansion of premodern humans into Europe 40,000 ybp led to the eventual replacement of the Neanderthals by modern humans 28,000 ybp. Here we report the second mitochondrial DNA (mtdna) analysis of a Neanderthal, and the first such analysis on clearly dated Neanderthal remains. The specimen is from one of the eastern-most Neanderthal populations, recovered from Mezmaiskaya Cave in the northern Caucasus. Radiocarbon dating estimated the specimen to be 29,000 years old and therefore from one of the latest living Neanderthals. continued... Molecular analysis of Neanderthal DNA from the northern Caucasus Ovchinnikov et al Nature 404, Affidavit by Michael D. Brown, Ph.D. (Emory University) SUBSCRIBED AND SWORN to before me this day of September, Figure 2 Variable sites in the DNA sequences of the PCR fragments from the Neanderthal from Mezmaiskaya Cave, the human reference sequence11 and the sequence of the Neanderthal from Feldhofer Cave4. A. indicates that the sequence is the same as the reference. The two Neanderthals share 19 substitutions relative to the ref. seq. Figure 3 Phylogenetic relationship of the two Neanderthals and modern humans. b, A maximum parsimony branch and bound search with the two Neanderthal sequences; three chimpanzee sequences were used as an outgroup. The numbers in both diagrams refer to the bootstrap frequencies (%) obtained from 1,000 replicates. Phylogenetic analysis places the two Neanderthals together in a clade that is distinct from modern humans, suggesting that their mtdna types have not contributed to the modern human mtdna pool. Comparison with modern populations provides no evidence for the multiregional hypothesis of modern human evolution lution. A view of Neanderthal genetic diversity. Krings et al Nature Genet. 26, Article No evidence of Neandertal mtdna contribution to early modern humans. Serre, D. et al PLoS Biol. 2, Article mtdna is a useful genetic system for studies into human origins and migrations. m The mtdna has a high sequence evolution (or mutation) rate which ensures differentiation between populations, which in turn facilitates genetic identification. Also, the mtdna does not undergo recombination like its nuclear counterpart. {mitochondria derived from haploid prokaryotic endosymbiont Fig 25.12} The mtdna is strictly maternally transmitted in humans. Thus, mtdnas have evolved by the sequential accumulation of mutations along radiating maternal lineages. As women migrated out of Africa into different continents about 130,000 years ago, they accumulated mtdna mutations which today are seen as high-frequency, continent specific mtdna sequence polymorphisms (~mutations). These polymorphisms are associated or linked with other polymorphisms to form specific mtdna haplotypes (a collection of all mutations/polymorphisms held by an individual's mtdna), and groups of related haplotypes are termed "haplogroup". Haplogroups are defined by one or more unique mtdna mutations which... sets the haplogroup apart from other mtdna haplogroups.

6 Mitochondrial Eve is the name given by researchers to the woman who is the most recent common matrilineal ancestor of all living humans. Eve was a member of a population living around 150,000 years ago in Africa. We know about Eve because of mitochondria organelles that are only passed from mother to offspring. Each mitochondrion contains Mitochondrial DNA, and the comparison of DNA sequences from Mt DNA reveals a phylogeny. Based on the molecular clock technique of correlating elapsed time with observed genetic drift, Eve is believed to have lived about 150,000 years ago. The Seven Daughters of Eve is a book by Bryan Sykes that presents the theory of mitochondrial genetics in a clear and non-specialistic manner. Sykes traces back human migrations, discusses the out of Africa theory. The title of the book comes from one of the principal achievements of mitochondrial genetics, which is the classification of all modern humans into one of several mitochondrial lineages. Sykes claims there are seven mitochondrial lineages for modern Europeans (though others put the number at 11 or 12) and he therefore speaks of the "Seven {European} Daughters of Eve". {alt migratory routes possible} A common misconception is that Mitochondrial Eve was the only living female of her time she was not. Many women alive at the same time as Mitochondrial Eve have descendants alive today. However, only Mitochondrial Eve produced an unbroken line of daughters that persists today each of the other matrilineal lineages was broken when a woman had only sons, or no children at all. Many researchers take the mitochondrial evidence as support for the "single-origin or Out-of-Africa model. {of human phylogeny} Note: if you have mixed-racial ancestry, your diploid nuclear chromosomes are a mixture but your haploid mitochondrial DNA is from your maternal lineage & if you have a y chromosome, it s from your paternal lineage mtdnatable.html