3. Variations on the Phylogenetic Scheme

Trouble-shooting:

Trouble-shooting: The absence of a synapomorphy for an internotde (within the ingroup) is a red flag: if all evolutionary novelties (apomorphies) are accounted for and there is an internode that lacks an synapomorphy, then the tree is probably wrong. 

-All branching in your preferred tree should be dichotomous. If there is a polytomy (three descendants attached to a node) in tree you have constructed this, is a red flag and you have made an error; if you cannot figure out where you went wrong, then start again. 

Variations on the Phylogenetic Scheme  sunflowers

-Some species have evolved from hybrid crosses between two different ancestors, a pattern especially common in plants. In these cases of hybrid speciation (reticulation) various phenotypic features and DNA markers throughout the genome reveal the two ancestors. 

- Studies of chloroplast DNA and nuclear ribosomal DNA reveals the sunflowers Helianthus anomalus, H. deserticola, and H. paradoxus are hybrids of H. annuus and H. petiolaris. 

HGT

-Unusual phenomena may be the result of horizontal gene transfer (HGT). Pea aphids are able to synthesize carotenoid pigments. Carotenoids are plant and fungal pigments and not normally synthesized by animals. Genetic analysis indicates that these aphids acquired the carotenoid-coding gene from a fungus.  

-Accordingly, the ability to synthesize carotenoid pigments is a synapomorphy of the clade of Acyrthosiphon (+ Myzus) within aphids and the gene to synthesize carotenoid pigments arose through HGT. 

HGT is common enough in prokaryotes that the phylogeny of bacteria is almost more net-like than tree-like. Major pathogens such as MRSA have been called superbugs because they have developed resistance to antibiotics, achieved partly because of HGT (via conjugation, transformation, transduction).  

Phylogenetic systematics can also be used to _____

Phylogenetic systematics can also be used to investigate the evolutionary history of single genes or gene families, yielding gene trees or a gene genealogy. A gene tree can differ from the species tree, so this is why many genes need to be sampled when using molecular data.  

Gene duplication

-Understanding the phenomenon of gene duplication can be important at broader levels of investigation. Genomes are enlarged by gene duplication, e.g. hox gene families, of which polyploidy is the wholesale duplication of the entire genome.  

-Gene families involve the concepts of orthology (vertical relationships of genes) and paralogy (horizontal relationships of genes). The history of globin genes in vertebrates is a classic example. Hemoglobin and myoglobin are oxygen-storing proteins in vertebrates: hemoglobin in red blood cells and myoglobin in muscle cells. 

Orthologic gene

Orthologic genes have an ancestor to dependent relationship, it is derived from a primitive sequence (vertical relationship). Paralagous genes are genes found in closely related species (horizontal relationship).

Hemoglobin and myoglobin

The genes for hemoglobin and myoglobin are reconstructed to have originated in the common ancestor of lampreys and jawed vertebrates. the hemoglobin gene is then inferred to have undergone duplication in the ancestor of jawed vertebrates, yielding alpha and beta hemoglobin genes. These underwent there own duplication events in mammals, placental mammals, and humans.  

Some of the duplicates, indicated by Ψ (Greek letter psi), are pseudogenes (non-functional genes). 

Evolution and characters 

-Practioners of Linnean classification used any and all types of characters, or the absence of characters, to group taxa together. Some characters were thought to be more important that others.  

-For example, the defining characteristic of birds is the presence of feathers, so any vertebrate with a feather would be a member of Class Aves. Class Reptilia was defined as scaled tetrapods that had neither hair nor feathers. 

Theropod dinosaurs

-In the 1980s it was suspected that some theropod dinosaurs had feathers, and in the mid-1980s phylogenetic analyses were published with birds nested within clades of theropod dinosaurs.  

-At the same time, other researchers were publishing cladograms showing that some fossil groups assigned to Class Reptilia (Subclass Synapsida) were forming clades with mammals to the exclusion of clades formed by turtles, lixards, snakes, and crocodiles and their close fossil relatives. The consensus now is Mammalia is nested within clade Synapsida. 

From the view of phylogenetic systematists

-From the view of phylogenetic systematists, practitioners of Linnean classification were using homologous and analogous characters to recognize taxa, leading to the creation of artificial taxa (taxa that do not exist in nature).  

-Phylogenetic systematists use only synapomorphies (shared derived characters) and eschew analogous/convergent characters in creating taxa. By using only synapomorphies, phylogenetic systematists endeavor to reconstruct taxa that were created by evolutionary processes and therefore inferred to be natural; these groups are described as monophyletic. 

Mosaic Evolution

 

When it comes to morphology, evolution is not necessarily shaping all parts of organisms at the same rate. This has been observed in many different groups and has been term mosaic evolution. 

 For example, modern species of the genus Equus are monodactyl, cursorial (good runners), and exhibit molars with tall crowns (associated with grazing), but their ancestors were polydactyl, capable of running but not cursorial, and had low-crowned molars (associated with browsing (eating leaves)). These changes did not occur simultaneously over the course of equid evolution. 

Human ex. Derived features include large cranial size and single jaw bone. Ancestral features include 5 fingers on the hand. 

Frog Ex. Ancestral features include short ribs, small cranium and multiple bones in the lower jaw (not visible). Derived features include loss of teeth in lower jaw and reduction of 5 to 4 fingers. 

Processed pseudogenes

With regards to molecular characters, some genes mutate at a consistent rate. This has been useful in two aspects. 

 Some genes, called processed pseudogenes, are junk genes that result when embedded RNA genes in the genome are expressed and their proteins translate random RNA strands into DNA and randomly insert these into the genome. Such pseudogenes can be recognized as synapomorphies, but also because mutation at any given site occurs at a steady rate (i.e. no selection on junk genes), older psudogenes exhibit more mutations than more recent pseudogenes. 

Some because of attacks by RNA viruses? If it gets into the sex cells and the cells don’t die in the process.   Older pseudogenes should have more mutations because they were around longer.      Pseudogenes are possibly neutral so aren't expressed physically and this not naturally selected upon so they just hang around? 

 

Shared pseudogenes from humans gorillas…..

-The processed pseudogene α-enolase Ψ1 is shared by humans, gorillas and chimpanzees, and CALM II Ψ2 is shared by humans, gorillas, chimpanzees, and orangutans. CALM II Ψ2, as expected (being older), has more mutations than α-enolase Ψ1.  

-Other genes also mutate at a steady rate and this has been used to construct molecular clocks to estimate the time that major groups evolved or when particular speciation events occurred. For example, the speciation event that produced Homo (humans) and Pan (chimpanzees and bonobos) is estimated to have occurred 5-7 million years ago 

How phylogenies are useful 

-Work by early naturalists such as Linnaeus created formal names for the organisms that they studied and organized these names into classifications: prosaic lists of ranked taxa (Kingdom Animalia, Phylum Chordata, Class Mammalia, etc.).  

-The Linnean system of classification was widely used until a few decades ago until some phylogeneticists started abandoning ranks (finding that, e.g. that groups ranked at the family level in a given order were not equivalent, i.e. not sister groups) 

-Most of the taxonomic terminology and concepts used in Linnean classification were retained by phylogenetic systematists. For example, the terms and concepts of monophyly, paraphyly and polyphyly were better envisioned using phylogenetic trees.

-Monophyly refers to a single origin for a group, i.e. a monophyletic taxon or monophyletic group is comprised of all the descendants of a common ancestor together with that ancestor, and so is a group that exists in nature as a product of evolutionary (natural) processes. 

Parphyly

-The phylogenetic systematist term for a monophyletic taxon is clade. Paraphyly and polyphyly refer to groups that are not natural because at least one descendant or an ancestor is missing from a group. 

- A paraphyletic group excludes at least one descendant from the common ancestor of the included taxa. An example: Class Reptilia was a paraphyletic group because it excluded birds (Class Aves) and mammals   The animals in those orders turned out to be more closely related to mammals than any other reptiles4 

Polyphyletic group

-A polyphyletic group excludes the common ancestor of the included taxa (and excludes some descendants of that ancestor as a result).  

-Order Falconiformes formerly included falcons, hawks, and eagles, but phylogenetic work indicates that falcons are more closely related to parrots and songbirds, so hawks and eagles form a group on their own, Accipitriformes. Another, older example, is Hematothermia, proposed for a group consisting solely of mammals and birds, united because species of both groups are endothermic (homeothermic)