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39

First, a note on spelling. Both "ortholog" and "orthologue" are correct, one is the American and the other the British spelling. The same is true for homolog and paralog. On to the biology. Homology is the blanket term, both ortho- and paralogs are homologs. So, when in doubt use "homologs". However: Orthologs are homologous genes that are the result of a ...


36

Short answer It is a flying lemur (there exist only 2 species). Flying lemurs and primates are together a sister clade to treeshrews. Easy source of information Have a look at the post The best free and most up to date phylogenetic tree on the internet?. In short, you can have a look at onezoom.org, tolweb.org or opentreeoflife.org by yourself! Tree of ...


30

1. Sheep are fearless 2. English common names are misleading when it comes to the genetic differences between goats and sheep You posted a picture of Mountain Goats (Oreamnos americanus), which are a different genus than Domestic Goats (Capra aegagrus). Both Capra and Oreamnos are members of the Subfamily Caprinae, as are Domestic Sheep (Ovis aries). ...


23

The most closely related animals to primates are colugos (order Dermoptera). The next most closely related after colugos are tree shrews (order Scandentia). The next most closely related after tree shrews are rodents (order Rodentia) and lagomorphs (order Lagomorpha) (rabbits, hares, and pikas). Sources: Wikipedia's section on the evolutionary history of ...


18

This is from Darwin's Notebook B: Transmutation of species from 1837–1838. From what I understand, the tree is a hypothetical depiction of descent used to discuss differences and relatedness between forms/species. This is the text that accompanies and follows the sketch (notebook pages 36-44): I think (sketch) Case must be that one generation ...


14

Basically just search "thing you want" and "phylogeny" and you'll find a million results on Google. For you, I might recommend the Botanist in the Kitchen blog, which has a whole page on the subject and has assembled this phylogeny, including many, many others. It's pretty impressive!


14

Horizontal gene transfer Don't expect to have a tree! Horizontal gene transfer happens and therefore we would end up with a network, not a tree. Gene trees Different DNA sequences have different evolutionary histories. See, in particular, the question of incomplete lineage sorting. This means that one may compute a tree for a given DNA sequence that must ...


13

You are correct that the reason is similar to that of convergent evolution of the eye. Both snakes and legless lizards are lizards (Squamata) that have lost their legs. However they have done so entirely separately much as octopus and human eyes have evolved entirely separately. An easier analogy is between whales and sea cows. Both are legless mammals but ...


13

Cats and monkeys have a common ancestor, both are placental mammals, so at the very least they must have both evolved from the first placental mammal. Cats are members of the Laurasiatheria group and primates are members of Euarchontoglires. These groups of mammals probably split off from each other about 100 millionish years ago. For more information about ...


12

You should also bear in mind that the fact that they are great climbers does not make them fearless. For example, if I were to find myself floating 500 meters above the ground, I would be terrified. The fact that birds do not appear to be scared in the same situation does not make them fearless, it just makes them fliers. Similarly, I am sure a fish would ...


12

Peach, apricot, plum, pear, apple, cherry trees are plants of the same family, Rosaceae, so they are closely related. They share many more aspects than the five petals. In fact, other plants in this family, and even many other dicots have five petal, simply because their share a common ancestry.


12

Long story short, use sequence information if you can. The long story long: Sequence information and the trees generated from them are strictly more reliable than morphological characters. For instance: sharks are pretty much the same shape they were millions of years ago, but they've been accumulating genetic differences 'invisibly' that allows us to group ...


12

"Evolving from another species" versus "Most Recent Common Ancestor (MRCA)" One cannot say about two extant species that one evolved from the other. It just doesn't make any sense. It is not only true for cats and chimpanzees (just to pick one species of monkey) but it is true for any pair of extant species. One extant species has never evolved from another ...


11

The simplest way of course is to add it to the supplementary materials. However, 220 species are not that many, you should be able to fit that into a page. You have not shown us your tree so it is kind of hard to give specific advice but I am guessing that you have a linear rather than circular tree. If you convert it to a circular tree you should be able to ...


11

There exists a bunch of population genetics forward and backward (coalescence) simulation platforms. Here is a non-exhaustive list. They all differ and you'll have to go through their manual to see what is more adapted to your needs. List of softwares Here is a long list of such platforms. The list might arguably be a little bit outdated today though and ...


9

The hybridization situation you describe could be found in ring species, and is partially related to this concept. For instance, the three species A, B and C could have partially overlapping distributions, such as: In such a situation (assuming that the relative distributions have been stable over evolutionary time), A and C might be able to produce ...


9

Available ressources I would recommend oneZoom.org is probably the best ressource. oneZoom.org is based on openTreeOfLife.org (for phylogenetic relationships) and eol.org (Encyclopedia Of Life) (mainly for the pictures I think). If you do not fancy to much the display and links of oneZoom/org, then I would just recommend openTreeOfLife.org. There is also ...


8

Both orthologs and paralogs are types of homologs, that is, they denote genes that derive from the same ancestral sequence. Orthologs are corresponding genes in different lineages and are a result of speciation, whereas paralogs result from a gene duplication. This often has important implications: while orthologs often fulfill the same role, paralogs tend ...


8

Dendroscope Using Dendroscope, I opened the provided example file trees.new. This opens a new window with 16 trees in it. Shift click on the first two trees (Tree1 and Tree2). Choose Algorithms $\rightarrow$ Tanglegram... This will compute the tanglegram and open a new window. At this point, I get: There is nothing special in the trees.new file, just 16 ...


8

A taxon (Plur. taxa) is any (monophyletic or not) group of species. For example the group of yellow flowers is a taxon. The group of primates is a taxon. The taxon of aquatic animals is a taxon. A clade is a monophyletic taxon or monophyletic group if you prefer. A monophyletic taxon (or a clade) is defined as a taxon that contains only all descendants of a ...


8

Let's start with a short comment. You say [..]evolution is nowadays pretty much analyzed through phylogenetic trees[..]. Many evolutionary biologist make extensive use of phylogenetic methods but a good part of evolutionary biologist (most of them I would say) do not work directly with phylogenetic methods. I am not sure I understand your question but I ...


8

The idea of parsimony is that when constructing phylogenetic trees a simple hypothesis (e.g., four evolutionary changes are necessary to connect two taxa) is more likely to be true than a more complex hypothesis (e.g., 15 evolutionary changes) (source: Berkeley University). The reason is that for a certain taxon to evolve, there must be a certain number of ...


7

In general, many sequence alignment programs can use multiple substitution models, distinguishing between nucleotides, amino acids, and codons. A protein sequence has functional information that is not directly visible in the nucleotide sequence. The papers you link deal with horizontal gene transfer, where a gene is passed to more distant organism. ...


7

In general for plants, before you start trying to make your own phylogeny, you should try to find an existing phylogeny. Phylogenetics is complex, and a lot of people have already done the hard work. You can start by looking at the Angiosperm Phylogeny to figure out which species are most closely related. To make use of the tree you will usually have to look ...


7

This is a very fundamental, and in my opinion, interesting question. You might not find many sources that directly cover this question because it is hard to test. If speciation did happen in two separate locations and the resulting species were so similar that they could breed with one another and not the original species, how would we be able to tell if the ...


7

In addition to @Gerardo's answer: Reptiles The term Reptiles as used in popular language does not represent a monophyletic group. When using the term Reptiles, one is typically thinking of turtles, snakes and lizards but excluding birds and mammals (and a few other things not worth mentioning). There are two clades (monophyletic groups) whose name sounds ...


6

There are many definitions of species - look at the wikipedia page for an overview (this is a large and tricky subject). Some hybridization is not uncommon between "proper" species (often in narrow contact zones), also with fully or partially fertile hybrids. Definitions of species in these cases often comes down to genetic similarity/dissimilarity of ...


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