When and how should the "breeding-back" projects cooperate?

Today in the 2020s, there are several “breeding-back” projects focusing on the European aurochs. I think that there can be no question that it would be most beneficial for “breeding-back” as a whole in order to achieve the goal – that is, a population of cattle that is as aurochs-like and at the same time as genetically diverse as possible to be fit for a reintroduction into Europe’s nature – if the projects would one day cooperate in some sort. The question is: when and how should the projects cooperate? 

First of all, it has to be visualized why cooperating between the different “breeding-back” projects would be beneficial. It would be helpful to maintain a higher level of genetic diversity than if the projects would work separately. Maintaining a certain level of genetic diversity while at the same time creating a homogeneously aurochs-like population is one of the challenges of “breeding-back”. This is less of a challenge when there are several projects that cooperate. When the crossbred cattle used in the breeding projects are bred selectively for a more homogeneous phenotype, some alleles become fixed. In the process of homogenizing the population, the genetic diversity is reduced. However, in each different project, different alleles become fixed. And when the populations of the projects are eventually combined to one large gene pool, the genetic diversity is larger than it would be if there was only one project. As an example, Project 1 has a cattle population with the alleles A, B, C and D on loci responsible for any trait that is not affected by the breeding objectives of “breeding-back” but relevant for genetic health. Project 2 has a cattle population with the alleles E, F, G, and H. Both projects establish a homogeneous aurochs-like phenotypes, and reduced their genetic diversity in the process. In Project 1, only the alleles B and D remained in the populations, being present homozygous now. D is deleterious when homozygous. In Project 2, only the alleles F and H remained in the now very aurochs-like animals, and allele F is deleterious when homozygous. So both projects achieved a very aurochs-like phenotype at the expense of genetic diversity. When both projects combine their gene pools into one large gene pool, we have a population with the alleles B, D, F and H. Now the allelic diversity is larger again and the number of individuals being homozygous for deleterious alleles dropped significantly and since both projects have very aurochs-like animals, the degree of aurochs-likeness was not affected by combining the two lineages. This is of course a simplified example, but combining two or more lineages always results in a greater allelic diversity and if all the individuals of those lineages are very aurochs-like, genetic diversity would not go at the expense of resemblance to the aurochs, which would be the case if a not related non-“breeding-back” breed was crossed in to increase the genetic diversity. 

While combining the different “breeding-back” lineages would be beneficial in the long run, it does not make sense if the different projects are yet at different levels of “breeding-back” progress. For example, if one project has great animals and another project is just starting or has animals of modest resemblance to the aurochs, and they exchange animals, the result being one project benefiting in terms of aurochs-likeness and one project perhaps introducing undesired traits from the breeds of the other projects, while the genetic diversity would not necessarily increase because the process of achieving very aurochs-like animals is not completed yet. Rather it could lead to the contrary, because the project with the less good animals will use the great animal from the other project on a larger scale in order to improve the aurochs-likeness of their animals, thereby narrowing its genetic diversity. Thus, I think exchanging animals between the “breeding-back” projects really only makes sense if all of them are at the same level of aurochs-likeness. 

When one project has an animal with a trait that all the other projects lack, for example if one project has absolutely perfectly aurochs-like horns and all the animals of the other projects have bad horns, it certainly would be beneficial for the aurochs-likeness of the other projects to acquire animals from the project with the perfect horns, but it would also narrow the genetic diversity in all of them. Therefore, it would be smarter before exchanging animals to ask the following questions: Why are the animals of the other project better in this respect? Did they use a breed that contributed the traits that are lacking in the one project, and could this or another breed with that trait be used in the project? For example, if one project used only medium-sized breeds as founding breeds, and another project included a very large breed and thus has larger animals, it would be the best decision for the overall genetic diversity of the “breeding-back” pool to cross-in very large founding animals instead of depleting the diversity by using an individual from the other project. 

Therefore, I think that for now, the different “breeding-back” projects should focus on their own gene pool and how they can improve the aurochs-likeness of their animals within the gene pool. That is not to say that never ever should individuals, cows in particular, be exchanged between the projects. Only the large-scale use of individuals from other projects, f.e. as sires for many years, however aurochs-like it may be, should be avoided so that the overall genetic diversity is not reduced. But once all of the projects achieved the same level of aurochs-likeness, i.e. that all of the animals of all of the projects are large, have the right colour, the right horns, the right sexual dimorphism, the right morphology et cetera, I suggest to exchange animals at a regular basis in order to create genetically diverse and healthy individuals. In zoos and reserves, the animals are exchanged on a regular basis in order not to diminish the genetic diversity of the herds, and “breeding-back” should do so as well once all projects have reached the same level of quality. The result would be one large and genetically diverse population of very aurochs-like cattle that are fit to be established in European wildlife reserves. 

 

 

An animation of an aurochs running

I have not seen an anatomically correct animation of an aurochs yet, so I decided to try one myself. I made a little video of an aurochs bull running. It was done by making animated GIF consisting of 16 drawings of the same individual during running, based on a GIF of an American bison running. I converted the GIF into a video, and here is the result: 

Should we allow paraphyletic genera?

This post is a rather theoretic one, and some might wonder what it has to do with the main topics of my blog. However, the question if we should allow paraphyly in some cases in taxonomy is relevant for the naming of species, some of which are in the focus of this blog. 

For those who are not familiar with the term “paraphyletic”, it describes when a group is not a natural group in the phylogenetic sense, a group that has a common ancestor but does not include all descendants of this common ancestor. Paraphyletic groups are avoided in modern taxonomy because treating them as if they were the same as mono- or holophyletic groups (such that have a common ancestor and include all of its descendants) is comparing apples to bananas. To illustrate that, I take my favourite vertebrate group as an example: dinosaurs (I am actually quite a big fan of Mesozoic paleontology ever since I was a kid). It is nowadays very well-established that birds descend from non-avian dinosaurs, so that they are part of the Dinosauria clade. Why? Because Velociraptor is closer to birds than Tyrannosaurus, and Tyrannosaurus is closer to birds than a Triceratops. If birds weren’t dinosaurs, Velociraptor isn’t a dinosaur either. But in this case, Tyrannosaurus would not be a dinosaur either, because it is closer to birds and Velociraptor than to Triceratops. And so on. Consequently, birds are dinosaurs because they are nested on the dinosaur branch of the phylogentic tree. Dinosaurs themselves are part of what has traditionally been called reptiles. That means that birds should be reptiles, because birds are dinosaurs. That sounds crazy when comparing a lizard with a duck, but that’s evolution. A crocodile is closer to birds than it is to lizards, and a Tyrannosaurus is closer to birds than a crocodile. Thus, the group of reptiles in the classical sense is not a natural group because there is that decision to regard some members of this clade not as members of this group for historical reasons that go back to the time of Linnaeus. This is called paraphyly. Therefore, Reptilia is not the same as Aves (an impression that can be created by the traditional rank system of four tetrapod “classes”), rather there is the Sauropsida clade, that includes a common ancestor and all its descendants, living and extinct. On this clade, there is the Aves clade, which includes all birds. Reptilia, however, is not a clade. It is a collective term for all sauropsids that are not birds, including not very bird-like animals such as lizards, and extremely bird-like animals such as Velociraptor mongoliensis. Since paraphyletic groups make the taxonomical system much more arbitrary than it already is, they are discarded in the modern (phylogenetic) systematics, otherwise one would compare apples and bananas. Systema naturae came 101 years before Darwin’s On the Origin of species and our knowledge of extinct organisms. 

Another problematic reminiscence of the original taxonomy that came before our knowledge of evolution are “ranks” for clades. That is the hierarchical system of species, genus, family, order, class and so forth. Nobody was ever able to define these ranks objectively and universally – how can we know that Hominidae, Tyrannosauridae and Canidae are of the same “rank”? There is no definition. Aves, for example, is considered one of four tetrapod “classes”, descending from reptiles, which were considered a “class” themselves. Now we know that Reptilia is not a natural group and most researchers use the name Sauropsida instead, but Sauropsida and Aves cannot both have the same “rank” as Sauropsida is a much more inclusive group. The same problem exists with any rank. For example, the Raphidae (dodos and its close relative Pezophaps solitaria) was downgraded to a subfamiliy (Raphinae) because it is obviously nested within the Columbidae (pigeons), so both cannot be the same “rank”. Therefore, “ranks” make taxonomy even more arbitrary and only worked back in Linnaeus’ time when we had no knowledge of evolution and extinct animals (as a side note, I wonder if Linnaeus would have questioned his own system if he would have had the possibility to classify living Velociraptor or Brachiosaurus, which are obviously between the “classes” of reptiles and birds in his understanding). “Ranks” for clades are not considered to be of any factual relevance in modern systematics anymore. 

This brings us to genera, which are ranks as well. However, genera cannot simply be ignored as they are perpetuated by the binominal nomenclature in biology. Each name for a species is composed of a genus epitheton and a species epitheton. Some species share the genus epitheton because they are considered members of the same “genus” (for example Panthera leo and Panthera tigris). A genus is based on a type species, and all the other species are assigned to that “genus” when they are considered “similar enough” to the type species to be considered members of the same “genus”. The problem is, however, nobody ever defined how to measure this similarity objectively and universally and how much of that measured similarity is “similar enough”. At least not that I am aware of. But we would need something like that in order to create a consistent concept of a “genus” that is necessary because it is relevant for the naming of species. The perception of what is “similar enough” also shifts with time. Back in the 18^th century, a “genus” was about as inclusive as is a “family” is nowadays – at least in some cases (take elephants: back in the 18^th century, there was Elephas maximus, Elephas africanus and Elephas primigenius, which are nowadays considered three different genera, Elephas, Loxodonta, Mammuthus). If that was not problematic enough, there is the evolutional process going on. Species evolve into new species, the phylogenetic tree continues to grow. And as a consequence, there is inevitably the case that one genus evolves into another. On the cladogram, the resulting “genus” is paraphyletic. For example, the Haast’s eagle Harpagornis moorei is nested within the “genus” Hieraaetus, the two Bison species nest within the “genus” Bos. But saying “that genus is paraphyletic” may be not entirely correct, as a “genus” is not a clade but a “rank” that is often congruent with a given clade. A genus is defined as all species that are “similar enough” to the type species and the type species itself. Nobody defined a “genus” as a clade, so it cannot actually be paraphyletic. So, is Harpagornis moorei “similar enough” to the type species of Hieraaetus, H. pennatus? Are Bison bonasus and Bison bison similar enough to the type species of Bos, B. taurus/primigenius to be considered members of that genus? The answer is entirely subjective, and there is no way to objectively and consistently measure “similar enough”. Perhaps Harpagornis moorei is more distinct from Hieraaetus pennatus than Bison bison is from Bosprimigenius. Including Harpagornis moorei into Hieraaetus means that also a hypothetical descendant of H. mooreiwould have to be included into Hieraaetus because it nests on this clade. That means that till the end of all days all species that would have evolved from Harpagornis or another member of the Hieraaetus clade, however distinct from the Hieraaetus type species they may be, have to be included into the “genus” Hieraaetus to avoid paraphyly. And considering that each genus descends from another genus, right down to the last common ancestor of all organisms classified under the rules of the ICZN, all animals are necessarily members of the same, ancestral “genus”, if a paraphyletic “genus” is to be avoided. That means that all genera are essentially synonymous. This makes the concept of a genus meaningless, if we are consistent with the approach that a “genus” should never be paraphyletic. But a “genus” is a rank and not a clade, and ranks are based on arbitrary subjective decisions based on similarity to a defined type species, and not on clades. They are often congruent with clades, yes. And regardless of how we name the species, Bison bison is a member of the Bos clade, and Harpagornis moorei is a member of the Hieraaetus clade (by the way, the same problem also goes for species. There is no definition of a species that works universally, but if we look at the individual level, all species in the history of evolution are paraphyletic on a cladogram, because some individuals assigned to the ancestral species will necessarily closer to the new species than to the earliest member of the ancestral species. Looking at the time scale, the concept of a species is artificial and arbitrary, and species are definitely not clades). Another way to avoid genus paraphyly instead of lumping is splitting. For example, Loxodontaafricana and Loxodonta cyclotis are “similar enough” to be considered a member of the same “genus”. But it turned out in recent genetic research that L. cyclotis is actually closer to Palaeoloxodon than to L. africana. How to avoid the paraphyly? If L. cyclotis is not “similar enough” to Palaeoloxodon, it might be assigned to its own “genus” because it is closer to Palaeoloxodon, but not similar enough to be a Palaeoloxodon species. That might work when looking only at Loxodonta and Palaeoloxodon. But all genera evolved from another genus. There will always be species that are closer to the descending genus than to the type species of a given genus. As a consequence, each species would end up with its own genus, making the concept of a genus moot. So, both approaches to avoid genus paraphyly, both lumping and splitting, would, when applied consistently to all organisms, make the genus as a rank useless – the problem is more fundamental, because a rank is treated as a clade here. 

So, considering that the concept of a “genus” as a rank is arbitrary and subjective, and the concept of a “genus” as a clade makes the term absurd because all living organisms would either be members of the same ancestral genus or each species would be its own genus so that no genus is paraphyletic, what should we do? At the moment, the way it is, it is inconsistent. See the example with Harpagornis. The concept of a genus, however, is tied to the binominal nomenclature. If we change the binominal nomenclature, we will have to change the names of millions of organisms. And naming a species with two words is more definite than just one word. But we could do something intermediate: erecting a new first epitheton for each species that is not a type species of an already existing “genus”. That would also be a lot of work, but it would be more consistent and compatible with the evolution of species and the cladistic system. In some cases it would work easily, when the species epitheton is a latin name on its own. Take Panthera as an example. I was unable to find out what the type species of Panthera is, but it would work in all five species: Parduspardus, Leo leo, Tigris tigris, Onca onca, Uncia uncia. Taking the Bos clade, it would work as well, because a number of synonynomous genera or subgenera have been erected or some species epitheta are just a latinized version of the name of the species: Bos primigenius, Gaurus gaurus (gaur), Bibos javanicus (banteng), Novibos sauveli (kouprey), Poephagus mutus (yak), Bonasus bonasus (wisent, bonasus is just another name for bison, by the way) and Bison bison(American bison). For a lot of species, new first epitheta would have to be erected, especially for fossil taxa. That would be a lot of paperwork, but let us be honest, each scientist dreams of naming a new taxon, so that “Name, Year” will be mentioned next to the name forever. So, I think that many would not mind and take that opportunity to immortalize their own name by naming a new taxonomical name. And since it is not the description of a new genus that includes several species and has to be differentiated from other genera, no profound diagnosis is necessary because the species it refers to already has been diagnosed. 

I know that this is a radical approach, and it would take decades until it is established and the rules of the ICZN would have to be changed. But it would be consistent, less arbitrary, and compatible with evolution. As already mentioned, Linneaus came 101 years before Darwin, and taxonomy has already reacted by discarding paraphyletic groups. Maybe the next little revolution that is necessary to transfer taxonomy into the 21^st century is to abandon the concept of a genus. The alternative is, if taxonomy is supposed to be consistent, to allow “paraphyletic” genera (which are not really paraphyletic since they are not clades).