Species Concept

[Garrett Schantz]

Suppose I will mention the species concept just in case anyone wants to discuss it here - fits in with some landraces-grexes. A few definitions here: https://www.merriam-webster.com/dictionary/species or "Species, in biology, classification comprising related organisms that share common characteristics and are capable of interbreeding. This biological species concept is widely used in biology and related fields of study."

 What happens if you find a few groups of Solanum chilense that can freely interbreed with Solanum peruvianum. But other groups of Solanum chilense can't cross with Solanum peruvianum, but they can cross with the interfertile groups of Solanum chilense.

 Some people use the "Reproductive isolation" classification as well, which doesn't work very well for the diverging "tomato clade" due to a large number of exceptions.

 A good bit of Agastache species overlap and occasionally interbreed. The same goes for some Physalis, Sanguisorba, Rudbeckia, Echinacea and Asclepias species. Occasionally citruses can cross in nature as well. Escaped crabapples or other Malus species can also cross freely. White oak species can overlap and cross pretty easily as well - happens frequently.

 Also factoring in escaped related species such as Oriental bittersweet(Celastrus orbiculatus) which can then cross with things like American bittersweet(Celastrus scandens) - the offspring between these are considered hybrids. But left to their own devices, they would technically meet the criteria for a new species after stabilizing out, being isolated from regular orbiculatus/scandens species, filling in different areas than either parent, and both parent species still existing in different isolated areas.

 I'm assuming Agastache rugosa from Asia has intermixed with certain groups of Agastache in North America as well.

 Also assuming that Vitis(Grape) species probably cross with American / Japanese / European species every so often, offspring probably dominates because of introduced diseases, pests that certain species are resistant to. Which could lead to separation of the parent species and the hybrid offspring after a period of time.

 Physalis longifolia x Physalis virginiana hybrids have been noted to be more vigorous than either parent, quickly replacing both parent species in an area. Which means that the hybrids should become a new species eventually, rather than having the hybrid designation. 

 A good bit of Fragaria chiloensis x Fragaria virginiana should have probably had some offspring split into a separate species by now - especially ones that escaped. Certain Fragaria species do overlap as well.

 Columbine species can cross / overlap frequently as well, but we still designate them as separate species.

 Not really going to touch on mammals due to this being a plant breeding forum, but Bison and Bos(Cow) species can breed fairly easily, same goes for Sus(Pig/Boar/Hog) species.

 In my opinion, most (not all) species are just "variable populations" from other members in a genus. I believe there should be a different terminology or classification for species that can cross but are noticeably different. The definition of "species" doesn't work in many cases - or it only half-works. Sub-species aren't accepted in many cases either for whatever reason.

A lot of older Latin species classifications are becoming incorrect as well, now that we can compare genetics between different species.

 I could try making a list of genus's with species that freely cross, could help with people wanting to make landraces/grexes of things that they didn't know could be done with little effort.

 Hoping that this starts some new thoughts / ideas / projects, some people seem to only focus on one species in a genus, without realizing that it can interbreed easily. Would be nice if certain species mentioned here attract more people to the forum as well. Would also be helpful if people here listed things such species here as well, maybe we could start breeding projects that we wouldn't have thought of on our own. I have saw others here mention that "species are a human concept" which is correct.

[William Schlegel]

Using what they freely cross with is a good way to think of a species. There are geographic, and biological reasons why species or populations do not cross.

Geographic barriers are very important to giving populations time to diverge. Some plants and species divided by geography when brought back together cross freely.

Biological reasons include things like timing, pollinators, flower shape, inability of pollen to germinate on the wrong species, or the miss match of embryo and endosperm causing incompatibility and abortion.

Plants are real rule breakers with all of this especially over deep time.

I suspect also that low level gene flow is advantageous between species.

One cool thing about white oaks is that small acorn species are dispersed short distances and large acorn species long distance. Some small acorn species have gothen around this by making long distance hybrids with the large acorn species and thus leapfrogging into new distant habitats. For one example.

Hybrid swarms that we create when we create hybrids between species of squash and tomatoes probably will most likely drift back into one species or the other. Creating a new species is less likely of an outcome. Genetically though this is more likely in one instance when the hybrid has a different ploidy than the parents. The tomatoes and squash we work with aren't crossing across ploidy.

Wheat on the other hand can be a multi-ploidy mess even within one diverse field.

[Garrett Schantz]

Continents seem to be the largest species barrier. Otherwise hybrids pop up fairly often.

 Physalis hybrids becoming new species can be possible due to ploidy I suppose. Plus perennial types will have rhizomes plus hybrid vigor, which would weed out the parents(parents can't backcross very well in a lot of
 physalis hybrids).

 Assuming escaped tomato hybrids could easily become a new species considering they wouldn't be backcrossing with the parents - plus the climates would be different from Peru.

 Squash, yeah probably going to stop accepting pollen from other species if you stopped crossing it with both parents.

 Species from different continents though could just make some new things.
 Snakebark maples, Vitis-Grapes, whole lot of plants could cross and end up with something superior to the parents.

 Celastrus orbiculatus and Celastrus scandens made good examples because they grow to different heights, one is more tolerant of shade - but they can grow in areas that neither parent would have done well in. Which
 then opens the possibility for a new species. Physalis heterophyllax Physalis virginiana is a good example of this.

 Diseases and pests that went between continents are good examples of how "low level gene flow" from hybrids could be quite helpful.

 Good bit of hybrids can grow in new areas, which probably ends up isolating them after awhile. Seems to be how the tomato clades came about.

 I'm growing a few different white oak hybrids just to see what happens in the future, squirrels should enjoy the diversity I suppose. (deer killed a few though)

 Jaltomatas seem to be a fun group to look at when thinking of a species. Different species are pollinated by different things, and they are usually isolated from each other.

Species, in biology, classification comprising related organisms that share common characteristics and are capable of interbreeding. This biological species concept is widely used in biology and related fields of study.
appears to be the widely accepted definition, with geographic / biological differences being stated as exceptions.

 But we have species that aren't isolated and cross every so often. Which is where that definition needs a bit of touching up on.
 

[Garrett Schantz]

Figured I would add on to this. Animals make good examples so I will mention them as well I suppose...

Although phenotypes are caused by genetic differences / mutations /differences, it doesn't necessarily mean that they are much different from each other based on the phenotypes. (Dogs vs Wolves)

 Selection by humans and other factors have changed cats from others compared to their genus/ancestors. Feral cats can form hunting groups. Other Felis species tend to prefer a solitary lifestyle - and are difficult to tame. A feral cat is still tamable due to recent domestication. The only other real "cat" that I can think of that forms social groups are lions.
 Humans being social animals probably selected for social groups / cats that accept other species. Cats naturally selected for traits to tolerate humans as well, which probably means that we ended up getting multiple groups coming in every so often rather than us taking in one group. Humans creating "breeds" probably reduces genetics quite a bit due to inbreeding.
 
 North American wolves - or coyotes can add quite a bit of genetic diversity into dogs which usually come from a few populations of wolves in Europe (few other places as well).  That might fit well into an analogy.

 Interestingly, Wikipedia (https://en.wikipedia.org/wiki/Ethiopian_wolf) mentions "Animals resulting from Ethiopian wolf-dog hybridization tend to be more heavily built than pure wolves, and have shorter muzzles and different coat patterns." - In the Hybridization section of the Ethiopian Wolf page, there is mention that such cases can result in outbreeding depression, "reduced fitness" which pretty much means bad genes could have been possibly introduced.
Although those bad genes would naturally get kicked out if/when the hybrids die - good genes would probably stay present. Seems like the hybrids are killed if found - to preserve the species or something...

 But we currently have evidence of Grey wolf(Canis lupus) and Coyotes(Canis latrans) moving into the same areas / hybridizing. Which is now creating populations of "hybrids" which are more adaptable than either parent, larger, able to hunt deer quite effectively.
 Purists seem to hate outcrossing for whatever reason, even though it seems to happen naturally in many cases...  There are sources attached as well on the Wikipedia page that I referenced.

 Species in the same genus seem to hybridize easily. Equines such as - Zebra x Horse - Donkey x Horse etc. And of course for big cats we have Ligers, Tigons and many more. Most of the hybrids happen in zoos due to the parent species being isolated from one another naturally. Normally you hear that these are sterile - although a good bit of females in the big cats hybrid offspring have turned out to be fertile or semi fertile.
 Fertile mules aren't commonly recorded - although this could be due to them being sterilized in order to prevent aggression.(https://horses.extension.org/is-there-a-chance-that-a-mule-may-reproduce-if-bred/)

 Outbreeding seems to be common in a lot of plant species as well. I haven't noticed any issues with hybrids either - our climates probably select against bad traits, along with our own selections.

 This link (https://www.jstor.org/stable/2989729?seq=1) mentions fertile hybrids found within the Solanum genus (some of which are found on different continents). Helps broaden areas in which the offspring can grow successfully.

Pretty sure that habrochaites and domestics are pretty closely related as well. A lot of the differences are just slight changes in their coding(still much better than commonly available domestics). Seems like the "tomato group/clade" are in the process of branching off into different species, or already have. If they were too far apart they might not be viable to create hybrids without embryo rescue etc.
 
 Joseph's idea of sending off a bunch of unstable hybrids into different climates is quite nice in this regard. Hopefully we will end up with variable plants that are naturally adapted to just about anywhere in a short period of time. Only having the domestic tomato to start off with would take much longer - relying on mutations and other such things. Leaf types, disease resistances, growth type, root systems, salt /humidity tolerances are available in a short amount of time - all due to Peru's various climates.

 Would be nice if we could cross tomatoes with something even more distant than habrochaites - peruvianum etc. If I recall there has been mention of a solanum sisymbriifolium hybrid, although that would probably require embryo rescue. Anything from the Jaltomata genus would be great as well. Widely diverse flower types / flavors, things that we aren't getting from tomatoes. Probably possible to create something favorable to pollinators more commonly found in people's climate - country etc. These would add in a ton of genetic diversity compared to habrochaites and the like.
(https://www.semanticscholar.org/paper/Heterochronic-developmental-shifts-underlie-floral-Kostyun-Preston/e39f069576de9f9ce2682b6cdcdd58f92b4f7ea0/figure/0)

I will be attempting a Lycium intraspecific hybridization project in the future - probably experimenting with Jaltomatas as well. I have managed to obtain quite a few Physalis species too, those might be a pain though due to certain reproductive barriers. Not planning on trying to put any of these into a tomato because embryo rescue would be required - and it might not work in some cases(if not enough genes match up).

 I'm assuming that a good bit of hybrids isolated from their parents - either by genetics or by location will eventually become a new species rather quickly (if not they could add in some useful genes) - for animals this could be that they gained access to new prey, food etc - for plants it could be that they can survive in different areas than either parent was able to.

 Genus's generally seem to be a very short ways away from an individual species. So yeah look into related genus's maybe you can create a new or better hybrid species.
 

[reed]

I don't think I really understand the species thing. I used to think it meant that things in the same family were related, things of the same species were well, the same. Actually I still think that but what I've come to realize is that a long time ago when people started naming things they didn't have clue what they were doing so if two things looked somewhat alike they just assigned them to the same family or species.

I guess to a large degree that worked, take oak trees for example, they make acorns, lots of different sizes and shapes but still recognizable as acorns so it makes sense to assume the are related.  That said though, if they can cross with each as I believe many can why assign different species names? Or maybe species is a phenotype distinction rather than one of genotype? If that's the case then it is just the same as a variety.

To me, it gets all mixed up and confused so I mostly just ignore it. I figure if two things can cross sexually by natural means and produce healthy offspring then they were always the same thing anyway. I have a few specific varieties whose phenotype I want to preserve and I do some intentional selection but mostly in my gardens I don't consider different varieties as different at all. I mostly grow species, rather than varieties and I don't worry too much that I don't really know what a species is.

[Jeremy Weiss]

I keep being told by the more scientific minded people I know that binomial nomenclature is on it's way out and that eventually, everything will be simply known by it's cladistic placement based on it's DNA karyotype (which I suppose means that eventually, we will be expected to memorize the DNA karyotype of every living thing, or, more likely have some little computer widget that can do it for us.)

Species seem to be more aggressively divided (in that it is harder to get interspecies fertile crosses) in animals than in plants. And there is always the matter of genetic engineering and DNA splicing (if you splice a gene from one species into another one, is it still the same species. If you get to the point where you can put together an organism wholly from assembled pieces of DNA [which I think we eventually will be able to do] how does it fit into the cladistic tree?"

And there are common plants I grow all the time whose species I am unsure of (for example garden pansies, how to they relate to violas and violets? Is the only difference between a pansy and a viola how big it gets?)

[S.Simonsen]

I agree that binomial nomenclature is on its way out, and the higher levels like tribes and orders are also a bit wobbly (at least in terms of their comparability across different types of organisms- eg does an order in animals mean the same thing as in plants?). DNA analysis has produced a lot of data, and mostly mirrored earlier morphology based classifications with a few notable surprises, but DNA based analysis is also based on the model of diverging ancestral species. This is at odds with the reality that a lot of speciation happens through hybridisation, something the models do a poor job of accounting for usually, though if you look for it you find it everywhere. If you analyse a group of organisms based on different genes you end up with different family trees for example, so what you usually see are "consensus" trees which agree with the most genes that they happened to look at.
I prefer to look at a species as a very porous concept. Just as individuals swap DNA wholesale to make new individuals, whole populations (species) also swap DNA wholesale regularly to create new species through hybridisation, kind of just the next layer up. And then you have huge amounts of smaller bits of DNA being moved between organisms by viruses and bacteria, plus whole microbial symbiont populations being exchanged which are effectively part of a functional organisms genome.

[Garrett Schantz]

 Species like the Lonicera fly(Rhagoletis mendax x Rhagoletis zephyria) are interesting as well. A hybrid isolated from both parents and feeding on a different genus of plants from either parent. Should probably get
 its own species name in my opinion.

 DNA analysis seems to indicate that a good bit of species in the Cervidae family (includes white tailed deer, sika deer, elk etc) could be further split up. Same goes for Ursus. Good bit of brown bear-grizzly bears are genetically
 distinct / separated enough that they stand out. Seems to be the same story with others in the Ursidae family. This could mean that we have more endangered species than previously thought. Assuming this applies to different plant species as well - some Physalis species have subspecies that can differ quite a bit from the main type for example.

 Good-King-Henry is another example of where binomial nomenclature didn't work too well, though it was close. Seems its closer to spinach than chenopodium species.

 Binomial nomenclature did work pretty well, but we now have the means of creating something better or more accurate.

 Unsure of how long binomial nomenclature will take to get replaced. Need to find an alternative first - and then a majority of scientists across the world need to agree on it.