Evolution: Speciation: Primary, and secondary speciation

Primary, and secondary speciation

https://reasonandscience.catsboard.com/t2360-evolution-speciation-primary-and-secondary-speciation

In 1997, evolutionary biologist Keith Stewart Thomson wrote: “A matter of unfinished business for biologists is the identification of evolution’s smoking gun,” and “the smoking gun of evolution is speciation, not local adaptation and differentiation of populations.”  

Secondary speciation does not solve Darwin’s problem. Only primary speciation — the splitting of one species into two by natural selection — would be capable of producing the branching-tree pattern of Darwinian evolution. But no one has ever observed primary speciation. Evolution’s smoking gun has never been found.  there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of twenty to thirty minutes, and populations achieved after eighteen hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another.”
https://evolutionnews.org/2009/05/selection_and_speciation_why_d/#footnote49


There are observed instances of secondary speciation -- which is not what Darwinism needs -- but no observed instances of primary speciation, not even in bacteria.

primary speciation
The splitting of one species into two, usually resulting from natural selection favoring different gene complexes in geographically isolated populations.

secondary speciation
the fusion through hybridization of two species that were formerly geographically isolated, followed by the establishment of a new adaptive norm ...

Secondary speciation in the genus level is possible, but at the family level and beyond is not. Organisms can evolve only up to different genera, but not different families.

British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: "None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of twenty to thirty minutes, and populations achieved after eighteen hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another.

Observed cases of speciation by polyploidy are limited to flowering plants. 2 Furthermore, according to American evolutionary biologist Douglas J. Futuyma, polyploidy — known as “ secondary speciation ” — “ does not confer major new morphological characteristics” and does not cause the evolution of higher levels in the biological hierarchy. Darwinism depends on the splitting of one species into two, which then diverge and split and diverge and split, over and over again — a process known as “primary speciation”—to produce the branching-tree pattern required by Darwin’s theory.

Allopolyploidy, i.e. hybridization followed by chromosome doubling, is a frequent mode of secondary speciation in vascular plants (Leitch and Bennett 1997; Haufler 2008). 3The occurrence of diploids and their derived polyploids in the same area provides an excellent natural experiment to test the unique environmental responses that may exist across ploidy levels.

primary speciation : The splitting of one species into two, usually resulting from natural selection favoring different gene complexes in geographically isolated populations. 4

PRIMARY AND SECONDARY TRANSITION ZONES IN SPECIATION AND POPULATION DIFFERENTIATION: A PHYLOGENETIC ANALYSIS OF RANGE EXPANSION
https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1984.tb00281.x

Phylogeography of speciation: Allopatric divergence and secondary contact between outcrossing and selfing Clarkia
There is a distinction between allopatric divergence (followed by secondary contact) versus primary intergradation (parapatric speciation) as alternative divergence histories.
https://experts.umn.edu/en/publications/phylogeography-of-speciation-allopatric-divergence-and-secondary-

Evolution and Diversification of Land Plants page 296

We have lots of evidence of secondary speciation. We have good reason to believe, for example, that all cats belong to the same created kind. A house cat can't breed with a lion, but it can breed with other small cat species, which can breed with other cat species, which could eventually breed with a lion. We can link all of the cat species (except the clouded leopard) together through a network of known hybrids. Not all of the known hybrids survived very long and many are infertile, but the fact that they can produce offspring shows a fundamental compatibility of the genomes and indicates that they came from a common ancestral stock. They belong to the same created kind. So if the 36 species of cats came from a common ancestral kind, then secondary speciation has occurred and done so multiple times. Something similar is true for the 7 species of equids (horses and donkeys), the 8 species of bears, and many other animal families. 

Primary speciation 
has been used to encompass the most basic and commonly recognized ways of initiating new species, the divergence of diploid populations to the level of species. Having a clear and well-supported phylogeny for the group of taxa being studied is particularly important in developing hypotheses about primary speciation. Unless sister taxa are compared, erroneous conclusions about the processes involved will be obtained. Within this major mode are more specific categories including allopatric speciation, the divergence of populations to the species level through isolation by geographic separation, parapatric speciation, divergence of popUlations to the species level even though populations maintain contiguous but nonoverlapping geographic distributions, and sympatric speciation, divergence of populations to the species level even though the populations occupy the same geographic region. Given the complex biotic and behavioral interactions that have been associated with sympatric speciation and the high probability that simple isolating mechanisms characterize pteridophytes, it seems unlikely that they speciate sympatrically at the diploid level.

Secondary Speciation
Theoretically, reproductive barriers arise when geographically separated populations diverge genetically. But Coyne describes five “cases of real-time speciation” that involve a different mechanism: chromosome doubling, or “polyploidy.” This usually follows hybridization between two existing plant species. Most hybrids are sterile because their mismatched chromosomes can’t separate properly to produce fertile pollen and ovaries; occasionally, however, the chromosomes in a hybrid spontaneously double, producing two perfectly matched sets and making reproduction possible. The result is a fertile plant that is reproductively isolated from the two parents — a new species, according to the BSC. But speciation by polyploidy (“secondary speciation”) has been observed only in plants. It does not provide evidence for Darwin’s theory that species originate through natural selection, nor for the neo-Darwinian theory of speciation by geographic separation and genetic divergence. Indeed, according to evolutionary biologist Douglas J. Futuyma, polyploidy “does not confer major new morphological characteristics… [and] does not cause the evolution of new genera” or higher levels in the biological hierarchy.

When it can be demonstrated that the speciation under investigation involved genomic-level changes, such as hybridization or polyploidy, a separate mode is proposed. The magnitude of genetic modification in secondary speciation often can be characterized, and it appears to be qualitatively different from that caused by the more incremental changes that are typical of primary speciation. Further, secondary speciation usually involves interactions between distinct and separate lineages that remain intact (autopolyploidy is the exception). These interactions result in the production of a new lineage that is reproductively isolated from its progenitors, shares significant portions of its genome with them, and is usually intermediate in morphology between them. Thus, instead of a single lineage evolving into two new lineages (as in primary speciation), two lineages interact to yield a third lineage, and all three lineages persist. Characterization of a variety of patterns provides circumstantial evidence of different kinds of secondary speciation. When different ploidy levels are detected among individuals that are morphologically uniform, autopolyploidy is suspected. Some summaries of speciation have used autopolyploidy as an example of "sympatric" speciation. However, autopolyploidy involves genome duplication, a mechanism that is quite different from those leading to the origin of diploid lineages. As reviewed by Gastony [34], speciation by chromosome doubling within pteridophyte species has been largely overlooked as a significant mechanism. In some groups, however, especially when accompanied by apomixis, autopolyploidy may occur frequently.


ERNST MAYR SPECIATION AND MACROEVOLUTION March 15, 1982
https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1982.tb05483.x
Kinds of Speciation: The term speciation has been used ambiguously throughout much of the history of evolutionary biology. For evolutionists in the vertical tradition, it meant phyletic speciation ( primary speciation), that is the transformation of one species into another one. For those in the horizontal tradition, it meant the multiplication of species ( allopatric, or secondary speciation), that is the establishment of separate populations that are incipient species.
Much of the current conflict about the validity of punctuated equilibria is actually the subconscious perpetuation of the old ambiguity as to what speciation really is. Some of those who support phyletic gradualism are still thinking in terms of phyletic speciation. There is now little doubt that, at least as far as animals are concerned, the prevailing mode of speciation is allopatric. I defined this in 1942 as follows: "A new species develops if a population which has become geographically isolated from its parental species acquires during this period of isolation characters which promote or guarantee reproductive isolation when the external barriers break down."

My comment: Mayr goes on to mention various kinds of speciation, namely: a) Sympatric speciation. b) Stasipatric speciation. c) Parapatric speciation. d) Peripatric speciation

When in a superspecies or species group there is a highly divergent population or taxon, it is invariably found in a peripherally isolated location. In many cases, when I traced a series of closely related allopatric species,
I found that the most distant, the most peripheral, species, was so distinct that ornithologists had described it as a separate genus or at least had not recognized at all its true relationship. In genus after genus I found the most peripheral species to be the most distinct. It is on this strictly the empirical, strictly observational basis that I proposed in 1954 my theory of peripatric speciation. My conclusion was that any drastic re-organization of the gene pool is far more easily accomplished in a small founder population than in any other kind of population. Indeed I was unable to find any evidence whatsoever of the occurrence of a drastic evolutionary acceleration and genetic reconstruction in widespread, populous species. When a drastic change occurs, it occurs in a relatively small and isolated population.

Genetically unbalanced populations may be ideally suited to shift into new niches such as will be available under the changed environmental conditions of the location of the founder population. 5. The genetic reorganization might be sufficiently drastic to have weakened genetic homeostasis sufficiently to facilitate the acquisition of morphological innovations. . The drastically different physical as well as the biotic environment of the founder population will exert greatly increased selection pressures. Since the early generations will be rather small, stochastic processes will play an important role in genetic reorganization. I concluded that the combination of
all these different factors might result in agenetic turnover that was by several orders of magnitude larger than that occurring in a normal deme that is part of a populous widespread species. I referred to such a drastic reorganization as a genetic revolution. My concept of the genetic revolution was based on the idea. of the genetic milieu of each gene. Since my ideas have often been misunderstood or misrepresented let me quote exactly from my 1954 paper: "Isolating a few individuals from a variable population . . . will produce a sudden change of the genetic environment of most loci. This change, in fact, is the most drastic genetic change . . .that may occur in a natural population, since it may affect all loci at once. Indeed, it may have the character of a veritable 'genetic revolution.' Furthermore, this 'genetic revolution,' released by the isolation of the founder population, may well have the character of a chain reaction. Changes in any locus will, in turn, affect the selective values at many other loci, until finally, the system has reached a new state of equilibrium."
My systematic studies of literally thousands of peripherally isolated populations during the preceding 25 years had shown me that such a drastic change occurs only very occasionally.

Those of us who for a long time have been on the road toward the explanation of speciation and evolution and who thought that we were nearing the goal now feel suddenly like the player in a parlor game who is told to go back to position zero. Indeed as far as our understanding of the genetics of speciation is concerned we are almost at position zero.

Chromosomal reconstruction.
Since in eukaryotes virtually all the genetic material is located on the chromosomes, no one will question that the chromosomes are important in speciation, the only question being, in what way? Carson's Hawaiian
Drosophila shows that chromosomal reorganization is not a necessary condition for speciation. For 15 or more years various authors have speculated on the importance of speciation of regulatory genes (in analogy to the findings in prokaryotes) and there seems to be indeed a great deal of evidence for the role of such regulatory mechanisms.

My remark: This is a remarkable admission for a 1982 paper. Back then, already, it was known that the gene regulatory network has a decisive role in speciation, and not the genetic information "per sé". This was confirmed by Davidson many years later.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/
It erroneously assumes that change in protein-coding sequence is the basic cause of change in the developmental program, and it erroneously assumes that evolutionary change in body plan morphology occurs by a continuous process. All of these assumptions are basically counterfactual.


1. http://www.evolutionnews.org/2009/05/selection_and_speciation_why_d020411.html
2. http://www.utitokyo.sakura.ne.jp/uti-index-papers-e-Jonathan-Wells-evolution-02.pdf
3. http://aobpla.oxfordjournals.org/content/7/plv047.full
4. http://www.oxfordreference.com/view/10.1093/oi/authority.20110803100345475
5. Lindsay Marks Harold 

First degree of speciation - Macro - Evolutionary claims are  pseudo scientific
https://reasonandscience.catsboard.com/t1712-first-degree-of-speciation-macro-evolutionary-claims-are-pseudo-scientific

a rebuttal of 26 different species concepts, highlighting the utter unscientific nature of this unfalsifiable and clearly pseudo-scientific concept.

"1. Agamospecies
Specifications: Asexual lineages, uniparental organisms, that cluster together in terms of their genome. Maybe secondarily uniparental from biparental ancestors."

Note: a lineage depicts ancestry, ToE claims universal ancestry, by this definition ALL asexual or uniparental organisms can then all be classified as the same "species".
This definition claims this concept of "species" in genome clustering but gives ZERO parameters to allow for any type of objective testing.

"2. Autapomorphic species
Specification: A geographically constrained group of individuals with some unique apomorphous characters, the unit of evolutionary significance"

So through geography, a non-biological line is drawn to denote "species", a biological entity. Assigning the term species to unique apomorphous characteristics, usually used to determine organisms at the Clade level, based on things such as babies digressing their mother's milk, which would indicate the classification of mammal. This species concept can then be used to clasify all mammals in a geographic location as a single species.

"3. Biospecies
Specifications: Inclusive Mendelian population of sexually reproducing organisms, interbreeding natural population isolated from other such groups"

Mendelian populations are subjectively decided based on phenotypic traits expressed, such as colour, or shape. So this definition allows subjective divisions in interfertile populations, based on phenotypic boundaries based on things like skin color, eye color, hair texture etc. If this definition was applied to humans her racist undertones are undeniable.

"4. Cladospecies
Specifications: Set of organisms between speciation events or between speciation event and extinction, a segment of a phylogenetic lineage between nodes. Upon speciation the ancestral species is extinguished and two new species are named."

Not only is "speciation" claims clearly subjective opinion, but the definition allows the creation of species, based on the extinction of a claimed ancestral "species" none of which is testable by this or other definitions for "species".

"5. Cohesion species
Specifications: Evolutionary lineages bounded by cohesion mechanisms that cause reproductive communities, particularly genetic exchange, and ecological interchangeability."

Bound by cohesion mechanisms never explained or given a set of testable parameters to establish "cohesion". It's also described as populations with genetic or demographic cohesion, again never defined to give any sort of verifiability if claims.

"6. Compilospecies
Specifications: A species pair where one species "plunders" the genetic resources of another via introgressive interbreeding."

Note: a species PAIR (ie. wolf and cayotee) where there is generic interchange between populations actually would classify such issues as a singular "species", if this was uniformly applied to ring species for instance, it would classify all such groups as a singular "species".

"7. Composite Species
Specifications: All organisms belonging to an internodal and its descendants until any subsequent internodon. An internodon is defined as a set of organisms whose parent-child relations are not split"

This attempt tries to identify specifically extinct "species". An internodon is determined again by subjective opinion and no testable parameters are presented. In essence it assigns species according to subjective characteristics dependant on the observer.

"8. Ecospecies
Specifications: A lineage (or closely related set of lineages) which occupies an adaptive zone minimally different from that of any other lineage in its range and which evolves separately from all lineages outside its range."

This describes a "species" which is genotypically adapted to specific environmental conditions, regardless of other factors such as breedability or phenotypic similarities, this is how Lenski's ecoli is justified as a new species, regardless of the enormous genetic similarities between two different populations. If universally applied this could classify lactose intolerance, or sickle cell as speciation events.

"9. Evolutionary species
Specifications: A single lineage of ancestor-descendant populations of organisms which maintains its identity from other such lineages [in space and time] and which has its own evolutionary tendencies and historical fate?

This is an attempt to classify the same organism as separate species based on it's assumed time or place of existence. Living fossils are distinguished from their fossil relatives as seperate "species" based on paid time seperating populations but also geographic location, regardless of phenotypical characteristics identifying then as the same organism.

"10. Evolutionary significant unit
Specifications: A population (or group of populations) that (1) is substantially reproductively isolated from other conspecific population units, and (2) represents an important component in the evolutionary legacy of the species."

Again no consideration is given to generic similarity, based purely on reproductive isolation due to geography, sexual behavior or even diet. Again a purely subjective attempt to "create" ever more "species" divisions where none actually exist genetically.

"11. Genealogical concordance species
Specifications: Population subdivisions concordantly identified by multiple independent genetic traits constitute the population units worthy of recognition as phylogenetic taxa"

A theoretical phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies, contrasted by those based on morphology and reproductive behavior. I could find only one fungi this definition was used on.

"12. Genic species
Specifications: A species formed by the fixation of all isolating genetic traits in the common genome of the entire population."

This concept ignores entire genome and even sexual reproductive capabilities, it differentiates "species" upon individual isolated genes. This definition regards any isolated traits to distinguish a different "species". Under these tenets, the exchange of any part of the genomes between diverging groups is thought to destroy their integrity. It's final conclusion leads again to an utterly racist view of "species" which would distinguish any genetic trait isolated in a population as a "speciation" event. And would consider any cross race genetic transference as destroying the population's integrity.

"13. Genetic species
Specifications: Group of organisms that may inherit characters from each other, common gene pool, reproductive community that forms a genetic unit"

This is by far the most testable of species concepts considering any possible genetic transfer to constitute a singular species, if this were applied universally the amount of species classified would drop significantly. Most canines, bears, and many snakes, as well as various birds, lizards, cats and fish, not even mentioning insects and microbes will need to be reclassified. This will not be done by the evolutionary community due to its absolute falsification of most species claims. This definition is however still unable to identify extinct species.

"14. Genotypic cluster
Specifications: Clusters of monotypic or polytypic biological entities, identified using morphology or genetics, forming groups that have few or no intermediates when in contact."

This concepts classifies species not in the basis of the observed organism, but rather the absence of intermediaries. This is laughable ironic as ToE claims uninterrupted intermediaries from LUCA to all living organisms observed to exist. So if ToE could ever show overrating evidence of it's claims, then it would classify all life as a singular species. One if those utterly meaningless definitions merely attempting to hide the inadequacies if the entire "species" concept

"15. Hennigian species
Specifications: A tokogenetic community that arises when a stem species is dissolved into two new species and ends when it goes extinct or speciates."

Once again an utterly subjective and circular reasoning. Species is defined by species. How this is not considered ludicrous by any free thinker is beyond me.

"16. Internodal species
Specifications: Organisms are conspecific in virtue of their common membership of a part of a genealogical network between two permanent splitting events or a splitting event and extinction"

Nothing more than a repetition of number 15. Not worth any further response.

"17. Least Inclusive Taxonomic Unit (LITUs)
Specifications: A taxonomic group that is diagnosable in terms of its autapomorphies, but has no fixed rank or binomial."

Another completely subjective claim, with no parameters set given to indicate the least inclusive group. Can be extended to mean any isolated difference, similar to number 12.

"18. Morphospecies
Specifications: Species are the smallest groups that are consistently and persistently distinct, and distinguishable by ordinary means (Cronquist)."

Once again an utterly subjective method of clasifying "species" similar again to number 12 and 15.

"19. Non-dimensional species
Specifications: Species delimitation in a non-dimensional system (a system without the dimensions of space and time, Mayr 1963)"

Utterly meaningless

"20. Nothospecies
Specifications: Species formed from the hybridization of two distinct parental species, often by polyploidy."

This highlights the unfalsifiability of "species" it's in absolute contradiction to biological "species" that are breedable.

"21 Phylogenetic Taxon species
Specifications: A species is the smallest diagnosable cluster of individual organisms within which there is a parental pattern of ancestry and descent (Cracraft)"

When I read statements like these even I am dumbfounded as to a response. It's utter vagueness as to any method of verifying claims under this concept renders it utterly unfalsifiable. It's far worse when one considers the evolutionary claim of common ancestry to all life, again if their theory is correct, this idiocy would classify all life as a singular species. The extension of this concept which I didn't include here seemingly tries to rectifying by insisting that common ancestor in this case refers to monophyletic groups, which seems then to ignore paraphyletic groups as species altogether. A perfect example of how attempts to justify these concepts turns even their own ideas on it's head.

"22. Phenospecies
Specifications: A cluster of characters that statistically covary, a family resemblance concept in which possession of most characters is required for inclusion in a species, but not all. A class of organisms that share most of a set of characters."

Absolutely subjective opinion on the side if the observer, scientifically meaningless as are most important these.

"23. Recognition species
Specifications: A species is that most inclusive population of individual, biparental organisms which share a common fertilization system"

A population of individuals. That's just utterly circular. Biparental will exclude all asexual organisms as being species. Common fertilization system could mean anything, again an utterly unfalsifiable statement that didn't have any scientific merit.

"24. Reproductive competition species
Specifications: The most extensive units in the natural economy such that reproductive competition occurs among their parts."

So again this deliminates all ring "species" as singular species. Also all natural fertile hybrids.

"25. Successional species
Specifications: Arbitrary anagenetic stages in morphological forms, mainly in the paleontological record."

By it's own definitiory admission it's arbitrary. No further rebuttal required but it's own definition.

" 26. Taxonomic species
Specifications: Specimens considered by a taxonomist to be members of a kind on the evidence or on the assumption they are as alike as their offspring of hereditary relatives within a few generations. Whatever a competent taxonomist chooses to call a species"

Nothing more than a fallacious argument suggesting that a taxonomist's destinction is automatically scientific. Utterly nonsensical.

https://biomed.brown.edu/Courses/BIO48/21.Models.HTML

Speciation is a fundamental issue in evolutionary biology, but it is both fascinating and frustrating: we know it does happen but it its an historical phenomenon so it is difficult to observe. The two camps of evolutionary biologists best equipped to deal with speciation (in terms of mechanism, population geneticists; in terms of time-frames, paleontologists) are both incapable of "seeing" speciation except in very special situations. We must rely on strong inference to properly understand speciation. This inference is in many cases very rigorous and scientific although it is historical, i.e., requires an interpretation of what has gone on in the past.

The terms primary and secondary speciation refer to different stages in the process of speciation, which is the formation of new species from a pre-existing population.

Primary speciation refers to the initial separation of populations into two or more groups that become reproductively isolated from each other. This separation can occur through a variety of mechanisms, such as geographic isolation (e.g., by the formation of a physical barrier like a mountain range or a body of water), ecological isolation (e.g., by occupying different niches within the same habitat), or behavioral isolation (e.g., by evolving different mating behaviors or preferences).

Once the populations are reproductively isolated, genetic and evolutionary processes can lead to the accumulation of differences between the two groups, such as mutations and genetic drift. Over time, these differences can become substantial enough that the two groups can no longer interbreed, resulting in the formation of two distinct species.

Secondary speciation, on the other hand, refers to the formation of additional species from a population that has already undergone primary speciation. This can occur when a previously isolated population itself becomes further subdivided and undergoes additional genetic and evolutionary changes, resulting in the formation of new species.

Overall, the distinction between primary and secondary speciation is a matter of temporal sequence. Primary speciation refers to the initial separation of populations into reproductively isolated groups, while secondary speciation refers to the formation of new species that arise from previously separated groups.