Plants and Animals

Most change watched in wild and domestic plants and animals ran on variation already present, as creationists predicted and mainstream reviews agree. The peppered moth ran on a new mutation. None of the watched changes is a gain of function, and the old variation carries ages young-earth models have not answered.

By AI (Claude Opus 5.5, thinking level unavailable) Draft:  October 2026

"adaptation is likely to be faster from standing variation than from new mutation" — Rowan Barrett and Dolph Schluter, 20081

"approximately 200 years (generations) old, during which time it has gone from a single mutation to near fixation (regionally) to near extinction" — Arjen van't Hof and colleagues, on the black peppered moth, 20162

Summary

The eight articles in this section report change that people have watched in wild and domestic populations of plants and animals:  moths, finches, sticklebacks, lizards, dogs, polyploid plants, flies and cichlid fish.  This overview asks one question of all of them.  How much of the change ran on variation that was already in the population, and how much on new mutations?  Each change is scored with the four classes of Measuring Biological Information:  gain, loss, modification or transfer of function.

Young-earth writers have long predicted the answer.  Kurt Wise wrote in 1994 that in dog and pigeon breeding the variety "was always extant (sometimes largely in latent form) and merely expressed".3  Robert Carter describes created kinds "front-loaded with a large amount of genetic diversity".4  John Sanford's team wrote in 2018 that with designed alleles "no extended “waiting time” is required."5  Mainstream biologists now say the same about speed:  Rowan Barrett and Dolph Schluter's 2008 review opens with the point that adaptation from standing variation is faster.1

The findings:

  1. Most of the watched change ran on variation that was already there. The finch beak changes, the stickleback armour change, the cichlid radiation, the apple race of the apple maggot fly, the tame silver foxes and most of the variants that define dog breeds all drew on variants present before the change began. On this point the creationist prediction is right, and both sides agree.
  2. One textbook case ran on a new mutation. The black peppered moth comes from a single insertion of a transposable element into the gene cortex. Its discoverers date the insertion to 1819 at the most likely point of a skewed estimate whose median is 1763. The black form was first recorded in 1848, 29 years after the most likely date.2 2 Its spread was watched; its origin was inferred. In dogs, the whippet's myostatin deletion probably arose in the breed era, and new copies of the FGF4 gene are still appearing.6 7 So the claim holds for most cases, not for all of them.
  3. "Already there" means older than the watching. It does not mean created. The reused stickleback allele is about 1.9 million generations old by a measured pedigree mutation rate.8 The finch beak haplotypes are dated by their authors to about 900,000 years for ALX1 and 1 million years for HMGA2.9 The creationist geneticist Jean Lightner judges that the dog coat variants "have arisen through mutation" after the Ark.10 No young-earth author has published a test that could tell created variation from accumulated mutation.
  4. No change in these cases, watched or inferred, scores as a gain of function. The changes are transfers by hybridisation, losses, and modifications that turn an existing gene up or down. The black moth's insertion is a modification, up, by copy. The dog variants are four losses, two modifications down, four up and three unmeasured.
  5. One famous case is not yet inherited change at all. The Pod Mrčaru lizards' gut valves disappeared on an insect diet, and their head differences did not persist in a common garden.11 12
  6. The absence of new mutations is a weak test. The watched wild populations were small and the windows short. Forty years of Daphne Major finches carried about 170,000 new mutations, so the chance that any one named single-letter change appeared was about one in 19,000. Only dogs were numerous enough to try every single-letter change many times over, and no gain was documented there either, under selection that was not looking for one.13
  7. New species have been watched forming only in plants. Chromosome doubling of a hybrid made Tragopogon mirus and T. miscellus in the American Northwest before 1949.14 It added no new sequence. In animals only partial isolation has been watched, and the count of new sequence reads zero even where a new breeding group formed.

Verdict.  The creationist claim that fast change runs on variation already present is borne out in nearly every case in this section, and the mainstream literature agrees.  It is not borne out in every case:  the peppered moth ran on a new mutation that arose shortly before the watched change.  What the cases do not show is where the old variation came from.  Measured mutation rates date it to about 1.9 million generations in sticklebacks and to hundreds of thousands of years in Lake Malawi cichlids, and the young-earth answer, that it was created, has not been put to the test that could check it.

How the cases are judged

Three questions are asked of each case, in the same words throughout.

  1. Was it watched or inferred? A change is watched when people recorded it while it happened: counts of moths in a given year, finches measured every season, breeds registered in stud books. It is inferred when it is read from comparing living genomes or from a dated layer. The section's membership rule is that it covers what was watched, and each article says where it relies on inference.
  2. Was the variant standing or new? Here "standing" means the variant was in the population before the watched change began. "New" means it arose by mutation during the change or shortly before it. Whether standing variation was created or accumulated by older mutations is a separate question, taken up in Part 8 and in the issues.
  3. How does it score? Each article uses the four classes of Measuring Biological Information. A rise in the frequency of an old allele involves no mutation and is not scored at all. Hybridisation is a transfer. The ledger counts unique functional sequence created, and it reads zero for a transfer or a copy even when something real happened.

The figures in years for the age of a variant, a lake or a lineage are those of the sources named beside them, and are reported as theirs.  Durations of watching are calendar years.

Part 1: Peppered moths

The black form of the peppered moth, carbonaria, was first recorded near Manchester in 1848.2  It came to make up about 99% of moths in its industrial heartland and has fallen below 5% since 1970.2  Michael Majerus's experiment of 2001 to 2006 released 4,864 moths at natural densities.  Black moths survived each day at 91% of the rate of pale ones, and the authors judge visual predation by birds "the major cause" of the frequency changes.15 15 15  The black form is a new mutation, not an old allele:  one transposable element inserted into the gene cortex.2  Its authors call it "approximately 200 years (generations) old", gone "from a single mutation to near fixation (regionally) to near extinction".2  It turns up a gene already active in the wing, so it scores as modification, up, by copy, with no unique functional sequence added.

The moth is the clearest case in this section of selection watched acting on a variant that arose within recorded history.  The full case, including the fraud charge and its source, is in Peppered Moths.

Part 2: Darwin's finches

Peter and Rosemary Grant measured nearly every finch on Daphne Major from 1973 to 2012.  Selection on beak size was strong and heritable.  Beak size is about 80% heritable.16  Selection favoured larger birds in the 1977 drought and smaller ones in 1984-85 and again in 2004-05.16 17  Comparing 1973 with 2001, mean beak size was unchanged, while body size was smaller and beak shape had changed.18  Every variant behind the change was old.  The authors date the ALX1 haplotype groups to about 900,000 years and the HMGA2 groups to about 1 million,9 and genome sequencing of 3,955 birds found allele frequency changes of 2 to 30% at six beak loci, with no new mutation reported.19  The Grants estimate that interbreeding adds variation "three or more orders of magnitude greater than variation introduced by new mutations per generation".16

The one new breeding group, the Big Bird lineage, came from an immigrant Geospiza conirostris breeding with a local medium ground finch, and became isolated in three generations.20 20  That scores as a transfer.  Robert Carter of Creation Ministries International concedes that the beak variants "are clearly mutations", not created diversity.21  The full case is in Darwin's Finches.

Part 3: Sticklebacks

Sea-run sticklebacks that colonise fresh water lose their armour plates within decades.  In Loberg Lake, Alaska, the low-armour form was absent in 1990 and made up 75% of the fish by 2001.22  In Cheney and Scout Lakes, stocked with about 3,000 sea-run fish each in 2009 and 2011, the low allele of Eda rose "from an initial frequency of <1% to over 50% within 8 years".23 23  It was standing variation:  the low allele sits in sea-run fish at 0.2% to 3.8%,24 and 323 of the 344 regions that changed fastest in the lakes were regions already known to differ between old freshwater and marine populations.23  The low allele's cause is one letter in an enhancer that weakens the gene's response in the armour plates, a modification, down.25

The pelvis is lost a different way.  Nine pelvic-reduced populations carry nine different deletions of one Pitx1 enhancer, overlapping in the same region.26  These are separate losses that arose in each population, inferred from genomes, not watched.  The weakness for the young-earth side is the age of the reused Eda allele:  about 1.9 million generations by a measured pedigree mutation rate.8  The full case is in Sticklebacks.

Part 4: Italian wall lizards

In 1971 ten Italian wall lizards were moved from Pod Kopište to the islet of Pod Mrčaru in the Adriatic.  Sampled from 2004 to 2006, they ate far more plants, 34% to 61% of their food against 4% to 7% on the source islet, and had bigger heads, harder bites and cecal valves in the gut.27  The discoverers themselves wrote that the roles of plasticity and maternal effects still needed testing.27  The tests that followed point to plasticity.  None of twenty lizards kept on insects had valves, against twelve of sixteen caught wild,11 and a later study with Herrel as co-author called the valves "not fixed features".28  Head and bite differences "did not persist in a common garden environment".12  A genome scan found a founder effect and a handful of outlying loci tied to no trait.29

So neither "standing" nor "new" applies yet, because no inherited change has been shown.  The case is not yet scoreable.  A capacity to grow a working valve on a plant diet is itself something that needs explaining.  The full case is in Italian Wall Lizards.

Part 5: Dog breeds

About 350 dog breeds were formed, most of them in the Victorian era, about 1830 to 1900, as closed breeding populations.30 31  The variants that define them are mostly older than the breeds, but most are not wolf variation.  The small-size allele at the IGF1 locus is the ancestral state in wild canids.32  The short-leg FGF4 copies sit on dog haplotypes and arose after domestication.7  Jean Lightner judges that the coat variants "have arisen through mutation".10  At least one variant, the whippet's myostatin deletion, is "a relatively new mutation in the purebred dog population".6  Of thirteen variants the dog article scores, four are losses, two are modifications down, four are modifications up, three of them by extra gene copies, and three are unmeasured.  None is shown to be a gain.

Two related experiments sharpen the question.  The tame silver foxes bred at Novosibirsk from 1959 came from fur-farm stock "already tamer than their wild relatives", and a 2018 genome study found 103 regions of reduced variation or increased divergence among tame, aggressive and ordinary farm foxes, with no new mutation reported.33 33 34  The Illinois maize lines, selected for kernel oil since 1896, went from 4.7% oil to 19.3% in the high line by generation 89.35  Whether that century of response came from new mutation is disputed.  Bruce Walsh argued that most of it did.  Peter Keightley replied that a response fed by new mutation tends to jump, and this one was smooth.35  Stephen Moose's team found the remaining diversity "too high to be explained by mutation".36  The mapping team said its results had no "direct bearing on the importance of new mutations."35  The full case is in Dog Breeds.

Part 6: Observed speciation

New species have been watched forming, in plants, by polyploidy.  Three Tragopogon species brought from Europe to western North America in the early 1900s hybridised.  In 1949 Marion Ownbey found four small populations with doubled chromosome sets, and in 1950 he named two new species from them.37 14  T. mirus has formed at least 13 times and T. miscellus possibly 21 times.38  Primula kewensis did the same in greenhouses in 1905, 1923 and 1926.39  The young species then lose duplicate genes:  about 20% of the loci studied in each T. miscellus plant had already lost one parent's copy.40

Both answers apply here.  The genomes are the two parents' standing genomes, added together.  The doubling is a new event each time, and it recurs.  It scores as a transfer and a modification by copy, with no unique functional sequence.  In animals, what has been watched is partial isolation:  the apple and hawthorn races of the apple maggot fly still exchange about 6% of their genes each generation,41 and the apple race was "extracted, in part, from preexisting adaptive inversion clines".42  In laboratory selection experiments, "in no case was reproductive isolation complete".43  The London Underground mosquito, long offered as a case, arose above ground more than a thousand years ago.44  Creation Ministries International lists "No new species have been produced" among arguments creationists should not use.45  The full case is in Observed Speciation.

Part 7: Cichlid radiations

Lake Victoria holds about 500 species of haplochromine cichlids found nowhere else.  Cores show the lake dried out "before 12,400 carbon-14 years before the present",46 which Ole Seehausen converts to a refilling 14,600 years ago and calls "the fastest large-scale species radiation known."47  Later cores found wetlands with permanent shallow ponds in the basin before the deep lake returned, so fish may have survived there.48  Nobody watched a cichlid species form.  The radiation is read from genomes.

It ran mostly on standing variation mixed by hybridisation.  The flock descends from a hybrid swarm of two river lineages whose split Joana Meier's team dates to "~1.6–5.8 million years ago" on a mitochondrial tree dated with four sets of calibration points.49  Each of the two classes of the main red-light opsin allele comes from one parent.49  Not every differentiating site is shown to be old:  in the same study's figure, about 151 of 340 outlier sites fall in the class "novel LV allele or unsampled in parental lineages".49  On the one cichlid mutation rate measured in parents and offspring, splits inside Lake Malawi date to 390,000 to 460,000 years.50 50  Scored, the hybridisation is a transfer and the sorting is not scored.  The full case, with the rate arithmetic on each clock, is in Cichlid Radiations.

Part 8: The creation model of rapid speciation

The Creation Model of Rapid Speciation states the young-earth models in their own words and tests them against the seven case articles.  There are at least four models, and they disagree with each other.  Carter, Nathaniel Jeanson and Sanford say kinds were created carrying variety;  Jeanson writes that the ancestors of modern species "were created with heterozygous chromosome pairs."51  The central mechanism, fast change from stored variation, is well supported, and the mainstream says the same:  David Marques, Joana Meier and Ole Seehausen write that recombining old variation works fast "as there is no waiting time for relevant mutations".52  The required rate is fast but not absurd.  Counted per line of descent, the average kind must double its species about every 740 to 790 years after the Flood, about twice as fast as Lake Victoria on its radiocarbon clock.53

The model is in trouble on three points.  The stored variation is dated far older than the Flood by measured mutation rates where those exist:  about 1.9 million generations for the stickleback Eda allele and 390,000 to 460,000 years for splits inside Lake Malawi.8 50  Randy Guliuzza's claim that organisms track their environment by directed variation fails at Eda, where offspring were born in the plain Mendelian 1:2:1 ratio before selection moved the frequency.54  And no proponent has tested whether the old differences look created or accumulated.  That article's verdict is that the mechanism stands and the chronology does not.  The full case is in The Creation Model of Rapid Speciation.

Part 9: The cases side by side

The table answers the section's question case by case.  "0" in the last column means no unique functional sequence was added.  The evidence for each cell is cited in the Part above and set out in full in the case's own article.

Case Watched What changed Standing or new, and the evidence Score
Peppered moth, Britain First record 1848; counts to 2014; predation experiment 2001-2006 Black form rose to about 99% near Manchester, then fell below 5% New. One transposon insertion with a single origin, dated by its discoverers to 1819 at the most likely point and 1763 at the median. The origin is inferred; the spread was watched Modification, up, by copy; 0
Darwin's finches, Daphne Major 1973-2012 Beak size up after 1977, down after 1984-85 and 2004-05; smaller bodies and pointier beaks by 2001 Standing. ALX1 and HMGA2 haplotypes dated by their authors to about 900,000 and 1 million years; 3,955 genomes show frequency shifts and no new mutation Frequency shifts not scored; 0
Big Bird lineage, Daphne Major 1981 to the 2010s A breeding group isolated by song and size in three generations Transfer. An immigrant G. conirostris bred with a local medium ground finch Transfer; 0
Sticklebacks, Alaska Loberg 1990-2017; Cheney 2009-2017; Scout 2011-2017 Armour lost; low Eda allele from under 1% to over 50% in 8 years Standing for armour: the low allele is at 0.2% to 3.8% in sea-run fish, and 94% of the fastest-changing regions match old freshwater differences. New for the pelvis: nine different Pitx1 deletions, inferred Eda: modification, down. Pitx1: loss. 0
Italian wall lizards, Pod Mrčaru Introduced 1971; sampled 2004-2006 and after Plant diet, bigger heads, harder bite, gut valves Neither shown. Valves vanish on an insect diet; head differences vanish in a common garden Not yet scoreable
Dog breeds Most founded about 1830-1900 About 350 breeds Mostly standing, but mostly dog mutations, not wolf variation. The small IGF1 allele is ancestral; the FGF4 copies arose after domestication; the whippet myostatin deletion is probably breed-era; new FGF4 copies still arise 4 losses, 2 down, 4 up, 3 unmeasured; no gain
Silver foxes, Novosibirsk From 1959 Tameness Standing. The founders were already tamer than wild foxes; no new mutation reported Not scored
Illinois maize oil From 1896 High line from 4.7% to 19.3% oil by generation 89 Disputed. Walsh: mostly new mutation. Keightley and Moose: mostly standing Not scored
Tragopogon and other polyploids Parents introduced in the early 1900s; found 1949; about 40 generations since New species, isolated by chromosome number Both. Two standing parental genomes; the doubling is new each time, at least 13 times for T. mirus Transfer and modification by copy; 0
Apple maggot fly Apple attacks noticed in the 1860s55 A host race with about 6% gene flow a generation Standing. Built in part from older inversions Not scored
Lake Victoria cichlids No speciation watched About 500 species, in a lake that refilled 14,600 years ago on Seehausen's reading Mostly standing. A hybrid swarm of two lineages split 1.6 to 5.8 million years ago on a calibrated tree; about 151 of 340 outlier sites are novel or unsampled in the parents Transfer, then sorting; no gain

Three patterns stand out.  First, nine rows have an answer, and in eight of them the change ran mainly on variants present before it began.  The moth is the exception, and the stickleback pelvis and the dogs carry new mutations beside the old.  Second, no row contains a gain of function.  The variants that were new are losses, in the stickleback pelvis and the whippet;  a copy that turned up an existing gene, in the moth;  and a doubling that copies whole genomes, in the polyploid plants.  Third, every row with a deep age carries it from a mainstream clock, and no young-earth author has published a test of the claim that those old differences were created.

How much was searched

The absence of a watched new mutation means little unless enough mutations were tried for one to be expected.  Each child article that could do so worked out a ledger.13

Case Births searched New mutations Times one named single-letter change is expected
Darwin's finches, 1973-2012 about 7,800 hatchlings about 1.7 × 10⁵ about 1 in 19,000
Sticklebacks, Cheney and Scout at least 42,000 fish-generations about 2 × 10⁵ at most about 1 in 7,000
Italian wall lizards at most 1.6 × 10⁴ to 2.8 × 10⁵ hatchlings 5.7 × 10⁵ to 1.0 × 10⁷ 1.3 × 10⁻⁴ to 2.2 × 10⁻³
Peppered moth, 1819-1848 2.9 × 10⁵ to 4.35 × 10⁶ moth-generations not computed; no Biston mutation rate not computed
Dogs, about 200 years at most 4.7 × 10¹⁰ dog-generations about 10¹² about 140 each
Lake Victoria cichlids not computed; census unknown

In the wild cases the expected count for any one named change is far below one, so finding no adaptive new mutation is what both views predict.  It is an absence of evidence, not a measured zero, as the stickleback article says of its own lakes.  The Pitx1 deletions fit the same arithmetic from the other side.  The enhancer sits at a fragile site, and Kathleen Xie's team estimate that mutations there arise at about 10⁻⁵ against about 10⁻⁹ for ordinary single-letter changes, so that they "would arise often".56  Dogs are the only case with enough search to try every single-letter change many times over.  There, new mutations did turn up, and the ones that were selected are a broken gene and extra copies of working genes.

Part 10: Where two articles disagree

Reading the eight articles together turns up two disagreements.  Both are settled here from the sources the articles themselves verified.

Did every case with known genetics run on old variation?  The Creation Model of Rapid Speciation says that in every case where the genetics is known, the change drew on variation that was already there.  Its table lists sticklebacks, cichlids, dogs, polyploid plants and the apple maggot fly.  Peppered Moths shows a case it did not list where the selected variant was new.  The discoverers write that in about 200 generations the black form's insertion went "from a single mutation to near fixation (regionally) to near extinction".2  Dog Breeds adds the whippet deletion and the FGF4 copies still arising.  The settled statement is that most watched change ran on old variation and some ran on new mutations, none of which scores as a gain.

Is the cichlid split dated by a measured mutation rate?  The creation-model article says in its Summary that the variation is dated far older than 4,400 years by measured mutation rates, and lists the cichlid parent lineages' split of 1.6 to 5.8 million years under it.  Cichlid Radiations reports that split from a mitochondrial tree dated with four sets of calibration points.49  The cichlid figure that does rest on a rate measured in parents and offspring is 390,000 to 460,000 years for splits within Lake Malawi.50  The creation-model article's conclusion stands, because the stickleback age it lists beside the cichlid one does come from a measured rate.  Its label for the cichlid figure should change.

Objections and responses

"Standing variation is only old mutation.  Calling it 'already there' hides where it came from."  That is right, and it is the real dispute.  The cases show that sorting is fast.  They do not show that the sorted variants were created.  Where a mutation rate has been measured, the reused variants come out old:  about 1.9 million generations for the stickleback Eda allele.8  Answers in Genesis calls the reused stickleback genes "the genetic information God provided",57 and the stickleback and cichlid articles each name a test that could check it:  compare the kinds of letter changes in the old differences with the kinds that new mutations make.  Nobody on either side has run it.

"The peppered moth proves that new mutations drive adaptation within decades."  It shows that a new mutation can arise and be selected within recorded history, and this site says so.  It is one mutation, an insertion of copied DNA that turned up an existing gene, and the moth ended where it began once the soot was gone.2  It is the best case in the section for new mutation and a poor one for new function.

"Finding no new mutations in a forty-year study supports creation."  It does not.  The ledgers above show that no one should have expected a particular new mutation in the finch, stickleback or lizard studies.  The zero is what an evolutionist expects too.  Only the dogs searched enough to make the zero informative, and there new variants did arise.

"All of this is variation within a kind, and none of it adds information."  The scores agree that no change in these cases is a gain of function.  "Loss of information" is still the wrong summary.  Hybridisation transfers working variants, extra gene copies turn genes up, and polyploidy makes a new species while adding no new sequence.  Dog Breeds and Observed Speciation both warn that a count of new sequence can read zero while something biologically real happens.

"The lizards evolved a new organ in 36 years."  The discoverers did not claim it was genetic, and every test since points to a response to diet.27 11 12  The case is not yet evidence of inherited change.

"The young-earth timeline needs speciation far faster than anything known."  Per line of descent the average kind needs about twice Lake Victoria's rate on its radiocarbon clock.53  That is fast but not absurd.  One published case, Todd Wood's 150 horse species in about 400 years, is about thirty times faster than any radiation known, as The Creation Model of Rapid Speciation shows.

Issues and unanswered questions

  1. Where the standing variation came from. This is the open question the whole section leaves. The mutation-spectrum test named above could separate created from accumulated differences in sticklebacks and cichlids, using a stickleback spectrum of new mutations that has already been measured.58
  2. The peppered moth's date. The 1819 date is the peak of a skewed model estimate. Genotyping museum moths from before 1848 would test it directly, and none has been found.
  3. The Illinois maize lines. Whether a century of response came from new mutation or from the starting variation is unresolved in the mainstream literature. It is the one long selection experiment here where new mutation may have done much of the work.
  4. Copies under new control. The dog FGF4 copies and the stickleback Fads2 copies are scored as modifications because they add dose where the gene already works. If either were shown active where the parent gene is silent, it would move to gain by copy.
  5. The lizard valves in a common garden. Whether the common-garden study examined guts could not be read. Hatching eggs from both islets on both diets would settle the case.
  6. Whether the Big Bird lineage stays apart. Its isolation is three generations old and rests on song and size.

Verdict

The creationist claim that change in wild and domestic populations runs mostly on variation already there is right.  In the finches, the sticklebacks' armour, the cichlids, the apple maggot fly, the silver foxes and most dog breeds, selection sorted variants that were present before the change began, and mainstream reviews say the same.  The claim is not right in every case.  The black peppered moth spread from a new mutation that arose shortly before the watched change, and dogs carry at least one breed-era mutation and keep making new gene copies.  None of the changes, old or new, scores as a gain of function.  They are transfers, losses and modifications.

What the cases do not settle is the origin of the old variation.  Measured mutation rates date the reused stickleback allele to about 1.9 million generations, and splits inside Lake Malawi to 390,000 to 460,000 years.  The young-earth answer, that such differences were created, is coherent and has not been tested.  A skeptic is right that the clocks give ages far beyond a young earth.  A creationist is right that the speed of change was never the problem it was made out to be.

Sources

  1. 1.

    Barrett, Rowan D. H., and Dolph Schluter.  “Adaptation from standing genetic variation.”  Trends in Ecology and Evolution 23(1):38–44.  2008.  Review by Rowan Barrett and Dolph Schluter of adaptation from standing genetic variation.  It sets out why adaptation from variants already present is faster than from new mutation and lists the known cases.  Here it is the mainstream statement of the creationist prediction this section tests.  Mirror:  Zoology.ubc.ca

    1. 1a.

      Page 38:  “First, adaptation is likely to be faster from standing variation than from new mutation, not only because beneficial alleles are immediately available, but also because they usually start at higher frequencies”. ↩ ↩

  2. 2.

    van't Hof, Arjen E. et al.  “The industrial melanism mutation in British peppered moths is a transposable element.”  Nature 534(7605):102–105.  2016.  Genome study from Ilik Saccheri's laboratory that found the mutation behind the black peppered moth:  a transposable element inserted in the gene cortex, carried by nearly all black moths tested and no pale ones.  Recombination around the insert, fitted to the historical frequency record, dates it.  Page numbers are those of the accepted manuscript, not of Nature.  Mirror:  Livrepository.liverpool.ac.uk

    1. 2a.

      Manuscript page 4:  “By contrast, we have shown that the carb-TE is young, approximately 200 years (generations) old, during which time it has gone from a single mutation to near fixation (regionally) to near extinction – driven by a pulse of environmental change.” ↩ ↩ ↩

    2. 2b.

      Manuscript page 3:  “The probability density for the date of the carb-TE mutation event (Fig. 2d) is highly skewed (median = 1763, interquartile range = 1681-1806) with a maximum likelihood at 1819, a date highly consistent with a detectable frequency being achieved in the mid-1840s.” ↩

    3. 2c.

      Manuscript page 3:  “1848 Manchester is generally regarded as the first reported sighting of the carbonaria form, although the wording of the record implies that it was rare but not completely unknown at this time.”  A superscript reference number after "form" is omitted. ↩ ↩

    4. 2d.

      Manuscript page 3:  “Tenure of the carb-TE has been transient, having declined from ~99% to less than 5% in its industrial heartland since 1970”.  A reference number between "in" and "its" is omitted. ↩ ↩

    5. 2e.

      Manuscript page 1:  “Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element (TE) into the first intron of the gene cortex.”  Manuscript page 2:  Page 2 reports the 87 candidate differences and their elimination down to the one insert. ↩

  3. 3.

    Wise, Kurt P.  “Australopithecus ramidus and the fossil record.”  Creation Ex Nihilo Technical Journal 8(2):160–165.  1994.  Article by Kurt Wise, a young-earth palaeontologist, in Creation Ministries International's technical journal.  Its notes state the young-earth view that post-Flood change expressed variety that was already present.

    1. 3a.

      Page 164:  “the finally assumed morphological diversity was always extant (sometimes largely in latent form) and merely expressed”.  Note 35. ↩

  4. 4.

    Carter, Robert.  “Species were designed to change, part 1.”  Creation Ministries International.  Jun 14, 2021.  Retrieved Sep 27, 2026.  First part of a three-part series by Robert Carter, a geneticist at Creation Ministries International, on how created kinds were made able to change into many species.

    1. 4a.

      “The prevailing idea within creationist circles is that God created distinct “kinds” that were front-loaded with a large amount of genetic diversity that could then be used as the kinds turned into our modern species.” ↩

  5. 5.

    Sanford, John C. et al.  “Adam and Eve, designed diversity, and allele frequencies.”  Proceedings of the Eighth International Conference on Creationism, 200–216.  Creation Science Fellowship.  2018.  Conference paper by John Sanford and colleagues modelling the allele frequencies expected if the first humans were created with designed genetic diversity.  It argues that designed alleles allow fast adaptation with no wait for mutations.

    1. 5a.

      Page 212:  “Designed alleles represent the most effective and the most rapid way to cause selection-driven adaptation. This is because no extended “waiting time” is required. All the required genetic variants are present from the first generation, and are already present at high frequency, enabling very rapid selective progress.” ↩

  6. 6.

    Mosher, Dana S. et al.  “A Mutation in the Myostatin Gene Increases Muscle Mass and Enhances Racing Performance in Heterozygote Dogs.”  PLoS Genetics 3(5):e79.  2007.  Genetic study that found a two-letter deletion in the myostatin gene of whippets, which makes heterozygous dogs faster racers.  Its haplotype and breed data suggest the mutation is recent.  Mirror:  PMC

    1. 6a.

      Section Discussion:  “The mh mutation occurs only on haplotype six, which is identical to haplotype seven except for the deletion itself.”  “Finally, the mutation may not be carried in the greyhound population at all, indicating that it is a relatively new mutation in the purebred dog population.” ↩ ↩

  7. 7.

    Batcher, Kevin et al.  “Multiple FGF4 Retrocopies Recently Derived within Canids.”  Genes 11(8):839.  2020.  Genome study that found five more FGF4 gene copies in canids beyond the two known in short-legged dogs, one of them in red wolves.  The copies in dogs sit on dog haplotypes, so they arose after domestication.  Mirror:  PMC

    1. 7a.

      Section Abstract:  “Five additional and distinct FGF4 retrocopies were identified in canids including a copy unique to red wolves (Canis rufus). The FGF4 retrocopies identified in domestic dogs were identical to domestic dog FGF4 haplotypes, which are distinct from modern wolf FGF4 haplotypes, indicating that these retrotransposition events likely occurred after domestication.” ↩ ↩

  8. 8.

    Colosimo's synonymous difference between the complete and low Eda haplotypes is Ks = 0.01938.24  Two lineages that split t generations ago each collect mutations, so under neutrality Ks ≈ 2μt and t = Ks ÷ 2μ.  With the pedigree rate μ = 5.11 × 10⁻⁹ per base per generation,58 t = 0.01938 ÷ (2 × 5.11 × 10⁻⁹) = 1.90 × 10⁶ generations.  Across Zhang's 95% interval, 4.08 to 6.14 × 10⁻⁹, t runs from 1.58 to 2.38 million generations.  At one generation a year that is 1.9 million years;  at the three years Zhang's team assumed for sea-run fish, 5.7 million.  Caveats:  a genome-wide per-base rate is applied to synonymous sites, which are not all neutral, and the Ks comes from the few genes in the shared region. ↩ ↩ ↩ ↩

  9. 9.

    Han, Fan et al.  “Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches.”  Genome Research 27(6):1004–1015.  2017.  Genome comparison of Darwin's finch species which found that adaptive variants are shared across species through old polymorphism and gene flow, and dated the ALX1 and HMGA2 haplotype groups.  Mirror:  PMC

    1. 9a.

      Section Discussion:  “According to our previous estimates, the haplogroups of ALX1 began to form ∼900,000 years ago, and HMGA2 formed ∼1 million years ago, when finches had just started to radiate”. ↩ ↩

  10. 10.

    Lightner, Jean K.  “Hairy New Findings in Dog Variation: A Different Coat Is as Simple as One, Two, Three.”  Answers in Depth 4.  Sep 16, 2009.  Retrieved Sep 27, 2026.  Article by Jean Lightner, a veterinarian and creationist researcher writing for Answers in Genesis, on the three gene variants behind dog coat types.  She judges that they arose by mutation after the Ark rather than being created.

    1. 10a.

      Section footnote 9:  “Theoretically, God could have created several alleles for different coat characteristics. In these three genes, I think it is more likely that these alleles have arisen through mutation. First, it doesn’t look like these alleles exist in other canids (wolves, coyotes, etc.). If they were represented by the pair on the Ark, these alleles should be quite common in all sorts of canids.” ↩ ↩

  11. 11.

    Vervust, Bart et al.  “Anatomical and physiological changes associated with a recent dietary shift in the lizard Podarcis sicula.”  Physiological and Biochemical Zoology 83(4):632–642.  2010.  Feeding experiment on Pod Mrčaru lizards:  twenty were kept on an insect diet and dissected, and none had cecal valves, against twelve of sixteen caught wild.  Mirror:  Jstor.org

    1. 11a.

      Page 635:  “Lizards maintained on an arthropod diet showed a reduction in the weight of the small intestine and the hindgut. In addition, we found no evidence of cecal valves in any of the twenty specimens that had been fed arthropods. This was in sharp contrast to the high proportion (12/16) of individuals with valves among the freshly caught individuals”. ↩ ↩ ↩

  12. 12.

    Sabolić, I. et al.  “Plastic and genomic change of a newly established lizard population following a founder event.”  Molecular Ecology 33(2):e17255.  2024.  Crossing, common-garden and genome study of the Pod Mrčaru lizards and their source population.  Head and bite traits were heritable, but the differences between the populations did not persist when lizards were raised in the same conditions.

    1. 12a.

      Section Abstract:  “Diverged traits related to head size and shape or bite force showed moderate heritability in a crossing experiment, but between-population differences in these traits did not persist in a common garden environment. Our results confirm the existence of sufficient additive genetic variance for traits to evolve under selection while also demonstrating that phenotypic plasticity and/or genotype by environment interactions are the main drivers of population differentiation at this early evolutionary stage.” ↩ ↩ ↩

  13. 13.

    Each row is copied from the ledger note of the case's own article, where every input is cited:  Darwin's Finches and Sticklebacks, in their notes on the ledger;  Italian Wall Lizards, in its note on the ledger arithmetic;  Peppered Moths and Dog Breeds, in their notes on the ledger.  Each multiplies births by the new mutations a newborn carries, from a genome size and a mutation rate, and compares the total with the number of possible single-letter changes, about three per base.  The stickleback and dog rates were measured in those species.  The finch and lizard rows borrow the average rates measured for birds and for reptiles, because none has been measured in those species.  No mutation rate has been measured in the peppered moth, and no census exists for the Lake Victoria cichlids, so those cells are empty.  Each figure is a rough bound, uncertain by a factor of a few. ↩ ↩

  14. 14.

    Ownbey, Marion.  “Natural hybridization and amphiploidy in the genus Tragopogon.”  American Journal of Botany 37(7):487–499.  1950.  Field and chromosome study by Marion Ownbey that found and named two new Tragopogon species in eastern Washington and Idaho, each with the doubled chromosome sets of a hybrid between two introduced species.

    1. 14a.

      Page 498, section Summary:  “Four small amphiploid populations were discovered in 1949. These represent apparently four recent and independent instances of the doubling of the chromosome sets, two cases each for the T. dubius x porrifolius and T. dubius x pratensis hybrids.” ↩ ↩

  15. 15.

    Cook, L. M. et al.  “Selective bird predation on the peppered moth: the last experiment of Michael Majerus.”  Biology Letters 8:609–612.  2012.  Report of Michael Majerus's predation experiment near Cambridge, 2001 to 2006, written up after his death by three colleagues.  Moths were released at natural densities and birds were watched taking them;  black moths survived less well.

    1. 15a.

      Page 609:  “Majerus released 4864 moths in his six-year experiment, the largest ever attempted for any similar study.”  Page 611, table 2:  Table 2 lists releases for 2001 to 2006;  the 2007 row gives only the local frequency of black moths. ↩

    2. 15b.

      Page 611:  “This gives daily relative survival estimates for melanics of 91 per cent (84–97%) of that of the typical forms.”  The sentence before it gives the maximum-likelihood coefficient against melanics as 0.091 per day, 95% interval 0.028 to 0.157. ↩

    3. 15c.

      Page 611:  “it is virtually impossible to escape the previously accepted conclusion that visual predation by birds is the major cause of rapid changes in frequency of melanic peppered moths”. ↩

  16. 16.

    Grant, Peter R., and B. Rosemary Grant.  40 Years of Evolution: Darwin's Finches on Daphne Major Island.  Princeton University Press.  2014.  Book by Peter and Rosemary Grant summarising forty years of fieldwork on the finches of Daphne Major, 1973 to 2012, including heritability, the reversals of selection and the role of hybridisation in supplying variation.

    1. 16a.

      Page 53:  “When corrected for this bias the heritability of beak size is 0.83 and for beak shape it is 0.88. They are exceptionally high values for wild bird populations.”  The same page gives the rate of extra-pair paternity as "approximately 20%". ↩

    2. 16b.

      Page 72:  “all selection differentials (s) were negative in 1984-85, whereas they were all positive in 1976-77”. ↩

    3. 16c.

      Page 174:  “is three or more orders of magnitude greater than variation introduced by new mutations per generation”.  Only the end of the sentence is quoted. ↩

  17. 17.

    Grant, Peter R., and B. Rosemary Grant.  “Evolution of character displacement in Darwin's finches.”  Science 313(5784):224–226.  2006.  Report by Peter and Rosemary Grant on the 2004-05 drought on Daphne Major, when a larger competitor finch ate the large seeds and selection favoured small-beaked medium ground finches.

    1. 17a.

      Page 224:  “Average selection differentials in standard deviation units for the six measured traits that quantify bill size and shape and body size were 0.774 for males and 0.649 for females.”  The same paragraph says the differentials "were uniformly negative". ↩

  18. 18.

    Grant, Peter R., and B. Rosemary Grant.  “Unpredictable evolution in a 30-year study of Darwin's finches.”  Science 296(5568):707–711.  2002.  Report by Peter and Rosemary Grant on thirty years of measurements of two finch species on Daphne Major.  It compares the first and last samples and finds beak size unchanged but body size and beak shape changed.

    1. 18a.

      Page 711, note 21:  “Mean beak size did not differ between years in either G. fortis (F1,166 = 0.004, P = 0.9480) or G. scandens (F1,50 = 3.108, P = 0.0840)”.  “Beak shape differed between years in both species.”  The note compares the first samples, 1973, with the last, 2001.  The same note reports mean body size significantly smaller in 2001 in both species. ↩

  19. 19.

    Enbody, Erik D. et al.  “Community-wide genome sequencing reveals 30 years of Darwin's finch evolution.”  Science 381(6665):eadf6218.  2023.  Genome sequencing of 3,955 finches of the Daphne Major community by Leif Andersson's and the Grants' groups.  It tracked allele frequencies at six beak loci over thirty years and found the changes were shifts in old variants.

    1. 19a.

      Page 6, article page 6 of 9:  “Allele frequency changes at the six loci (2 to 30%) are greater in G. fortis than in G. scandens (1 to 10%)”. ↩

  20. 20.

    Lamichhaney, Sangeet et al.  “Rapid hybrid speciation in Darwin's finches.”  Science 359(6372):224–228.  2018.  Genome study of the Big Bird lineage on Daphne Major, founded in 1981 by an immigrant male and a local medium ground finch.  It identified the founder's species and showed the lineage bred only within itself from the second generation.

    1. 20a.

      Page 1 of 4:  “A phylogenetic tree analysis showed that the founder male (individual 5110) was not a G. fortis × G. scandens hybrid as previously hypothesized (12), but rather a G. conirostris”.  The abstract adds that he "originated on Española >100 kilometers from Daphne Major." ↩

    2. 20b.

      Section Abstract:  “This example shows that reproductive isolation, which typically develops over hundreds of generations, can be established in only three.” ↩

  21. 21.

    Carter, Robert.  Galápagos finches, rapid speciation, and recent creation.  Creation Ministries International.  Nov 9, 2023.  Article by Robert Carter of Creation Ministries International on what the Daphne Major genomics means for a young-earth model.  He concedes that the beak variants are mutations rather than created diversity.

    1. 21a.

      Section the discussion of mutation near the end:  “When a genetic variant only appears in one animal, one species, or a small group of species within a baramin, we can be fairly certain that this is a new mutation, not created diversity. Thus, the genetic variants that affect beak size and shape among these birds are clearly mutations.” ↩

  22. 22.

    Bell, Michael A. et al.  “Twelve Years of Contemporary Armor Evolution in a Threespine Stickleback Population.”  Evolution 58(4):814–824.  2004.  Field study of Loberg Lake, Alaska, recolonised by sea-run sticklebacks after its fish were poisoned.  Armour forms were counted each year from 1990 to 2001, and the low-armour form went from absent to 75%.

    1. 22a.

      Section Abstract:  “The 1990 sample was nearly monomorphic for the complete plate morph, which is monomorphic in local sea-run populations; the low plate morph, which is usually monomorphic in local freshwater populations, was absent. By 2001, the frequency of completes had declined to 11%, and lows had increased to 75%.”  “Contemporary evolution in this population indicates that threespine stickleback adapt to freshwater habitats within decades after invasion from the ocean”. ↩

  23. 23.

    Roberts Kingman, Garrett A. et al.  “Predicting Future from Past:  The Genomic Basis of Recurrent and Rapid Stickleback Evolution.”  Science Advances 7(25).  Jun 18, 2021.  Genome study from David Kingsley's laboratory of Alaskan lakes founded by sea-run sticklebacks, sampled year by year to 2017 and compared with long-established freshwater and marine populations.  The regions that changed fastest were almost all regions already known to differ between old freshwater and marine fish.  Mirror:  PMC

    1. 23a.

      Section Rapid contemporary evolution and TempoPeak identification:  “Bell et al. (47) introduced ~3000 anadromous RS fish into each of two other Cook Inlet lakes without outlets that had been similarly treated to exterminate fish: Cheney Lake (CH) in 2009 and Scout Lake (SC) in 2011. Low–armor-plated (~5 to 7 plates per side) stickleback began to appear in the second and third generation after founding in CH and SC respectively, and, by 2017, they had increased to 20 to 30% (Fig. 2B).” ↩

    2. 23b.

      Section Rapid contemporary evolution and TempoPeak identification:  “In both CH and SC, the G allele increases rapidly from an initial frequency of <1% to over 50% within 8 years, while approaching fixation in LB by 15 years.” ↩

    3. 23c.

      Section Rapid contemporary evolution and TempoPeak identification:  “we identified 524 sensitive and 344 specific TempoPeaks. Despite operating over very different time spans, the visual correspondence between the Pacific EcoPeaks in long-established populations and the TempoPeaks in recently established populations is notable, particularly for the specific TempoPeaks, of which 323 of 344 (94%) overlap with the sensitive Pacific EcoPeaks”. ↩

  24. 24.

    Colosimo, Pamela F. et al.  “Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles.”  Science 307(5717):1928–1933.  Mar 25, 2005.  Genetic study that found Eda as the gene behind armour loss and showed that low-armour freshwater populations around the world share one old low allele, which also occurs at low frequency in sea-run fish.  It dated the allele against lineages dated by geology.  Mirror:  Zoology.ubc.ca

    1. 24a.

      Page 1930:  “Eight of 109 completely plated fish from NAV were heterozygous for complete and low-morph alleles at both markers, which gave an estimated frequency of low-morph alleles of 3.8% (8/218 chromosomes). One of 302 completely plated marine sticklebacks collected from LITC was also heterozygous at both markers and gave an estimated allele frequency of 0.2% (1/604 chromosomes).” ↩

    2. 24b.

      Page 1930:  “To estimate the age of the shared haplotype, we examined the rate of neutral sequence evolution at third–base pair positions from all genes (EDA to Garp) in the shared region.”  Pages 1930–1931:  “thought to have diverged”.  “on the basis of genetic and geological estimates”.  “on the basis of the split between Pacific and Atlantic populations”.  Page 1931:  “(Ks values of 0.01938, 0.01384, and 0.05875, respectively). The common clade of low-plated alleles thus probably arose between 2 and 10 million years ago.”  The calibration sentences are quoted in pieces;  the approximate calibration dates between the pieces are left out. ↩

  25. 25.

    O'Brown, Natasha M. et al.  “A Recurrent Regulatory Change Underlying Altered Expression and Wnt Response of the Stickleback Armor Plates Gene EDA.”  eLife 4:e05290.  Jan 28, 2015.  Laboratory study from David Kingsley's group that traced the shared low-armour allele to one T to G change in an Eda enhancer.  Recreating the change in a marine enhancer lowered expression in the armour plates and left other tissues alone.  Mirror:  PMC

    1. 25a.

      Section Abstract:  “Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates.”  “Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.” ↩

  26. 26.

    Chan, Yingguang Frank et al.  “Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer.”  Science 327(5963):302–305.  2010.  Genetic study of 34 stickleback populations from David Kingsley's laboratory that traced pelvic loss to deletions of one enhancer of the Pitx1 gene.  Different populations carry different deletions, each overlapping the same region.  Mirror:  PMC

    1. 26a.

      Section Nature of mutations in pelvic-reduced fish:  “Nine of the 13 pelvic-reduced stickleback populations—but zero out of 21 pelvic-complete populations—showed consistent missing genotypes for multiple consecutive SNP markers located in and around the Pel enhancer”.  “The larger genotyping survey identified a total of nine different haplotypes with different staggered deletions, each consistently seen within a pelvic-reduced population, and each overlapping or completely removing the Pel enhancer region (Figs. 4 and S8).” ↩

  27. 27.

    Herrel, Anthony et al.  “Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource.”  Proceedings of the National Academy of Sciences 105(12):4792–4795.  Mar 25, 2008.  Field study from Anthony Herrel's group comparing the Italian wall lizards of Pod Mrčaru, introduced in 1971, with their source population on Pod Kopište.  It reported plant eating, bigger heads, harder bites and cecal valves, and called for tests of plasticity and maternal effects.  Mirror:  PMC

    1. 27a.

      Page 4792:  “plants composing between 34% (spring) and 61% (summer) of the total volume of the food eaten”.  “In contrast, plant consumption was low (7% to 4%) and did not differ seasonally for lizards from the source population”.  Page 4795:  Methods:  330 lizards stomach-flushed, 119 from Pod Kopište and 211 from Pod Mrčaru. ↩

    2. 27b.

      Page 4794:  “Although the presence of cecal valves and large heads in hatchlings and juveniles suggests a genetic basis for these differences, further studies investigating the potential role of phenotypic plasticity and/or maternal effects in the divergence between populations are needed.” ↩ ↩

  28. 28.

    Wehrle, Beck A. et al.  “Rapid dietary shift in Podarcis siculus resulted in localized changes in gut function.”  Physiological and Biochemical Zoology 93(5):396–415.  2020.  Study of gut function in the two lizard populations, with Anthony Herrel as a co-author.  It found that the valves vary between individuals and judged them not fixed features of the Pod Mrčaru lizards.  Mirror:  Hal.science

    1. 28a.

      Page 409:  “convince us that, although usually present, the HG valves in P. siculus may be flexible in their morphology or even in their presence, and”.  Page 410:  “they are not fixed features in the Pod Mrčaru lizards.” ↩

  29. 29.

    Sherpa, Stéphanie et al.  “Genetic depletion does not prevent rapid evolution in island-introduced lizards.”  Ecology and Evolution 13(11):e10721.  2023.  Genome scan of about 82,000 loci in the introduced and source lizard populations.  It found a founder effect and a handful of loci with large allele shifts, none tied to a trait.  Mirror:  PMC

    1. 29a.

      Section Abstract:  “Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction and very low neutral genetic differentiation between the introduced population and its source.”  “Our genome‐scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large‐effect loci and/or that phenotypic plasticity plays a major role in phenotypic changes.” ↩

  30. 30.

    Parker, Heidi G. et al.  “Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development.”  Cell Reports 19(4):697–708.  2017.  Genome study of dog breeds from Elaine Ostrander's laboratory at the US National Human Genome Research Institute.  It builds a tree of breeds and recovers their documented crosses from DNA.  Mirror:  PMC

    1. 30a.

      Section Introduction:  “the diversity of talents and phenotypes combined with an unequalled emotional connection between dog and man has led to the creation of more than 350 distinct breeds, each of which is a closed breeding population that reflects a collage of defining traits”. ↩

  31. 31.

    vonHoldt, Bridgett M. et al.  “Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication.”  Nature 464(7290):898–902.  2010.  Genome survey of dogs and grey wolves that traced dogs to wolves, mainly of the Middle East, and placed the making of modern breeds in the Victorian era.  Mirror:  PMC

    1. 31a.

      Section main text, first paragraph:  “Given that modern breeds are the products of controlled breeding practices of the Victorian era (circa 1830–1900)”.  The same paper traces dogs to grey wolves, mainly of the Middle East. ↩

  32. 32.

    Plassais, Jocelyn et al.  “Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids.”  Current Biology 32(4):889–897.  2022.  Genome study of an IGF1 size variant in modern dogs, wild canids and ancient wolves.  It found that the small-size allele is the ancestral state in canids and that the large allele arose in wolves.  Mirror:  PMC

    1. 32a.

      Section Results and Discussion:  “Interestingly, except for the two red wolves from North America (20–35kg), all canids (coyotes, jackals, African wolves and hunting dogs, dholes and foxes) possessed the small allele in a homozygous state, suggesting that the small allele is the ancestral state.” ↩

  33. 33.

    Trut, Lyudmila N.  “Early Canid Domestication: The Farm-Fox Experiment.”  American Scientist 87(2):160–169.  1999.  Account by Lyudmila Trut, head of the research group, of forty years of the Novosibirsk experiment selecting silver foxes for tameness alone.

    1. 33a.

      Page 161:  “Belyaev began his experiment in 1959”. ↩

    2. 33b.

      Page 163:  “He began with 30 male foxes and 100 vixens, most of them from a commercial fur farm in Estonia. The founding foxes were already tamer than their wild relatives.” ↩

  34. 34.

    Kukekova, Anna V. et al.  “Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours.”  Nature Ecology & Evolution 2(9):1479–1491.  2018.  Genome study that sequenced tame, aggressive and ordinary farm foxes from the Novosibirsk lines and looked for regions where selection had reduced variation or increased divergence.  Mirror:  PMC

    1. 34a.

      Section Abstract:  “Analysis of the resequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations.” ↩

  35. 35.

    Laurie, Cathy C. et al.  “The Genetic Architecture of Response to Long-Term Artificial Selection for Oil Concentration in the Maize Kernel.”  Genetics 168(4):2141–2155.  2004.  Genetic mapping study of the Illinois Long-Term Selection Experiment on maize kernel oil, begun in 1896.  It mapped more than 50 loci behind the response and discussed whether new mutation or the starting variation drove a century of change.  Mirror:  PMC

    1. 35a.

      Section Introduction:  “At generation 89, selection in ILO was discontinued because of poor viability and an oil concentration so low that it cannot be measured accurately. At this point, the populations had changed from 4.7% oil to 19.3% in IHO and 1.1% in ILO.” ↩

    2. 35b.

      Section Discussion:  “Furthermore, Walsh (2004) used population genetics theory to suggest that the majority of response in IHO and ILO was due to new mutation, primarily because most of the initial variation would be rapidly fixed by selection and/or random drift in the small population sizes experienced by the selection lines (Ne ∼ 10). However, Keightley (2004) notes that responses due to new mutation often involve sudden changes in mean performance, while those due to standing variation tend to be relatively smooth (like the Illinois selection responses).” ↩

    3. 35c.

      Section Discussion:  “Unfortunately, the genetic architecture results do not seem to have a direct bearing on the importance of new mutations.” ↩

  36. 36.

    Moose, Stephen P. et al.  “Maize selection passes the century mark: a unique resource for 21st century genomics.”  Trends in Plant Science 9(7):358–364.  2004.  Review of the Illinois maize selection lines at their hundredth generation by researchers at the University of Illinois, including how much genetic diversity remains in them.

    1. 36a.

      Page 362:  “The degrees of allelic diversity and heterozygosity remaining in the Illinois Selection Strains are too high to be explained by mutation”. ↩

  37. 37.

    Chester, Michael et al.  “Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae).”  Proceedings of the National Academy of Sciences 109(4):1176–1181.  2012.  Chromosome study of natural Tragopogon miscellus populations, which gives the species' age as about 80 years and 40 generations.  Mirror:  PMC

    1. 37a.

      Section Introduction:  “This species is ∼80 y old (ca. 40 generations for this biennial), having formed repeatedly in North America after the introduction of its diploid (2n = 12) progenitors, Tragopogon dubius and Tragopogon pratensis, from Europe in the early 1900s”. ↩

  38. 38.

    Lim, K. Yoong et al.  “Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae).”  PLoS ONE 3(10):e3353.  Oct 9, 2008.  Chromosome study of the two young Tragopogon polyploids, which reports their present range and how many times each has formed.

    1. 38a.

      Section Introduction:  “The two allotetraploids now occupy a large geographic area of eastern Washington and adjacent Idaho, USA, and comprise many thousands of individuals in several populations. Molecular analyses have revealed that T. mirus has recurrently formed at least 13 times and T. miscellus possibly as many as 21 times”. ↩

  39. 39.

    Newton, W. C. F., and Caroline Pellew.  “Primula kewensis and its derivatives.”  Journal of Genetics 20(3):405–467.  1929.  Report from the John Innes Horticultural Institution on Primula kewensis, a sterile hybrid that three times produced fertile plants with doubled chromosomes.

    1. 39a.

      Page 424:  “The diploid hybrid has been observed to set seed on three occasions, and each time the seed produced has given rise to tetraploid plants. The first was in 1905, five years after the first appearance of the hybrid, in the nurseries of Messrs Veitch; the second, in 1923, at Kew; and the third, in 1926, at this Institution.”  “This Institution” is the John Innes Horticultural Institution. ↩

  40. 40.

    Buggs, Richard J. A. et al.  “Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin.”  Current Biology 22(3):248–252.  2012.  Genome study of natural Tragopogon miscellus populations of separate origin, which measured how many duplicate gene copies had already been lost since the doubling.

    1. 40a.

      Section Frequency of Homeolog Loss:  “An average of 13 (∼20%) of the 70 loci investigated in each plant of T. miscellus were missing alleles of one homeolog, with high variation (min = 0, max = 33, SD = 6.8).”  “on average at least 7.7% (SD = 4.3) of the original 280 allele copies have been lost in an individual plant's lineage since WGD.”  WGD is whole-genome duplication.  A homeolog is one of the two parental copies of a gene. ↩

  41. 41.

    Feder, Jeffrey L. et al.  “Host fidelity is an effective premating barrier between sympatric races of the apple maggot fly.”  Proceedings of the National Academy of Sciences 91(17):7990–7994.  1994.  Field study of the apple and hawthorn races of the apple maggot fly, which measured how far the flies' fidelity to their host plant restricts gene flow between the races.  Mirror:  PMC

    1. 41a.

      Page 7990:  “we confirm that host fidelity (i.e., the tendency of an insect to reproduce on the same host species that it used in earlier life-history stages) restricts gene flow between sympatric apple- and hawthorn-infesting races of Rhagoletis pomonella (Diptera: Tephritidae) to ≈6% per generation.” ↩

  42. 42.

    Feder, Jeffrey L. et al.  “Allopatric genetic origins for sympatric host-plant shifts and race formation in Rhagoletis.”  Proceedings of the National Academy of Sciences 100(18):10314–10319.  2003.  Genetic study of the apple maggot fly which traced the chromosomal inversions behind the apple and hawthorn races to an older split between Mexican and northern populations.  Mirror:  PMC

    1. 42a.

      Section Introduction:  “Thus, the sympatrically derived apple race was extracted, in part, from preexisting adaptive inversion clines in the haw race.”  The abstract dates the separation of the Mexican and northern populations to about 1.57 million years ago, from sequence differences. ↩

  43. 43.

    Coyne, Jerry A., and H. Allen Orr.  Speciation.  Sinauer Associates.  2004.  Standard textbook on speciation by Jerry Coyne and H. Allen Orr.  It reviews the laboratory selection experiments and the evidence for polyploid speciation.

    1. 43a.

      Pages 90–91:  “More than half of the published experiments showed either pre- or postzygotic isolation. Although this proportion may reflect a publication bias, obtaining isolation as a byproduct of selection cannot be rare. More surprisingly, such isolation can evolve within 10-100 generations, a blink of the eye in evolutionary time. Although in no case was reproductive isolation complete, one does not expect full speciation to occur in so few generations.”  The passage crosses from page 90 to page 91 in the middle of the word “proportion”. ↩

  44. 44.

    Haba, Yuki et al.  “Ancient origin of an urban underground mosquito.”  Science 390.  Oct 23, 2025.  Genome study of about 350 modern and museum mosquitoes that traced the London Underground mosquito to the Mediterranean or Middle East more than a thousand years ago, overturning the story that it evolved in the Underground.  Mirror:  Africamuseum.be

    1. 44a.

      Page 1:  “Population genomic analysis of ~350 contemporary and historical samples counters the popular hypothesis that molestus originated belowground in London <200 years ago. Instead, we show that molestus first adapted to human environments aboveground in the Mediterranean or Middle East over the course of more than 1000 years, possibly in association with ancient agricultural civilizations of the Middle East.” ↩

  45. 45.

    Sarfati, Jonathan.  “Arguments we think creationists should NOT use.”  Creation Ministries International.  2026.  Creation Ministries International's standing list of arguments it advises creationists not to use, maintained by Jonathan Sarfati.

    1. 45a.

      Section Which arguments should definitely not be used?:  “This is not true—new species have been observed to form. In fact, rapid speciation is an important part of the creation model. But this speciation is within the ‘kind’, and involves no new genetic information”.  The list entry is headed “No new species have been produced.” ↩

  46. 46.

    Johnson, Thomas C. et al.  “Late Pleistocene desiccation of Lake Victoria and rapid evolution of cichlid fishes.”  Science 273(5278):1091–1093.  Aug 23, 1996.  Geological study that took seismic profiles and piston cores of the Lake Victoria floor and found an old soil showing that the lake dried out.  Its authors concluded that the cichlid flock evolved very fast.  Mirror:  Jstor.org

    1. 46a.

      Page 1091:  “Lake Victoria is the largest lake in Africa and harbors more than 300 endemic species of haplochromine cichlid fish. Seismic reflection profiles and piston cores show that the lake not only was at a low stand but dried up completely during the Late Pleistocene, before 12,400 carbon-14 years before the present. These results imply that the rate of speciation of cichlid fish in this tropical lake has been extremely rapid.” ↩

  47. 47.

    Seehausen, Ole.  “Patterns in fish radiation are compatible with Pleistocene desiccation of Lake Victoria and 14 600 year history for its cichlid species flock.”  Proceedings of the Royal Society of London B 269:491–497.  2002.  Analysis by Ole Seehausen of species-formation rates across fish radiations, defending the short history of the Lake Victoria flock.  It defines the doubling-time measure of speciation rate used in this series.  Mirror:  PMC

    1. 47a.

      Page 491:  “Geophysical data are currently being interpreted as evidence for a late Pleistocene desiccation of Lake Victoria and its refilling 14 600 years ago. This implies that between 500 and 1000 endemic cichlid fish species must have evolved in 14 600 years, the fastest large-scale species radiation known.” ↩ ↩

    2. 47b.

      Page 492:  “Net speciation intervals (SI, where net speciation = gross speciation − extinction) in thousands of years are calculated as the mean doubling time of species number”.  The logarithmic model, same page:  SIlog = t × ln 2 ÷ (ln Nt − ln N0). ↩

  48. 48.

    Wienhues, Giulia et al.  “From desiccation to wetlands and outflow:  Rapid re-filling of Lake Victoria during the Latest Pleistocene 14–13 ka.”  Journal of Great Lakes Research 50(3):102246.  2023.  Core study of Lake Victoria's refilling which found wetlands with permanent shallow ponds in the basin before the deep lake returned.  Mirror:  Boris.unibe.ch

    1. 48a.

      Page 1:  “At our coring site in the central basin, local Typha wetlands existed >16.7 ka, alternating with periods of desiccation. Moisture increased slightly between ca. 16.7 – 14.5 ka and wetlands with permanent, shallow ponds established simultaneously in the center and the marginal, more elevated parts of the flat lake basin.”  “Whereas consensus exists on widespread desiccation of Lake Victoria ∼18 – 17 ka, the re-filling history (16 – 13 ka) has remained highly controversial.” ↩

  49. 49.

    Meier, Joana I. et al.  “Ancient hybridization fuels rapid cichlid fish adaptive radiations.”  Nature Communications 8:14363.  Feb 10, 2017.  Genome study which found that the Lake Victoria region cichlid flock descends from a hybrid swarm of two river lineages, and that its adaptive variants were mostly sorted from those parents.

    1. 49a.

      Page 3:  “we estimate the split of this lineage from the Congolese lineage to date to ~1.6–5.8 million years ago, coincident with the uplift of the flanks of the Western branch of the East African Rift”.  Methods, page 8:  dated with BEAST on mitochondrial D-loop and ND2 sequences and four different sets of calibration nodes. ↩ ↩

    2. 49b.

      Page 5:  “the two haplotype classes51 in the LVRS are each shared exclusively with just one of these parental lineages”.  The 51 is a reference numeral. ↩

    3. 49c.

      Page 7, figure 5a:  “novel LV allele or unsampled in parental lineages”.  Category counts and outlier shares from the figure:  category 1, 10,799 sites, 1.4%;  category 2, 1,053, 7.9%;  category 3, 1,038, 9.7%;  category 4, 100, 20%.  10,799 × 0.014 ≈ 151 of the 340 outliers.  The legend gives 12,890 SNPs and 340 outliers. ↩

  50. 50.

    Malinsky, Milan et al.  “Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow.”  Nature Ecology & Evolution 2:1940–1955.  2018.  Genome study of Lake Malawi cichlids that measured a cichlid mutation rate from parents and offspring and used it to date splits within the lake.  Mirror:  PMC

    1. 50a.

      Section Low per-generation mutation rate:  “The overall mutation rate (μ) was estimated at 3.5×10-9 (95%CI: 1.6×10-9 to 4.6×10-9) per bp per generation, approximately three to four times lower than in human27, although, given much shorter mean generation times, the per-year rate is still expected to be higher in cichlids than in humans.” ↩

    2. 50b.

      Section Origins of the radiation:  “Applying our per-generation mutation rate to observed genomic divergences we obtained mean divergence time estimates between these lineages between 460 thousand years ago (ka) [95%CI: (350ka to 990ka)] and 390ka [95%CI: (300ka to 860ka)] (Fig. 4f), assuming three years per generation as in ref. 55.” ↩ ↩ ↩

  51. 51.

    Jeanson, Nathaniel T.  Replacing Darwin:  The New Origin of Species.  Master Books, Green Forest, Arkansas.  2017.  Book by Nathaniel Jeanson, a young-earth biologist, setting out his model of created heterozygosity and post-Flood speciation.

    1. 51a.

      Page 234:  “In other words, I claimed that the ancestors to modern species were created with heterozygous chromosome pairs.” ↩

  52. 52.

    Marques, David A. et al.  “A Combinatorial View on Speciation and Adaptive Radiation.”  Trends in Ecology and Evolution 34(6):531–544.  2019.  Review by David Marques, Joana Meier and Ole Seehausen arguing that rapid speciation and adaptive radiation mostly reassemble old genetic variation into new combinations.  Mirror:  Repository.cam.ac.uk

    1. 52a.

      Section The combinatorial mechanism:  “A combinatorial mechanism allows early and rapid speciation at the time ecological opportunity arises even when geographical isolation is lacking, as there is no waiting time for relevant mutations”.  Manuscript page 9. ↩

  53. 53.

    Doubling times use Ole Seehausen's net speciation interval, years × ln 2 ÷ ln(final species ÷ starting lineages).47  The average kind:  628 kinds to 39,586 living species in 4,400 years gives 4,400 × 0.693 ÷ ln 63.0 = 736 years.  Mammal kinds:  137 kinds to 6,650 land species gives 4,400 × 0.693 ÷ ln 48.5 = 786 years.  The inputs and their sources are in the rate note of The Creation Model of Rapid Speciation.  Lake Victoria:  500 species from one or two founding lineages in 14,600 years47 gives 14,600 × 0.693 ÷ ln 500 = 1,628 years and 14,600 × 0.693 ÷ ln 250 = 1,833 years, as worked in the rate note of Cichlid Radiations.  The ratios run from 1,628 ÷ 786 = 2.1 to 1,833 ÷ 736 = 2.5.  The 4,400 years is the round figure the series uses for the time since the Flood, and the 14,600 years is Seehausen's reading of a radiocarbon date. ↩ ↩

  54. 54.

    Barrett, Rowan D. H. et al.  “Natural Selection on a Major Armor Gene in Threespine Stickleback.”  Science 322(5899):255–257.  Oct 10, 2008.  Pond experiment from Dolph Schluter's laboratory in which sea-run sticklebacks carrying both Eda alleles bred in freshwater ponds and their offspring were genotyped through a season.  The offspring were born in Mendelian ratios, and selection then moved the allele frequency.  Mirror:  Zoology.ubc.ca

    1. 54a.

      Page 256:  “Genotype frequencies at Eda in the F1 generation were not significantly different from the predicted 1:2:1 ratio (Fig. 2A)”. ↩

  55. 55.

    Walsh, Benjamin D.  “The apple-worm and the apple-maggot.”  The American Journal of Horticulture and Florist’s Companion 2:338–343.  J. E. Tilton.  1867.  Note by Benjamin Walsh, an entomologist, recording that the apple maggot had recently begun to attack cultivated apples in New England and New York.

    1. 55a.

      Page 338:  “The second larva, the apple-maggot, is a native-American species, and breeds naturally in our wild haws and crabs, but, within the last few years, has been noticed to attack the cultivated apple in Massachusetts, in Connecticut, in New York, and probably in Vermont also.” ↩

  56. 56.

    Xie, Kathleen T. et al.  “DNA Fragility in the Parallel Evolution of Pelvic Reduction in Stickleback Fish.”  Science 363(6422):81–84.  Jan 4, 2019.  Laboratory and modelling study from David Kingsley's group showing that the Pitx1 pelvic enhancer sits in a fragile stretch of DNA that breaks unusually often.  Mirror:  PMC

    1. 56a.

      Section Main text, paragraph beginning Could elevated mutation rates:  “Population genetic modeling indicates that new mutations occurring at the low rates of typical single nucleotide changes (~10⁻⁹) would rarely arise at a particular locus in postglacial stickleback populations, while mutations occurring at elevated rates (~10⁻⁵ for fragile sites) would arise often.” ↩

  57. 57.

    Mitchell, Elizabeth.  “Sticklebacks Recycling Ancient Genetic Information.”  Answers in Genesis, News to Know.  Apr 14, 2012.  Retrieved Sep 27, 2026.  News article by Elizabeth Mitchell of Answers in Genesis on the 2012 stickleback genome study, stating the young-earth reading of the reused genes.

    1. 57a.

      “The “ancient genes” the fish seems to switch on and off are the genetic information God provided in order to enable this fish to adapt to various environments, with the ultimate variety in each environment regulated by natural selection and other factors.”  “This variation is not accomplished by acquiring new information but by reshuffling, regulating, and sometimes losing old information.” ↩

  58. 58.

    Zhang, Chaowei et al.  “Rate of De Novo Mutations in the Three-Spined Stickleback.”  Heredity 134(7):387–395.  2025.  Pedigree study that sequenced stickleback parents and offspring and counted 115 new mutations, giving a directly measured mutation rate and spectrum for the species.  Mirror:  PMC

    1. 58a.

      Section Results:  “In addition to the typically high proportion of C > T mutations, whether at CpG sites or not, an elevated number of C > A mutations was observed in both species as well”.  Section Discussion:  “CpG sites outside CpG islands (CGIs) exhibit higher µ than the genome-wide average in three-spined sticklebacks”. ↩

    2. 58b.

      Section Results:  “After applying a series of filters, 115 unique de novo mutations (DNMs) were detected”.  “The overall average per-generation point DNM rate was estimated to be µ = 5.11 × 10^−9/bp/gen (95% confidence interval: 4.08–6.14 × 10^−9/bp/gen, with zero-inflated method being 5.07 × 10^−9/bp/gen)”.  “Assuming a generation time of 3 years for the marine three-spined sticklebacks, the yearly mutation rate would be, on average, 1.70 × 10^−9/bp/year.” ↩