On pages 6 and 7 of this topic thread, Sea Breeze (probably this site's
foremost outspoken young Earth creationist critic of evolution) says
that the science of genetics (combined with the idea of information
theory) prove that mutations and natural selection could not have have resulted in macroevolution, but he is wrong.
Yesterday I found a science essay article which presents very strong genetic evidence of what causes most macroevolution, including such having happened in a punctuated equilibrium manner! See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7029956/ . It has an abstract of an article from February 2022 called "The Developmental Gene Hypothesis for
Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes
and Transposable Elements". It provides the answer I have been looking for years. It is similar to partial answers I have found years ago, but it is expansion of those. According to my understanding of the article, the cause of macroevolution in a punctuated equilibrium manner is as follows. Most the needed mutations for such happen in noncoding sections of the genome which acquired insertions of transposable
elements (TE). Since that area is noncoding such mutations did not harm organisms. Later some of the insertions were transposed to in or near transcriptional and
developmental genes. When such insertions were beneficial it resulted in sudden macroevolution (but when they were unfavorable the result was "... typically incompatible with life and often lead to
miscarriage or serious functional impairment preventing further
inheritance"). The DevReg genes were thus were high conserved, with only the beneficial changes being passed on from individuals' offspring beyond one generation. [Regarding one instance the article says the following. "In this instance, the variation intolerance of DevReg genes provides an
active safeguard against mutational events. Surprisingly, CNE within
long genes such as DevReg genes are not mutation cold spots despite
their functional sensitivity. Instead, such mutations are typically
incompatible with life and often lead to miscarriage or serious
functional impairment preventing further inheritance. [41,42] "] The article says the following.
'Theories of the genetics underlying Punctuated Equilibrium (PE) have
been vague to date. Here we propose the Developmental Gene Hypothesis,
which states that: 1) developmental regulatory (DevReg) genes are
responsible for the orchestration of metazoan morphogenesis and their
extreme conservation and mutation intolerance generates the equilibrium
or stasis present throughout much of the fossil record; and 2) the
accumulation of regulatory elements and recombination within these same
genes—often derived from transposable elements—drives punctuated bursts
of morphological divergence and speciation across metazoa. This two-part
hypothesis helps to explain the features that characterize PE,
providing a theoretical genetic basis for the once-controversial theory.
... Detractors of punctuated equilibrium have previously chided
the theory as a mechanism with “no scientific use” as they claimed it
could not be tested at the genetic level. [2]
However, with the advent of large-scale genomic sequencing and
extensive molecular and computational study of numerous genomes, our
wealth of available data has grown substantially since the early battles
over Gould and Eldredge’s theory. [3]
Since that time we have been able to study not only transposable
elements (TE) (i.e., “selfish DNA”) and their roles in molecular
evolution, but also the subset of genes responsible for the regulation
of morphogenesis reflected in the fossil record.
Here,
we propose that there is a native genetic complement to TE insertions
leading to features of punctuated equilibria in both the vertebrate and
invertebrate fossil records. Specifically, this complement lies within
the developmental regulatory (DevReg) genes responsible for
morphogenesis and their unique mutational patterns, as well as the
elements that regulate their expression. The genes’ relative mutation
intolerance suggests a means by which morphology is actively conserved
even in the face of exaggerated TE activity. [4]
Yet they also exhibit a clear history of TE insertion that is strongly
correlated to the presence of conserved noncoding elements (CNE) and
changes to gene regulation and phenotype by acting as promoters,
enhancers, repressors, terminators, insulators, and post-transcriptional
effectors.[4–7]
In addition, TE-derived RNA may act as direct regulators of these
important developmental genes, strongly reminiscent of Barbara
McClintock’s “controlling elements”. [7,8] Alongside the TE-Thrust Hypothesis [9] and the TE-epigenomic arms race proposed by Zeh et al. [10], as well as the large body of work spearheaded by Eric Davidson [11,12] concerning the roles of the regulome in speciation, we believe the Developmental Gene Hypothesis
may help explain the long periods of active morphological stasis within
the fossil record bookended by rare TE-associated mutational events
that have long lasting effects on phenotype and have been tightly
conserved over evolutionary time [4,13] (Fig. 1).
... Although evolution of the eukaryotic exome has been relatively conserved
across time, evolution of the regulome seems to account for
considerable interspecies variation. [11,13]
The regulome is both a seat of rapid evolutionary development, as in
the case of species-specific TE regulatory exaptation, and extreme
conservation in the form of conserved (CNE) and ultraconserved noncoding
elements (UCNE). [14–16]
UCNE networks are likewise strongly conserved across species in the
form of gene regulatory blocks surrounding important developmental
genes. [17]
... Many of the UCNE are located in or near transcriptional and
developmental genes, as are many of the younger less conserved noncoding
elements unique to later phylogenetic branches, suggesting a strong
directional selection for the retention and exaptation of potential
noncoding elements in these regions [15,18]
... While genetic isolation and ultimately hybrid dysgenesis ensure
speciation, the evolution of DevReg genes plays a fundamental role in
the type of morphological divergence that originally inspired the
Linnaean classification system. [45] ... it has subsequently been demonstrated that morphological evolution
correlates better with regulatory gene divergence rather than with
overall rates of molecular evolution. [48–50]
Thus, the variation intolerance we see in DevReg genes appears to be
responsible for the significant periods of morphological stasis present
in the fossil record. Meanwhile, other gene groups evolve at a more
rapid, and perhaps more constant, rate.
... Since the publication of the theory of punctuated equilibrium,
detractors have sometimes criticized its dependence on an imperfect
fossil record and the lack of an underlying genetic theory. [1] Oliver and Greene [9] and Zeh et al. [10]
made significant strides by proposing genetic and epigenetic mechanisms
that help explain the long periods of stasis bookended by periods of
comparatively rapid change. Likewise, the body of work by Eric Davidson
clearly outlines numerous regulatory mechanisms leading to morphological
divergence across species. [11,12]
These works, however, do not recognize the active role DevReg genes
play in maintaining morphological stasis, their propensity to collect
TE-derived noncoding elements over time, or their tendency to be
regulated by TE-derived RNA. [8]
All of these presumably underlie changes in gene function and
morphology relevant to the patterns within the fossil record first
recognized by Gould and Eldredge. [3] The Developmental Gene Hypothesis helps to fill in these important gaps.
... Within mammals, there are strong links between TE activity and speciation. [56,57]
As mentioned, TEs provide a prime source of potential regulatory
material to the host genome and the primate lineage is an excellent
example of such a relationship.
... TE insertions have also played an important role in the evolution of
pregnancy, particularly in the decidualization of the connective tissue
within the uterus. For instance, certain endogenous retroviruses (ERV)
are highly expressed in mammalian uterus in a tissue-specific manner
and, among other things, help to drive cell fusion within the
trophoblast layers via action of the ERV-derived envelope glycoprotein,
syncytin. [75,76] Interestingly, the Mabuya
lizard, which evolved approximately 25 million years ago (mya), is
viviparous and has an unusually mammalian-like placenta that also
expresses an ERV-derived envelope glycoprotein functionally identical to
mammalian syncytin. [77]
Similarly, fossilized evidence of the Jurassic marine reptiles,
ichthyosaurs, show they were also viviparous, indicating that live birth
has evolved multiple times in the reptilian lineage and may commonly be
linked with the exaptation of retroviruses (see Fig. 4).
Thousands of other transposon-derived cis-regulatory elements
have been identified that also regulate placental function, many of
which have been exapted as hormone response elements (HRE). [78] For instance, Alu elements have been shown to house high-affinity binding sites for the estrogen, thyroid, and retinoic acid receptors. [79] SVA elements likewise appear to house HRE half-sites and also bind the glucocorticoid receptor. [80]
Therefore, evidence suggests that both TE-derived HRE and ERV-derived
envelope glycoproteins have played important roles in the evolution of
mammalian pregnancy.
... 4. Conclusions and Outlook
While punctuated equilibrium as a theory
has stood the test of time, until now there has been no clear genetic
explanation for the trends present within the fossil record. Work by
Oliver and Greene [9], Zeh et al. [10], and Davidson [11] provide admirable starting points and, we think, vital pieces of the larger story.
The
Developmental Gene Hypothesis, however, proposes a clear and testable
mechanism for stasis via the strong purifying selection acting upon
DevReg genes. Likewise, a measurable record of transposable element
insertion, exaptation, and recombination within these same genes
provides a primary mechanism for bursts of adaptation and evidence of
accelerated evolution in these genes across select species lends further
support to this notion.'
