Very interesting article and corresponding research which lends an applied
science perspective to some of the recent conversations on the forum.
In the ScienceDaily article ‘Genome study reveals 30 years of Darwin's finch
evolution <https://www.sciencedaily.com/releases/2023/09/230929171007.htm> ’
we read:
‘An international team of researchers has released a landmark study on
contemporary evolutionary change in natural populations. Their study uses
one of the largest genomic datasets ever produced for animals in their
natural environment, comprising nearly 4,000 Darwin's finches. The study has
revealed the genetic basis of adaptation in this iconic group.’
‘The strength of Darwin's finches as a study organism lies in what they can
show about the early stages of speciation. Peter and Rosemary Grant
(Princeton University) tracked nearly every individual on Daphne Major
starting in the 1970s. Their work demonstrates that the finches of Daphne
Major evolved in response to changes in the environment and interactions
among species. An international team has sequenced the genomes of nearly
every finch studied on Daphne and revealed the genetic architecture of
adaptive change.’
‘Over the three decades studied, the beak of the Medium Ground-Finch has
become smaller. Using the genomes of all the finches on Daphne, the
researchers show that this results from genes transferring from the Small
Ground-Finch through hybridisation and periods of drought where individuals
with smaller beaks survived better.’
‘This study paints a dynamic picture of how species adapt to changing
environments through a combination of genetic changes of large phenotypic
effects that are sometimes transferred between species. As the global
environment continues to change, the finches of the Galápagos island will
provide a valuable window into understanding how birds, their genetic
constitution, and their environment interact to shape the future of wild
populations.’
In the background published research (attached), I’ve endeavored to
summarize the background, the two main observations and the concluding
take-away as follows:
1. Background: ‘We followed the fates of individually marked and
measured birds of four Geospiza species on Daphne Major Island for 40 years
to investigate contemporary evolution. We combined observations on fitness
with whole-genome sequencing to reveal and interpret the genetic
architecture of evolutionary change.’
‘We collected data from 3955 individuals from a community of four species of
Geospiza ground finches (G. fortis, G. fuliginosa, G. magnirostris, and G.
scandens) in their shared environment of Daphne Major Island each year for
more than 30 years and measured their phenotypic evolution, genomic
composition, and fitness variation. Finches were marked with distinct
combinations of colored leg bands to allow direct determination of
individual fitness (survival). We identified, quantified, and documented the
importance of six large-effect loci and showed how allelic variation has
changed under contrasting influences of natural selection and introgressive
hybridization. One of the loci comprising four genes in strong linkage
disequilibrium (LD) acts as a supergene. Extrapolating from these findings,
we suggest that a few loci of large effect contributed disproportionately to
the rapid diversification of species in this classical example of adaptive
radiation. These findings demonstrate the potential to leverage long-term
genomic monitoring to understand short and long-term processes that shape
natural populations.’
2. Changes in Allele Frequency: ‘We show that a few loci of large
effect have had a major impact on the trajectory of Darwin’s finch
populations on the small island of Daphne Major. They affect fitness through
their association with survival in relation to competition for food,
particularly during extreme climatic events, and have been passed between
species through hybridization.’
‘The average size of G. fortis and G. scandens beak dimensions oscillated in
response to changing ecological conditions over the 30 years of monitoring
(Fig. 5A) (33, 59). Changes in allele frequency at the six large-effect loci
identified in our GWAS changed concordantly with morphology, generally
exceeding annual shifts in allele frequency at random loci (Fig. 5, B and C,
and fig. S22). The strongest shift occurred in G. fortis during 2.5 years of
drought from late 2003 to early 2005 (60). The beaks of G. fortis became
smaller on average because of differential mortality resulting from
competition with the much larger G. magnirostris. The frequency of the G03 S
allele (Fig. 5A) increased sharply from 0.50 in 2004 to 0.63 in 2005 (17).
In a generalized linear-mixed model, G03 alone predicts survival with a
selection coefficient of 0.49 (Fisher’s exact test, P < 0.05). Three other
loci show a very similar change with an increase of the allele associated
with small beak size (and two others trend in this direction). Indeed, three
loci (G01, G03, and G29) in combination predict survival from 2004 to 2005
better than G03 alone in a repeated leave-one out analysis [Akaike
information criterion (AIC); AICcombined = 89.4 versus AICG03 = 97.6] (z =
3.1, P < 0.01) (Fig. 5D). Shifts in allele frequencies at these three loci
can account for 51% of the phenotypic shift in beak size due to natural
selection.’
3. Hybridization Effects: ‘Changes in ancestry are strongly correlated
with phenotypic shifts.’
‘Changes in ancestry (Fig. 1C) affected allele frequencies at these six
loci. Allele frequency changes at the six loci (2 to 30%) are greater in G.
fortis than in G. scandens (1 to 10%) (Fig. 5A). The phenotypic change
toward a blunter beak in G. scandens is the outcome of incremental gene flow
from G. fortis beginning in the 1990s (Fig. 1C) (29, 59). A spike in allele
frequency change at the turn of the century (Fig. 5C) is likely due to this
introgression in the El Niño year of 1998: The frequency of hybridization
increased in the next two dry years with no breeding when many finches died
from starvation, and then decreased in the following year (Fig. 1) (33). At
the locus with the largest phenotypic effect on beak shape (G07/ ALX1), G.
scandens carrying a Blunt allele were more likely to have G. fortis ancestry
than those carrying a Pointed allele (Generalized linear model, GLM: F =
1.1, P < 0.0001; fig. S23A and supplementary note 1). Similarly, G. fortis
carrying the S allele at G03, the locus of greatest phenotypic effect on
beak size, were more likely to have G. fuliginosa ancestry (GLM: F = –1.1, P
< 0.0001; fig. S23B) and G. fuliginosa–associated SNPs (fig. S23, C and D).
G. fortis and G. scandens converged in allele frequency at G07 but diverged
at G03 (Fig. 5F). Divergence is a consequence of hybridization between G.
fortis and G. fuliginosa and strong selection in the 2004–2005 period,
resulting in a higher frequency of the S allele at G03 in G. fortis (Fig. 5,
E and F).’
4. Conclusion: ‘These findings offer a snapshot into the
population-level processes that underlie the long-term processes of
speciation and adaptive radiation.’
‘Adaptive radiations are the product of a favorable genetic potential and
environmental opportunity for evolutionary change (3–5). The value of
Darwin’s finches lies in what they reveal about these features in the early
stages of speciation in a young adaptive radiation, when ecological
divergence has occurred repeatedly and strongly but without the kind of
genetic divergence that impairs fertility and viability (72). Focusing on
genetic potential, we have shown that a few identified loci have large
effects, individually and in combination, on quantitative, fitness-related,
phenotypic traits. Allele frequencies at the loci fluctuate through
directional natural selection and introgressive hybridization, thereby
revealing the evolutionary dynamics of a classical case of adaptive
radiation.’
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