Abstract:
Embryology, or developmental biology, has been widely studied since centuries,
as a field that contains answers to several fundamental questions in biology. One
such persistent biological question has been that of evolution, with many
classical evolutionists turning to comparative embryology in their quest for
answers and explanations. However, with the rediscovery of Mendel’s laws and
subsequent advent of genetics in the early and mid-20th century, followed by the
identification of DNA as the primary carrier of genetic information across
generations, DNA and genes have taken centre stage in explaining how species
evolve from pre-existing species, at the neglect of other aspects, such as
development and ecology. Over the last years, though, a combination of factors -
such as (re)merging of evolutionary and developmental biology, advent of a
wide array of model organisms for comparative developmental studies, and
technological advances in the field of molecular and computational biology -
have led to a growing need to redress and reassess the fundamentals of evolution
and origins of species diversity. In this context, the nematode Pristionchus
pacificus has emerged as a key model system. P. pacificus, along with its famous
distant relative Caenorhabditis elegans, provides us with a great opportunity to
understand the finer aspects of contemporary evolutionary developmental
biology (evo-devo) through comparative analyses between the two species.
Specifically, P. pacificus has emerged has a keystone species to study
developmental plasticity, a phenomenon in which organisms have the ability to
give rise to alternative phenotypes on the basis of their environmental
experiences during development. In this context, a wealth of knowledge has
been accumulated with regards to the effects of environmental factors on
developmentally plastic traits of P. pacificus, as well as on the underlying genetic
machinery manifesting and regulating said plastic traits. However, the
mediating link connecting the environmental reception to the morphological
manifestation is only starting to be peered into in P. pacificus.
In this doctoral thesis, I, with support from my colleagues, improve the genomic
reference of the orthologues of C. elegans genes in P. pacificus genome, using it to
subsequently identify, using comparative spatial tomography, a dissociation
between genomic and morphological homology between the two nematode
species, and further explore the spatial expression of evolutionarily young genes,
one of the keystone evolutionary facilitators of morphological novelty and evolutionary diversity, in the masculine part of the gonads, providing the first
example in support of the ‘out-of-testis’ hypothesis from nematodes. Next, I
present the first developmentally resolved small RNA transcriptome of P.
pacificus. Small non-coding RNAs have emerged as important post-
transcriptional regulators, and implicated in wide-ranging biological
phenomena, including development, genome protection, and environmental
response, among others. Temporal resolution of the P. pacificus small RNAs gives
us the opportunity to look at the role of conserved microRNAs in the worm’s
development, and explore their evolutionary divergence between P. pacificus and
other nematodes, including C. elegans. In addition to being the first of their kind
for P. pacificus, the developmental small RNA transcriptome also sets up the stage
for elucidating the potential roles of small RNAs in mediating the crosstalk
between environmental influence and the genetic machinery controlling
developmental plasticity within the species. Lastly, I contribute in exploring how
the environment itself may regulate developmental decision-making without
any genetic perturbation in perfectly isogenic worm populations.
Pristionchus pacificus