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DTSTAMP:20260424T114328Z
UID:1758898800@ist.ac.at
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DESCRIPTION:Speaker: Arka Pal\nhosted by Ilaria Caiazzo\nAbstract: Understa
 nding the mechanisms underlying speciation is a central aim of evolutionar
 y biology. A persistent challenge in the field is to identify loci that co
 ntribute to reproductive isolation\, while disentangling signals of select
 ion from demography\, linkage and intrinsic genomic features. Traditional 
 population genomic approaches that rely on site-based statistics in arbitr
 ary fixed windows face inherent limitations\, as they conflate historical 
 and contemporary processes of divergence and overlook haplotype structure.
  Recent advances in whole-genome sequencing and methods to infer ancestral
  recombination graphs (ARGs) now offer the opportunity to study genealogic
 al relationships explicitly\, revealing how lineages coalesce and recombin
 e through time. By directly analysing haplotype clustering by species or p
 henotype and their patterns of coalescence\, ARG-based methods show promis
 e for diagnosing sweeps\, identifying barrier loci maintained under diverg
 ent selection amid gene flow\, and tracing their evolutionary history. In 
 this thesis\, I explore the utility of genealogical approaches for studyin
 g species divergence. I start by proposing a conceptual framework for defi
 ning haplotype blocks through the structure of the ARG\, using simulations
  and empirical data to highlight how genealogical processes generate rich 
 and often overlooked haplotypic patterns. In the following chapters\, I st
 udy the genomic basis of species divergence in two study systems. First\,
  I examine the genomic basis of a key evolutionary innovation in marine sn
 ails Littorina. These snails offer a unique opportunity to study an innova
 tion because they include a very recent transition from egg-laying to live
  bearing\, yet snails with the different reproductive modes are not recipr
 ocally monophyletic. I exploited this by using topology clustering in ARG 
 derived local genealogical trees to pinpoint narrow genomic regions or hap
 lotype blocks that carry swept alleles\, thus revealing that the transitio
 n from egg laying to live bearing involves multiple\, live bearer specific
  sweeps.Second\, I investigate the genomic basis of flower colour variatio
 n in Antirrhinum majus. Across two replicate hybrid zones\, ARG based topo
 logy clustering uncovered parallel reuse of colour associated haplotypes\,
  even where differentiation outlier scans failed to resolve meaningful sig
 nals. Integrating these genealogical approaches with genome wide associati
 on studies not only confirmed major effect loci underlying pigmentation\, 
 but also suggested the presence of a previously unknown regulatory factor.
  Finally\, preliminary analysis of the Rosea/Eluta genomic region showed t
 hat it comprises multiple divergent colour associated loci\, shaped by sta
 ggered selective sweeps and localised barriers to gene flow.Together\, the
 se chapters add to the increasing pool of studies using genealogical appro
 aches to complement and extend site-based statistics to use haplotype stru
 ctures in speciation research. By tracking haplotypes directly and connect
 ing genealogical clustering to population processes\, ARG-based inference 
 shows promise of providing new insights into how local selective pressures
 \, demographic history\, and long-term barriers interact to shape the geno
 mic architecture of divergence. Despite underscoring the value of ARGs in 
 revealing the fine-scale origins and maintenance of biodiversity\, this th
 esis presents cautious optimism about the benefits of using genealogical i
 nference to learn more than what site-based statistics could tell us.
LOCATION:Central Bldg / O1 / Mondi 2a (I01.O1.008) and Zoom\, ISTA
ORGANIZER:
SUMMARY:Arka Pal: Thesis Defense: Using Genealogies to Study the Genomic Ba
 sis of Species Divergence
URL:https://talks-calendar.ista.ac.at/events/6031
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