The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans
Date
2016
Authors
Blom, Mozes
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Abstract
Understanding the evolutionary processes that generate and
maintain biodiversity is a fundamental objective in ecology and
evolution. In this dissertation, I characterize phylogenetic
patterns in a recent radiation of Australian skinks, discuss the
ecological context of diversification and how this has translated
into macroevolutionary change across the continent. By also
reconstructing the evolutionary history of all Cryptoblepharus
species globally, I shed further light on the evolutionary and
biogeographic processes that have shaped the diversity of the
genus. This dissertation project has generated an empirical
framework for future studies into the continuous nature between
micro- and macroevolutionary change.
To infer the phylogeny of Australian Cryptoblepharus, I generated
an exon- capture dataset and designed a bioinformatic pipeline to
generate quality filtered sequence alignments (Appendix A).
Multi-locus datasets are required to confidently infer species
trees for rapidly speciating clades due to a high prevalence of
gene tree incongruence among loci. In Chapter I, I use the
Cryptoblepharus radiation as an empirical example and describe
how to account for differences in gene tree resolution when
employing summary-coalescent methods for species tree inference.
Our study highlights the importance of phylogenetically
informative loci but simultaneously demonstrates that the
addition of non-informative loci does not introduce phylogenetic
noise.
In Chapter II, I then use comparative methods and morphological
measurements for over 800 individuals, to examine the ecological
context of diversification in Australian Cryptoblepharus.
Specifically, I focus on whether habitat specialisation can
explain current patterns of variation in ecologically relevant
traits. I observed significant differences in morphology between
species that occur in distinct environments (rock, arboreal and
littoral) and species that occur within the same habitat are
often cryptic. These findings suggest that isolated analogous
habitats have provided ecological opportunity and repeatedly
promoted adaptive diversification, while speciation within
habitat has accrued without ecomorphological change. In contrast
to well known adaptive radiations in insular environments,
continental radiations are likely driven by alternative
diversification processes that jointly stimulate species
proliferation.
In Chapter III, I explore patterns of introgression between
phylogenetically divergent species. I combine population and
phylogenetic tools, to quantify the extent of introgression
between ecomorphologically distinct and similar taxa. I describe
the frequent occurrence of mitochondrial haplotype sharing across
species boundaries and the complete replacement of the
mitochondrial genome in one species. Furthermore, non-sister
species often share more nuclear variants than as expected under
a model of incomplete lineage sorting only, suggesting
substantial historical introgression.
Finally, Cryptoblepharus skinks are renowned for their widespread
distribution, across continents and many island archipelagoes,
while they have only emerged and diversified recently (i.e. since
late Miocene/early Pliocene). In Chapter IV, I reconstruct the
global phylogeny and discuss the importance of trait-based
dispersal. Large scale range expansions across the Indian and
Pacific Ocean have only occurred relatively recently, after an
ancestor adapted to a more littoral habitat, and many
extralimital taxa still only occur in close vicinity to coastal
areas (Appendix B). These lizards therefore exemplify how
ecological traits can increase the propensity of dispersal and
that disjunct geographic distributions are not solely explained
by a vicariance model.
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Cryptoblepharus, Scincidae, phylogenomics, introgression, speciation, macroevolution, biogeography, continental radiation, exon capture
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