| dc.description.abstract | Phylogenetics in Space & the Evolution of the Haustoriidae is a dissertation in two volumes: 1) the systematics, biogeography, genome evolution, and phylogenetics of sand-burrowing amphipods of the family Haustoriidae; and 2) the impacts of spatial population structure on aspects of phylogenetic inference.
Volume I: Sand-burrowing amphipods of the family Haustoriidae are predominately distributed in the northern hemisphere where they are one of the most abundant members of the benthic beach fauna. Despite their ubiquity and numerical abundance, their phylogenetic affinities have remained a mystery, both within the family and in the broader context of the Amphipoda. In this dissertation, I take a hierarchical approach to unraveling the relationships within and between haustoriids. In Chapter I, using a handful of molecular markers, I examine the relationships between four haustoriid species distributed across the Gulf of Mexico: presumed sister species Haustorius galvezi and H. jayneae, H. allardi, and a widespread species, Lepidactylus triarticulatus. The Gulf of Mexico has long been of interest to biogeography as fauna are often characterized by a stark east-west distribution pattern, indicating a historic zone of vicariance in the Gulf. A myriad of hypotheses have been put forth to explain these patterns; for this chapter, I examined three possible causes for population splitting: 1) cold-water pulses down the Mississippi River at the end of the last Ice Age; 2) freshwater influx due to the confluence of several rivers into the Tennessee River that fed into Mobile Bay; and 3) a Miocene sedimentation event in which increased silt and clay were deposited at the mouth of the Mississippi ~5 million years ago. The molecular evidence supported an ancient split between H. galvezi and H. jayneae, and, surprisingly, that L. triarticulatus is a species complex composed of two major clades separated by the Mississippi River. Each split supported a Miocene sedimentation event. In addition, widespread cryptic diversity was found among the haustoriids sampled indicating the possibility for cryptic species. This was most pronounced in L. triarticulatus, where each sampled location supported a unique genetic cluster.
In addition to having strong population structure and deep divergences, haustoriid amphipods display wide genome size variation. Genome sizes vary by orders of magnitude across the Tree of Life and lack any correlation with organismal complexity. Some crustacean orders, including amphipods, have genome sizes that correlate with body size, temperature, and water depth, indicating that natural selection may constrain genome sizes due to physiological pressures. In Chapter II, I examine the relationship between genome size, repetitive content, and environmental variables on haustoriids that are distributed across the Gulf of Mexico and the North Atlantic. I uncover a 6-fold genome size variation within a clade that is less than 7 million years old. Unlike previous studies, I find no correlation between genome size and latitude, but do uncover a significant relationship between genome size and body length. Further, I find that the genome size predicts proportions of repetitive content, and that the largest genomes appear to be driven by expansions of LINEs. Finally, I find evidence of genomic purging and body size reduction in two lineages that have independently colonized warm brackish waters, possibly indicating a strong physiological constraint of transitioning from surf-swept beaches to protected bays.
Volume II: Isolation-by-distance is a widespread pattern in nature that describes the reduction of genetic correlation between subpopulations with increased geographic distance. In the population ancestral to modern sister species, this pattern may hypothetically inflate population divergence time estimation due to allele frequency differences in subpopulations at the ends of the ancestral population. In Chapter III, I analyze the relationship between the time to the most recent common ancestor and the population divergence time when the ancestral population model is a linear stepping-stone. Using coalescent simulations, I compare the coalescent time to the population divergence time for various ratios of the divergence time over the population size. Next, I simulate whole genomes to obtain SNPs, and use the Bayesian coalescent program SNAPP to estimate divergence times. I find that as the rate of migration between neighboring demes decreases, the coalescent time becomes significantly greater than the population divergence time when sampled from end demes. Divergence-time overestimation in SNAPP becomes severe when the divergence-to-population size ratio < 10 and migration is low. Finally, I demonstrate the impact of ancestral isolation-by-distance on divergence-time estimation using an empirical dataset of squamates (Tropidurus) endemic to Brazil. I conclude that studies estimating divergence times be cognizant of the potential ancestral population structure in an explicitly spatial context or risk dramatically overestimating the timing of population splits.
The tendency to discretize biology permeates taxonomy and systematics, leading to models that simplify the often-continuous nature of populations. Even when the assumption of panmixia is relaxed, most models still assume some degree of discrete structure. The multispecies coalescent has emerged as a powerful model in phylogenetics, but in its common implementation is entirely space-independent – what I call the “missing z-axis”. In Chapter IV, I review the many lines of evidence for how continuous spatial structure can impact phylogenetic inference. I illustrate and expand on these by using complex continuous-space demographic models that include distinct modes of speciation. I find that the impact of spatial structure permeates all aspects of phylogenetic inference, including gene tree stoichiometry, topological and branch-length variance, network estimation, and species delimitation. I conclude by utilizing my results to suggest how researchers can identify spatial structure in phylogenetic datasets. | en |
