The evolutionary consequences of genetic adaptation to parasitism

The processes driving and maintaining variable immune responses are poorly understood compared with other aspects of an organism’s ecology. This is particularly true from an evolutionary perspective, as the evolutionary relationships between immune responses and other traits and processes in nature remain inadequately explored. I investigated these associations in this thesis using the three-spined stickleback system as an evolutionary and immunological model. I combined sampling of wild individuals with genomic analyses to demonstrate phenotypic and genomic associations between immune responses and life history evolution across multiple populations. I also observe how experimental changes in daylength, a seasonal cue, modulate immune responses and increase parasite susceptibility in a controlled laboratory experiment. These findings occur independently of natural variation in parasite resistance. Stickleback are also a model for studies of speciation. I used sampling of wild hybrids to assess the significance of immune variation in postzygotic isolating mechanisms between diverging ecotypes; although my findings suggest a minor role. Finally, I demonstrate that genomic responses to parasitism and abiotic environmental variation are repeatable across independent, intercontinental adaptive radiation events in sticklebacks; conferring a repeatability of the evolutionary relationships of immune variation documented in this thesis. The findings within this thesis therefore provide novel insights into poorly explored or open areas of research regarding how variable immune responses evolve in nature

The evolutionary consequences of genetic adaptation to parasitism

The processes driving and maintaining variable immune responses are poorly understood compared with other aspects of an organism’s ecology. This is particularly true from an evolutionary perspective, as the evolutionary relationships between immune responses and other traits and processes in nature remain inadequately explored. I investigated these associations in this thesis using the three-spined stickleback system as an evolutionary and immunological model. I combined sampling of wild individuals with genomic analyses to demonstrate phenotypic and genomic associations between immune responses and life history evolution across multiple populations. I also observe how experimental changes in daylength, a seasonal cue, modulate immune responses and increase parasite susceptibility in a controlled laboratory experiment. These findings occur independently of natural variation in parasite resistance. Stickleback are also a model for studies of speciation. I used sampling of wild hybrids to assess the significance of immune variation in postzygotic isolating mechanisms between diverging ecotypes; although my findings suggest a minor role. Finally, I demonstrate that genomic responses to parasitism and abiotic environmental variation are repeatable across independent, intercontinental adaptive radiation events in sticklebacks; conferring a repeatability of the evolutionary relationships of immune variation documented in this thesis. The findings within this thesis therefore provide novel insights into poorly explored or open areas of research regarding how variable immune responses evolve in nature

Wildlife linkages: volumes and values of residual timber in riparian zones in eastern Texas

In regenerating southern pine, maintenance of riparian zones (RZs) is a major land concession for soil and water protection and wildlife habitat enhancement. However, there are few data quantifying the volume and value of residual timber in such areas. We inventoried merchantable timber in nine RZs of three widths in sapling-class East Texas pine plantations. Present, discounted, and projected volumes and values of residual timber were determined. Average per-acre volumes of narrow, medium, and wide RZs were 337, 1438, and 2542 board feet (Doyle log rule) and 4.6, 8.2, and 7.2 cords, respectively. At US $154.00 and US$57.00 per thousand board feet for pine and hardwood saw timber, respectively, and US $15.00 and US$5.00 per cord for pine and hardwood pulpwood, respectively, average present per-acre values were US $46.41, US$209.93 and US $352.75 for narrow, medium, and wide RZs. Interest rates for the growth of trees from 1981 to 1989 ranged 3.7$4.52, US $20.46, and US$34.38, respectively. Stumpage values at the time of harvest projected at 7% compound interest for 30 years ranged US $10.66-US$3547.54 per acre and for 80 years ranged US $313.93-US$104 499.95 per acre. The impact of these results on wildlife is discusse

An HI absorption distance to the black hole candidate X-ray binary MAXI J1535-571

With the Australian Square Kilometre Array Pathfinder (ASKAP) we monitored the black hole candidate X-ray binary MAXI J1535--571 over seven epochs from 21 September to 2 October 2017. Using ASKAP observations, we studied the HI absorption spectrum from gas clouds along the line-of-sight and thereby constrained the distance to the source. The maximum negative radial velocities measured from the HI absorption spectra for MAXI J1535--571 and an extragalactic source in the same field of view are $-69\pm4$ km s$^{-1}$ and $-89\pm4$ km s$^{-1}$, respectively. This rules out the far kinematic distance ($9.3^{+0.5}_{-0.6}$ kpc), giving a most likely distance of $4.1^{+0.6}_{-0.5}$ kpc, with a strong upper limit of the tangent point at $6.7^{+0.1}_{-0.2}$ kpc. At our preferred distance, the peak unabsorbed luminosity of MAXI J1535--571 was $>78$ per cent of the Eddington luminosity, and shows that the soft-to-hard spectral state transition occurred at the very low luminosity of 1.2 -- 3.4 $\times$ 10$^{-5}$ times the Eddington luminosity. Finally, this study highlights the capabilities of new wide-field radio telescopes to probe Galactic transient outbursts, by allowing us to observe both a target source and a background comparison source in a single telescope pointing.Comment: Revised after favorable referee report from MNRAS Letter

The Performance and Calibration of the CRAFT Fly's Eye Fast Radio Burst Survey

Since January 2017, the Commensal Real-time ASKAP Fast Transients survey (CRAFT) has been utilising commissioning antennas of the Australian SKA Pathfinder (ASKAP) to survey for fast radio bursts (FRBs) in fly's eye mode. This is the first extensive astronomical survey using phased array feeds (PAFs), and a total of 20 FRBs have been reported. Here we present a calculation of the sensitivity and total exposure of this survey, using the pulsars B1641-45 (J1644-4559) and B0833-45 (J0835-4510, i.e.\ Vela) as calibrators. The design of the survey allows us to benchmark effects due to PAF beamshape, antenna-dependent system noise, radio-frequency interference, and fluctuations during commissioning on timescales from one hour to a year. Observation time, solid-angle, and search efficiency are calculated as a function of FRB fluence threshold. Using this metric, effective survey exposures and sensitivities are calculated as a function of the source counts distribution. The implied FRB rate is significantly lower than the $37$\,sky$^{-1}$\,day$^{-1}$ calculated using nominal exposures and sensitivities for this same sample by \citet{craft_nature}. At the Euclidean power-law index of $-1.5$, the rate is $10.7_{-1.8}^{+2.7}\,{\rm (sys)} \, \pm \, 3\,{\rm (stat)}$\,sky$^{-1}$\,day$^{-1}$ above a threshold of $57\pm6\,{\rm (sys)}$\,Jy\,ms, while for the best-fit index for this sample of $-2.1$, it is $16.6_{-1.5}^{+1.9} \,{\rm (sys)}\, \pm 4.7\,{\rm (stat)}$\,sky$^{-1}$\,day$^{-1}$ above a threshold of $41.6\pm1.5\,{\rm (sys)}$\,Jy\,ms. This strongly suggests that these calculations be performed for other FRB-hunting experiments, allowing meaningful comparisons to be made between them.Comment: 21 pages, 15 figures, 2 tables, accepted for publication in PAS

Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds

Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species

Energy of Isolated Systems at Retarded Times as the Null Limit of Quasilocal Energy

We define the energy of a perfectly isolated system at a given retarded time as the suitable null limit of the quasilocal energy $E$. The result coincides with the Bondi-Sachs mass. Our $E$ is the lapse-unity shift-zero boundary value of the gravitational Hamiltonian appropriate for the partial system $\Sigma$ contained within a finite topologically spherical boundary $B = \partial \Sigma$. Moreover, we show that with an arbitrary lapse and zero shift the same null limit of the Hamiltonian defines a physically meaningful element in the space dual to supertranslations. This result is specialized to yield an expression for the full Bondi-Sachs four-momentum in terms of Hamiltonian values.Comment: REVTEX, 16 pages, 1 figur

Prior exposure to long-day photoperiods alters immune responses and increases susceptibility to parasitic infection in stickleback

Seasonal disease and parasitic infection are common across organisms, including humans, and there is increasing evidence for intrinsic seasonal variation in immune systems. Changes are orchestrated through organisms' physiological clocks using cues such as day length. Ample research in diverse taxa has demonstrated multiple immune responses are modulated by photoperiod, but to date, there have been few experimental demonstrations that photoperiod cues alter susceptibility to infection. We investigated the interactions among photoperiod history, immunity and susceptibility in laboratory-bred three-spined stickleback (a long-day breeding fish) and its external, directly reproducing monogenean parasite Gyrodactylus gasterostei. We demonstrate that previous exposure to long-day photoperiods (PLD) increases susceptibility to infection relative to previous exposure to short days (PSD), and modifies the response to infection for the mucin gene muc2 and Treg cytokine foxp3a in skin tissues in an intermediate 12 L : 12 D photoperiod experimental trial. Expression of skin muc2 is reduced in PLD fish, and negatively associated with parasite abundance. We also observe inflammatory gene expression variation associated with natural inter-population variation in resistance, but find that photoperiod modulation of susceptibility is consistent across host populations. Thus, photoperiod modulation of the response to infection is important for host susceptibility, highlighting new mechanisms affecting seasonality of host-parasite interactions

Reproductive isolation in a three‐way contact zone

Contact zones between divergent forms within a species provide insight into the role of gene flow in adaptation and speciation. Previous work has focused on contact zones involving only two divergent forms, but in nature, many more than two populations may overlap simultaneously and experience gene flow. Patterns of introgression in wild populations are, therefore, likely much more complicated than is often assumed. We begin to address this gap in current knowledge by investigating patterns of divergence and introgression across a complex natural contact zone. We use phenotypic and genomic data to confirm the existence of a three-way contact zone among divergent freshwater resident, saltwater resident and saltwater migratory three-spined stickleback (Gasterosteus aculeatus) on the island of North Uist, Scottish Western Isles. We find evidence for hybridization, mostly between saltwater resident and saltwater migratory forms. Despite hybridization, genomic analyses reveal pairwise islands of divergence between all forms that are maintained across the contact zone. Genomic cline analyses also provide evidence for selection and/or hybrid incompatibilities in divergent regions. Divergent genomic regions occur across multiple chromosomes and involve many known adaptive loci and several chromosomal inversions. We also identify distinct immune gene expression profiles between forms, but no evidence for transgressive expression in hybrids. Our results suggest that reproductive isolation is maintained in this three-way contact zone, despite some hybridization, and that reduced recombination in chromosomal inversions may play an important role in maintaining this isolation