Jonathan L. Richardson

Microgeographic adaptation and the spatial scale of evolution

Local adaptation has been a major focus of evolutionary ecologists working across diverse systems for decades. However, little of this research has explored variation at microgeographic scales because it has often been assumed that high rates of gene flow will prevent adaptive divergence at fine spatial scales. Here, we establish a quantitative definition of microgeographic adaptation based on Wrights dispersal neighborhood that standardizes dispersal abilities, enabling this measure to be compared across species. We use this definition to evaluate growing evidence of evolutionary divergence at fine spatial scales. We identify the main mechanisms known to facilitate this adaptation and highlight illustrative examples of microgeographic evolution in nature. Collectively, this evidence requires that we revisit our understanding of the spatial scale of adaptation and consider how microgeographic adaptation and its driving mechanisms can fundamentally alter ecological and evolutionary dynamics in nature.

Divergent landscape effects on population connectivity in two co-occurring amphibian species.

The physical and environmental attributes of landscapes often shape patterns of population connectivity by influencing dispersal and gene flow. Landscape effects on movement are typically evaluated for single species. However, inferences from multiple species are required for multi‐species management strategies increasingly being applied in conservation. In this study, I compared the spatial genetic patterns of two amphibian species across the northeastern United States and estimated the influence of specific landscape features on the observed genetic structure. The spotted salamander (Ambystoma maculatum) and wood frog (Rana sylvatica) share many ecological attributes related to habitat use, phenology and site fidelity. However, I hypothesized that important differences in their movement patterns and life history would create distinct genetic patterns for each species. Using 14 microsatellite loci, I tested for differences in the level of genetic differentiation between the two species across 22 breeding ponds. The effects of eight landscape features were also estimated by evaluating 32 landscape resistance models. Spotted salamanders exhibited significantly higher genetic differentiation than wood frogs. Different landscape features were also identified as potential drivers of the genetic patterns in each species, with little overlap in model support between species. Collectively, these results provide strong evidence that these two amphibian species interact with the landscape in measurably different ways. The distinct genetic patterns observed are consistent with key differences in movement ability and life history between A. maculatum and R. sylvatica. These results highlight the importance of considering more than one species when assessing the impacts of the landscape matrix on population connectivity, even for ecologically similar species within the same habitats.

Plasticity and genetic adaptation mediate amphibian and reptile responses to climate change

Phenotypic plasticity and genetic adaptation are predicted to mitigate some of the negative biotic consequences of climate change. Here, we evaluate evidence for plastic and evolutionary responses to climate variation in amphibians and reptiles via a literature review and meta‐analysis. We included studies that either document phenotypic changes through time or space. Plasticity had a clear and ubiquitous role in promoting phenotypic changes in response to climate variation. For adaptive evolution, we found no direct evidence for evolution of amphibians or reptiles in response to climate change over time. However, we found many studies that documented adaptive responses to climate along spatial gradients. Plasticity provided a mixture of adaptive and maladaptive responses to climate change, highlighting that plasticity frequently, but not always, could ameliorate climate change. Based on our review, we advocate for more experiments that survey genetic changes through time in response to climate change. Overall, plastic and genetic variation in amphibians and reptiles could buffer some of the formidable threats from climate change, but large uncertainties remain owing to limited data.

The halo occupation distribution of active galactic nuclei

Using a fully cosmological hydrodynamic simulation that self-consistently incorporates the growth and feedback of supermassive black holes and the physics of galaxy formation, we examine the effects of environmental factors (e.g., local gas density, black hole feedback) on the halo occupation distribution of low luminosity active galactic nuclei (AGN). We decompose the mean occupation function into central and satellite contribution and compute the conditional luminosity functions (CLF). The CLF of the central AGN follows a log-normal distribution with the mean increasing and scatter decreasing with increasing redshifts. We analyze the light curves of individual AGN and show that the peak luminosity of the AGN has a tighter correlation with halo mass compared to instantaneous luminosity. We also compute the CLF of satellite AGN at a given central AGN luminosity. We do not see any significant correlation between the number of satellites with the luminosity of the central AGN at a fixed halo mass. We also show that for a sample of AGN with luminosity above 10 42 ergs/s the mean occupation function can be modeled as a softened step function for central AGN and a power law for the satellite population. The radial distribution of AGN inside halos follows a power law at all redshifts with a mean index of 2.33 ± 0.08. Incorporating the environmental dependence of supermassive black hole accretion and feedback, our formalism provides a theoretical tool for interpreting current and future measurements of AGN clustering.

Strong selection barriers explain microgeographic adaptation in wild salamander populations.

Microgeographic adaptation occurs when populations evolve divergent fitness advantages across the spatial scales at which focal organisms regularly disperse. Although an increasing number of studies find evidence for microgeographic adaptation, the underlying causes often remain unknown. Adaptive divergence requires some combination of limited gene flow and strong divergent natural selection among populations. In this study, we estimated the relative influence of selection, gene flow, and the spatial arrangement of populations in shaping patterns of adaptive divergence in natural populations of the spotted salamander (Ambystoma maculatum). Within the study region, A. maculatum co‐occur with the predatory marbled salamander (Ambystoma opacum) in some ponds, and past studies have established a link between predation risk and adaptive trait variation in A. maculatum. Using 14 microsatellite loci, we found a significant pattern of genetic divergence among A. maculatum populations corresponding to levels of A. opacum predation risk. Additionally, A. maculatum foraging rate was strongly associated with predation risk, genetic divergence, and the spatial relationship of ponds on the landscape. Our results indicate the sorting of adaptive genotypes by selection regime and strongly suggest that substantial selective barriers operate against gene flow. This outcome suggests that microgeographic adaptation in A. maculatum is possible because strong antagonistic selection quickly eliminates maladapted phenotypes despite ongoing and substantial immigration. Increasing evidence for microgeographic adaptation suggests a strong role for selective barriers in counteracting the homogenizing influence of gene flow.

Worldwide phylogeography of the invasive ctenophore Mnemiopsis leidyi (Ctenophora) based on nuclear and mitochondrial DNA data

The ctenophore Mnemiopsis leidyi is one of the most successful marine bioinvaders on record. Native to the Atlantic coast of the Americas, M. leidyi invaded the Black Sea, Caspian and Mediterranean Seas beginning the in late 1980s, followed by the North and Baltic Seas starting in 2006, with major concomitant alterations in pelagic ecology, including fishery collapses in some cases. Using extensive native range sampling (21 sites), along with 11 invasive sites in the Black, Caspian, Mediterranean, North and Baltic Seas, we examined M. leidyi worldwide phylogeographic patterns using data from mitochondrial cytochrome b (cytb) and six nuclear microsatellite loci. Cytb and microsatellite data sets showed different levels of genetic differentiation in the native range. Analyses of cytb data revealed considerable genetic differentiation, recovering three major clusters (northwestern Atlantic, Caribbean, and South America) and further divided northwestern Atlantic sampling sites into three groups, separated approximately at Cape Hatteras on the US Atlantic coast and at the Floridian peninsula, separating the Gulf of Mexico and Atlantic coasts. In contrast, microsatellite data only distinguished samples north and south of Cape Hatteras, and suggested considerable gene flow among native samples with clear evidence of isolation by distance. Both cytb and microsatellite data sets indicated that the northern invaders (North/Baltic Seas) originated from north of Cape Hatteras, with cytb data pointing to Delaware and north. Microsatellite data indicated a source for the southern invaders (Black, Caspian and Mediterranean Seas) to be south of Cape Hatteras, while cytb data narrowed the source location to the Gulf of Mexico region. Both cytb and microsatellite data sets suggested that the southern invasion was associated with genetic bottlenecks while evidence was equivocal for the northern invasion. By increasing the native range spatial sampling, our dataset was able to sufficiently characterize patterns and levels of genetic differentiation in the native range of M. leidyi and identify likely biogeographic boundaries, allowing for the most complete characterization of M. leidyi’s invasion histories and most realistic estimates of its source region(s) to date.

The halo occupation distribution of black holes

We investigate the halo occupation distribution (HOD) of black holes within a hydrodynamic cosmological simulation that directly follows black hole growth. Similar to the HOD of galaxies/subhalos, we find that the black hole occupation number can be described by the form N_BH proportional to 1+ (M_Host)^alpha where alpha evolves mildly with redshift indicating that a given mass halo (M_Host) at low redshift tends to host fewer BHs than at high redshift (as expected as a result of galaxy and BH mergers). We further divide the occupation number into contributions from black holes residing in central and satellite galaxies within a halo. The distribution of M_BH within halos tends to consist of a single massive BH (distributed about a peak mass strongly correlated with M_Host), and a collection of relatively low-mass secondary BHs, with weaker correlation with M_Host. We also examine the spatial distribution of BHs within their host halos, and find they typically follow a power-law radial distribution (i.e. much more centrally concentrated than the subhalo distribution). Finally, we characterize the host mass for which BH growth is feedback dominated (e.g. star formation quenched). We show that halos with M_Host > 3 * 10^12 M_sun have primary BHs that are feedback dominated by z~3 with lower mass halos becoming increasingly more affected at lower redshift.

The Halo Occupation Distribution of Black Holes: Dependence on Mass

We investigate the halo occupation distribution (HOD) of black holes within a hydrodynamic cosmological simulation that directly follows black hole growth. Similar to the HOD of galaxies/subhalos, we find that the black hole occupation number can be described by the form N_BH proportional to 1+ (M_Host)^alpha where alpha evolves mildly with redshift indicating that a given mass halo (M_Host) at low redshift tends to host fewer BHs than at high redshift (as expected as a result of galaxy and BH mergers). We further divide the occupation number into contributions from black holes residing in central and satellite galaxies within a halo. The distribution of M_BH within halos tends to consist of a single massive BH (distributed about a peak mass strongly correlated with M_Host), and a collection of relatively low-mass secondary BHs, with weaker correlation with M_Host. We also examine the spatial distribution of BHs within their host halos, and find they typically follow a power-law radial distribution (i.e. much more centrally concentrated than the subhalo distribution). Finally, we characterize the host mass for which BH growth is feedback dominated (e.g. star formation quenched). We show that halos with M_Host > 3 * 10^12 M_sun have primary BHs that are feedback dominated by z~3 with lower mass halos becoming increasingly more affected at lower redshift.

Using fine scale spatial genetics of Norway rats to improve control efforts and reduce leptospirosis risk in urban slum environments

The Norway rat (Rattus norvegicus) is a key pest species globally and responsible for seasonal outbreaks of the zoonotic bacterial disease leptospirosis in the tropics. The city of Salvador, Brazil, has seen recent and dramatic increases in human population residing in slums, where conditions foster high rat density and increasing leptospirosis infection rates. Intervention campaigns have been used to drastically reduce rat numbers. In planning these interventions, it is important to define the eradication units ‐ the spatial scale at which rats constitute continuous populations and from where rats are likely recolonizing, post‐intervention. To provide this information, we applied spatial genetic analyses to 706 rats collected across Salvador and genotyped at 16 microsatellite loci. We performed spatially explicit analyses and estimated migration levels to identify distinct genetic units and landscape features associated with genetic divergence at different spatial scales, ranging from valleys within a slum community to city‐wide analyses. Clear genetic breaks exist between rats not only across Salvador but also between valleys of slums separated by <100 m—well within the dispersal capacity of rats. The genetic data indicate that valleys may be considered separate units and identified high‐traffic roads as strong impediments to rat movement. Migration data suggest that most (71–90%) movement is contained within valleys, with no clear source population contributing to migrant rats. We use these data to recommend eradication units and discuss the importance of carrying out individual‐based analyses at different spatial scales in urban landscapes.

The evolution of foraging rate across local and geographic gradients in predation risk and competition.

Multiple theories predict the evolution of foraging rates in response to environmental variation in predation risk, intraspecific competition, time constraints, and temperature. We tested six hypotheses for the evolution of foraging rate in 24 spotted salamander (Ambystoma maculatum) populations from three latitudinally divergent sites using structural equation models derived from theory and applied to our system. We raised salamander larvae in a common-garden experiment and then assayed foraging rate under controlled conditions. Gape-limited predation risk from marbled salamanders solely explained foraging rate variation among populations at the southern site, which was dominated by this form of selection. However, at the middle and northern sites, populations evolved different foraging rates depending on their unique responses to local intraspecific density. The coupling of gape-limited predation risk from marbled salamanders and high intraspecific density at the middle site jointly contributed to selection for rapid foraging rate. At the northernmost site, intraspecific density alone explained 97% of the interpopulation variation in foraging rate. These results suggest that foraging rate has evolved multiple times in response to varying contributions from predation risk and intraspecific competition. Predation risk often varies along environmental gradients, and, thus, organisms might often shift evolutionary responses from minimizing predation risk to maximizing intraspecific competitive performance.