Patricia E. Maloney

Present and past old-growth forests of the Lake Tahoe Basin, Sierra Nevada, US

Abstract We described 38 relictual old-growth stands – with data on the mortality, regeneration, floristic richness, fuel load and disease incidence in our study area in the Tahoe Basin of California and Nevada. The stands are within the lower and upper montane zones (1900–2400 m a.s.l.) and they are rare, occupying < 2% of the land in the Basins watershed. Correlation matrices and ANOVAs of forest types and conifer species with environmental gradients revealed significant relationships with elevation, distance east of the Sierran crest, slope aspect, annual precipitation, date of complete snow melt, litter depth and degree of soil profile development. Pathogens, parasites and wood-boring insects were present on 23% of living trees; 16% of all trees were dead. We compared these stands to a reconstruction of pre-contact Basin forests and to ecologically analogous old-growth forests of Baja California that have never experienced fire suppression management. Currently, overstorey trees (> 180 yr old) in the Basin stands have ca. 33% cover, 54 m2.ha−1 basal area and 107 individuals.ha−1, values very similar to reconstructions of pre-contact Basin forests and to modern Baja California forests. Understorey trees (60–180 yr old), however, are several times more dense than historic levels and species composition is strongly dominated by A. concolor, regardless of the overstorey composition. The ratio of Pinus : Abies has increased – and the age structure of extant stands predicts that it will continue to increase – from approximately 1:1 in pre-contact time to 1:7 within the next century. Disease incidence and mortality in Baja forests were lower. Although we quantitatively defined current Basin old-growth forests – in terms of stand structure – we realize that our definition will differ from that of both past and future old-growth forests unless management protocols are changed. Nomenclature: Hickman (1993) for vascular plants; Furniss & Carolin (1977) for bark beetles; Hansen & Lewis (1997) for pathogens.

Initial tree mortality, and insect and pathogen response to fire and thinning restoration treatments in an old growth, mixed-conifer forest of the Sierra Nevada, California

Fire and thinning restoration treatments in fire-suppressed forests often damage or stress leave trees, altering pathogen and insect affects. We compared types of insect- and pathogen-mediated mortality on mixed-conifer trees 3 years after treatment. The number of bark beetle attacked trees was greater in burn treatments compared with no-burn treat- ments, and in some cases, larger pine trees were preferentially attacked. Restoration treatments are not expected to change the trajectory of spread and intensification of dwarf mistletoe. Thinning treatments may have provided a sanitation effect in which large leave trees have lower levels of dwarf mistletoe. Although thinning treatments are known to exacerbate root disease, <12% of cut stumps were infected with root pathogens (Armillaria gallica and Heterobasidion annosum). Treatments increased Ribes (alternate host for white pine blister rust) frequency and abundance, which may have very lo- calized impacts on white pine blister rust dynamics. In some instances, fire, insects, and pathogens appear to conflict with forest restoration goals by reducing the percentage of pine and producing proportionally higher rates of tree mortality in large-diameter size classes. To better understand the long-term effects of restoration treatments on pathogens and insects, continued monitoring over the course of varying climatic conditions will be needed.

Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA

Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n = 116 231 SNPs) to describe signatures of fine‐scale adaptation within eight whitebark pine (Pinus albicaulis Engelm.) populations across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (FST = 0.0069), there is strong evidence for adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we build upon evidence from a common garden study and find that allele frequencies of loci associated with four phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher signals of selection (covariance of allele frequencies) than could be expected to arise, given the data. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results replicate empirical support for theoretical expectations of local adaptation for populations exhibiting strong gene flow and high selective pressures and suggest that ongoing adaptation of many P. albicaulis populations within the Lake Tahoe Basin will not be constrained by the lack of genetic variation. Even so, some populations exhibit low levels of heritability for the traits presumed to be related to fitness. These instances could be used to prioritize management to maintain adaptive potential. Overall, we suggest that established practices regarding whitebark pine conservation be maintained, with the additional context of fine‐scale adaptation.

Dwarf mistletoe-host interactions in mixed-conifer forests in the sierra nevada.

ABSTRACT We determined the spatial pattern of dwarf mistletoe (Arceuthobium spp.) associated with two different conifer hosts, white fir (Abies concolor) and Jeffrey pine (Pinus jeffreyi), in forests around the Lake Tahoe Basin and at the Teakettle Experimental Forest, both located in the Sierra Nevada. We also examined a number of host variables and bark beetle incidence to determine how these factors might be involved in the Arceuthobium-conifer interaction. There was no significant relationship between dwarf mistletoe-infected trees and associated bark beetles. We found the highest incidence of dwarf mistletoe on Jeffrey pine in Lake Tahoe (87%), followed by dwarf mistletoe on white fir in Lake Tahoe (30%), with the lowest incidence on white fir at Teakettle (27%). Dwarf mistletoe incidence on white fir in our Lake Tahoe grid was not correlated to density but the dwarf mistletoe rating (DMR) was positively correlated to host size. At the Teakettle Forest, dwarf mistletoe incidence on white fir was not correlated with host density but the DMR was correlated with host size. Dwarf mistletoe incidence and DMR on Jeffrey pine were correlated with host density. Individuals, of both conifer species, in all diameter size classes were susceptible to dwarf mistletoe, with the lowest infection rate in the seedling-10-cm-diameter class. Arceuthobium on white fir in Lake Tahoe showed spatial dependence to a range of 20 m. However, Arceuthobium on Jeffrey pine in Lake Tahoe and on white fir at Teakettle showed no clear pattern of spatial structuring. The degree of infection and stand history appear to be important in the spatial dynamics of Arceuthobium spp.

Effect of fire and thinning on fine-scale genetic structure and gene flow in fire-suppressed populations of sugar pine (Pinus lambertiana Douglas)

Historically, frequent, low-severity fires in dry western North American forests were a major driver of ecological patterns and processes, creating resilient ecosystems dominated by widely spaced pine species. However, a century of fire-suppression has caused overcrowding, altering forest composition to shade-tolerant species, while increasing competition and leaving trees stressed and susceptible to pathogens, insects, and high-severity fire. Exacerbating the issue, fire incidence is expected to increase with changing climate, while fire season has been observed to begin earlier and last longer than historic trends. Forest thinning and prescribed fire have been identified as important management tools to mitigate these risks. Yet little is known of how thinning, fire, or their interaction affect contemporary evolutionary processes of constituent pine species that influence fitness and play an important role in the opportunity for selection and population persistence. We assessed the impact of widely used fuel reduction treatments and prescribed fire on fine-scale gene flow on an ecologically important and historically dominant shade-intolerant pine species of the Sierra Nevada, Pinus lambertiana Dougl. Treatment prescription (no-thin-no-fire, thin-no-fire, and fire-and-thin) was found to differentially affect both fine-scale spatial and genetic structure as well as effective gene flow in this species. Specifically, the thin-no-fire prescription increases genetic structure (spatial autocorrelation of relatives) between adults and seedlings, while seed and pollen dispersal increase and decrease, respectively, as a function of increasing disturbance intensity. While these results may be specific to the stands at our study site, they indicate how assumptions relating to genetic effects based on spatial structure can be misleading. It is likely that these disequilibrated systems will continue to evolve on unknown evolutionary trajectories. The long-term impacts of management practices on reduced fitness from inbreeding depression should be continually monitored to ensure resilience to increasingly frequent and severe fire, drought, and pest stresses.

Comparative transcriptomics among four white pine species

Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola), limber pine (Pinus flexilis), whitebark pine (Pinus albicaulis), and sugar pine (Pinus lambertiana) was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.

The genetic architecture of local adaptation II: The QTL landscape of water-use efficiency for foxtail pine (Pinus balfouriana Grev. & Balf.)

Water availability is an important driver of the geographic distribution of many plant species, although its importance relative to other climatic variables varies across climate regimes and species. A common indirect measure of water-use efficiency (WUE) is the ratio of carbon isotopes (δ13C) fixed during photosynthesis, especially when analyzed in conjunction with a measure of leaf-level resource utilization (δ15N). Here, we test two hypotheses about the genetic architecture of WUE for foxtail pine (Pinus balfouriana Grev. & Balf.) using a novel mixture of double digest restriction site associated DNA sequencing, species distribution modeling, and quantitative genetics. First, we test the hypothesis that water availability is an important determinant of the geographical range of foxtail pine. Second, we test the hypothesis that variation in δ13C and δ15N is genetically based, differentiated between regional populations, and has genetic architectures that include loci of large effect. We show that precipitation-related variables structured the geographical range of foxtail pine, climate-based niches differed between regional populations, and δ13C and δ15N were heritable with moderate signals of differentiation between regional populations. A set of large-effect QTLs (n = 11 for δ13C; n = 10 for δ15N) underlying δ13C and δ15N variation, with little to no evidence of pleiotropy, was discovered using multiple-marker, half-sibling regression models. Our results represent a first approximation to the genetic architecture of these phenotypic traits, including documentation of several patterns consistent with δ13C being a fitness-related trait affected by natural selection.

When local means local: Polygenic signatures of local adaptation within whitebark pine (Pinus albicaulis Engelm.) across the Lake Tahoe Basin, USA

For populations exhibiting high levels of gene flow, the genetic architecture of fitness-related traits is expected to be polygenic and underlain by many small-effect loci that covary across a network of linked genomic regions. For most coniferous taxa, studies describing this architecture have been limited to single-locus approaches, possibly leaving the vast majority of the underlying genetic architecture undescribed. Even so, molecular investigations rarely search for patterns indicative of an underlying polygenic basis, despite prior expectations for this signal. Here, using a polygenic perspective, we employ single and multilocus analyses of genome-wide data (n = 116,231 SNPs) to describe the genetic architecture of adaptation within whitebark pine (Pinus albicaulis Engelm.) across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation ( = 0.0069) there is strong evidence for polygenic adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we find little evidence for large-effect loci and that the frequencies of loci associated with 4/5 phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher covariance than random SNPs. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results provide replicative support for theoretical expectations and highlight advantages of a polygenic perspective, as unremarkable loci when viewed from a single-locus perspective are noteworthy when viewed through a polygenic lens, particularly when considering protective measures such as conservation guidelines and restoration strategies.Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n = 116,231 SNPs) to describe signatures of fine-scale adaptation within eight whitebark pine (Pinus albicaulis Engelm.) populations across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (FST = 0.0069) there is strong evidence for adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we build upon evidence from a common garden study and find that allele frequencies of loci associated with four phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher signals of selection (covariance of allele frequencies) than could be expected to arise, given the data. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results replicate empirical support for theoretical expectations of local adaptation for populations exhibiting strong gene flow and high selective pressures, and suggest that ongoing adaptation of many P. albicaulis populations within the Lake Tahoe Basin will not be constrained by the lack of genetic variation. Even so, some populations exhibit low levels of heritability for the traits presumed to be related to fitness. These instances could be used to prioritize management to maintain adaptive potential. Overall, we suggest that established practices regarding whitebark pine conservation be maintained, with the additional context of fine-scale adaptation.