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1. Pervasive Genomic Signatures of Local Adaptation to Altitude Across Highland Specialist Andean Hummingbird Populations

   https://doi.org/10.1093/jhered/esab008  

   Lim, Marisa C; Bi, Ke; Witt, Christopher C; Graham, Catherine H; Dávalos, Liliana M (February 2021, Journal of Heredity)

   Chapman, Mark (Ed.)

   Abstract Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow, and genetic drift. In montane systems, where species are often restricted to narrow ranges of elevation, it is unclear whether the selection is strong enough to influence functional differentiation of subpopulations differing by a few hundred meters in elevation. We used targeted capture of 12 501 exons from across the genome, including 271 genes previously implicated in altitude adaptation, to test for adaptation to local elevations for 2 highland hummingbird species, Coeligena violifer (n = 62) and Colibri coruscans (n = 101). For each species, we described population genetic structure across the complex geography of the Peruvian Andes and, while accounting for this structure, we tested whether elevational allele frequency clines in single nucleotide polymorphisms (SNPs) showed evidence for local adaptation to elevation. Although the 2 species exhibited contrasting population genetic structures, we found signatures of clinal genetic variation with shifts in elevation in both. The genes with SNP-elevation associations included candidate genes previously discovered for high-elevation adaptation as well as others not previously identified, with cellular functions related to hypoxia response, energy metabolism, and immune function, among others. Despite the homogenizing effects of gene flow and genetic drift, natural selection on parts of the genome evidently optimizes elevation-specific cellular function even within elevation range-restricted montane populations. Consequently, our results suggest local adaptation occurring in narrow elevation bands in tropical mountains, such as the Andes, may effectively make them “taller” biogeographic barriers. 

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2. Whole‐exome sequencing reveals a long‐term decline in effective population size of red spruce ( Picea rubens )

   https://doi.org/10.1111/eva.12985  

   Capblancq, Thibaut; Butnor, John R.; Deyoung, Sonia; Thibault, Ethan; Munson, Helena; Nelson, David M.; Fitzpatrick, Matthew C.; Keller, Stephen R. (May 2020, Evolutionary Applications)

   Understanding the factors influencing the current distribution of genetic diversity across a species range is one of the main questions of evolutionary biology, especially given the increasing threat to biodiversity posed by climate change. Historical demographic processes such as population expansion or bottlenecks and decline are known to exert a predominant influence on past and current levels of genetic diversity, and revealing this demo‐genetic history can have immediate conservation implications. We used a whole‐exome capture sequencing approach to analyze polymorphism across the gene space of red spruce (Picea rubens Sarg.), an endemic and emblematic tree species of eastern North America high‐elevation forests that are facing the combined threat of global warming and increasing human activities. We sampled a total of 340 individuals, including populations from the current core of the range in northeastern USA and southeastern Canada and from the southern portions of its range along the Appalachian Mountains, where populations occur as highly fragmented mountaintop “sky islands.” Exome capture baits were designed from the closely relative white spruce (P. glauca Voss) transcriptome, and sequencing successfully captured most regions on or near our target genes, resulting in the generation of a new and expansive genomic resource for studying standing genetic variation in red spruce applicable to its conservation. Our results, based on over 2 million exome‐derived variants, indicate that red spruce is structured into three distinct ancestry groups that occupy different geographic regions of its highly fragmented range. Moreover, these groups show small Ne , with a temporal history of sustained population decline that has been ongoing for thousands (or even hundreds of thousands) of years. These results demonstrate the broad potential of genomic studies for revealing details of the demographic history that can inform management and conservation efforts of nonmodel species with active restoration programs, such as red spruce. 

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3. Studies in Lichens and Lichenicolous Fungi - No. 23: Notes on Appalachian taxa including newly reported disjunctions and multiple species new to North America

   https://doi.org/10.5962/p.388460  

   Lendemer, James C (January 2023, Opuscula philolichenum)

   Arthonia ligniariella is reported for the first time from eastern North America based on a collection growing on lignum in North Carolina, U.S.A. Biatora appalachensis, an Appalachian endemic, is shown to be widespread throughout the Appalachian Mountains, primarily at high elevations. The only report of Fellhanera parvula from North America (Tennessee, U.S.A.) is considered to be F. bouteillei. Fellhanera subtilis, previously reported in North America from the Pacific Northwest, is reported for the first time from eastern North America (southern Appalachian Mountains). Gyalideopsis mexicana, previously reported in North America from the Yukon, Canada and New Mexico, U.S.A. is newly reported from eastern North America (southern Appalachian Mountains, North Carolina, U.S.A.). Lepra ouahensis, a sorediate species with lichexanthone and stictic acid, is reported from disjunct areas of the southern Appalachian Mountains and the Southeastern Coastal Plain. Its distribution is compared to the lichexanthone producing chemotypes of L. trachythallina and Varicellaria velata. Rockefellera crossophylla, a rare species considered extinct in Pennsylvania, U.S.A. is reported to be extant in that state. Psoronactis dilleniana is newly reported from North America from high elevations of the central and southern Appalachian Mountains (North Carolina and Virginia U.S.A.). Xenonectriella streimannii is newly reported for North America based on a collection found growing on Anaptychia palmulata in Georgia, U.S.A. 

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4. Two new species of lichenicolous Arthonia (Arthoniaceae) from southeastern North America highlight the need for comparative studies of lichen parasites and their hosts

   https://doi.org/10.1639/0007-2745-127.1.001  

   Hollinger, Jason P; Scott, Perry A; Lendemer, James C (January 2024, The Bryologist)

   Arthonia frostiicola and A. galligena are described as new to science based on collections from mountainous regions of southeastern North America. Arthonia frostiicola infects the saxicolous lichen Dirinaria frostii, producing emarginate black apothecia which erupt from within the host thallus. It is characterized by a dark hypothecium and 1-septate, obovoid ascospores which turn brownish and verruculose in age. It is known from five collections made in the southern Appalachian Mountains and Ozark Mountains in southeastern North America. Arthonia galligena produces galls in the thallus and apothecia of the corticolous lichens Lecanora masana and L. rugosella, and is apparently endemic to the high elevations of the southern Appalachian Mountains. It is characterized by a variably pigmented, pale to red-brown hypothecium and 2-septate, macrocephalic ascospores which turn brownish and verruculose in age. Keys to the species of Arthonia on Caliciales and Lecanoraceae are provided. 

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5. Genotypic variation and plasticity in climate-adaptive traits after range expansion and fragmentation of red spruce ( Picea rubens Sarg.)

   https://doi.org/10.1098/rstb.2021.0008  

   Prakash, Anoob; DeYoung, Sonia; Lachmuth, Susanne; Adams, Jacquelyne L.; Johnsen, Kurt; Butnor, John R.; Nelson, David M.; Fitzpatrick, Matthew C.; Keller, Stephen R. (April 2022, Philosophical Transactions of the Royal Society B: Biological Sciences)

   Shifting range limits are predicted for many species as the climate warms. However, the rapid pace of climate change will challenge the natural dispersal capacity of long-lived, sessile organisms such as forest trees. Adaptive responses of populations will, therefore, depend on levels of genetic variation and plasticity for climate-responsive traits, which likely vary across the range due to expansion history and current patterns of selection. Here, we study levels of genetic and plastic variation for phenology and growth traits in populations of red spruce ( Picea rubens ), from the range core to the highly fragmented trailing edge. We measured more than 5000 offspring sampled from three genetically distinct regions (core, margin and edge) grown in three common gardens replicated along a latitudinal gradient. Genetic variation in phenology and growth showed low to moderate heritability and differentiation among regions, suggesting some potential to respond to selection. Phenology traits were highly plastic, but this plasticity was generally neutral or maladaptive in the effect on growth, revealing a potential liability under warmer climates. These results suggest future climate adaptation will depend on the regional availability of genetic variation in red spruce and provide a resource for the design and management of assisted gene flow. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’. 

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