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1. Contrasting Phylogeographic Patterns of Sandy vs. Rocky Sympatric Sister Species of Supralittoral Tylos Isopods in Chile

   https://doi.org/10.1002/ece3.71803  

   Hurtado, Luis A; Mateos, Mariana; Wang, Chang; Ndeda, Violet M; Pérez‐Schultheiss, Jorge; Thiel, Martin (July 2025, Ecology and Evolution)

   ABSTRACT Sister taxa that have diverged and persisted in sympatry have likely been exposed to the same general environmental changes throughout their evolutionary history and may thus exhibit similar phylogeographies. Here, we compare the phylogeographic patterns of two sister species of isopods (genusTylos) that have broadly overlapping distributions but distinct habitat preferences in the supralittoral zone of Chile. The dynamic geoclimatic history of this region during the Quaternary has been implicated in shaping the evolutionary histories of other coastal taxa.Tylos spinulosusis found in sandy beaches at latitudes ~27°–30° S, whereasTylos chilensishas been found in rocky shores at ~27°–33° S and at ~39°–42° S. We sampled both species across their ranges (collectively from 20 localities) and obtained sequences from at least one mitochondrial gene for 95 T. chilensisand 41 T. spinulosus. We used phylogenetics and population genetics methods to analyze four single‐gene and one concatenated datasets: 12S rDNA (n = 130); 16S rDNA (n = 31); Cytochrome oxidase subunit I (n = 28); Cytochrome b (n = 24); concatenation of the four genes (n = 24). Both species show high levels of isolation of local populations, consistent with expectations from their limited autonomous dispersal potential. However, they exhibit strikingly different mitochondrial phylogeographic patterns.Tylos chilensisshows evidence of multiple relatively deep divergence events leading to geographically restricted lineages that appear to have persisted over multiple glaciations. Surprisingly, one lineage ofT. chilensiswas found in geographically distant localities, suggesting the possibility of human‐mediated dispersal.Tylos spinulosusappears to have undergone a relatively recent bottleneck followed by a population/range expansion. Differences in life histories and habitat preferences or stochasticity may have contributed to these striking phylogeographic differences. Finally, the high levels of differentiation and isolation among populations indicate that they are highly vulnerable to extirpation. We discuss threats to their persistence and recommendations for their conservation. 

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2. Hybrid Zone Analysis Using Coalescent‐Based Estimates of Introgression and Migration in Plateau Fence Lizards ( Sceloporus tristichus )

   https://doi.org/10.1111/mec.17819  

   Leaché, Adam D; Davis, Hayden R; Singhal, Sonal (July 2025, Molecular Ecology)

   ABSTRACT Coalescent modelling of hybrid zones can provide novel insights into the historical demography of populations, including divergence times, population sizes, introgression proportions, migration rates and the timing of hybrid zone formation. We used coalescent analysis to determine whether the hybrid zone between phylogeographic lineages of the Plateau Fence Lizard (Sceloporus tristichus) in Arizona formed recently due to human‐induced landscape changes, or if it originated during Pleistocene climatic shifts. Given the presence of mitochondrial DNA from another species in the hybrid zone (Southwestern Fence Lizard,S. cowlesi), we tested for the presence ofS. cowlesinuclear DNA in the hybrid zone as well as reassessed the species boundary betweenS. tristichusandS. cowlesi. No evidence ofS. cowlesinuclear DNA is found in the hybrid zone, and the paraphyly of both species raises concerns about their taxonomic validity. Introgression analysis placed the divergence time between the parental hybrid zone populations at approximately 140 kya and their secondary contact and hybridization at approximately 11 kya at the end of the Pleistocene. Introgression proportions estimated for hybrid populations are correlated with their geographic distance from parental populations. The multispecies coalescent with migration provided significant support for unidirectional migration moving from south to north, which is consistent with spatial cline analyses that suggest a slow but steady northward shift of the centre of the hybrid zone over the last two decades. When analysing hybrid populations sampled along a linear transect, coalescent methods can provide novel insights into hybrid zone dynamics. 

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3. Comparative Analyses of Four Reference Genomes Reveal Exceptional Diversity and Weak Linked Selection in the Yellow Monkeyflower ( Mimulus guttatus ) Complex

   https://doi.org/10.1111/1755-0998.70012  

   Lovell, John T; Walstead, Rachel; Lawrence, Amelia; Stark‐Dykema, Evan; Farnitano, Matthew C; Harder, Avril; Brůna, Tomáš; Barry, Kerrie; Goodstein, David; Jenkins, Jerry; et al (July 2025, Molecular Ecology Resources)

   ABSTRACT Yellow monkeyflowers (Mimulus guttatuscomplex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan‐genomics in this group, we present four chromosome‐scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a singleM. guttatuspopulation, one from the closely related selfing speciesM. nasutus, and one from a more divergent speciesM. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat‐rich, gene‐poor regions that large portions of the genome are unalignable across accessions. As a result, thisMimuluspan‐genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence–absence, investigate the recombination landscape using high‐resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high—even in regions of very low recombination—reaching ~3.2% within a singleM. guttatuspopulation, ~7% within the interfertileM. guttatusspecies complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolatedM. tilingii. Genome‐wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high‐recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation forMimulusresearch and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes. 

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4. Mycorrhizal Fungi Influence on Mature Tree Growth: Stronger in High‐Nitrogen Soils for an EMF ‐Associated Tree and in Low‐Nitrogen Soils for Two AMF ‐Associated Trees

   https://doi.org/10.1002/pei3.70055  

   Ibáñez, Inés; McPherson, Morgan R; Upchurch, Rima A; Zak, Donald R (June 2025, Plant-Environment Interactions)

   Wiley (Ed.)

   ABSTRACT The plant–mycorrhizal fungi relationship can range from mutualistic to parasitic as a function of the fungal taxa involved, plant ontogeny, as well as the availability of resources. Despite the implications this relationship may have on forest carbon cycling and storage, we know little about how mature trees may be impacted by mycorrhizae and how this impact may vary across the landscape. We collected growth data of two arbuscular mycorrhizal fungi (AMF)‐associated tree species,Acer rubrumandA. saccharum, and one ectomycorrhizal fungi (EMF)‐associated tree species,Quercus rubra, to assess how the mycorrhizal fungi–plant association may vary along a gradient of nitrogen (N) availability. Individual assessments of fungal taxa relative abundances showed non‐linear associations with tree growth; positive associations for the two AMF‐associated trees were mostly under low N, whereas positive to neutral associations for the EMF‐associated tree mainly took place at high N. OnlyA. rubrumexhibited greater tree growth with its tree soil‐specific mycorrhizal community when compared with predictions under a random mycorrhizal soil community. Because mycorrhizal fungi are likely to mediate how plants respond to warming, increasing levels of N deposition and of atmospheric CO₂, understanding these relationships is critical to accurately forecasting tree growth. 

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5. Recently Delisted Songbird Harbors Extensive Genomic Evidence of Inbreeding, Potentially Complicating Future Recovery

   https://doi.org/10.1111/eva.70052  

   Calderón, Anna María; Wood, Andrew W; Szpiech, Zachary A; Toews, David PL (December 2024, Evolutionary Applications)

   The Kirtland's warbler (Setophaga kirtlandi) is a rare migratory passerine species and habitat specialist of the North American Jack Pine Forests. Their near extinction in the 1970s classified them as endangered and protected under the Endangered Species Act of 1973. After decades of intense conservation management, their population size recovered, and they were delisted from federal protection in 2019. We explore the genomic consequences of this harsh bottleneck and recovery by comparing the genomic architecture of two closely related species whose population sizes have remained large and stable, Hooded Warblers (Setophaga citrina) and American Redstarts (Setophaga ruticilla). We used whole‐genome sequencing to characterize the distribution of runs of homozygosity and deleterious genetic variation. We find evidence that Kirtland's warblers exhibit genetic patterns consistent with recent inbreeding. Our results also show that Kirtland's warblers carry an excess proportion of deleterious variation, which could complicate management for this conservation‐reliant species. This analysis provides a genetically informed perspective that should be thoroughly considered when delisting other species from federal protections. Through the increasing accessibility of genome sequencing technology, it will be more feasible to monitor the genetic landscape of recovering populations to ensure their long‐term survival independent of conservation intervention. 

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