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1. Genetic Diversity and Population Structure in Cities Is Not Consistent Among Cosmopolitan Plant Species

   https://doi.org/10.1111/mec.70261  

   Hoffman, Ava M; Cocciardi, Jennifer M; Manna, Prothama; Alvarado‐Serrano, Diego F; Cavender‐Bares, Jeannine; Groffman, Peter M; Hall, Sharon J; Hobbie, Sarah E; Lerman, Susannah B; Padullés_Cubino, Josep; et al (February 2026, Molecular Ecology)

   ABSTRACT. Urbanisation has led to increasing homogenization of plant communities across cities. However, it is unclear whether these patterns extend to cosmopolitan plant species at the genetic level. We examined genome‐wide genetic patterns in six widespread plant species (three Poaceae and three Asteraceae) across five cities in the USA (Boston, Baltimore, Minneapolis‐St. Paul, Phoenix, and Los Angeles) using reduced‐representation sequencing. We assessed genetic structure, differentiation, and patterns of isolation by distance (IBD) and environment (IBE) to determine if species were genetically homogeneous or differentiated by city, percentage of impervious surface, or both. Most species exhibited limited population structure overall, withPoa annua(annual bluegrass),Taraxacum officinale(dandelion), andCynodon dactylon(Bermuda grass) showing no significant genetic differentiation among cities, a pattern consistent with high gene flow mediated by human activity. Notable exceptions included city‐level differences inErigeron canadensis(horseweed) andLactuca serriola(prickly lettuce), especially in Phoenix. We also observed low genetic diversity inDigitaria sanguinalis(crabgrass) from Phoenix, suggesting recent founder effects or selection via environmental filtering.Erigeron canadensis,the only native species studied, displayed stronger differentiation by city, along with significant isolation by temperature and distance. Among all species, we found no evidence for population structure by impervious surface. Our findings indicate that widespread population genetic structure patterns of cosmopolitan plants are likely to depend more on species attributes (e.g., self‐compatibility) and human‐mediated dispersal than on urbanisation per se. 

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2. Recent Climate Change and Historical Population Structure Predict Spatial Patterns of Admixture Between Two Host‐Specialised Pine Sawfly Species

   https://doi.org/10.1111/mec.70183  

   Glover, Ashleigh N; Linnen, Catherine R (December 2025, Molecular Ecology)

   ABSTRACT Human disturbance can have profound effects on biodiversity, including increasing hybridization between reproductively isolated species. One approach for understanding how human activity affects hybridization dynamics is to evaluate correlations between disturbance (e.g., urbanisation, temperature change) and hybridization. Because variation in hybridization can also arise from historical factors unrelated to recent human disturbance, it is essential to account for population structure to avoid spurious correlations. Here, we combine environmental and high‐coverage whole‐genome resequencing data to investigate how human disturbance and population structure affect hybridization dynamics between a pair of pine sawflies adapted to different pines,Neodiprion leconteiandNeodiprion pinetum. We find thatN. leconteiandN. pinetumexhibit strikingly different patterns of population structure, which we hypothesise stem from differences in host use. We also find that recent admixture is both asymmetric and geographically variable. Linear regression analyses reveal that admixture proportion is predicted by indirect human disturbance (i.e., climate change) and not direct human disturbance (e.g., urbanisation) in bothN. leconteiandN. pinetum. Lastly, inN. pinetum, we find evidence of a spurious association between admixture and direct human disturbance that disappears when regression models account for population structure via inclusion of genetic principal component scores as covariates. Together, our data suggest that indirect human disturbance and population structure both contribute to geographic variation in admixture betweenN. leconteiandN. pinetum. Our study also highlights the importance of adequately controlling for population structure when attempting to identify environmental predictors (human disturbance‐related or not) of hybridization. 

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3. 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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4. 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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5. 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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