Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.

The Russian dandelion, Taraxacum kok-saghyz (TKS), is a perennial species native to Central Asia that produces high quality, natural rubber. Despite its potential to help maintain a stable worldwide rubber supply, little is known about genetic variation in this species. To facilitate future germplasm improvement efforts, we developed simple-sequence repeat (SSR) markers from available expressed-sequence tag (EST) data and used them to investigate patterns of population genetic diversity in this nascent crop species. We identified numerous SSRs (1,510 total) in 1,248 unigenes from a larger set of 6,960 unigenes (derived from 16,441 ESTs) and designed PCR primers targeting 767 of these loci. Screening of a subset of 192 of these primer pairs resulted in the identification of 48 pairs that appeared to produce single-locus polymorphisms. We then used the most reliable 17 of these primer pairs to genotype 176 individuals from 17 natural TKS populations. We observed an average of 4.8 alleles per locus with population-level expected heterozygosities ranging from 0.28 to 0.50. An average pairwise FST of 0.11 indicated moderate but statistically significant levels of genetic differentiation, though there was no clear geographic patterning to this differentiation. We also tested these 17 primer pairs in the widespread common dandelion, T. officinale, and a majority successfully produced apparently single-locus amplicons. This result demonstrates the potential utility of these markers for genetic analyses in other species in the genus.

12Hybrid incompatibilities play a critical role in the evolution and maintenance of species. We 13 have discovered a simple genetic incompatibility that causes lethality in hybrids between two 14 closely related species of yellow monkeyflower (Mimulus guttatus and M. nasutus). This hybrid 15 incompatibility, which causes one sixteenth of F 2 hybrid seedlings to lack chlorophyll and die 16 shortly after germination, occurs between sympatric populations that are connected by 17 ongoing interspecific gene flow. Using complimentary genetic mapping and gene expression 18 analyses, we show that lethality occurs in hybrids that lack a functional copy of the critical 19 photosynthetic gene pTAC14. In M. guttatus, this gene was duplicated, but the ancestral copy is 20 no longer expressed. In M. nasutus, the duplication is missing altogether. As a result, hybrids 21 die when they are homozygous for the nonfunctional M. guttatus copy and missing the 22 peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/201392 doi: bioRxiv preprint first posted online 2 duplicate from M. nasutus, apparently due to misregulated transcription of key photosynthetic 23 genes. Our study indicates that neutral evolutionary processes may play an important role in 24 the evolution of hybrid incompatibilities and opens the door to direct investigations of their 25 contribution to reproductive isolation among naturally hybridizing species. 26 27 Author Summary 28Hybrid incompatibilities play an important role in speciation, because they act to limit gene flow 29 between species. Identifying the genes that underlie these barriers sheds light on the 30 evolutionary forces and genetic mechanisms that give rise to new species. We identified a 31 reproductive barrier that causes lethality in the F2 offspring of sympatric species of yellow 32 monkeyflower (Mimulus guttatus and M. nasutus). We show that lethality occurs in hybrids that 33 lack a functional copy of the critical photosynthetic gene pTAC14. This gene was duplicated in M. 34 guttatus, but the ancestral copy subsequently lost function. In M. nasutus, no duplication 35 occurred. As a consequence, F2 hybrids that are homozygous for non-functional M. guttatus 36 copies at one locus and missing M. nasutus duplicates at the other locus completely lack 37 functional pTAC14 and die. Our data indicate that non-functionalization of ancestral pTAC14 in 38 M. guttatus occurred via neutral evolutionary change. These results suggest that neutral 39 evolutionary forces may play an important role in speciation. 40 41

Hybrid incompatibilities play a critical role in the evolution and maintenance of species. We have discovered a simple genetic incompatibility that causes lethality in hybrids between two closely related species of yellow monkeyflower (Mimulus guttatus and M. nasutus). This hybrid incompatibility, which causes one sixteenth of F2 hybrid seedlings to lack chlorophyll and die shortly after germination, occurs between sympatric populations that are connected by ongoing interspecific gene flow. Using complimentary genetic mapping and gene expression analyses, we show that lethality occurs in hybrids that lack a functional copy of the critical photosynthetic gene pTAC14. In M. guttatus, this gene was duplicated, but the ancestral copy is no longer expressed. In M. nasutus, the duplication is missing altogether. As a result, hybrids die when they are homozygous for the nonfunctional M. guttatus copy and missing the duplicate from M. nasutus, apparently due to misregulated transcription of key photosynthetic genes. Our study indicates that neutral evolutionary processes may play an important role in the evolution of hybrid incompatibilities and opens the door to direct investigations of their contribution to reproductive isolation among naturally hybridizing species.

Reproductive isolation, which is essential for the maintenance of species in sympatry, is often incomplete between closely related species. In these taxa, reproductive barriers must evolve within species, without being degraded by ongoing gene flow. To better understand this dynamic, we investigated the frequency and geographic distribution of alleles underlying a two-locus, hybrid lethality system between naturally hybridizing species of monkeyflower (Mimulus guttatus and M. nasutus). We found that M. guttatus typically carries hybrid lethality alleles at one locus (hl13) and M. nasutus typically carries hybrid lethality alleles at the other locus (hl14). As a result, natural hybrids carry incompatible alleles at both loci, and express hybrid lethality in later generations. We also discovered considerable polymorphism at both hl13 and hl14 within both species. For M. guttatus, polymorphism at both loci occurs within populations, meaning that incompatible allele pairings likely arise through intraspecific gene flow. Genetic variation at markers linked to hl13 and hl14 suggest that introgression from M. nasutus is the primary driver of this polymorphism within M. guttatus. Additionally, patterns of introgression at the two hybrid lethality loci suggest that natural selection eliminates incompatible allele pairings, suggesting that even weak reproductive barriers might promote genomic divergence between species.