Spatiotemporally consistent genomic signatures of reproductive isolation in a moving hybrid zone

Studies of hybrid zone dynamics often investigate a single sampling period and draw conclusions from that temporal snapshot. Stochasticity can, however, result in loci with spurious outlier patterns, which is exacerbated by limited temporal or geographic sampling. Comparing admixed populations from different geographic regions is one way to detect repeatedly divergent genomic regions potentially involved in reproductive isolation. Temporal comparisons also allow us to control partially for the role of stochasticity, but the power of temporal sampling has not yet been adequately explored. In North America, black‐capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadees hybridize in a contact zone extending from New Jersey to Kansas. The hybrid zone is likely maintained by strong intrinsic selection against hybrids, and it is moving north. We used a reduced representation genomic approach and temporally spaced sampling—two samples of ～80 individuals separated by a decade—to determine the pattern and consistency of selection and genomic introgression in the chickadee hybrid zone. We report consistently low introgression for highly divergent loci between P. atricapillus and P. carolinensis in this moving hybrid zone. This is strong evidence that these loci may be linked to genomic regions involved in reproductive isolation between chickadees.     

Divergent population structure and climate associations of a chromosomal inversion polymorphism across the Mimulus guttatus species complex

Chromosomal rearrangement polymorphisms are common and increasingly found to be associated with adaptive ecological divergence and speciation. Rearrangements, such as inversions, reduce recombination in heterozygous individuals and thus can protect favourable allelic combinations at linked loci, facilitating their spread in the presence of gene flow. Recently, we identified a chromosomal inversion polymorphism that contributes to ecological adaptation and reproductive isolation between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus. Here we evaluate the population genetic structure of this inverted region in comparison with the collinear regions of the genome across the M. guttatus species complex. We tested whether annual and perennial M. guttatus exhibit different patterns of divergence for loci in the inverted and noninverted regions of the genome. We then evaluated whether there are contrasting climate associations with these genomic regions through redundancy analysis. We found that the inversion exhibits broadly different patterns of divergence among annual and perennial M. guttatus and is associated with environmental variation across population accessions. This study is the first widespread population genetic survey of the diversity of the M. guttatus species complex. Our findings contribute to a greater understanding of morphological, ecological, and genetic evolutionary divergence across this highly diverse group of closely related ecotypes and species. Finally, understanding species relationships among M. guttatus sp. has hitherto been stymied by accumulated evidence of substantial gene flow among populations as well as designated species. Nevertheless, our results shed light on these relationships and provide insight into adaptation in life history traits within the complex.     

Serial founder effects and genetic differentiation during worldwide range expansion of monarch butterflies

Range expansions can result in founder effects, increasing genetic differentiation between expanding populations and reducing genetic diversity along the expansion front. However, few studies have addressed these effects in long-distance migratory species, for which high dispersal ability might counter the effects of genetic drift. Monarchs (Danaus plexippus) are best known for undertaking a long-distance annual migration in North America, but have also dispersed around the world to form populations that do not migrate or travel only short distances. Here, we used microsatellite markers to assess genetic differentiation among 18 monarch populations and to determine worldwide colonization routes. Our results indicate that North American monarch populations connected by land show limited differentiation, probably because of the monarch''s ability to migrate long distances. Conversely, we found high genetic differentiation between populations separated by large bodies of water. Moreover, we show evidence for serial founder effects across the Pacific, suggesting stepwise dispersal from a North American origin. These findings demonstrate that genetic drift played a major role in shaping allele frequencies and created genetic differentiation among newly formed populations. Thus, range expansion can give rise to genetic differentiation and declines in genetic diversity, even in highly mobile species.     

Investigating latitudinal clines for life history and stress resistance traits in Drosophila simulans from eastern Australia

Latitudinal clines have been demonstrated for many quantitative traits in Drosophila and are assumed to be due to climatic selection. However, clinal studies are often performed in species of Drosophila that contain common cosmopolitan inversion polymorphisms that also show clinal patterns. These inversion polymorphisms may be responsible for much of the observed clinal variation. Here, we consider latitudinal clines for quantitative traits in Drosophila simulans from eastern Australia. Drosophila simulans does not contain cosmopolitan inversion polymorphisms, so allows the study of clinal selection on quantitative traits that are not confounded by associations with inversions. Body size showed a strong linear cline for both females and males. Starvation resistance exhibited a weak linear cline in females, whereas chill-coma recovery exhibited a significant nonlinear cline in females only. No clinal pattern was evident for development time, male chill-coma recovery, desiccation or heat resistance. We discuss these results with reference to the role inversion polymorphisms play in generating clines in quantitative traits of Drosophila.     

Grow with the flow: a latitudinal cline in physiology is associated with more variable precipitation in Erythranthe cardinalis

Local adaptation is commonly observed in nature: organisms perform well in their natal environment, but poorly outside it. Correlations between traits and latitude, or latitudinal clines, are among the most common pieces of evidence for local adaptation, but identifying the traits under selection and the selective agents is challenging. Here, we investigated a latitudinal cline in growth and photosynthesis across 16 populations of the perennial herb Erythranthe cardinalis (Phrymaceae). Using machine learning methods, we identify interannual variation in precipitation as a likely selective agent: southern populations from more variable environments had higher photosynthetic rates and grew faster. We hypothesize that selection may favour a more annualized life history – grow now rather than save for next year – in environments where severe droughts occur more often. Thus, our study provides insight into how species may adapt if Mediterranean climates become more variable due to climate change.     

Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and nonecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genomewide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species‐diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate‐mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate‐mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.     

Hybrid zone formation and contrasting outcomes of secondary contact over transects in common toads

Much progress in speciation research stems from documenting patterns of morphological and genetic variation in hybrid zones. Contrasting patterns of marker introgression in different sections of the contact can provide valuable insights on the relative importance of various evolutionary mechanisms maintaining species differences in the face of hybridization and gene flow and on hybrid zone temporal and spatial dynamics. We studied species interactions in the common toads Bufo bufo and B. spinosus in France and northwestern Italy using morphological and molecular data from the mitochondrial and nuclear genomes in an extensive survey, including two independent transects west and east of the Alps. At both, we found sharp, coincident and concordant nuclear genetic transitions. However, morphological clines were wider or absent and mtDNA introgression was asymmetric. We discuss alternative, nonexclusive hypotheses about evolutionary processes generating these patterns, including drift, selection, long‐distance dispersal and spatial shifts in hybrid zone location and structure. The distribution of intraspecific mtDNA lineages supports a scenario in which B. bufo held a local refugium during the last glacial maximum. Present‐day genetic profiles are best explained by an advance of B. spinosus from a nearby Iberian refugium, largely superseding the local B. bufo population, followed by an advance of B. bufo from the Balkans, with prongs north and south of the Alps, driving B. spinosus southwards. A pendulum moving hybrid zone, first northwards and then southwards, explains the wide areas of introgression at either side of the current position of the contact zones.     

黑果蝇（D.virilis）自然群体遗传多态研究

利用９种限制性内切酶对Ｄ．ｖｉｒｉｌｉｓ兰州群体作了ｍｔＤＮＡ的ＲＦＬＰ分析,结合其他地区Ｄ．ｖｉｒｉｌｉｓ群体的ｍｔＤＮＡ的ＲＦＬＰ数据,用ＵＰＧＭＡ法构建了聚类图。发现大陆Ｄ．ｖｉｒｉｌｉｓ聚成明显的３支：兰州和青岛群体、华东群体、福建群体,呈一纬度梯度分布。单纯以地理隔离不能解释Ｄ．ｖｉｒｉｌｉｓ自然群体间的遗传差异。温度依赖性的选择可能是纬度梯度分布的维持机制。     

Patterns of diversification and genetic population structure of small mammals in Taiwan

Taiwan is a mountainous island off the coast of the Asian continent. The island is located on the continental shelf and rises to an elevation of nearly 4000 m. It became an island approximately 4 million years ago and has been connected to the continent more than once since its emergence. Therefore, the elevational zonation of two Taiwanese pairs of congeners in the rodent genera Apodemus and Niviventer can be explained by one of two competing hypotheses. One hypothesis assumes that speciation of the two congeners occurred in situ after an ancestral species migrated from the continent. In contrast, the second hypothesis argues the zonation resulted from separate incursion events during the connections. The phylogenetic analyses, which are based on electrophoretic allozyme data, reject the first of these hypotheses. Furthermore, genetic population structure and gene flow of three species of Taiwanese rodents (Apodemus semotus, Niviventer culturatus and Microtus kikuchii) are studied in relation to their patterns of elevational distribution. The genetic structure of A. semotus and N. culturatus, which have extensive elevational distribution, is rather homogeneous and no genie discontinuity or cline in allele frequency was detected. Gene flow among subpopulations for these two species is rather substantial; therefore, the potential isolating effect imposed by deep river valleys is minimal. Conversely, isolation of populations of M. kikuchii on different mountaintops is quite complete as mirrored by the high level of genie differentiation and low gene flow.