Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes

Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone

Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene expression plasticity by comparing expression profiles in parental species and their hybrids following a 2-week thermal challenge. Hybrid expression plasticity was most often like one parent or the other (50%). However, a large fraction of genes (26%) showed transgressive expression plasticity (i.e. the change in gene expression was either greater or lesser than that of both parent species), while only 2% were intermediately plastic in hybrids. Despite their close phylogenetic relationship, there was limited overlap in the differentially expressed genes responding to temperature, indicating interspecific differences in the responses to high temperature in which responses from hybrids are distinct from both parent species. We also identified differentially expressed long non-coding RNAs (lncRNAs), which we suggest may contribute to species-specific differences in thermal tolerance. Our findings provide important insight into the impact of hybridization on gene expression under warming. We propose transgressive hybrids may play an important role in population persistence under future warming conditions.

A de novo genome assembly and annotation of the southern flying squirrel (Glaucomys volans)

Northern (Glaucomys sabrinus) and southern (Glaucomys volans) flying squirrels are widespread species distributed across North America. Northern flying squirrels are common inhabitants of the boreal forest, also occurring in coniferous forest remnants farther south, whereas the southern flying squirrel range is centered in eastern temperate woodlands. These two flying squirrel species exhibit a hybrid zone across a latitudinal gradient in an area of recent secondary contact. Glaucomys hybrid offspring are viable and can successfully backcross with either parental species, however, the fitness implications of such events are currently unknown. Some populations of G. sabrinus are endangered, and thus, interspecific hybridization is a key conservation concern in flying squirrels. To provide a resource for future studies to evaluate hybridization and possible introgression, we sequenced and assembled a de novo long-read genome from a G. volans individual sampled in southern Ontario, Canada, while four short-read genomes (two G. sabrinus and two G. volans, all from Ontario) were resequenced on Illumina platforms. The final genome assembly consisted of approximately 2.40 Gb with a scaffold N50 of 455.26 Kb. Benchmarking Universal Single-Copy Orthologs reconstructed 3,742 (91.2%) complete mammalian genes and genome annotation using RNA-Seq identified the locations of 19,124 protein-coding genes. The four short-read individuals were aligned to our reference genome to investigate the demographic history of the two species. A principal component analysis clearly separated resequenced individuals, while inferring population size history using the Pairwise Sequentially Markovian Coalescent model noted an approximate species split 1 million years ago, and a single, possibly recently introgressed individual.

Butterfly Conservation in China: From Science to Action

About 10% of the Earth's butterfly species inhabit the highly diverse ecosystems of China. Important for the ecological, economic, and cultural services they provide, many butterfly species experience threats from land use shifts and climate change. China has recently adopted policies to protect the nation's biodiversity resources. This essay examines the current management of butterflies in China and suggests various easily implementable actions that could improve these conservation efforts. Our recommendations are based on the observations of a transdisciplinary group of entomologists and environmental policy specialists. Our analysis draws on other successful examples around the world that China may wish to consider. China needs to modify its scientific methodologies behind butterfly conservation management: revising the criteria for listing protected species, focusing on umbrella species for broader protection, identifying high priority areas and refugia for conservation, among others. Rural and urban land uses that provide heterogeneous habitats, as well as butterfly host and nectar plants, must be promoted. Butterfly ranching and farming may also provide opportunities for sustainable community development. Many possibilities exist for incorporating observations of citizen scientists into butterfly data collection at broad spatial and temporal scales. Our recommendations further the ten Priority Areas of China's National Biodiversity Conservation Strategy and Action Plan (2011-2030).

Assessing ecological and physiological costs of melanism in North American Papilio glaucus females: two decades of dark morph frequency declines

Polymorphisms for melanic form of insects may provide various selective advantages. However, melanic alleles may have significant/subtle pleiotrophic "costs." Several potential pleiotrophic effects of the W (=Y)-linked melanism gene in Papilio glaucus L. (Lepidoptera) showed no costs for melanic versus yellow in adult size, oviposition preferences, fecundity, egg viability, larval survival/growth rates, cold stress tolerance, or postdiapause emergence times. Sexual selection (males choosing yellow rather than mimetic dark females) had been suggested to provide a balanced polymorphism in P. glaucus, but spermatophore counts in wild females and direct field tethering studies of size-matched pairs of virgin females (dark and yellow), show that male preferences are random or frequency-dependent from Florida to Michigan, providing no yellow counter-advantages. Recent frequency declines of dark (melanic/mimetic) females in P. glaucus populations are shown in several major populations from Florida (27.3°N latitude) to Ohio (38.5° N). Summer temperatures have increased significantly at all these locations during this time (1999-2018), but whether dark morphs may be more vulnerable (in any stage) to such climate warming remains to be determined. Additional potential reasons for the frequency declines in mimetic females are discussed: (i) genetic introgression of Z-linked melanism suppressor genes from P. canadensis (R & J) and the hybrid species, P. appalachiensis (Pavulaan & Wright), (ii) differential developmental incompatibilities, or Haldane effects, known to occur in hybrids, (iii) selection against intermediately melanic ("dusty") females (with the W-linked melanic gene, b+) which higher temperatures can cause.

Projecting Suitability and Climate Vulnerability of Bhutanitis thaidina (Blanchard) (Lepidoptera: Papilionidae) with Conservation Implications

Bhutanitis thaidina is an endemic, rare, and protected swallowtail in China. Deforestation, habitat fragmentation, illegal commercialised capture, and exploitation of larval food plants are believed to be the four major causes of population decline of B. thaidina in the recent decade. However, little attention was paid to the impact of climate change. This study used ecological niche factor analysis and species distribution model to analyse the current suitable areas for B. thaidina with BioClim variables as well as its future suitable areas under four future climate scenarios (represented by four Representative Concentration Pathways: RCP2.6, RCP4.5, RCP6.0, and RCP8.5). Statistical analysis was carried out to compare the possible area and altitude changes to the distribution of B. thaidina under changing climate. Our analyses showed that the suitable areas for B. thaidina are fragmented under the current climate, with four suitable centres in northwestern Yunnan, northeastern Yunnan and northwestern Guizhou, the western margin of Sichuan Basin, and Qinling mountains. Apart from further habitat fragmentation under climate change, slight range expansion (average 6.0–8.9%) was detected under the RCP2.6 and RCP4.5 scenarios, while more range contraction (average 1.3–26.9%) was detected under the RCP6.0 and RCP8.5 scenarios, with the two southern suitable centres suffering most. Also, a tendency of contraction (2,500–3,500 m) and upslope shift (~600 m) in suitable altitude range were detected. The findings of this study supported the climate-vulnerable hypothesis of B. thaidina, especially under future climate like the RCP6.0 and RCP8.5 scenarios, in terms of contraction in suitable areas and altitude ranges. Conservation priority should be given to northwestern Yunnan, northeastern Yunnan, and northwestern Guizhou to alleviate the stress of massive habitat loss and extinction. Refugial areas should be established in all four suitable centres to maintain genetic diversity of B. thaidina in China.

Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling

Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity, and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over the course of a 32-y period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict a 68-km shift of this hybrid zone. To empirically test this prediction, we assessed genetic and phenotypic changes using contemporary and museum collections and document a 40-km northward shift of this hybrid zone. Interactions between the two species appear relatively unchanged during hybrid zone movement. We found no change in the frequency of hybridization, and regions of the genome that experience little to no introgression moved largely in concert with the shifting hybrid zone. Model predictions based on climate scenarios predict this hybrid zone will continue to move northward, but with substantial spatial heterogeneity in the velocity (55-144 km/1 °C), shape, and contiguity of movement. Our findings suggest that the presence of nonclimatic barriers (e.g., genetic incompatibilities) and/or nonlinear responses to climatic gradients may preserve species boundaries as the species shift. Further, we show that variation in the geography of hybrid zone movement could result in evolutionary responses that differ for geographically distinct populations spanning hybrid zones, and thus have implications for the conservation and management of genetic diversity.

Butterfly community shifts over two centuries

Environmental changes strongly impact the distribution of species and subsequently the composition of species assemblages. Although most community ecology studies represent temporal snap shots, long-term observations are rather rare. However, only such time series allow the identification of species composition shifts over several decades or even centuries. We analyzed changes in the species composition of a southeastern German butterfly and burnet moth community over nearly 2 centuries (1840-2013). We classified all species observed over this period according to their ecological tolerance, thereby assessing their degree of habitat specialisation. This classification was based on traits of the butterfly and burnet moth species and on their larval host plants. We collected data on temperature and precipitation for our study area over the same period. The number of species declined substantially from 1840 (117 species) to 2013 (71 species). The proportion of habitat specialists decreased, and most of these are currently endangered. In contrast, the proportion of habitat generalists increased. Species with restricted dispersal behavior and species in need of areas poor in soil nutrients had severe losses. Furthermore, our data indicated a decrease in species composition similarity between different decades over time. These data on species composition changes and the general trends of modifications may reflect effects from climate change and atmospheric nitrogen loads, as indicated by the ecological characteristics of host plant species and local changes in habitat configuration with increasing fragmentation. Our observation of major declines over time of currently threatened and protected species shows the importance of efficient conservation strategies.

Hybridization and the spread of the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), in the northwestern United States

Hybridization may be an important process interjecting variation into insect populations enabling host plant shifts and the origin of new economic pests. Here, we examine whether hybridization between the native snowberry-infesting fruit fly Rhagoletis zephyria (Snow) and the introduced quarantine pest R. pomonella (Walsh) is occurring and may aid the spread of the latter into more arid commercial apple-growing regions of central Washington state, USA. Results for 19 microsatellites implied hybridization occurring at a rate of 1.44% per generation between the species. However, there was no evidence for increased hybridization in central Washington. Allele frequencies for seven microsatellites in R. pomonella were more 'R. zephyria-like' in central Washington, suggesting that genes conferring resistance to desiccation may be adaptively introgressing from R. zephyria. However, in only one case was the putatively introgressing allele from R. zephyria not found in R. pomonella in the eastern USA. Thus, many of the alleles changing in frequency may have been prestanding in the introduced R. pomonella population. The dynamics of hybridization are therefore complex and nuanced for R. pomonella, with various causes and factors, including introgression for a portion, but not all of the genome, potentially contributing to the pest insect's spread.

Adaptations to "Thermal Time" Constraints in Papilio: Latitudinal and Local Size Clines Differ in Response to Regional Climate Change

Adaptations to "thermal time" (=Degree-day) constraints on developmental rates and voltinism for North American tiger swallowtail butterflies involve most life stages, and at higher latitudes include: smaller pupae/adults; larger eggs; oviposition on most nutritious larval host plants; earlier spring adult emergences; faster larval growth and shorter molting durations at lower temperatures. Here we report on forewing sizes through 30 years for both the northern univoltine P. canadensis (with obligate diapause) from the Great Lakes historical hybrid zone northward to central Alaska (65° N latitude), and the multivoltine, P. glaucus from this hybrid zone southward to central Florida (27° N latitude). Despite recent climate warming, no increases in mean forewing lengths of P. glaucus were observed at any major collection location (FL to MI) from the 1980s to 2013 across this long latitudinal transect (which reflects the "converse of Bergmann's size Rule", with smaller females at higher latitudes). Unlike lower latitudes, the Alaska, Ontonogon, and Chippewa/Mackinac locations (for P. canadensis) showed no significant increases in D-day accumulations, which could explain lack of size change in these northernmost locations. As a result of 3-4 decades of empirical data from major collection sites across these latitudinal clines of North America, a general "voltinism/size/D-day" model is presented, which more closely predicts female size based on D-day accumulations, than does latitude. However, local "climatic cold pockets" in northern Michigan and Wisconsin historically appeared to exert especially strong size constraints on female forewing lengths, but forewing lengths quickly increased with local summer warming during the recent decade, especially near the warming edges of the cold pockets. Results of fine-scale analyses of these "cold pockets" are in contrast to non-significant changes for other Papilio populations seen across the latitudinal transect for P. glaucus and P. canadensis in general, highlighting the importance of scale in adaptations to climate change. Furthermore, we also show that rapid size increases in cold pocket P. canadensis females with recent summer warming are more likely to result from phenotypic plasticity than genotypic introgression from P. glaucus, which does increase size in late-flight hybrids and P. appalachiensis.