Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime - Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species' phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually - similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2006.03061.x

Comparative phylogeography of unglaciated eastern North America.

Selection is a central process in nature. Although our understanding of the strength and form of selection has increased, a general understanding of the temporal dynamics of selection in nature is lacking. Here, we assembled a database of temporal replicates of selection from studies of wild populations to synthesize what we do (and do not) know about the temporal dynamics of selection. Our database contains 5519 estimates of selection from 89 studies, including estimates of both direct and indirect selection as well as linear and nonlinear selection. Morphological traits and studies focused on vertebrates were well-represented, with other traits and taxonomic groups less well-represented. Overall, three major features characterize the temporal dynamics of selection. First, the strength of selection often varies considerably from year to year, although random sampling error of selection coefficients may impose bias in estimates of the magnitude of such variation. Second, changes in the direction of selection are frequent. Third, changes in the form of selection are likely common, but harder to quantify. Although few studies have identified causal mechanisms underlying temporal variation in the strength, direction and form of selection, variation in environmental conditions driven by climatic fluctuations appear to be common and important.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1461-0248.2009.01381.x

It's about time: the temporal dynamics of phenotypic selection in the wild.

Glacial cycles have played a dominant role in shaping the genetic structure and distribution of biota in northwestern North America. The two major ice age refugia of Beringia and the Pacific Northwest were connected by major mountain chains and bordered by the Pacific Ocean. As a result, numerous refugial options were available for the regions taxa during glacial advances. We reviewed the importance of glaciations and refugia in shaping northwestern North America’s phylogeographic history. We also tested whether ecological variables were associated with refugial history. The recurrent phylogeographic patterns that emerged were the following: (i) additional complexity, i.e. refugia within refugia, in both Beringia and the Pacific Northwest; and (ii) strong evidence for cryptic refugia in the Alexander Archipelago and Haida Gwaii, the Canadian Arctic and within the ice-sheets. Species with contemporary ranges that covered multiple refugia, or those with high dispersal ability, were significantly more likely to have resided in multiple refugia. Most of the shared phylogeographic patterns can be attributed to multiple refugial locales during the last glacial maximum or major physiographic barriers like rivers and glaciers. However, some of the observed patterns are much older and appear connected to the orogeny of the Cascade-Sierra chain or allopatric differentiation during historic glacial advances. The emergent patterns from this review suggest we should refine the classic Beringian-southern refugial paradigm for northwestern North American biota and highlight the ecological and evolutionary consequences of colonization from multiple refugia.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2010.04828.x

Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America.

Summary
1. In this essay I summarize current trends in the evolutionary ecology of plant defence, while advocating for approaches that integrate community ecology with specific tests of classic evolutionary hypotheses. Several conclusions emerge.

2. The microevolution of defence is perhaps best studied by reciprocal transplant experiments of differentiated plant populations while simultaneously manipulating the presence of the herbivore(s) hypothesized to be the agent(s) of natural selection.

3. Although there is continued interest in the costs of defence, I argue that some empirical approaches to estimating costs (e.g. genetic engineering) may provide limited insight into evolutionary processes.

4. Essentially all plants employ several different lines of defence against herbivory. It is thus time to abandon searching for single silver bullet traits and the simple trade-off model (where traits are arbitrarily expected to negatively covary across genotypes or species). We still know very little about which trait combinations are most effective and have repeatedly evolved together. Thus, some of our prominent theories (e.g. a predicted trade-off between direct and indirect defence) need to be revised.

5. Studies of the macroevolution of plant defence are enjoying renewed interest due to available phylogenies and analytical methods. Although general trends are not currently surmisable, we will soon have strong case studies evaluating both biotic and abiotic drivers of convergent evolution in defence strategies and the role of defence evolution in the adaptive radiation of plant lineages.

6. The evolution of specificity is proposed as a final frontier in understanding complexity in plant–herbivore interactions. Although it is abundantly clear that plants can deploy highly specific defensive responses that are differentially perceived by herbivore species, how such responses evolve and are physiologically regulated remains an important gap. Relatively straightforward methodologies are now available to close the loop between plant perception of herbivory, hormonal responses, and production of defensive end-products across genotype or species.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2435.2010.01796.x

Current trends in the evolutionary ecology of plant defence

Variation among sites and years in the local ecological outcome of interspecific interactions can generate a geographic mosaic of coevolution, as indicated by recent mathematical models. We evaluated whether local temporal dynamics of ecological outcome in the interaction between the moth Greya politella (Prodoxidae) and its host plant Lithophragma parviflorum (Saxifragaceae) are likely to mitigate or magnify geographic differences in ecological outcome found in earlier studies. The moths are highly host-specific pollinating floral parasites, and the mutualism can be swamped in some populations by the presence of effective co-pollinators. Hence, differing community contexts can shift the outcome of the interaction from mutualism to commensalism or antagonism. During each of four years, we evaluated the effect of Greya oviposition on seed development through a paired design that controlled for plant genotype and microenvironment. At Turnbull National Wildlife Refuge in Washington State, the interaction was significantly mutualistic in all four years. Mutualism in this population was indicated by a higher probability of development of capsules visited by ovipositing Greya than capsules not visited by Greya on the same plant. At Rapid River, Idaho, the interaction was commensalistic in three years and antagonistic in one year. Antagonism in this population was indicated by selective withering of capsules containing Greya eggs. Overall, the results suggest stable geographic differences in the range of ecological outcomes in this plant–insect interaction under different community contexts.

Temporal dynamics of antagonism and mutualism in a geographically variable plant-insect interaction.

The common cushion moss Grimmia laevigata (Bridel) Bridel grows on bare rock in a broad range of environments on every continent except Antarctica. As such, it must harbor adaptations to a remarkably broad set of environmental stresses, the extremes of which can include very high temperatures, prolonged nearly complete desiccation, and high ultraviolet B (UVB) exposure. Yet, like many mosses, G. laevigata shows very little morphological variability across its cosmopolitan range. This presents an evolutionary puzzle, the solution to which lies in understanding the phylogeographic structure of this morphologically simple organism. Here we report the results of an analysis of amplified fragment length polymorphisms (AFLPs) in G. laevigata, focusing on individuals from the California Floristic Province. We found evidence that populations within California constitute two distinct geographically overlapping cryptic species. Each clade harbors multiple private alleles, indicating they have been genetically isolated for some time. We suggest that the existence of cryptic species within G. laevigata, in combination with its life history, growth habits, and extreme desiccation tolerance, makes this moss an ideal research tool and a candidate for a biological indicator of climate change and pollution.

https://www.pnas.org/content/pnas/103/3/637.full.pdf

Cryptic species within the cosmopolitan desiccation-tolerant moss Grimmia laevigata

Understanding the historical framework in which species interactions have diversified across landscapes may help to partition the effects of vicariance and geographically variable selection in shaping the geographical mosaic of coevolving species. We used phylogeographical analyses of the pollinating seed parasite Greya politella (Lepidoptera: Prodoxidae) to define the historical processes that may have structured interactions of this species with its host plants across major biogeographical breaks in western North America. Using 648 bp of cytochrome oxidase I and amplified fragment length polymorphisims, we identified deep genetic breaks among some populations consistent with some definitions of cryptic species. A combination of phylogenetic and population genetic approaches indicates that different historical processes may have structured G. politella genetic diversity in four regions: northern Pacific Northwest, southern Oregon, southern Sierra Nevada, and the remainder of California. The northern Pacific Northwest had high genetic diversity likely due to glacial refugia and subsequent spatial expansion, concordant with some other taxa. Populations in southern Oregon possessed unique, closely related haplotypes with restricted gene flow, possibly indicating a long-standing set of populations in this endemic-rich region. Analyses of California populations showed evidence of restricted gene flow and spatial expansion with many closely related haplotypes that occupy a broad geographical range. Southern Sierra Nevada populations were genetically distinct and highly diverse, possibly due to a localized glacial refugium. Together, these results suggest that vicariance and population expansion, possibly in combination with geographically variable selection, have shaped the diversification of G. politella and its interactions with its host plants.

Catherine C. Fernandez

Papers

Temporal dynamics of antagonism and mutualism in a geographically variable plant-insect interaction.

Cryptic species within the cosmopolitan desiccation-tolerant moss Grimmia laevigata

Diverse historical processes shape deep phylogeographical divergence in the pollinating seed parasite Greya politella.