Robert G. Laport

How fast is fast? Eco-evolutionary dynamics and rates of change in populations and phenotypes.

Abstract It is increasingly recognized that evolution may occur in ecological time. It is not clear, however, how fast evolution – or phenotypic change more generally – may be in comparison with the associated ecology, or whether systems with fast ecological dynamics generally have relatively fast rates of phenotypic change. We developed a new dataset on standardized rates of change in population size and phenotypic traits for a wide range of species and taxonomic groups. We show that rates of change in phenotypes are generally no more than 2/3, and on average about 1/4, the concurrent rates of change in population size. There was no relationship between rates of population change and rates of phenotypic change across systems. We also found that the variance of both phenotypic and ecological rates increased with the mean across studies following a power law with an exponent of two, while temporal variation in phenotypic rates was lower than in ecological rates. Our results are consistent with the view that ecology and evolution may occur at similar time scales, but clarify that only rarely do populations change as fast in traits as they do in abundance.

Ecological niche modeling implicates climatic adaptation, competitive exclusion, and niche conservatism amongLarrea tridentatacytotypes in North American deserts 1,2

Abstract Larrea tridentata is a dominant and widespread shrub of North American warm deserts. The species comprises three “chromosomal races,” including diploids (Chihuahuan Desert), tetraploids (Sonoran Desert), hexaploids (Mojave and western Sonoran Deserts), as well as the geographically restricted tetraploid L. tridentata var. arenaria. Creosote bush is a recent arrival to the North American continent, and it is hypothesized that its geographic dispersion reflects rapid ecological divergence mediated by polyploidization. Here we use species distribution modeling to quantitatively evaluate alternate hypotheses for cytotype distributions, based on comprehensive field sampling of creosote bush populations over four years. Using ecological niche models and analyses of field-collected soils, we test whether (1) the climatic niche of the three cytotypes are differentiated; (2) there is evidence for strong climatic gradients at the distributional boundaries of the cytotypes; and (3) cytotype ranges are distinguished by edaphic features. Quantitative tests of niche equivalence indicated that distribution models for all cytotypes were significantly different from one other, suggesting that cytotype races occupy unique and distinctive habitats. However, tests of niche similarity suggest a pattern of niche conservatism, wherein cytotypes tend to occur in climatically similar regions of their respective deserts. Moreover, the modeled diploid distribution was projected to intrude into the geographic range of tetraploids, and the modeled tetraploid distribution was projected to intrude into the range of hexaploids, suggesting that intercytotype competition is a factor influencing cytotype distributions. The range boundary between the dune endemic L. tridentata var. arenaria and hexaploid L. tridentata was noteworthy for exhibiting a strong climatic gradient and striking differences in soil texture (increased sand, decreased gravel). More generally, soil texture differed statistically between sites occupied by diploid, tetraploid, and hexaploid L. tridentata, albeit with considerable overlap across the geographic ranges of the three cytotypes. Taken together, our findings suggest that multiple factors affect the distribution of creosote bush chromosome races, including but not limited to ecological divergence.

Phylogeny and Cytogeography of the North American Creosote Bush (Larrea tridentata, Zygophyllaceae)

Abstract The North American creosote bush (Larrea tridentata, Zygophyllaceae) is a widespread and ecologically dominant taxon of North American warm deserts. The species is comprised of diploid, tetraploid, and hexaploid populations, and touted as a classical example of an autopolyploid taxonomic complex. Here we use flow cytometry and DNA sequence data (non-coding cpDNA and nuclear ribosomal DNA) to evaluate spatial and evolutionary relationships among cytotype races, as well as the origins of the species from its South American ancestors. We find the geographic distribution of North American cytotypes to be highly structured, with limited co-occurrence within populations. Diploids reside only in the Chihuahuan Desert, as reported in previous biosystematic surveys, but tetraploid and hexaploid populations interdigitate along the margins of the Sonoran and Mojave Deserts. In phylogenetic analyses, North American plants comprise a monophyletic grouping that is sister to the South American diploid species, L. divaricata. North American populations exhibit genetic signatures of rapid demographic expansion, including a star-shaped genealogy, unimodal distribution of pairwise haplotype differences, and low genetic structure. Nonetheless, polyploid cytotypes are consistently distinguished from diploid cytotypes by a cpDNA indel character, suggesting a single origin of tetraploidy in the species. These findings suggest a recent origin of the North American creosote bush via long distance dispersal, with establishment of polyploid populations accompanying its rapid spread through the Northern Hemisphere.

Occupation of active Xylocopa virginica nests by the recently invasive Megachile sculpturalis in upstate New York.

The Asian native Giant Resin Bee, Megachile sculpturalis Smith, was inadvertently introduced to the southeastern United States in the early 1990’s (Mangum and Brooks, 1997; Mangum and Sumner, 2003; Hinojosa-Diaz, 2008). Since its introduction, it has rapidly spread throughout much of the eastern US from its North Carolina center of introduction (Magnum and Brooks, 1997), reaching north as far as New York and southern Ontario by 2000 and 2002, respectively (Ascher, 2001; Paiero and Buck, 2003), and as far west as Michigan and eastern Kansas by 2008 (Hinojosa-Diaz, 2008; O’Brien and Craves, 2008). Despite the rapid spread, the ecological impact and affect on native bee fauna by M. sculpturalis has not been widely studied. It has been assumed that the invasion of the Giant Resin Bee is relatively benign except that it may preferentially pollinate plant species introduced to North America (Koelreuteria paniculata Laxm., Ligustrum lucidum Aiton, Pueraria lobata DC., Sophora japonica L.) from its native range. The presence of these plant species may have aided the establishment of M. sculpturalis in the U.S. (Mangum and Sumner, 2003). Possible negative effects of M. sculpturalis on native North American bees are unstudied (HinojosaDiaz, 2005). Megachile sculpturalis nests have been reported in empty tree cavities, crevices, downed logs, and other debris sometimes used by native bees, as well as vacant burrows of the Eastern Carpenter Bee (Xylocopa virginica L.; Mangum and Brooks, 1997; Batra, 1998). It remains unknown, however, whether M. sculpturalis utilizes active X. virginica nests, evicting the resident female. Here we report a usurpation and occupation of active X. virginica burrows by M. sculpturalis in upstate New York.

Low-Cost DNA Extraction

The methods described in this chapter were developed to avoid toxic organic phase separation utilized in many low-cost DNA extraction protocols such as the CTAB method. The steps involve: (1) lysis of the plant material, (2) binding of DNA to silica powder under chaotropic conditions, (3) washing the bound DNA, and (4) elution of DNA from the silica powder. This method has been tested in several plant species and the applicability of such DNA preparations for molecular marker studies in barley is shown in Chap. 8.

PCR Amplification for Low-Cost Mutation Discovery

PCR is used to amplify regions to be interrogated for the presence of mutations (SNP and small indel polymorphisms). While PCR is a common practice and many protocols exist, reaction conditions are provided here that are optimized for TILLING and Ecotilling assays utilizing native agarose gel electrophoresis.

Sample Collection and Storage

Of importance to the successful extraction of genomic DNA from plant tissues is the collection of the suitable material and proper storage of the tissues before DNA isolation. If the samples are not properly treated, DNA can be degraded prior to isolation. The rate of sample degradation can vary dramatically from species to species depending on the method of sample collection. Mechanisms of genomic DNA degradation include exposure to endogenous nucleases due to organellar and cellular lysis. To prevent this from occurring, leaf or root tissues are commonly flash frozen in liquid nitrogen and then stored at −80 °C. At these temperatures, nucleases remain inactive and DNA is stable. Thawing of tissue in some species can lead to rapid degradation. Therefore, during the extraction procedure, it may be necessary to grind the tissue to a fine powder in the presence of liquid nitrogen and expose frozen tissue immediately to a lysis buffer containing EDTA, which inhibits nuclease activity. This chapter provides an alternative method for sample collection and storage. Silica gel is used to desiccate tissues at room temperature. This avoids the use of liquid nitrogen and storage at −80 °C.

Health and Safety Considerations

All laboratories should have standardized health and safety rules and practices. These can vary from region to region due to differences in legislation. Before beginning new experiments, please consult your local safety guidelines. Failure to follow these rules could result in accidents, fines, or a closure of the laboratory. Consider the following guidelines in this chapter applicable to all laboratories.

Alternative Enzymology for Mismatch Cleavage for TILLING and Ecotilling: Extraction of Enzymes from Common Weedy Plants

A crude celery extract containing the single-strand-specific nuclease CEL I, has been widely used in TILLING and Ecotilling projects around the world. Yet, celery is hard to come by in some countries. Sequences homologous to CEL I can be found in different plant species. Previous work showed that similar mismatch cleavage activities could be found in crude extracts of mung bean (Till BJ, Burtner C, Comai L, Henikoff S. Nucleic Acids Res 32:2632–2641, 2004). It is likely that the same activity can be recovered in many different plant species. Therefore, a protocol for the extraction of active enzyme was developed that uses plants common across the world, namely weeds. Monocotyledenous and dicotyledenous weedy plants from the grassland, field and waste grounds around crop fields are suitable for this protocol. Due to lower recovery of enzymatic activity compared to celery-based extractions, a centrifuge-based filter method is applied to concentrate the enzyme extract.