David M. Althoff

Employing Philosophical Dialogue in Collaborative Science

ABSTRACT Integrated research across disciplines is required to address many of the pressing environmental problems facing human societies. Often the integration involves disparate disciplines, including those in the biological sciences, and demands collaboration from problem formulation through hypothesis development, data analysis, interpretation, and application. Such projects raise conceptual and methodological challenges that are new to many researchers in the biological sciences and to their collaborators in other disciplines. In this article, we develop the theme that many of these challenges are fundamentally philosophical, a dimension that has been largely overlooked in the extensive literature on cross-disciplinary research and education. We present a “toolbox for philosophical dialogue,” consisting of a set of questions for self-examination that cross-disciplinary collaborators can use to identify and address their philosophical disparities and commonalities. We provide a brief users manual for this toolbox and evidence for its effectiveness in promoting successful integration across disciplines.

PLANT POLYPLOIDY AND INSECT/PLANT INTERACTIONS

We used flow cytometry and extensive geographic surveys of herbivore attack to test whether repeated evolution of autotetraploidy in the perennial herb Heuchera grossulariifolia Rydb. (Saxifragaceae) has created evolutionary barriers to attack by the specialist moth herbivore Greya politella (Prodoxidae). We found that the moth has colonized tetraploid as well as diploid populations, has colonized tetraploids of separate evolutionary origin, and, at least under some conditions, is more likely to attack tetraploids than diploids. Plant polyploidy therefore provides a potential route out of specialization as an evolutionary dead end in phytophagous insect taxa as well as a potentially important route to subsequent phylogenetic and geographic diversification of plant/insect interactions.

The Utility of Amplified Fragment Length Polymorphisms in Phylogenetics: A Comparison of Homology within and between Genomes

The amplified fragment length polymorphism (AFLP) technique is being increasingly used in phylogenetic studies, especially in groups of rapidly radiating taxa. One of the key issues in the phylogenetic suitability of this technique is whether the DNA fragments generated via the AFLP method are homologous within and among the taxa being studied. We used a bioinformatics approach to assess homology based on both chromosomal location and sequence similarity of AFLP fragments. The AFLP technique was electronically simulated on genomes from eight organisms that represented a range of genome sizes. The results demonstrated that within a genome, the number of fragments is positively associated with genome size, and the degree of homology decreases with increasing numbers of fragments generated. The average homology of fragments was 89% for small genomes (< 400 Mb) but decreased to 59% for large genomes (> 2 Gb). Fragment homology for large genomes can be increased by excluding smaller fragments, although there is no clear upper limit for the size of fragments to exclude. A second approach is to increase the number of selective nucleotides in the final selective amplification step. For strains of the same organism, homology based on chromosome location and sequence similarity of fragments was 100%. Fragment homology for more distantly related taxa, however, decreased with greater time since divergence. We conclude that AFLP data are best suited for examining phylogeographic patterns within species and among very recently diverged species.

Pattern and timing of diversification in Yucca (Agavaceae): specialized pollination does not escalate rates of diversification

The yucca–yucca moth interaction is one of the most well-known and remarkable obligate pollination mutualisms, and is an important study system for understanding coevolution. Previous research suggests that specialist pollinators can promote rapid diversification in plants, and theoretical work has predicted that obligate pollination mutualism promotes cospeciation between plants and their pollinators, resulting in contemporaneous, parallel diversification. However, a lack of information about the age of Yucca has impeded efforts to test these hypotheses. We used analyses of 4322 AFLP markers and cpDNA sequence data representing six non-protein-coding regions (trnT–trnL, trnL, trnL intron, trnL–trnF, rps16 and clpP intron 2) from all 34 species to recover a consensus organismal phylogeny, and used penalized likelihood to estimate divergence times and speciation rates in Yucca. The results indicate that the pollination mutualism did not accelerate diversification, as Yucca diversity (34 species) is not significantly greater than that of its non-moth-pollinated sister group, Agave sensu latissimus (240 species). The new phylogenetic estimates also corroborate the suggestion that the plant–moth pollination mutualism has at least two origins within the Agavaceae. Finally, age estimates show significant discord between the age of Yucca (ca 6–10 Myr) and the current best estimates for the age of their pollinators (32–40 Myr).

EXAMINING GENETIC STRUCTURE IN A BOGUS YUCCA MOTH: A SEQUENTIAL APPROACH TO PHYLOGEOGRAPHY

Abstract Understanding the phylogeography of a species requires not only elucidating patterns of genetic structure among populations, but also identifying the possible evolutionary events creating that structure. The use of a single phylogeographic test or analysis, however, usually provides a picture of genetic structure without revealing the possible underlying evolutionary causes. We used current analytical techniques in a sequential approach to examine genetic structure and its underlying causes in the bogus yucca moth Prodoxus decipiens (Lepidoptera: Prodoxidae). Both historical biogeography and recent human transplantations of the moths host plants provided a priori expectations of the pattern of genetic structure and its underlying causes. We evaluated these expectations by using a progression of phylogenetic, demographic, and population genetic analyses of mtDNA sequence data from 476 individuals distributed across 25 populations that encompassed the range of P. decipiens. The combination of these analyses revealed that much of the genetic structure has evolved more recently than suggested by historical biogeography, has been influenced by changes in demography, and can be best explained by long distance dispersal and isolation by distance. We suggest that performing a suite of analyses that focus on different temporal scales may be an effective approach to investigating the patterns and causes of genetic structure within species.

Testing for coevolutionary diversification: linking pattern with process

Coevolutionary diversification is cited as a major mechanism driving the evolution of diversity, particularly in plants and insects. However, tests of coevolutionary diversification have focused on elucidating macroevolutionary patterns rather than the processes giving rise to such patterns. Hence, there is weak evidence that coevolution promotes diversification. This is in part due to a lack of understanding about the mechanisms by which coevolution can cause speciation and the difficulty of integrating results across micro- and macroevolutionary scales. In this review, we highlight potential mechanisms of coevolutionary diversification, outline approaches to examine this process across temporal scales, and propose a set of minimal requirements for demonstrating coevolutionary diversification. Our aim is to stimulate research that tests more rigorously for coevolutionary diversification.

Geographic isolation trumps coevolution as a driver of yucca and yucca moth diversification.

Coevolution is thought to be especially important in diversification of obligate mutualistic interactions such as the one between yuccas and pollinating yucca moths. We took a three-step approach to examine if plant and pollinator speciation events were likely driven by coevolution. First, we tested whether there has been co-speciation between yuccas and pollinator yucca moths in the genus Tegeticula (Prodoxidae). Second, we tested whether co-speciation also occurred between yuccas and commensalistic yucca moths in the genus Prodoxus (Prodoxidae) in which reciprocal evolutionary change is unlikely. Finally, we examined the current range distributions of yuccas in relationship to pollinator speciation events to determine if plant and moth speciation events likely occurred in sympatry or allopatry. Co-speciation analyses of yuccas with their coexisting Tegeticula pollinator and commensalistic Prodoxus lineages demonstrated phylogenetic congruence between both groups of moths and yuccas, even though moth lineages differ in the type of interaction with yuccas. Furthermore, Yucca species within a lineage occur primarily in allopatry rather than sympatry. We conclude that biogeographic factors are the overriding force in plant and pollinator moth speciation and significant phylogenetic congruence between the moth and plant lineages is likely due to shared biogeography rather than coevolution.

COMPARATIVE GEOGRAPHIC STRUCTURES OF TWO PARASITOID-HOST INTERACTIONS

Recent studies of parasitoid‐host interactions have demonstrated that parasitoids and their hosts are geographically structured for traits such as virulence and encapsulation defenses, but no studies have yet compared the geographic structure of parasitoids and hosts using neutral genetic markers. Such studies of geographic structure are needed to evaluate the underlying geographic scale at which these interactions evolve and allow assessment of the relative effects of selection and gene flow on the geographic structure observed in traits under selection. We used sequence data from the mitochondrial DNA cytochrome oxidase I and II subunits to document and compare the geographic structures of the parasitoid Agathis thompsoni and its moth host Greya subalba. We also documented the geographic structure of G. enchrysa and compared it to the geographic structure of its parasitoid Agathis n. sp. The results demonstrated that parasitoids and their hosts may have incongruent patterns of geographic structure as assessed by molecular markers. As a consequence, the geographic scale at which the interaction evolves may be different for each species involved in the interaction. Depending on the interplay of selection and gene flow, there may not be a one‐to‐one correspondence of traits important in the interaction between parasitoids and their hosts at the level of local populations. The geographic structures of A. thompsoni and G. subalba and Agathis n. sp. and G. enchrysa provide further evidence of the potential importance of the formation of geographic mosaics in coevolving parasitoid‐host interactions and evolving interactions in general.

Geographic structure in the searching behaviour of a specialist parasitoid: combining molecular and behavioural approaches

An increasing number of studies have shown that the traits important to species interactions may differ geographically among populations or groups of populations within a single interacting species. We examined geographic structure in the searching behaviour of a recently discovered parasitoid in the genus Agathis (Hymenoptera: Braconidae) by examining the pattern of population structure obtained from sequence data of mitochondrial DNA cytochrome oxidase I and the pattern of population differentiation in female searching behaviour. Analyses of population structure showed no isolation by distance and suggested long distance dispersal among populations. This pattern is consistent with recent post‐glacial expansion of Agathis n. sp. Observations of searching behaviour demonstrated that populations of Agathis n. sp. differed in a subset of the behavioural traits examined and also one morphological trait. These population differences appear to be driven in part by local host plant characteristics, and based on the population structure of Agathis n. sp., have arisen relatively quickly in evolutionary time. This study suggests that the interaction between parasitoids and their host insects may exhibit substantial geographic variation, and studies that focus at the level of single populations or the species‐level may be missing much of the evolutionary dynamics of parasitoid–host interactions.

Phylogeny and life history evolution of Prodoxus yucca moths (Lepidoptera: Prodoxidae)

Abstract.  Yucca moths (Lep., Prodoxidae) are well‐known for their obligate pollination mutualism with yuccas. In addition to the pollinators, yuccas also host many non‐pollinating yucca moths. Here the genus Prodoxus, the non‐pollinating sister group of the pollinators, is revised using morphological and molecular data, their phylogenetic relationships are analysed, and the evolution of host tissue specialization explored. Twenty‐two species are recognized, including nine new species: Prodoxus gypsicolorsp.n., P. sonorensissp.n., P. carnerosanellussp.n., P. tamaulipellussp.n., P. weethumpisp.n., P. tehuacanensissp.n., P. californicussp.n., P. mapimiensissp.n. and P. atascosanellussp.n.Prodoxus y‐inversus Riley, P. coloradensis Riley and P. sordidus Riley are redescribed. The genus Agavenema is synonymized with Prodoxus. Phylogenetic analyses indicated that stalk‐feeding is basal within the group, that there are three separate origins of fruit‐feeding, and one origin of leaf‐mining from a stalk‐feeding ancestor. Although species with different feeding habits often coexist within hosts, the analyses suggest that ecological specialization and diversification within a host only may have occurred within one or possibly two hosts.