Publications by EEOB faculty November 1 - November 30

November 21, 2016
eeob 2016

Biodiversity and the Species Concept – Lineages are not Enough

John V. Freudenstein, Michael B. Broe, Ryan A. Folk and Brandon T. Sinn. 2016. Syst Biol. doi: 10.1093/sysbio/syw098


The nature and definition of species continue to be matters of debate. Current views of species often focus on their nature as lineages -- maximal reproductive communities through time. Whereas many authors point to the Evolutionary Species Concept as optimal, in its original form it stressed the ecological role of species as well as their history as lineages, but most recent authors have ignored the role aspect of the concept, making it difficult to apply unambiguously in a time-extended way. This trend has been exacerbated by the application of methods and concepts emphasizing the notion of monophyly, originally applied only at higher levels, to the level of individuals, as well as by the current emphasis on molecular data. Hence, some current authors recognize units that are no more than probable exclusive lineages as species. We argue that biodiversity is inherently a phenotypic concept and that role, as manifested in the organismal extended phenotype, is a necessary component of the species concept. Viewing species as historically connected populations with unique role brings together the temporal and phenotypic natures of species, providing a clear way to view species both in a time-limited and time-extended way. Doing so alleviates perceived issues with “paraphyletic species” and returns the focus of species to units that are most relevant for biodiversity.

Identifying cryptic diversity with predictive phylogeography.

Espíndola A, Ruffley M, Smith ML, Carstens BC, Tank DC, Sullivan J. 2016. Proc Biol Sci. 283(1841). pii: 20161529. DOI: 10.1098/rspb.2016.1529


Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.

Invasion of a dominant floral resource: effects on the floral community and pollination of native plants

Karen Goodell, Ingrid M. Parker. 2016. DOI: 10.1002/ecy.1639


Through competition for pollinators, invasive plants may suppress native flora. Community-level studies provide an integrative assessment of invasion impacts and insights into factors that influence the vulnerability of different native species. We investigated effects of the non-native herb Lythrum salicaria on pollination of native species in 14 fens of the eastern United States. We compared visitors per flower for 122 native plant species in invaded and uninvaded fens and incorporated a landscape-scale experiment, removing L. salicaria flowers from three of the invaded fens. Total flower densities were more than three times higher in invaded than uninvaded or removal sites when L. salicaria was blooming. Despite an increase in number of visitors with number of flowers per area, visitors per native flower declined with increasing numbers of flowers. Therefore, L. salicaria invasion depressed visitation to native flowers. In removal sites, visitation to native flowers was similar to uninvaded sites, confirming the observational results and also suggesting that invasion had not generated a persistent buildup of visitor populations.
To study species-level impacts, we examined effects of invasion on visitors per flower for the 36 plant species flowering in both invaded and uninvaded fens. On average, the effect of invasion represented about a 20% reduction in visits per flower. We measured the influence of plant traits on vulnerability to L. salicaria invasion using meta-analysis. Bilaterally symmetrical flowers experienced stronger impacts on visitation, and similarity in flower color to L. salicaria weakly intensified competition with the invader for visitors. Finally, we assessed the reproductive consequences of competition with the invader in a dominant flowering shrub, Dasiphora fruticosa. Despite the negative effect of invasion on pollinator visitation in this species, pollen limitation of seed production was not stronger in invaded than uninvaded sites, suggesting little impact of competition for pollinators on its population demography. Negative effects on pollination of native plants by this copiously-flowering invader appeared to be mediated by increases in total flower density that were not matched by increases in pollinator density. The strength of impact was modulated across native species by their floral traits and reproductive ecology.

Speciation with gene flow in North American Myotis bats

Ariadna E. Morales, Nathan D. Jackson, Tanya A. Dewey, Brian C. O’Meara and Bryan C. Carstens. 2016. Syst Biol. doi: 10.1093/sysbio/syw100


Growing evidence supports the idea that species can diverge in the presence of gene flow. However, most methods of phylogeny estimation do not consider this process, despite the fact that ignoring gene flow is known to bias phylogenetic inference. Furthermore, studies that do consider divergence-with-gene-flow typically do so by estimating rates of gene flow using a isolation-with-migration model (IM), rather than evaluating scenarios of gene flow (such as divergence-with-gene flow or secondary contact) that represent very different types of diversification. In this investigation, we aim to infer the recent phylogenetic history of a clade of western long-eared bats while evaluating a number of different models that parameterize gene flow in a variety of ways. We utilize PHRAPL, a new tool for phylogeographic model selection, to compare the fit of a broad set of demographic models that include divergence, migration, or both among Myotis evotis, M. thysanodes and M. keenii. A genomic dataset consisting of 808 loci of ultraconserved elements (UCEs) was used to explore such models in three steps using an incremental design where each successive set was informed by, and thus more focused than, the previous set of models. Specifically, the three steps were to (i) assess whether gene flow should be modeled and identify the best topologies, (ii) infer directionality of migration using the best topologies, and (iii) estimate the timing of gene flow. The best model (AIC model weight ~0.98) included two divergence events ((Myotis evotis, M. thysanodes), M. keenii) accompanied by gene flow at the initial stages of divergence. These results provide a striking example of speciation-with-gene-flow in an evolutionary lineage.

Niche partitioning among sexual and unisexual Ambystoma salamanders.

Greenwald, K. R., R. D. Denton, and H. L. Gibbs. 2016. Ecosphere 7(11): e01579. 10.1002/ecs2.1579


Organisms that have ecologically similar sexual and asexual forms present an evolutionary puzzle, as theory predicts that eventually one form should eliminate the other. However, both forms may persist if there is niche partitioning between them. Geographical parthenogenesis is a hypothesis that predicts that in terms of niche use the asexual form in such pairs should be more ecologically successful in marginal habitats. This model has rarely been considered for gynogenetic taxa, as they are sperm dependent and thus constrained to the geographical range of sexual “sperm donor” species. Unisexual Ambystoma salamanders present a unique opportunity to look for evidence of niche partitioning and geographical parthenogenesis in a gynogenetic lineage, as there are multiple possible sperm donor species and so the geographical distributions of unisexuals are less constrained. We used broad sampling, comparative ecological niche models, and a model selection approach to determine (1) whether niche partitioning occurs among sexual and unisexual salamanders and (2) whether unisexual lineages indeed occupy marginal habitat relative to their most similar sexual species. Nearly all unisexual and sexual types showed significant niche differentiation. Predictions consistent with geographical parthenogenesis were upheld for one sexual–unisexual pair (A. jeffersonianum and LJJ unisexuals), but not for a second pair (A. texanum and LTT unisexuals). Our study provides evidence that different biotypes within the unisexual lineage have distinct ecological interactions with sexual taxa, supporting a role for these differences as a mechanism promoting coexistence between some sexual and unisexual forms. However, geographical parthenogenesis is only a partial explanation for sexual–unisexual coexistence, suggesting that other ecological and genetic mechanisms also play important roles in mediating coexistence among these salamanders.