Evaluating Simplistic Methods to Understand Current Distributions and Forecast Distribution Changes Under Climate Change Scenarios: An Example With Coypu (Myocastor coypus)

Invasive species provide a unique opportunity to evaluate factors controlling biogeographic distributions; we can consider introduction success as an experiment testing suitability of environmental conditions. Predicting potential distributions of spreading species is not easy, and forecasting potential distributions with changing climate is even more difficult. Using the globally invasive coypu (Myocastor coypus [Molina, 1782]), we evaluate and compare the utility of a simplistic ecophysiological based model and a correlative model to predict current and future distribution. The ecophysiological model was based on winter temperature relationships with nutria survival. We developed correlative statistical models using the Software for Assisted Habitat Modeling and biologically relevant climate data with a global extent. We applied the ecophysiological based model to several global circulation model (GCM) predictions for mid-century. We used global coypu introduction data to evaluate these models and to explore a hypothesized physiological limitation, finding general agreement with known coypu distribution locally and globally and support for an upper thermal tolerance threshold. Global circulation model based model results showed variability in coypu predicted distribution among GCMs, but had general agreement of increasing suitable area in the USA. Our methods highlighted the dynamic nature of the edges of the coypu distribution due to climate non-equilibrium, and uncertainty associated with forecasting future distributions. Areas deemed suitable habitat, especially those on the edge of the current known range, could be used for early detection of the spread of coypu populations for management purposes. Combining approaches can be beneficial to predicting potential distributions of invasive species now and in the future and in exploring hypotheses of factors controlling distributions

The Explication Defence of Arguments from Reference

In a number of influential papers, Machery, Mallon, Nichols and Stich have presented a powerful critique of so-called arguments from reference, arguments that assume that a particular theory of reference is correct in order to establish a substantive conclusion. The critique is that, due to cross-cultural variation in semantic intuitions supposedly undermining the standard methodology for theorising about reference, the assumption that a theory of reference is correct is unjustified. I argue that the many extant responses to Machery et al.’s critique do little for the proponent of an argument from reference, as they do not show how to justify the problematic assumption. I then argue that it can in principle be justified by an appeal to Carnapian explication. I show how to apply the explication defence to arguments from reference given by Andreasen (for the biological reality of race) and by Churchland (against the existence of beliefs and desires)

Angiosperm Phylogeny: 17 Genes, 640 Taxa

• Premise of the study : Recent analyses employing up to fi ve genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. • Methods : We conducted two primary analyses based on 640 species representing 330 families. The fi rst included 25 260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19 846 aligned bp from 13 genes (representing only the nucleus and plastid). • Key results : Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms ( Mesangiospermae ), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae ]. Eudicotyledoneae contains a basal grade subtending Gunneridae . Within Gunneridae , Gunnerales are sister to the remainder ( Pentapetalae ), which comprises (1) Superrosidae , consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae , comprising Berberidopsidales, Santalales, Caryophyllales , Asteridae , and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae , most deep-level relationships are resolved with strong support. • Conclusions : Our analyses confi rm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics

Angiosperm phylogeny: 17 genes, 640 taxa

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/1/ajb20704-sup-0010.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/2/ajb20704.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/3/ajb20704-sup-0001.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/4/ajb20704-sup-0016.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/5/ajb20704-sup-0017.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/6/ajb20704-sup-0021.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/7/ajb20704-sup-0003.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/8/ajb20704-sup-0002.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/9/ajb20704-sup-0011.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/10/ajb20704-sup-0019.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/11/ajb20704-sup-0015.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/12/ajb20704-sup-0006.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/13/ajb20704-sup-0020.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/14/ajb20704-sup-0013.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/15/ajb20704-sup-0004.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/16/ajb20704-sup-0012.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/17/ajb20704-sup-0005.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/18/ajb20704-sup-0018.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/19/ajb20704-sup-0009.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/20/ajb20704-sup-0014.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/21/ajb20704-sup-0007.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/22/ajb20704-sup-0008.pd

Flammable biomes dominated by eucalypts originated at the Cretaceous-Palaeogene boundary

Fire is a major modifier of communities, but the evolutionary origins of its prevalent role in shaping current biomes are uncertain. Australia is among the most fire-prone continents, with most of the landmass occupied by the fire-dependent sclerophyll and savanna biomes. In contrast to biomes with similar climates in other continents, Australia has a tree flora dominated by a single genus, Eucalyptus, and related Myrtaceae. A unique mechanism in Myrtaceae for enduring and recovering from fire damage likely resulted in this dominance. Here, we find a conserved phylogenetic relationship between post-fire resprouting (epicormic) anatomy and biome evolution, dating from 60 to 62 Ma, in the earliest Palaeogene. Thus, fire-dependent communities likely existed 50 million years earlier than previously thought. We predict that epicormic resprouting could make eucalypt forests and woodlands an excellent long-term carbon bank for reducing atmospheric CO2 compared with biomes with similar fire regimes in other continents

Supporting Spartina: Interdisciplinary perspective shows Spartina as a distinct solid genus

In 2014 a DNA-based phylogenetic study confirming the paraphyly of the grass subtribe Sporobolinae proposed the creation of a large monophyletic genus Sporobolus, including (among others) species previously included in the genera Spartina, Calamovilfa, and Sporobolus. Spartina species have contributed substantially (and continue contributing) to our knowledge in multiple disciplines, including ecology, evolutionary biology, molecular biology, biogeography, experimental ecology, environmental management, restoration ecology, history, economics, and sociology. There is no rationale so compelling to subsume the name Spartina as a subgenus that could rival the striking, global iconic history and use of the name Spartina for over 200 years. We do not agree with the arguments underlying the proposal to change Spartina to Sporobolus. We understand the importance of taxonomy and of formalized nomenclature and hope that by opening this debate we will encourage positive feedback that will strengthen taxonomic decisions with an interdisciplinary perspective. We consider the strongly distinct, monophyletic clade Spartina should simply and efficiently be treated as the genus Spartina

Supporting Spartina: Interdisciplinary perspective shows Spartina as a distinct solid genus

In 2014, a DNA-based phylogenetic study confirming the paraphyly of the grass subtribe Sporobolinae proposed the creation of a large monophyletic genus Sporobolus, including (among others) species previously included in the genera Spartina, Calamovilfa, and Sporobolus. Spartina species have contributed substantially (and continue contributing) to our knowledge in multiple disciplines, including ecology, evolutionary biology, molecular biology, biogeography, experimental ecology, biological invasions, environmental management, restoration ecology, history, economics, and sociology. There is no rationale so compelling to subsume the name Spartina as a subgenus that could rival the striking, global iconic history and use of the name Spartina for over 200 yr. We do not agree with the subjective arguments underlying the proposal to change Spartina to Sporobolus. We understand the importance of both the objective phylogenetic insights and of the subjective formalized nomenclature and hope that by opening this debate we will encourage positive feedback that will strengthen taxonomic decisions with an interdisciplinary perspective. We consider that the strongly distinct, monophyletic clade Spartina should simply and efficiently be treated as the genus Spartina

Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL

We present the results of two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups. The data are exclusively from the chloroplast gene rbcL, which codes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO or RuBPCase). We used two different state-transformation assumptions resulting in two sets of cladograms: (i) equal-weighting for the 499-taxon analysis; and (ii) a procedure that differentially weights transversions over transitions within characters and codon positions among characters for the 475-taxon analysis. The degree of congruence between these results and other molecular, as well as morphological, cladistic studies indicates that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling. Because the topologies presented are necessarily approximate and cannot be evaluated adequately for internal support, these results should be assessed from the perspective of their predictive value and used to direct future studies, both molecular and morphological. In both analyses, the three genera of Gnetales are placed together as the sister group of the flowering plants, and the anomalous aquatic Ceratophyllum (Ceratophyllaceae) is sister to all other flowering plants. Several major lineages identified correspond well with at least some recent taxonomic schemes for angiosperms, particularly those of Dahlgren and Thorne. The basalmost clades within the angiosperms are orders of the apparently polyphyletic subclass Magnoliidae sensu Cronquist. The most conspicuous feature of the topology is that the major division is not monocot versus dicot, but rather one correlated with general pollen type: uniaperturate versus triaperturate. The Dilleniidae and Hamamelidae are the only subclasses that are grossly polyphyletic; an examination of the latter is presented as an example of the use of these broad analyses to focus more restricted studies. A broadly circumscribed Rosidae is paraphyletic to Asteridae and Dilleniidae. Subclass Caryophyllidae is monophyletic and derived from within Rosidae in the 475-taxon analysis but is sister to a group composed of broadly delineated Asteridae and Rosidae in the 499-taxon study