Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms)

The recognized potential of using mitogenomics in phylogenetics and the more accessible use of high-throughput sequencing (HTS) offer an opportunity to investigate groups of neglected organisms. Here, we leveraged HTS to execute the most comprehensive documentation of mitogenomes for cestodes based on the number of terminals sequenced. We adopted modern approaches to obtain the complete mitogenome sequences of 86 specimens representing five orders of cestodes (three reported for the first time: Phyllobothriidea, “Tetraphyllidea” and Trypanorhyncha). These complete mitogenomes represent an increase of 41% of the mitogenomes available for cestodes (61–147) and an addition of 33% in the representativeness of the cestode orders. The complete mitochondrial genomes are conserved, circular, encoded in the same strand, and transcribed in the same direction, following the pattern observed previously for tapeworms. Their length varies from 13,369 to 13,795 bp, containing 36 genes in total. Except for the Trypanorhyncha specimen, the gene order of the other four cestode orders sequenced here suggests that it could be a synapomorphy for the acetabulate group (with a reversion for taenids). Our results also suggest that no single gene can tell all the evolutionary history contained in the mitogenome. Therefore, cestodes phylogenies based on a single mitochondrial marker may fail to capture their evolutionary history. We predict that such phylogenies would be improved if conducted under a total evidence framework. The characterization of the new mitochondrial genomes is the first step to provide a valuable resource for future studies on the evolutionary relationships of these groups of parasites.

Misleading Higher-Order Evidence, Conflicting Ideals, and Defeasible Logic

Thinking about misleading higher-order evidence naturally leads to a puzzle about epistemic rationality: If one’s total evidence can be radically misleading regarding itself, then two widely-accepted requirements of rationality come into conflict, suggesting that there are rational dilemmas. This paper focuses on an often misunderstood and underexplored response to this (and similar) puzzles, the so-called conflicting-ideals view. Drawing on work from defeasible logic, I propose understanding this view as a move away from the default meta-epistemological position according to which rationality requirements are strict and governed by a strong, but never explicitly stated logic, toward the more unconventional view, according to which requirements are defeasible and governed by a comparatively weak logic. When understood this way, the response is not committed to dilemmas.

Impacts of Taxon-Sampling Schemes on Bayesian Molecular Dating under the Unresolved Fossilized Birth-Death Process

Evolutionary timescales can be estimated using a combination of genetic data and fossil evidence based on the molecular clock. Bayesian phylogenetic methods such as tip dating and total-evidence dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of these diversified sampling schemes on Bayesian molecular dating under the unresolved fossilized birth-death (FBD) process, in which fossil taxa are topologically constrained but their exact placements are not inferred. We used synthetic data generated by simulation of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses show that increasing sampling density does not substantially improve divergence-time estimates under benign conditions. However, when the tree topologies were fixed to those used for simulation or when evolutionary rates varied among lineages, the performance of Bayesian tip dating improves with sampling density. By exploring three situations of model mismatches, we find that including all relevant fossils without pruning off those inappropriate for the FBD process can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have useful implications for Bayesian molecular dating in the era of phylogenomics.

Appearance and Explanation

McCain and Moretti develop a new appearance/seemings-based theory of epistemic justification. This theory, Phenomenal Explanationism, takes as a reasonable starting point the idea that how things appear provides evidence about how the world is. However, unlike other appearance-based theories, Phenomenal Explanationism does not rely on an overly simplistic account of evidential support where things appearing a particular way is sufficient for rationally believing they are that way. Instead, Phenomenal Explanationism takes the insight that appearances are evidence and imbeds it into a broader explanationist framework. In this broader framework the world appearing a particular way provides sufficient justification for believing the world is that way just in case the world being the way it appears best explains the total evidence. Although Phenomenal Explanationism draws inspiration from Phenomenal Conservatism and explanationist theories, it is superior to both in that it offers a satisfying, complete theory of epistemic justification.

Human Evolution in Polynesia: a Molecular Biological Study

<p>Human evolution is an extremely interesting and contentious topic that incorporates data from a wide variety of disciplines. Molecular studies are becoming increasingly important for reconstructing human history, as new techniques allow faster recovery of results, and genetic tests provide an independent test for colonisation theories that are usually based on archaeological and linguistic evidence. Mitochondrial DNA (mtDNA) is an extremely useful genetic marker that is widely used in molecular biology for establishing phylogenetic links between individuals and populations. In the current study the 3' Hypervariable Region (3' HVI) of mtDNA from human populations living in New Zealand (Aotearoa) was analysed. The HVI mtDNA diversity in the New Zealand Maori population was significantly reduced compared with Polynesian and Melanesian populations, with an extremely high frequency (~87%) of the 'Polynesian CGT motif' haplotype. Additionally, the 9-bp deletion, common in Polynesian populations, has reached fixation (100%) in the Maori samples. These results support a settlement scenario with repeated population bottlenecks. The mtDNA HVI haplotype frequencies in this study, combined with those from previous studies, were used in computer simulations to estimate the number of females required to found the current Maori population. Approximately 56 women, and an equal or greater number of men, were estimated to have been present in the founding waka. This estimate is too large to support any settlement models with a small number of founders and effectively rules out the possibility of 'accidental discovery', instead supporting a planned settlement of Aotearoa in agreement with traditional knowledge. Analysis of interdisciplinary data has allowed current theories for the origins of the Polynesians and proto-Austronesians to be consolidated by introducing a 'Synthetic Total Evidence Theory'. It is likely that once published this theory will stimulate intense discussion and debate and will continue to grow as further evidence is obtained and incorporated into this model.</p>

Human Evolution in Polynesia: a Molecular Biological Study

<p>Human evolution is an extremely interesting and contentious topic that incorporates data from a wide variety of disciplines. Molecular studies are becoming increasingly important for reconstructing human history, as new techniques allow faster recovery of results, and genetic tests provide an independent test for colonisation theories that are usually based on archaeological and linguistic evidence. Mitochondrial DNA (mtDNA) is an extremely useful genetic marker that is widely used in molecular biology for establishing phylogenetic links between individuals and populations. In the current study the 3' Hypervariable Region (3' HVI) of mtDNA from human populations living in New Zealand (Aotearoa) was analysed. The HVI mtDNA diversity in the New Zealand Maori population was significantly reduced compared with Polynesian and Melanesian populations, with an extremely high frequency (~87%) of the 'Polynesian CGT motif' haplotype. Additionally, the 9-bp deletion, common in Polynesian populations, has reached fixation (100%) in the Maori samples. These results support a settlement scenario with repeated population bottlenecks. The mtDNA HVI haplotype frequencies in this study, combined with those from previous studies, were used in computer simulations to estimate the number of females required to found the current Maori population. Approximately 56 women, and an equal or greater number of men, were estimated to have been present in the founding waka. This estimate is too large to support any settlement models with a small number of founders and effectively rules out the possibility of 'accidental discovery', instead supporting a planned settlement of Aotearoa in agreement with traditional knowledge. Analysis of interdisciplinary data has allowed current theories for the origins of the Polynesians and proto-Austronesians to be consolidated by introducing a 'Synthetic Total Evidence Theory'. It is likely that once published this theory will stimulate intense discussion and debate and will continue to grow as further evidence is obtained and incorporated into this model.</p>

Molecular species delimitation refines the taxonomy of native and nonnative physinine snails in North America

Being able to associate an organism with a scientific name is fundamental to our understanding of its conservation status, ecology, and evolutionary history. Gastropods in the subfamily Physinae have been especially troublesome to identify because morphological variation can be unrelated to interspecific differences and there have been widespread introductions of an unknown number of species, which has led to a speculative taxonomy. To resolve uncertainty about species diversity in North America, we targeted an array of single-locus species delimitation methods at publically available specimens and new specimens collected from the Snake River basin, USA to generate species hypotheses, corroborated using nuclear analyses of the newly collected specimens. A total-evidence approach delineated 18 candidate species, revealing cryptic diversity within recognized taxa and a lack of support for other named taxa. Hypotheses regarding certain local endemics were confirmed, as were widespread introductions, including of an undescribed taxon likely belonging to a separate genus in southeastern Idaho for which the closest relatives are in southeast Asia. Overall, single-locus species delimitation was an effective first step toward understanding the diversity and distribution of species in Physinae and to guiding future investigation sampling and analyses of species hypotheses.

A multifaceted ecological assessment reveals the invasion of the freshwater red macroalga Montagnia macrospora (Batrachospermales, Rhodophyta) in Taiwan

Invasive freshwater macroalgae are rarely described. Recently, a freshwater red alga, Montagnia macrospora, was introduced from South America to East Asia via the global aquarium trade. The earliest occurrence record of this alga in Taiwan is dated 2005. To determine whether M. macrospora has become an invasive species in Taiwan and to understand its traits that facilitated its invasion, we took a total-evidence approach that combines examination of ecological background and population genetic analysis. Our island-wide survey showed that M. macrospora alga was widespread in the field across Taiwan, where the climate greatly differs from that of South America. Our population genetic analysis revealed that the cox2-3 sequences of all the specimens of M. macrospora from Taiwan were identical, consistent with the hypothesis that the alga expanded through asexual reproduction. Moreover, during our long-term ecological assessments and field surveys, we observed that M. macrospora is an ecological generalist that can self-sustain for a decade and bloom. Taken together, our data suggest that M. macrospora has successfully invaded the freshwater ecosystems in Taiwan due to its ability to disperse asexually and to grow under broad environmental conditions. We hope that our study brings attention to invasive freshwater algae, which have been overlooked in conservation planning and management.

A multifaceted ecological assessment reveals the invasion of the freshwater red macroalga Montagnia macrospora (Batrachospermales, Rhodophyta) in Taiwan

Invasive freshwater macroalgae are rarely described. Recently, a freshwater red alga, Montagnia macrospora, was introduced from South America to East Asia via the global aquarium trade. The earliest reported occurrence of this alga in Taiwan was dated 2005. To determine whether or not M. macrospora has become an invasive species in Taiwan and to understand its traits that facilitated its invasion, we took a total-evidence approach that combines ecological background examination and population genetic analysis. Our island-wide survey showed that this alga is widespread in the field in Taiwan, where the climate greatly differs from that of South America. Our population genetic analyses showed that the cox2-3 sequences were identical in all the samples of M. macrospora from Taiwan, consistent with our observations that the alga mainly expanded through asexual reproduction. Furthermore, our long-term ecological assessments and field observations revealed that M. macrospora can grow under a wide range of environmental conditions (e.g., temperature, pH, and light conditions), self-sustain for nearly a decade, and bloom in polluted waters. Taken together, these data suggest that M. macrospora has successfully invaded the freshwater ecosystems in Taiwan due to its ability to undergo asexual reproduction and to self-sustain under broad environmental conditions. We hope that our study brings attention to invasive freshwater algae, which have been overlooked in conservation planning and management.