Species are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to identify them are often unavailable to ...researchers. In such cases DNA sequence-based species delimitation has been proposed as a means of estimating species boundaries for further analysis. Several methods have been proposed to accomplish this. Here we present a Bayesian implementation of an evolutionary model-based method, the general mixed Yule-coalescent model (GMYC). Our implementation integrates over the parameters of the model and uncertainty in phylogenetic relationships using the output of widely available phylogenetic models and Markov-Chain Monte Carlo (MCMC) simulation in order to produce marginal probabilities of species identities.
We conducted simulations testing the effects of species evolutionary history, levels of intraspecific sampling and number of nucleotides sequenced. We also re-analyze the dataset used to introduce the original GMYC model. We found that the model results are improved with addition of DNA sequence and increased sampling, although these improvements have limits. The most important factor in the success of the model is the underlying phylogenetic history of the species under consideration. Recent and rapid divergences result in higher amounts of uncertainty in the model and eventually cause the model to fail to accurately assess uncertainty in species limits.
Our results suggest that the GMYC model can be useful under a wide variety of circumstances, particularly in cases where divergences are deeper, or taxon sampling is incomplete, as in many studies of ecological communities, but that, in accordance with expectations from coalescent theory, rapid, recent radiations may yield inaccurate results. Our implementation differs from existing ones in two ways: it allows for the accounting for important sources of uncertainty in the model (phylogenetic and in parameters specific to the model) and in the specification of informative prior distributions that can increase the precision of the model. We have incorporated this model into a user-friendly R package available on the authors' websites.
How to fail at species delimitation Carstens, Bryan C.; Pelletier, Tara A.; Reid, Noah M. ...
Molecular ecology,
September 2013, Letnik:
22, Številka:
17
Journal Article
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Species delimitation is the act of identifying species‐level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting ...species. However, most recent investigations only utilize a handful (i.e. 2–3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
Radical environmental change that provokes population decline can impose constraints on the sources of genetic variation that may enable evolutionary rescue. Adaptive toxicant resistance has rapidly ...evolved in Gulf killifish (
) that occupy polluted habitats. We show that resistance scales with pollution level and negatively correlates with inducibility of aryl hydrocarbon receptor (AHR) signaling. Loci with the strongest signatures of recent selection harbor genes regulating AHR signaling. Two of these loci introgressed recently (18 to 34 generations ago) from Atlantic killifish (
). One introgressed locus contains a deletion in
that confers a large adaptive advantage selection coefficient (
) = 0.8. Given the limited migration of killifish, recent adaptive introgression was likely mediated by human-assisted transport. We suggest that interspecies connectivity may be an important source of adaptive variation during extreme environmental change.
Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative ...transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor-based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicitymediating genes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.
For most species, evolutionary adaptation is not expected to be sufficiently rapid to buffer the effects of human‐mediated environmental changes, including environmental pollution. Here we review how ...key features of populations, the characteristics of environmental pollution, and the genetic architecture underlying adaptive traits, may interact to shape the likelihood of evolutionary rescue from pollution. Large populations of Atlantic killifish (Fundulus heteroclitus) persist in some of the most contaminated estuaries of the United States, and killifish studies have provided some of the first insights into the types of genomic changes that enable rapid evolutionary rescue from complexly degraded environments. We describe how selection by industrial pollutants and other stressors has acted on multiple populations of killifish and posit that extreme nucleotide diversity uniquely positions this species for successful evolutionary adaptation. Mechanistic studies have identified some of the genetic underpinnings of adaptation to a well‐studied class of toxic pollutants; however, multiple genetic regions under selection in wild populations seem to reflect more complex responses to diverse native stressors and/or compensatory responses to primary adaptation. The discovery of these pollution‐adapted killifish populations suggests that the evolutionary influence of anthropogenic stressors as selective agents occurs widely. Yet adaptation to chemical pollution in terrestrial and aquatic vertebrate wildlife may rarely be a successful “solution to pollution” because potentially adaptive phenotypes may be complex and incur fitness costs, and therefore be unlikely to evolve quickly enough, especially in species with small population sizes.
Summary
The origin of phenotypic novelty is one of the most challenging problems in evolutionary biology. Although genetic regulatory network rewiring or co‐option has been widely recognised as a ...major contributor, in most cases how such genetic rewiring/co‐option happens is completely unknown.
We have studied a novel foliar pigmentation pattern that evolved recently in the monkeyflower species Mimulus verbenaceus. Through genome‐wide association tests using wild‐collected samples, experimental crosses of laboratory inbred lines, gene expression analyses, and functional assays, we identified an anthocyanin‐activating R2R3‐MYB gene, STRIPY, as the causal gene triggering the emergence of the discrete, mediolateral anthocyanin stripe in the M. verbenaceus leaf.
Chemical mutagenesis revealed the existence of upstream activators and repressors that form a ‘hidden’ prepattern along the leaf proximodistal axis, potentiating the unique expression pattern of STRIPY. Population genomics analyses did not reveal signatures of positive selection, indicating that nonadaptive processes may be responsible for the establishment of this novel trait in the wild.
This study demonstrates that the origin of phenotypic novelty requires at least two separate phases, potentiation and actualisation. The foliar stripe pattern of M. verbenaceus provides an excellent platform to probe the molecular details of both processes in future studies.
Marine pollution is ubiquitous, and is one of the key factors influencing contemporary marine biodiversity worldwide. To protect marine biodiversity, how do we surveil, document and predict the ...short- and long-term impacts of pollutants on at-risk species? Modern genomics tools offer high-throughput, information-rich and increasingly cost-effective approaches for characterizing biological responses to environmental stress, and are important tools within an increasing sophisticated kit for surveiling and assessing impacts of pollutants on marine species. Through the lens of recent research in marine killifish, we illustrate how genomics tools may be useful for screening chemicals and pollutants for biological activity and to reveal specific mechanisms of action. The high dimensionality of transcriptomic responses enables their usage as highly specific fingerprints of exposure, and these fingerprints can be used to diagnose environmental problems. We also emphasize that molecular pathways recruited to respond at physiological timescales are the same pathways that may be targets for natural selection during chronic exposure to pollutants. Gene complement and sequence variation in those pathways can be related to variation in sensitivity to environmental pollutants within and among species. Furthermore, allelic variation associated with evolved tolerance in those pathways could be tracked to estimate the pace of environmental health decline and recovery. We finish by integrating these paradigms into a vision of how genomics approaches could anchor a modernized framework for advancing the predictive capacity of environmental and ecotoxicological science.
The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human‐altered environments can impose strong natural selection, where successful evolutionary ...adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts that adaptation is due to a few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype–phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and using RAD‐seq genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB‐126. We found that one to two large‐effect QTL loci accounted for resistance to PCB‐mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling. One QTL locus was shared across all populations and another was shared across three populations. One QTL locus showed strong signatures of recent natural selection in the corresponding wild population but another QTL locus did not. Some candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB‐126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB‐126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.
Among terrestrial ectotherms, hibernation is a common response to extreme cold temperatures and is associated with reduced physiological rates, including immunity. When winter wanes and temperatures ...increase, so too do vital rates of both ectothermic hosts and their parasites. Due to metabolic scaling, if parasite activity springs back faster than host immune functions then cold seasons and transitions between cold and warm seasons may represent periods of vulnerability for ectothermic hosts. Understanding host regulation of physiological rates at seasonal junctions is a first step toward identifying thermal mismatches between hosts and parasites. Here we show that immune gene expression is responsive to transitions into and out of the cold season in a winter-adapted amphibian, the wood frog (Lithobates sylvaticus), and that frogs experienced parasitism by at least two nematode species throughout the entirety of the cold season. In both splenic and skin tissues, we observed a decrease in immune gene expression going from fall to winter, observed no changes between winter and emergence from hibernation, and observed increases in immune gene expression after hibernation ended. At all timepoints, differentially expressed genes from spleens were more highly enriched for immune system processes than those from ventral skin, especially with respect to terms related to adaptive immune processes. Infection with nematode lungworms was also associated with upregulation of immune processes in the spleen. We suggest that rather than being a period of stagnation, during which physiological processes and infection potential cease, the cold season is immunologically dynamic, requiring coordinated regulation of many biological processes, and that the reemergence period may be an important time during which hosts invest in preparatory immunity.
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•Wood frog immune gene expression is decreased in the winter compared to the fall•A month after hibernation, many immune genes are still downregulated•Immune gene expression in the spleen is more seasonally dynamic than in the skin•Rhabdias sp. lung nematode parasitism is prevalent throughout the cold season•Frogs infected with Rhabdias sp. increase expression of immune genes in the spleen
Toe phalanx transplantation is a well-established technique for addressing bony deficiency in the reconstruction of hypoplastic digits in patients with congenital differences of the hand. Prior ...studies have commented on varying degrees of donor-site morbidity, although assessment of morbidity with validated outcome scores is lacking. This study seeks to evaluate donor-site morbidity after toe phalanx harvest using validated outcome measures.
We identified all children who underwent free, nonvascularized toe phalanx transfer to the hand at our institution from 2001 to 2011. We administered the Oxford Ankle Foot Questionnaire for Children (OXAFQ-C) and the Foot and Ankle Ability Measure (FAAM) to all patients, scaling results according to published scoring instructions.
Thirty-six patients with 83 toe phalanx transfers were able to be contacted, with a mean follow-up of 5.3 years (range, 18 months–11.2 years). The results of the OXAFQ-C showed mean scores of 99.96% (Physical), 100% (School and Play), and 96.01% (Emotional). The FAAM mean scores were 99.08% (Sports) and 99.17% (Activities of Daily Living). There were no lower extremity complications during the study period.
In contrast to varying degrees of donor-site morbidity reported in the current literature, this study demonstrates that toe phalanx harvest causes almost no measurable lower extremity morbidity or dysfunction over the mid- to long-term.
Therapeutic IV.
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