ABSTRACT Emerging Infectious Diseases (EID) pose a world-wide health and socio-economic threat. Accelerating climate change and globalization are exposing unforeseen ways that pathogens cope with their surroundings. The 2015 Zika virus (ZIKV) outbreak was an example of expansion into previously inaccessible fitness spaces, causing a sudden epidemic. Recent studies indicating the subsequent decrease in symptomatic cases means the virus is in remission, currently poses little threat, and therefore can be ignored. We present an evolutionary scenario derived from the Stockholm Paradigm, of oscillating phases of expansion and isolation, accompanied by changes in transmission, persistence, virulence, and pathology. Chief among these is the likelihood that asymptomatic strains are constantly transmitted sexually. This suggests that the currently quiescent virus retains capacities to reemerge abruptly and spread rapidly in an arena of changing opportunity.

It is time for an expansion and enrichment of evolutionary theory. The "back to the future" proposal contained herein is based on three postulates: 1) Neo-Darwinism is too impoverished for this task; 2) its predecessor, Darwinism, contained the necessary breadth of vision and metaphor to be the basis for an inclusive and unifying theory of biology; and 3) the necessary framework for this new stage in the evolution of evolutionary theory is largely in place. We make our case through the use of a number of metaphorical dualisms designed to help focus discussions toward a more cooperative and productive approach to the study of living systems. Along the way, we suggest a number of self-induced paradoxes in neo-Darwinian accounts of evolution that are resolved by our perspective.

A new species of Haematoloechus is described from the lungs of Rana boylii from Humboldt County, California. The new species is similar to Haematoloechus buttensis, Haematoloechus kernensis, and Haematoloechus complexus in general course of the uterus and gonad shape. It is similar to H. buttensis by having a cirrus sac terminating midway between the posterior margin of the pharynx and the anterior margin of the ovary, and having a smaller oral/ventral sucker ratio; to H. complexus by having the genital pore ventral to the pharynx, and it is similar to H. kernensis by having a larger oral sucker to pharynx width ratio. The new species is unique by lacking an extra-cecal longitudinal uterine loop from the hind-body. Molecularly, the new species differs 1.04-1.15% in partial 28S sequence with respect to H. complexus, and a monophyletic grouping of these specimens in a phylogenetic analysis of all available sequence data consistent with the species-specific status proposed herein. Evidence is also presented to suggest that specimens identified as H. buttensis in Rana pretiosa from British Columbia, Canada represents a new, but still undescribed species. The importance of conducting biological inventories of helminths, along with continued monitoring of populations, and collections based taxonomy are related.

Una especie nueva de Haematoloechus es descrita de los pulmones de Rana boylii de Humboldt County, California. La especie nueva guarda semejanza con Haematoloechus buttensis, Haematoloechus kernensis, y Haematoloechus complexus en la disposición general del útero y en la forma de las gónadas. Es similar a H. buttensis en que la bolsa del cirro finaliza entre el margen posterior de la faringe y el margen anterior del ovario, y en presentar una relación menor entre la ventosa oral y el acetábulo; a H. complexus por tener el poro genital ventral a la faringe, y a H. kernensis por tener una relación mayor del ancho de la ventosa oral contra la faringe. La especie nueva es única por carecer de asas uterinas extracecales longitudinales. Molecularmente, la especie nueva muestra 1.04-1.15% de diferencia en secuencias parciales de 28S con respecto H. complexus; esta información complementa las diferencias morfológicas. También se presenta evidencia para sugerir que ejemplares identificados como H. buttensis de Rana pretiosa en British Columbia, Canadá probablemente representan una especie nueva aún no descrita. Se aborda la importancia de la realización de inventarios biológicos de helmintos, el monitoreo continuo de las poblaciones y las colecciones basadas en la taxonomía.

The parasite paradox arises from the dual observations that parasites (broadly construed, including phytophagous insects) are resource specialists with restricted host ranges, and yet shifts onto relatively unrelated hosts are common in the phylogenetic diversification of parasite lineages and directly observable in ecological time. We synthesize the emerging solution to this paradox: phenotypic flexibility and phylogenetic conservatism in traits related to resource use, grouped under the term ecological fitting, provide substantial opportunities for rapid host switching in changing environments, in the absence of the evolution of novel host-utilization capabilities. We discuss mechanisms behind ecological fitting, its implications for defining specialists and generalists, and briefly review empirical examples of host shifts in the context of ecological fitting. We conclude that host shifts via ecological fitting provide the fuel for the expansion phase of the recently proposed oscillation hypothesis of host range and speciation, and, more generally, the generation of novel combinations of interacting species within the geographic mosaic theory of coevolution. Finally, we conclude that taxon pulses, driven by climate change and large-scale ecological perturbation are drivers of biotic mixing and resultant ecological fitting, which leads to increased rates of rapid host switching, including the agents of Emerging Infectious Disease.

We review Hennigian phylogenetics and compare it with Maximum parsimony, Maximum likelihood, and Bayesian likelihood approaches. All methods use the principle of parsimony in some form. Hennigian-based approaches are justified ontologically by the Darwinian concepts of phylogenetic conservatism and cohesion of homologies, embodied in Hennig's Auxiliary Principle, and applied by outgroup comparisons. Parsimony is used as an epistemological tool, applied a posteriori to choose the most robust hypothesis when there are conflicting data. Quantitative methods use parsimony as an ontological criterion: Maximum parsimony analysis uses unweighted parsimony, Maximum likelihood weight all characters equally that explain the data, and Bayesian likelihood relying on weighting each character partition that explains the data. Different results most often stem from insufficient data, in which case each quantitative method treats ambiguities differently. All quantitative methods produce networks. The networks can be converted into trees by rooting them. If the rooting is done in accordance with Hennig's Auxiliary Principle, using outgroup comparisons, the resulting tree can then be interpreted as a phylogenetic hypothesis. As the size of the data set increases, likelihood methods select models that allow an increasingly greater number of a priori possibilities, converging on the Hennigian perspective that nothing is prohibited a priori. Thus, all methods produce similar results, regardless of data type, especially when their networks are rooted using outgroups. Appeals to Popperian philosophy cannot justify any kind of phylogenetic analysis, because they argue from effect to cause rather than from cause to effect. Nor can particular methods be justified on the basis of statistical consistency, because all may be consistent or inconsistent depending on the data. If analyses using different types of data and/or different methods of phylogeny reconstruction do not produce the same results, more data are needed.

Se revisa la sistemática filogenética Hennigiana y se compara con las aproximaciones de Máxima Parsimonia, Máxima Verosimilitud y verosimilitud Bayesiana. Todos los métodos utilizan el principio de la parsimonia en alguna forma. Las aproximaciones con bases Hennigianas se justifican ontológicamente con los conceptos Darwinianos de conservacionismo filogenético y cohesión de las homologías, representados en el Principio Auxiliar de Hennig, y aplicado en la comparación con el grupo externo. La Parsimonia se utiliza como una herramienta epistemológica, aplicada a posteriori en la elección de la hipótesis más robusta cuando hay datos en conflicto. Los métodos cuantitativos utilizan la parsimonia como un criterio ontológico: los análisis de Máxima Parismonia utilizan la parsimonia sin pesaje, la Máxima Verosimilitud les asigna un peso igual a todos los caracteres que explican los datos, mientras que la verosimilitud Bayesiana depende del pesaje de cada una de las particiones de caracteres que explican los datos. Las diferencias en los resultados derivan de un muestreo insuficiente de datos, en cuyo caso cada método trata las ambigüedades de manera diferente. Todos los métodos cuantitativos producen redes. Las redes pueden convertirse en árboles al ser enraizadas. Si el enraizamiento se efectua de acuerdo con el Principio Auxiliar de Hennig, utilizando la comparación con un grupo externo, el árbol resultante puede considerarse como una hipótesis filogenética. Al incrementarse el número de datos, los métodos de verosimilitud selccionan modelos que permiten un número cada vez mayor de posibilidades a priori, convergiendo en la perspectiva Hennigiana de que nada está prohibido a priori. Por lo tanto, todos los métodos producen resultados similares independientemente del tipo de datos, especialmente cuando las redes se enraizan utilizando grupos externos. Las invocaciones a la filosofia Popperiana no pueden justificar ningún tipo de análisis filogenético, ya que sus argumentos van del efecto a la causa y no de la causa al efecto. Tampoco se puede justificar el uso de un método en particular con base en la consistencia estadística, ya que todos pueden ser consistentes o incosistentes dependiendo de los datos. Si los análisis con diferentes tipos de datos y/o métodos de reconstrucción filogenética no producen igual resultado, significa que es necesario reunir datos adicionales.

Traditional wisdom, based on assumptions of species-specific coevolutionary interactions between hosts and parasites, suggests that pathogens with multi-host life cycles are unlikely to move with their definitive hosts because their transmission requirements are so specialized. Ecological fitting provides a theory of diffuse coevolution, which allows introduced pathogens with complex life cycles to become established and spread rapidly into native hosts if the resource required at each stage of the life cycle is both phylogenetically conservative (distributed among numerous species) and geographically widespread. The external appearance of life cycle complexity does not, therefore, on its own, predict the potential for an organism to become an emerging infectious disease. We apply this concept to explain a potential enigma, the presence of a lung fluke, Haematoloechus floedae, endemic to North American bullfrogs, in Costa Rican leopard frogs, even though there are no bullfrogs extant in the country today, and none ever occurred where the parasite has been discovered. We then discuss how the integration of ecological and life history information within a phylogenetic framework can help biologists move from attempts to manage emerging infectious disease outbreaks to the ability to predict and thus circumvent the outbreak in the first place.

Con base en el supuesto de coevolución a nivel de especies de parásitos y hospederos, tradicionalmente se asume como poco probable que aquellos patógenos con ciclos de vida que involucran varios hospederos acompañen a su hospedero definitivo a un nuevo ambiente, por lo especializado de sus requerimientos de transmisión. El fenómeno de flexibilidad ecológica aporta una teoría de coevolución difusa, que permite a los patógenos con ciclos de vida complejos, que han sido introducidos, establecerse y dispersarse de una manera rápida en hospederos nativos, si el recurso requerido en cada etapa del ciclo de vida es filogenéticamente conservado (se distribuye en numerosas especies) y a la vez, tiene una distribución geográfica amplia. Por lo tanto, la complejidad de un ciclo de vida no predice, por sí misma, el potencial de un organismo para provocar una enfermedad infecciosa emergente. Aplicamos este concepto para explicar el caso particular de un digéneo del pulmón de anfibios, Haematoloechus floedae, endémico de ranas toro de Norteamérica, que fue recolectado en ranas leopardo de Costa Rica, aún cuando actualmente no existen ranas toro en ese país, y nunca existieron en la región en donde se encontró al parásito. Asimismo, se discute de qué manera la integración de la información ecológica y de ciclos de vida, en un marco filogenético, puede ayudar a los biólogos a pasar de los intentos para controlar brotes de enfermedades emergentes, hacia la predicción y el impedimento de dichos brotes en primera instancia.

Historical biogeography has recently experienced a significant advancement in three integrated areas. The first is the adoption of an ontology of complexity, replacing the traditional ontology of simplicity, or a priori parsimony; simple and elegant models of the biosphere are not sufficient for explaining the geographical context of the origin of species and their post-speciation movements, producing evolutionary radiations and complex multi-species biotas. The second is the development of a powerful method for producing area cladograms from complex data, especially cases of reticulated area relationships, without loss of information. That method, called Phylogenetic Analysis for Comparing trees (PACT), is described herein. The third element is the replacement of the model of maximum vicariance with the model called the Taxon Pulse hypothesis. Using PACT analysis for a data set of 33 different clades occurring in 9 different areas of endemism in Mexico, I show how taxon pulses can be detected. Finally, I show how PACT results can be used to provide a phylogenetic context for analyses of species-area relationships.

Recientemente, la biogeografía histórica ha experimentado un avance significativo en tres aspectos integrales. El primero, es la adopción de una ontología de la complejidad, que reemplaza a la tradicional ontología de la simplicidad o parsimonia a priori; los modelos elegantes y sencillos para representar a la biósfera no son suficientes para explicar el contexto geográfico del origen de las especies y sus movimientos posteriores, generadores de radiaciones evolutivas y biotas multiespecíficas complejas. El segundo es el desarrollo de un método capaz de producir cladogramas de área a partir de datos complejos, especialmente casos de relaciones reticuladas de áreas, sin pérdida de información. Aquí describo ese método, llamado Análisis Filogenético para la Comparación de Árboles (PACT por sus siglas en inglés). El tercer aspecto, es la sustitución del modelo de máxima vicarianza por el modelo llamado hipótesis de pulsación de los taxa. Utilizando PACT para analizar 33 clados diferentes que ocurren en 9 áreas de endemismo en México, muestro cómo pueden detectarse las pulsaciones de los taxa. Finalmente, muestro cómo pueden utilizarse los resultados de PACT para proveer un contexto filogenético para el análisis de relaciones especies- área.

Thanks to the phylogenetic systematics revolution, systematic parasitology is poised to make significant contributions in tropical medicine and public health, biodiversity science, and evolutionary biology. At the same time, the taxonomic impediment is acute within parasitology. Both systematists and non-systematists must be interested in working towards common goals and establishing collaborative efforts in order to re-vitalize and re-populate systematic parasitology.