An evaluation of narrow hybrid zones in vertebrates

A review of the literature on vertebrate hybridization reveals the existence of a number of narrow hybrid zones. Three hypotheses have been suggested to explain the occurrence of these zones. The ephemeral-zone hypothesis states that hybridization will end either in speciation or fusion of the hybridizing taxa by means of introgression. The dynamic-equilibrium hypothesis allows the possibility that narrow hybrid zones might be stable: where hybrids are confined to a small area by steep selection gradients, crystallization of an antihybridization mechanism might be prevented by naive immigrants from the parental populations even though hybrids are selected against. The hybrid-superiority hypothesis states that hybrids are more fit than parental phenotypes in some environments. The ephemeral-zone hypothesis fails to explain the antiquity and apparent stability of several hybrid zones. The dynamic-equilibrium hypothesis does not adequately explain the persistence of hybrid populations that do not receive a substantial influx of genes from both parental populations. The hybrid-superiority hypothesis is consistent with the various sizes, shapes, and positions reported for stable hybrid zones because, under this hypothesis, the range of a hybrid population is determined by the range of environmental conditions within which the hybrids are superior. Although there are exceptions, most vertebrate hybrid zones are, in fact, narrow. The hybridsuperiority hypothesis must accommodate this fact. The additional hypothesis is offered that hybrids, in some cases, can succeed in environments where competition from parental phenotypes is weak. Thus, hybrid populations are often found in areas devoid of stable ecological communities. Ecotones are one such area, and I suggest that stable hybrid zones are often narrow because they tend to occur in ecotones which are themselves narrow

Stability of small unisexual-bisexual populations of Poeciliopsis (Pisces: Poeciliidae)

All-female species of Poeciliopsis depend upon ♂ ♂ of closely related species for sperm. This relationship creates a competitive situation in which bisexual ♀ ♀ compete with unisexual ♀ ♀ for sperm from ♂ ♂ of the bisexual species. Earlier studies demonstrated a sufficient mechanism inherent in the behavior of ♂ ♂ for allowing coexistence in mixed unisexual-bisexual populations. Courtship preference of ♂ ♂ for conspecific ♀ ♀ is dynamically countered by social interaction among ♂ ♂ : subordinate males mate with unisexual ♀ ♀ in impetuous courtships. The Poeciliopsis monacha-Poeciliopsis 2 monacha-lucida complex occurs naturally in small isolated populations where stochastic factors are not negligible. This paper evaluates the stability of small populations of this complex by laboratory population experimentation and stochastic computer simulation. Three small mixed populations persisted in the laboratory for 2 yr but extinction of the bisexual species occurred in four of nine simulated replicates of these experiments. Life tables and fitness values calculated from estimates of birth and death rates showed the all-female species to be much more fit in the laboratory populations than was the bisexual species. Additional simulations done at relative fitness values more characteristic of natural populations indicated that extinctions in small isolates would be rare in nature. Isolated demes can become confluent during the annual rainy season. It was expected that this confluence, by effectively increasing population size, might enhance stability by reducing the effect of stochastic factors; simulations of two and four demes mixed annually did not support this hypothesis

A System for Accessible Artificial Intelligence

While artificial intelligence (AI) has become widespread, many commercial AI systems are not yet accessible to individual researchers nor the general public due to the deep knowledge of the systems required to use them. We believe that AI has matured to the point where it should be an accessible technology for everyone. We present an ongoing project whose ultimate goal is to deliver an open source, user-friendly AI system that is specialized for machine learning analysis of complex data in the biomedical and health care domains. We discuss how genetic programming can aid in this endeavor, and highlight specific examples where genetic programming has automated machine learning analyses in previous projects.Comment: 14 pages, 5 figures, submitted to Genetic Programming Theory and Practice 2017 worksho

Coexistence in unisexual-bisexual species complexes of Poeciliopsis (Pisces: Poeciliidae)

All-female forms of Poeciliopsis rely on males of closely related bisexual species for sperm. The natural habitat of Poeciliopsis in Sonora, Mexico, consists of a variety of small ponds connected by intermittent watercourses. Optimal areas, containing mixed female aggregates, are defended by territorial males. Social structure in natural populations very closely resembles that of laboratory experiments, wherein subordinant males show reduced mate discrimination and inseminate unisexuals. An equation relating male density to unisexual inseminations is used in a computer simulation model of a population. A stable equilibrium is inherent in unisexual-bisexual species complexes but the level of equilibrium is affected by the environment. Coexistence does not require niche separation. The simulations predict the percentage of unisexuals pregnant in natural populations and explain their distribution pattern. The strength of the mechanism is demonstrated by a natural population in which the percentage of unisexuals pregnant responded strongly to a modest change in unisexual-bisexual composition

Plumage convergence in Picoides woodpeckers based on a molecular phylogeny, with emphasis on convergence in downy and hairy woodpeckers

Adult and juvenile plumage characters were traced onto a well-resolved molecular based phylogeny for Picoides woodpeckers, and a simple phylogenetic test of homology, parallelism, and convergence of plumage characters was performed. Reconstruction of ancestral character states revealed multiple events of independent evolution of derived character states in most characters studied, and a concentrated changes test revealed that some plumage characters evolved in association with habitat type. For example, there was a statistically significant association between loss of dorsal barring and use of densely vegetated habitats among Picoides species. Two analyses indicated that convergence, as opposed to parallel evolution or shared ancestry, underlies the similarity in plumage patterns between the Downy (Picoides pubescens) and Hairy (P. villosus) Woodpeckers. Possible causal explanations for convergence in plumage patterns may include mimicry and interspecific territoriality

PMLB: A Large Benchmark Suite for Machine Learning Evaluation and Comparison

The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world and simulated benchmark datasets have emerged from different sources, but their organization and adoption as standards have been inconsistent. As such, selecting and curating specific benchmarks remains an unnecessary burden on machine learning practitioners and data scientists. The present study introduces an accessible, curated, and developing public benchmark resource to facilitate identification of the strengths and weaknesses of different machine learning methodologies. We compare meta-features among the current set of benchmark datasets in this resource to characterize the diversity of available data. Finally, we apply a number of established machine learning methods to the entire benchmark suite and analyze how datasets and algorithms cluster in terms of performance. This work is an important first step towards understanding the limitations of popular benchmarking suites and developing a resource that connects existing benchmarking standards to more diverse and efficient standards in the future.Comment: 14 pages, 5 figures, submitted for review to JML

Chapter 11: Genome-Wide Association Studies

Genome-wide association studies (GWAS) have evolved over the last ten years into a powerful tool for investigating the genetic architecture of human disease. In this work, we review the key concepts underlying GWAS, including the architecture of common diseases, the structure of common human genetic variation, technologies for capturing genetic information, study designs, and the statistical methods used for data analysis. We also look forward to the future beyond GWAS

Comparative reproductive success of Yellow-shafted, Red-shafted, and Hybrid Flickers across a hybrid zone

Alternative hypotheses of hybrid zones make specific predictions about reproductive components of fitness in the hybrids. The dynamic-equilibrium and reinforcement hypotheses are premised on reduced hybrid fitness, which should be apparent as reduced clutch or brood size or as increased embryonic mortality. The hybrid-superiority and introgression hypotheses predict normal clutch and brood size and embryonic mortality. Reproductive success was measured at four study sites on a transect across the hybrid zone between the Yellow- (Colaptes auratus auratus) and Red-shafted (C. a. cafer) subspecies of the Northern Flicker. Two additional clutch size samples representing pure Yellow- and Redshafted flickers were obtained from museum egg collections. Mean clutch size did not differ significantly among the six samples. Factorial ANOVAs showed that early clutches and broods are larger than late clutches and broods, but no significant difference was detected between hybrid and parental study sites. Analyses of the effect of phenotype (yellow-shafted, red-shafted, hybrid) also suggest that neither clutch size nor brood size is affected, with the exception that hybrid males sired significantly smaller broods. Finally, there were no significant effects of type of cross (red-shafted male x hybrid female, etc.) on the ratio broodsize / clutch-size. The only evidence for reduced hybrid fitness was in the test where males with hybrid phenotypes appear to have sired small broods. This may indicate that abnormal behavior of hybrid males affects female fecundity, but it is also plausible that this marginally significant result is a type I statistical error. The overall lack of evidence for reduced hybrid fitness is inconsistent with either the dynamic-equilibrium or reinforcement models. Of the two remaining alternatives, the bounded hybrid-superiority model appears the more likely explanation of the Northern Flicker hybrid zone because earlier work (Moore and Buchanan 1985) showed that the hybrid zone is not becoming broader, as predicted by the introgression model