Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

/pdf/fstat-version-1-2-a-computer-program-to-calculate-f-2fjvw732br.pdf

FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics

MUCH attention has been given to the Prisoners' Dilemma as a metaphor for the problems surrounding the evolution of coopera-tive behaviour1–6. This work has dealt with the relative merits of various strategies (such as tit-for-tat) when players who recognize each other meet repeatedly, and more recently with ensembles of strategies and with the effects of occasional errors. Here we neglect all strategical niceties or memories of past encounters, considering only two simple kinds of players: those who always cooperate and those who always defect. We explore the consequences of placing these players in a two-dimensional spatial array: in each round, every individual 'plays the game' with the immediate neighbours; after this, each site is occupied either by its original owner or by one of the neighbours, depending on who scores the highest total in that round; and so to the next round of the game. This simple, and purely deterministic, spatial version of the Prisoners' Dilemma, with no memories among players and no strategical elaboration, can generate chaotically changing spatial patterns, in which cooperators and defectors both persist indefinitely (in fluctuating proportions about predictable long-term averages). If the starting configurations are sufficiently symmetrical, these ever-changing sequences of spatial patterns—dynamic fractals—can be extraordinarily beautiful, and have interesting mathematical properties. There are potential implications for the dynamics of a wide variety of spatially extended systems in physics and biology.

Evolutionary games and spatial chaos

spag e d i version 1.0 is a software primarily designed to characterize the spatial genetic structure of mapped individuals or populations using genotype data of codominant markers. It computes various statistics describing genetic relatedness or differentiation between individuals or populations by pairwise comparisons and tests their significance by appropriate numerical resampling. spag e d i is useful for: (i) detecting isolation by distance within or among populations and estimating gene dispersal parameters; (ii) assessing genetic relatedness between individuals and its actual variance, a parameter of interest for marker based inferences of quantitative inheritance; (iii) assessing genetic differentiation among populations, including the case of haploids or autopolyploids.

spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels

LIITLEJOHN, M. J. 1965. Premating isolation in the Hyla ewingicomplex (Anura: Hylidae). Evolution 19:234-243. MAYR, E. 1963. Animal Species and Evolution. Belknap Press, Cambridge, MA. McCARLEY, H. 1964. Ethological isolation in the coenospecies Peromyscus leucopus. Evolution 18:331-32. McCARTAN, L., J. P. OWENS, B. W. BLACKWELDER, P. J. SZABO, D. F. BELKNAP, N. KRIAUSAKUL, R. M. MIITERER, AND J. F. WEHMILLER. 1982. Comparison of amino acid racemization geochronometry with lithostratigraphy, biostratigraphy, uranium-series coral dating, and magnetostratigraphy in the Atlantic coastal plain of the southeastern United States. Quat. Res. 18: 337-359. MECHAM, J. S. 1961. Isolating mechanisms in anuranamphibians, pp. 24-61. In W. F. Blair (ed.), Vertebrate Speciation. Univ, Texas Press, Austin. NELSON, J. S. 1968. Hybridization and isolating mechanisms between Catostomus commersoni and C. macrocheilus. J. Fish Res. Bd. Canada 25:101-150. ORTMANN, A. E. 1914. Studies in najades. Nautilus 28:41-47. REMINGTON, C. L. 1968. Suture-zones of hybrid interaction between recentlyjoined biotas. Evol. BioI. 2:321-428. SIBLEY, G. C. 1954. Hybridization in red-eyed towhees of Mexico. Evolution 8:252-290. --. 1961. Hybridization and isolating mechanisms, pp. 69-95. In W. F. Blair (ed.), Vertebrate Speciation. Univ. Texas Press, Austin.

On estimating relatedness using genetic markers.

Behavioural reciprocity can be evolutionarily stable1–3. Initial increase in frequency depends, however, on reciprocal altruists interacting predominantly with other reciprocal altruists either by associating within kin groups or by having sufficient memory to recognize and not aid nonreciprocators. Theory thus suggests that reciprocity should evolve more easily among animals which live in kin groups. Data are available separating reciprocity from nepotism only for unrelated nonhuman animals4. Here, I show that food sharing by regurgitation of blood among wild vampire bats (Desmodus rotundus) depends equally and independently on degree of relatedness and an index of opportunity for recipro cation. That reciprocity operates within groups containing both kin and nonkin is supported further with data on the availability of blood-sharing occasions, estimates of the economics of shar ing blood, and experiments which show that unrelated bats will reciprocally exchange blood in captivity.

Reciprocal food sharing in the vampire bat

The evolutionary theory of aging predicts that life span should decrease in response to the amount of mortality caused by extrinsic sources. Using this prediction, we selected six life history and ecological factors to use in a comparative analysis of longevity among 64 bat species. On average, the maximum recorded life span of a bat is 3.5 times greater than a non-flying placental mammal of similar size. Records of individuals surviving more than 30 years in the wild now exist for five species. Univariate and multivariate analyses of species data, as well as of phylogenetically independent contrasts obtained using a supertree of Chiroptera, reveal that bat life span significantly increases with hibernation, body mass and occasional cave use, but decreases with reproductive rate and is not influenced by diet, colony size or the source of the record. These results are largely consistent with extrinsic mortality risk acting as a determinant of bat longevity. Nevertheless, the strong association between life span and both reproductive rate and hibernation also suggests that bat longevity is strongly influenced by seasonal allocation of non-renewable resources to reproduction. We speculate that hibernation may provide a natural example of caloric restriction, which is known to increase longevity in other mammals.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1474-9728.2002.00020.x

Life history, ecology and longevity in bats

Length variation in D-loop mitochondrial DNA was observed after amplification with the polymerase chain reaction (PCR) in 28% of 195 evening bats, Nycticeius humeralis, from seven colonies. Nucleotide sequences of PCR products show that this heteroplasmy is characterized by an 81-bp region which is tandemly repeated five to eight times. Southern blots using PCR products as probes on HaeIII genomic digests confirm the presence of heteroplasmy. Furthermore, densitometry of electrophoresed PCR products from 109 mother-offspring pairs indicate that heteroplasmy is stably transmitted from mother to offspring with one exception: a heteroplasmic offspring had a homoplastic mother and sib. Nucleotide sequences from this family reveal that a repeat duplication and deletion occurred. The observed mutation rate per generation, mu, for length polymorphism is comparable to an independent estimate, mu = 10(-2), based on hierarchical diversity statistics. With the exception of the repeat nearest the proline tRNA gene, sequence similarities between repeats within bats are consistent with a model of concerted evolution due to unidirectional replication slippage. Selection is inferred to act on the first repeat because in comparison to other repeats it has the least sequence divergence among bats, the fewest transversions, and the lowest minimum free energy associated with folding.

https://www.genetics.org/content/genetics/128/3/607.full.pdf

Length and Sequence Variation in Evening Bat D-Loop Mtdna

Multicellularity is characterized by cooperation among cells for the development, maintenance and reproduction of the multicellular organism. Cancer can be viewed as cheating within this cooperative multicellular system. Complex multicellularity, and the cooperation underlying it, has evolved independently multiple times. We review the existing literature on cancer and cancer-like phenomena across life, not only focusing on complex multicellularity but also reviewing cancer-like phenomena across the tree of life more broadly. We find that cancer is characterized by a breakdown of the central features of cooperation that characterize multicellularity, including cheating in proliferation inhibition, cell death, division of labour, resource allocation and extracellular environment maintenance (which we term the five foundations of multicellularity). Cheating on division of labour, exhibited by a lack of differentiation and disorganized cell masses, has been observed in all forms of multicellularity. This suggests that deregulation of differentiation is a fundamental and universal aspect of carcinogenesis that may be underappreciated in cancer biology. Understanding cancer as a breakdown of multicellular cooperation provides novel insights into cancer hallmarks and suggests a set of assays and biomarkers that can be applied across species and characterize the fundamental requirements for generating a cancer.

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Gerald S. Wilkinson

Papers

On estimating relatedness using genetic markers.

Reciprocal food sharing in the vampire bat

Life history, ecology and longevity in bats

Length and Sequence Variation in Evening Bat D-Loop Mtdna

Cancer across the tree of life: cooperation and cheating in multicellularity