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Definition
| Aims to build a resource to help understand the genetic contribution to disease. Widely used to screen variants discovered in exome data from individuals with genetic disorders, and in cancer genome projects. Regions of low sequence complexity, satellite regions, large repeats, and large-scale structural variants including copy-number polymorphisms, segmental duplications, and inversions continue to present major challenge to short-read technologies. Because rare variants tend to be recent, and geographically restricted, it is important to sequence individuals from diverse populations, to characterize the spectrum of genetic variation and support disease studies across diverse groups. |
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Definition
| The strongest differentiation between African populations is within a neuron-restrictive silencer factor transcription-factor peak, PANC1 cell line, upstream of ST8SIA1, which is involved in ganglioside generation. Derived allele frequency distribution has substantial divergence between populations below a frequency of 40%, with individuals from African ancestry carrying up to three times as many low-frequency variants as Europeans or East Asians, reflecting ancestral bottlenecks in non-African populations. Have greater effective population size than other populations. |
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Definition
| An Oriental dog breed. Maximum offspring for sires is 306, and for dams 52. Average f value is 0.038. Effective population size is 45. |
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| Australopithecus afarensis |
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Definition
| Lived 3.2 million years ago. Included the fossil "Lucy". |
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| Australopithecus africanus |
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Definition
| Lived from 2.4 to 2.8 million years ago. Fossil found by Robert Broom and John T. Robinson in Sterkfontein, South Africa. |
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| Australopithecus anamensis |
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Definition
| Lived from 3.9 to 4.2 million years ago. Fossil found by Peter Nzube in Kanapoi, Kenya. |
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Definition
| A Mastiff dog breed. Maximum offspring for sires is 1101, and for dams 49. Average f value is 0.048. Effective population size is 45. |
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| A nematode in the Elegans supergroup. Has a lack of drift, and a huge effective population size. Has obligate sexual reproduction. Lives in the tropics. Based on nucleotide diversity, the effective population size is 1.52 x 106. There is low genome-wide linkage disequilibrium, equal to 0.6 for several million base pairs. Population size has likely been stable for a long time. |
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Definition
| A hermaphrodite. Have linkage disequilibrium equal to 0.2 within a few hundred base pairs, much less than C. brenneri. |
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Definition
| Assumed all founders (dogs with no previous pedigree record) to have an f value of zero, so inbreeding is underestimated. Reported average f values of dogs in generatiosn 6 and 7. Used principal-components analysis on the basis of the ancestor/descendent incidence matrix. |
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Pan
The closest living relatives of humans. Based on nucleotide diversity of 50 genes, the effective population size is 21,300. |
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| An Oriental dog breed. Maximum offspring for sires is 212, and for dams 35. Average f value is 0.051. Effective population size is 50. |
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| Variants present at 10% and over in humans. Found in almost all populations. Weakly differentiated, and most FST estimates are < 1%. Some show strong differentiation between populations within ancestry-based groups likely driven by local adaptation directly or through hitchhiking. Likely to have been present in moderate frequencies in the ancestral populations of all humans. Effective population size, and time since expansion has not allowed these variants to be lost locally by drift. When more recently derived, beneficial across all demes, spread by continual gene flow and balancing, frequency-dependent selection. |
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Definition
| The second closest living relative of dogs. |
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| Written in Toronto. Used Caenorhabditis brenneri populations from around the world. Found a very high relative level of linkage disequilibrium compared to other species. |
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| A population in Sudan thought to have little or no Neanderthal ancestry. Genomes were used to estimate the number of alleles attributed to Neanderthal ancestry in Oase 1. |
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Definition
Canis lupus familiaris
May be used as a model for human diseases. Populations are affected by inbreeding, genetic diversity, and population structure, which depend on breed-specific selective breeding patterns. Most breeds have an effective population size of 40 - 80, and most breeds have over 90% of genetic variants lost over six generations. Account for populaton structure in association studies. Around 20% of dogs have offspring, so effective population size is small. A few dogs give rise to lots of offspring. Originated in Europe and Asia separately. |
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Term
| Effective population size (Ne) |
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Definition
| The size of a Wright-Fisher population with an equal rate of drift as a real population. Always smaller than census size. As the variance in the number of gametes passed on to the next generation per individual goes up, effective population size goes down. With larger effective populaton size, there is less overall change in frequencies. Can be altered by fluctuating census size, different sex ratios, and different values of k and Vk. With small effective population size, drift is a more significant factor. Changes allele frequencies. May result in fixation of deleterious alleles by chance. |
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Definition
| Only a few males will reproduce with all of the females. Causes a reduced effective population size. |
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Definition
| A Mastiff dog breed. Maximum offspring for sires is 430, and for dams 36. Average f value is 0.057. Effective population size is 48. High levels of inbreeding, and low population structure. |
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Definition
| A Hunting dog breed. Maximum offspring for sires is 2538, and for dams 62. Average f value is 0.033. Effective population size is 72. Has low levels of inbreeding, but strong population structure, due to systemic choice of sires in a subpopulation representing 10% of the breed. |
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Definition
| Combines inbreeding in subpopulations with inbreeding between subpopulations, so it must be greater than FIS and FST. |
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Definition
| Based on nucleotide diversity of 252 genes, the effective population size is 106. |
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| The fact that Oase 1 is more related to East Asians and Native Americans than to Europeans suggests that humans expanded out of Africa into Europe and Asia before agriculture, and then after agriculture people from the Fertile Crescent displaced individuals living in Europe, and became modern Europeans. |
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Definition
| Comes from a selection of a finite number of gametes. |
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| A Shepherd dog breed. Maximum offspring for sires is 1479, and for dams 67. Average f value is 0.033. Effective population size is 76. |
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| A Hunting dog breed. Maximum offspring for sires is 1386, and for dams 59. Average f value is 0.035. Effective population size is 67. |
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Gorilla
The second closest living relatives of humans. |
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| The closest living relatives of dogs. |
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Definition
| A Shepherd dog breed. Maximum offspring for sires is 45, and for dams 17. Average f value is 0.058. Effective population size is 17. |
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| Lived from 0.4 to 1.2 million years ago. Fossil found by Towkiromo in Java, Indonesia. |
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Definition
Australopithecus habilis
Lived from 1.6 to 1.9 million years ago. Fossil found by Kamoya Kimeu in Koobi Fora, Kenya. |
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| Lived from 0.2 to 0.6 million years ago. Fossil found by Tom Zwigelaar in Kabwe, Zambia. |
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Definition
Homo sapiens
Based on nucleotide diversity of 50 genes, the effective populatioin size is historically 10,400. Have very high variance in number of successful gametes passed, producing an effective population size much smaller than the consensus population size of 7.9 billion. First appered 0.1 million years ago. A Cro-Magnon fossil from 30 - 32 thousand years ago was found by Louis Lartet and Henry Christy in Les Eyzies, France. Expanded out of Africa into Europe 1.1 million years ago, into Asia 1.6 million years ago, and into the Americas 20,000 years ago. There is a negative correlation between variant frequency and the median length of shared haplotypes; chromosomes with variants of 1% frequency share haplotypes with 100 - 150 kb. At the most highly conserved coding sites, 85% of non-synonymous variants, and over 90% of stop-gain and splice-disrupting variants are below 0.5% in frequency. |
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Definition
| There is increased homozygosity, and expression of recessive deleterious alleles. Selection is more effective. This counteracts the small effective population size in dogs. |
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| A human fossil found in western Russia. Dated to be 36 - 39 thousand years old. More closely related to later Europeans than to East Asians. |
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Definition
| A Hunting dog breed. Maximum offspring for sires is 1911, and for dams 72. Average f value is 0.024. Effective population size is 114. |
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Definition
| A species of ant. There is one reproductive queen per colony, hundreds of males, and thousands of non-reproductive females. Even with tens of thousands of reproductive males, the effective population size is only 600, because of consequences for drift. |
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| Linkage disequilibrium (LD) |
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Definition
| Happens when alleles at two loci are associated and occur together more commonly than expected. |
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| Loss-of-function alleles (LOF) |
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Definition
| Mostly heterozygous. Not all are expressed. May be recessive. |
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Definition
| Variants present at 0.5 - 5% in humans. Tend to be recent in origin, and exhibit increased levels of population differentiation. 17% are observed in just one ancestry group. There are many, because mutations arise, and there has not been enough time since expansion. |
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Definition
Homo neanderthalensis
Lived from 0.03 to 0.3 million years ago. Fossil found by Mario Grazioli in Rome, Italy. Disappeared from Europe 39 - 41 thousand years ago. Contributed to 1 - 3% of DNA of present-day Eurasians. Share more alleles with East Asians and Native Americans than with Europeans. Did not mix with humans in Europe, despite living in Europe. Mixed with humans 39 - 47 thousand years ago. |
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| Negative frequency dependent selection |
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Definition
| Produces polymorphic equilibrium because an allele has highest marginal fitness when it is rare, so it will increase in frequency. When an allele is common it has the lowest marginal fitness, and will decrease in frequency. |
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| A human fossil found in 2002 in Pestera cu Oase, Romania. Dated to be 37 - 42 thousand years old. One of the oldest modern human fossils found in Europe. The genome is 6 - 9% Neanderthal, more than any other human fossil found. There were segments of chromosomes over 50 cM in size suggesting Neanderthal contribution; he must have had a Neanderthal ancestor 4 - 6 generations back, not enough time for chromosomes to break up due to recombination. Interbred with Neanderthals in Europe before agriculture, before the second wave of expansion of Asians into Europe. Shares more alleles with East Asians and Native Americans than with modern Europeans. Shares equal amounts of alleles with pre-agricultural European fossils as with present-day East Asians and Native Americans. Belonged to a population that did not contribute much to present-day Europeans. |
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Pongo
The third closest living relatives to humans. |
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Definition
Australopithecus boisei
Lived from 1.4 to 2.3 million years ago. Fossil found by Richard Leaky and H. Mutua in Koobi Fora, Kenya. |
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| A breed of dog with a high portion of ancient ancestry. |
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Definition
| An important factor in genetic association studies. Can lead to spurious associations. Methods are available to diagnose and correct for population stratification from genome-wide marker data. It is desirable for researchers to be aware of potential stratification. |
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| Principal components analysis (PCA) |
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Definition
| Used in the Calboli et al paper to analyse contributions of gametes to the next generation. |
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Term
| Rare, deleterious variants |
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Definition
| Human individuals carry 76 - 190 rare, deleterious, non-synonymous variants, and up to 20 loss-of-function and disease-associated variants. Low frequency variation demonstrates pervasive efforts of purifying selection at functionally relevant sites, and how this can interact with population history leading to substantial differentiation, even when FST is small. There is selection balance: selection reduces frequency, and mutation increases frequency. Selection is not as effective on recessive alleles, allowing for these variants to be maintained in a population. Selection is stronger with inbreeding and homozygotes. Effects may be expressed later in life, after reproduction, causing no selection (cancer or aging related). There may be medical intervention, reducing selection. |
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Definition
| Variants present at less than 0.5% in humans. 53% are observed in just one population. Twice as likely to be within the same population, compared with random samples from their ancestry group. Individuals from all populations have enrichment of rare variants, reflecting recent explosive increases in population size, and the effects of geographic differentiation. Tend to be recent, and geographically restricted. Interpretations with a particular disease should be within the context of a local (geographic or ancestry-based) genetic background. |
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Definition
| Have not had enough time to incrase in frequency by drift or selection. Expected to be at a low frequency. No time to move into other demes. |
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| Has no effect on homozygotes; doesn't break the linkage disequilibrium. |
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| A big name in population genetics. |
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| A Shepherd dog breed. Maximum offspring for sires is 775, and for dams 39. Average f value is 0.073. Effective population size is 33. High levels of inbreeding, with modest population structure. |
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Definition
| Occurs when a beneficial allele is selected for and quickly reaches high frequency in a population. Alleles at other loci that are linked to this allele will simultaneously increase in frequency due to lack of recombination. Influence genome-level variation, causing linked alleles to be more likely to fix or be lost, decreasing nucleotide diversity. |
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| A big name in population genetics. Loved math and guinea pigs. |
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| A breed of dog with high portion of ancient ancestry. |
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Definition
| Had an insight in the 1980s to sequence DNA of fossils to investigate genetic history of humans. |
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| United Kingdom Kennel Club |
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Definition
| The oldest dog fanciers club in the world, founded in 1873. Has a compiled registration database for dog pedigrees, the most comprehensive record of UK dog breeds, and the largest pedigree record for dogs internationally. |
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| Variants present twice across the entire sample (f2) |
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Definition
| Within and between populations with recent shared ancestry, f2s are present on very short haplotypes. |
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| An undomesticated, semi-wild dog with no specific breed. |
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| An abstract concept. Applied to perennial plants. Most populations do not follow this model. It is an ideal that real populations are compared to. Easy to understand. |
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