Simulation was used to investigate the effects of population structure and migration on metrics of pairwise shared ancestry. Random and hierarchical structures, or migration geometries, were examined. Compared to panm...Simulation was used to investigate the effects of population structure and migration on metrics of pairwise shared ancestry. Random and hierarchical structures, or migration geometries, were examined. Compared to panmictic populations, progress to all qualitative metrics of pairwise ancestry is delayed in structured populations. However, unless migration is very low, the time required is generally less than triple and often less than twice that required in a panmictic population of the same total size. Population structure also increases, to a similar degree, the time required for a population-wide most recent common ancestor (MRCA). As a result, the relationships between various qualitative metrics of pairwise shared ancestry and MRCA time are relatively unaffected by population structure. For example, the mean time to most recent shared ancestor (MRSA) with global sampling of pairs is 40% - 50% of the MRCA time for almost all simulated structures and migration levels. Quantitative pairwise genealogical overlap is strongly affected by population structure. With global sampling, pairwise quantitative overlap never approaches 1.0, as it does in panmictic populations;and instead eventually becomes stationary at much lower values. Possible implications of the present results for human pairwise shared ancestry are discussed. For globally sampled pairs, the longest time to most recent shared ancestor (MRSA) for humans is suggested to be approximately 2100 years before the present. If generation time is 30 years, then all humans are 69th, or closer, cousins. For people with recent European ancestry, the MRSA time may be only half as long, about 1000 years.展开更多
In a panmictic population of constant size N, random pairs of individuals will have a most recent shared ancestor who lived slightly more than 0.5 log<sub>2</sub>N generations previously, on average. The p...In a panmictic population of constant size N, random pairs of individuals will have a most recent shared ancestor who lived slightly more than 0.5 log<sub>2</sub>N generations previously, on average. The probability that a random pair of individuals will share at least one ancestor who lived 0.5 log<sub>2</sub>N generations ago, or more recently, is about 50%. Those individuals, if they do share an ancestor from that generation, would be cousins of degree (0.5 log<sub>2</sub>N) - 1. Shared ancestry from progressively earlier generations increases rapidly until there is universal pairwise shared ancestry. At that point, every individual has one or more ancestors in common with every other individual in the population, although different pairs may share different ancestors. Those ancestors lived approximately 0.7 log<sub>2</sub>N generations in the past, or more recently. Qualitatively, the ancestries of random pairs have about 50% similarity for ancestors who lived about 0.9 log<sub>2</sub>N generations before the present. That is, about half of the ancestors from that generation belonging to one member of the pair are present also in the genealogy of the other member. Qualitative pairwise similarity increases to more than 99% for ancestors who lived about 1.4 log<sub>2</sub>N generations in the past. Similar results apply to a metric of quantitative pairwise genealogical overlap.展开更多
Transition from a nocturnal to a diurnal lifestyle represents a major shift in primate evolution, plays a central role in the adaptation of these species to new habitats, and is involved in modifications to their phys...Transition from a nocturnal to a diurnal lifestyle represents a major shift in primate evolution, plays a central role in the adaptation of these species to new habitats, and is involved in modifications to their physiological and social behaviors （Heesy and Ross, 2001; Shultz et al., 2011）. However, two core problems concerning the circadian rhythm transition re- mains unresolved. First, there is controversy concerning the activity pattern of the ancestral primate （Heesy and Ross, 2001; Tan et al., 2005）. Second, the transition process for circadian rhythm in primate evolutionary history is unre- solved. Although most research suggests that primates trans- formed from a nocturnal to a diurnal circadian rhythm in the lineage leading to the common ancestor of the anthropoids or the haplorrhines （anthropoids and tarsier） （Ross, 2000; Heesy and Ross, 2001）, evidence has been insufficient to determine whether this occurred in the lineage leading to the common ancestor of the haplorrhines or the anthroooids.展开更多
In this paper, we focus on efficient processing of XML keyword queries based on smallest lowest common ancestor （SLCA） semantics. For a given query Q with m keywords, we propose to use stable matches as the basis fo...In this paper, we focus on efficient processing of XML keyword queries based on smallest lowest common ancestor （SLCA） semantics. For a given query Q with m keywords, we propose to use stable matches as the basis for SLCA computation, where each stable match M consists of m nodes that belong to the m distinct keyword inverted lists of Q. M satisfies that no other lowest common ancestor （LCA） node of Q can be found to be located after the first node of M and be a descendant of the LCA of M, based on which the operation of locating a stable match can skip more useless nodes. We propose two stable match based algorithms for SLCA computation, i.e., BSLCA and HSLCA. BSLCA processes two keyword inverted lists each time from the shortest to the longest, while HSLCA processes all keyword inverted lists in a holistic way to avoid the problem of redundant computation invoked by BSLCA. Our extensive experimental results verify the performance advantages of our methods according to various evaluation metrics.展开更多
The characteristic of individual is described by the Penna model. Based oninformation entropy and the Penna model we define the entropy in the Penna modelto discuss common ancestors and genetic diversity for two repro...The characteristic of individual is described by the Penna model. Based oninformation entropy and the Penna model we define the entropy in the Penna modelto discuss common ancestors and genetic diversity for two reproduction modes withand without mutation. About the problem of common ancestor, we find that all livingindividuals at any time step have a set of common ancestors which belongs to differenttimes. They have the most recent common ancestor and earlier common ancestors.The analysis of genetic diversity shows that the complexity of ecosystems is caused bymutations and there is no contribution of sexual reproduction to conserving geneticdiversity at long time scales. Moreover, in stable environment genetic diversity inasexual reproduction mode is higher than that in the sexual case.展开更多
Motivated by sample path decomposition of the stationary continuous state branching process with immigration, a general population model is considered using the idea of immortal individual. We compute the joint distri...Motivated by sample path decomposition of the stationary continuous state branching process with immigration, a general population model is considered using the idea of immortal individual. We compute the joint distribution of the random variables： the time to the most recent common ancestor （MRCA）, the size of the current population, and the size of the population just before MRCA. We obtain the bottleneck effect as well. The distribution of the number of the oldest families is also established. These generalize the results obtained by Y. T. Chen and J. F. Delmas.展开更多
文摘Simulation was used to investigate the effects of population structure and migration on metrics of pairwise shared ancestry. Random and hierarchical structures, or migration geometries, were examined. Compared to panmictic populations, progress to all qualitative metrics of pairwise ancestry is delayed in structured populations. However, unless migration is very low, the time required is generally less than triple and often less than twice that required in a panmictic population of the same total size. Population structure also increases, to a similar degree, the time required for a population-wide most recent common ancestor (MRCA). As a result, the relationships between various qualitative metrics of pairwise shared ancestry and MRCA time are relatively unaffected by population structure. For example, the mean time to most recent shared ancestor (MRSA) with global sampling of pairs is 40% - 50% of the MRCA time for almost all simulated structures and migration levels. Quantitative pairwise genealogical overlap is strongly affected by population structure. With global sampling, pairwise quantitative overlap never approaches 1.0, as it does in panmictic populations;and instead eventually becomes stationary at much lower values. Possible implications of the present results for human pairwise shared ancestry are discussed. For globally sampled pairs, the longest time to most recent shared ancestor (MRSA) for humans is suggested to be approximately 2100 years before the present. If generation time is 30 years, then all humans are 69th, or closer, cousins. For people with recent European ancestry, the MRSA time may be only half as long, about 1000 years.
文摘In a panmictic population of constant size N, random pairs of individuals will have a most recent shared ancestor who lived slightly more than 0.5 log<sub>2</sub>N generations previously, on average. The probability that a random pair of individuals will share at least one ancestor who lived 0.5 log<sub>2</sub>N generations ago, or more recently, is about 50%. Those individuals, if they do share an ancestor from that generation, would be cousins of degree (0.5 log<sub>2</sub>N) - 1. Shared ancestry from progressively earlier generations increases rapidly until there is universal pairwise shared ancestry. At that point, every individual has one or more ancestors in common with every other individual in the population, although different pairs may share different ancestors. Those ancestors lived approximately 0.7 log<sub>2</sub>N generations in the past, or more recently. Qualitatively, the ancestries of random pairs have about 50% similarity for ancestors who lived about 0.9 log<sub>2</sub>N generations before the present. That is, about half of the ancestors from that generation belonging to one member of the pair are present also in the genealogy of the other member. Qualitative pairwise similarity increases to more than 99% for ancestors who lived about 1.4 log<sub>2</sub>N generations in the past. Similar results apply to a metric of quantitative pairwise genealogical overlap.
基金supported by the grants from the National Natural Science Foundation of China(Nos.2007CB411600 and 2008GA001)the Bureau of Science and Technology of Yunnan Province(No.31061160189)supported by the West Light Foundation of the Chinese Academy of Sciences
文摘Transition from a nocturnal to a diurnal lifestyle represents a major shift in primate evolution, plays a central role in the adaptation of these species to new habitats, and is involved in modifications to their physiological and social behaviors （Heesy and Ross, 2001; Shultz et al., 2011）. However, two core problems concerning the circadian rhythm transition re- mains unresolved. First, there is controversy concerning the activity pattern of the ancestral primate （Heesy and Ross, 2001; Tan et al., 2005）. Second, the transition process for circadian rhythm in primate evolutionary history is unre- solved. Although most research suggests that primates trans- formed from a nocturnal to a diurnal circadian rhythm in the lineage leading to the common ancestor of the anthropoids or the haplorrhines （anthropoids and tarsier） （Ross, 2000; Heesy and Ross, 2001）, evidence has been insufficient to determine whether this occurred in the lineage leading to the common ancestor of the haplorrhines or the anthroooids.
基金partially supported by the National Natural Science Foundation of China under Grant Nos. 61073060, 61040023,61272124the Science and Technology Research and Development Program of Hebei Province of China under Grant No. 11213578
文摘In this paper, we focus on efficient processing of XML keyword queries based on smallest lowest common ancestor （SLCA） semantics. For a given query Q with m keywords, we propose to use stable matches as the basis for SLCA computation, where each stable match M consists of m nodes that belong to the m distinct keyword inverted lists of Q. M satisfies that no other lowest common ancestor （LCA） node of Q can be found to be located after the first node of M and be a descendant of the LCA of M, based on which the operation of locating a stable match can skip more useless nodes. We propose two stable match based algorithms for SLCA computation, i.e., BSLCA and HSLCA. BSLCA processes two keyword inverted lists each time from the shortest to the longest, while HSLCA processes all keyword inverted lists in a holistic way to avoid the problem of redundant computation invoked by BSLCA. Our extensive experimental results verify the performance advantages of our methods according to various evaluation metrics.
文摘The characteristic of individual is described by the Penna model. Based oninformation entropy and the Penna model we define the entropy in the Penna modelto discuss common ancestors and genetic diversity for two reproduction modes withand without mutation. About the problem of common ancestor, we find that all livingindividuals at any time step have a set of common ancestors which belongs to differenttimes. They have the most recent common ancestor and earlier common ancestors.The analysis of genetic diversity shows that the complexity of ecosystems is caused bymutations and there is no contribution of sexual reproduction to conserving geneticdiversity at long time scales. Moreover, in stable environment genetic diversity inasexual reproduction mode is higher than that in the sexual case.
基金Acknowledgements The author would like to express his sincere thanks to his advisor Professor Zenghu Li for his persistent encouragements and suggestions and Professor J. F. Delmas for his careful check of this work. Thanks are also given to the anonymous referees for the suggestions. This work was supported in part by the National Natural Science Foundation of China （Grant No. 11131003） and the 985 Program.
文摘Motivated by sample path decomposition of the stationary continuous state branching process with immigration, a general population model is considered using the idea of immortal individual. We compute the joint distribution of the random variables： the time to the most recent common ancestor （MRCA）, the size of the current population, and the size of the population just before MRCA. We obtain the bottleneck effect as well. The distribution of the number of the oldest families is also established. These generalize the results obtained by Y. T. Chen and J. F. Delmas.
