scholarly journals Estimating Pan evolutionary history from nucleotide site patterns

2022 ◽  
Author(s):  
Colin M Brand ◽  
Frances J White ◽  
Alan R Rogers ◽  
Timothy H Webster
Keyword(s):  
Evolutionary History ◽  
Pan Paniscus ◽  
Population Variation ◽  
Deterministic Approach ◽  
Effective Population ◽  
Admixture Proportion ◽  
Demographic Models ◽  
Estimated Parameters ◽  
History Of ◽  
Divergence Dates

Introgression appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. However, accurately estimating introgression is difficult, particularly when 1) there are many parameters, 2) multiple models fit the data well, and 3) parameters are not simultaneously estimated. Here, we use the software Legofit to investigate the evolutionary history of bonobos (Pan paniscus) and chimpanzees (P. troglodytes) using whole genome sequences. This approach 1) ignores within-population variation, reducing the number of parameters requiring estimation, 2) allows for model selection, and 3) simultaneously estimates all parameters. We tabulated site patterns from the autosomes of 71 bonobos and chimpanzees representing all five extant Pan lineages. We then compared previously proposed demographic models and estimated parameters using a deterministic approach. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. Introgression from bonobos into the ancestor of eastern and central chimpanzees and from western into eastern chimpanzees best explained the autosomal site patterns. This second event was substantial with an estimated 0.21 admixture proportion. Estimates of effective population size and most divergence dates are consistent with previous findings; however, we observe a deeper divergence within chimpanzees at 987 ka. Finally, we identify male-biased reproduction in Pan evolutionary history and suggest that western to eastern chimpanzee introgression was driven by western males mating with eastern females.

Human Evolution

1984 ◽  
Vol 8 ◽  
pp. 182-198
Author(s):  
Catherine Badgley
Keyword(s):  
Human Evolution ◽  
Evolutionary History ◽  
Pan Paniscus ◽  
Homo Sapiens ◽  
Great Apes ◽  
Sister Group ◽  
The Family ◽  
History Of ◽  
Living Species ◽  
Single Living

The evolutionary history of humans is well understood in outline, compared to that of many other groups of mammals. But human evolution remains enigmatic in its details, and these are compelling both scientifically and personally because they relate to the biological uniqueness of humans. Humans are placed in the primate family Hominidae, which, in traditional classifications, contains a single living species, Homo sapiens. The closest living relatives of humans are great apes: the chimpanzees Pan paniscus and Pan troglodytes, the gorilla Gorilla gorilla, and the orangutan Pongo pygmaeus. These apes have traditionally been placed in the family Pongidae as the sister group of Hominidae. Living Hominidae and Pongidae, together with Hylobatidae (gibbons) comprise the modern representatives of the primate suborder Hominoidea.

scholarly journals Approximating the coalescent under facultative sex

2019 ◽  
Author(s):  
Matthew Hartfield
Keyword(s):  
Population Size ◽  
Evolutionary History ◽  
Sampling Strategies ◽  
Effective Population ◽  
Sexual Species ◽  
History Of ◽  
Mitotic Gene Conversion ◽  
Evolutionary Consequences ◽  
Insight Into ◽  
Coalescent Time

AbstractGenome studies of facultative sexual species, which can either reproduce sexually or asexually, are providing insight into the evolutionary consequences of mixed reproductive modes. It is currently unclear to what extent the evolutionary history of facultative sexuals’ genomes can be approximated by the standard coalescent, and if a coalescent effective population size Ne exists. Here, I determine if and when these approximations can be made. When sex is frequent (occurring at a frequency much greater than 1/N per reproduction per generation, for N the actual population size), the underlying genealogy can be approximated by the standard coalescent, with a coalescent Ne ≈ N. When sex is very rare (at frequency much lower than 1/N), approximations for the pairwise coalescent time can be obtained, which is strongly influenced by the frequencies of sex and mitotic gene conversion, rather than N. However, these terms do not translate into a coalescent Ne. These results are used to discuss the best sampling strategies for investigating the evolutionary history of facultative sexual species.

scholarly journals Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection

2021 ◽  
Author(s):  
Ellie E Armstrong ◽  
Anubhab Khan ◽  
Ryan W Taylor ◽  
Alexandre Gouy ◽  
Gili Greenbaum ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Species Conservation ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Metabolic Adaptation ◽  
Genetic Rescue ◽  
Weak Selection ◽  
Demographic Models ◽  
Show Evidence ◽  
History Of

Abstract Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, their evolutionary history and genomic variation remain poorly known, especially for Indian tigers. With 70% of the world’s wild tigers living in India, such knowledge is critical. We re-sequenced 65 individual tiger genomes representing most extant subspecies with a specific focus on tigers from India. As suggested by earlier studies, we found strong genetic differentiation between the putative tiger subspecies. Despite high total genomic diversity in India, individual tigers host longer runs of homozygosity, potentially suggesting recent inbreeding or founding events, possibly due to small and fragmented protected areas. We suggest the impacts of ongoing connectivity loss on inbreeding and persistence of Indian tigers be closely monitored. Surprisingly, demographic models suggest recent divergence (within the last 20,000 years) between subspecies and strong population bottlenecks. Amur tiger genomes revealed the strongest signals of selection related to metabolic adaptation to cold, whereas Sumatran tigers show evidence of weak selection for genes involved in body size regulation. We recommend detailed investigation of local adaptation in Amur and Sumatran tigers prior to initiating genetic rescue.

scholarly journals Minimal-assumption inference from population-genomic data

2016 ◽  
Author(s):  
Daniel B. Weissman ◽  
Oskar Hallatschek
Keyword(s):  
Evolutionary History ◽  
Simulated Data ◽  
Effective Population ◽  
Minimal Assumption ◽  
Genome Data ◽  
Human Genomes ◽  
Single Genome ◽  
Linkage Information ◽  
Time Histories ◽  
History Of

AbstractSamples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of this linkage information rely on models of recombination and coalescence, limiting the sample sizes and populations that they can analyze. We introduce a method, Minimal-Assumption Genomic Inference of Coalescence (MAGIC), that reconstructs key features of the evolutionary history, including the distribution of coalescence times, by integrating information across genomic length scales without using an explicit model of recombination, demography or selection. Using simulated data, we show that MAGIC’s performance is comparable to PSMC’ on single diploid samples generated with standard coalescent and recombination models. More importantly, MAGIC can also analyze arbitrarily large samples and is robust to changes in the coalescent and recombination processes. Using MAGIC, we show that the inferred coalescence time histories of samples of multiple human genomes exhibit inconsistencies with a description in terms of an effective population size based on single-genome data.

scholarly journals Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta

2021 ◽  
Vol 288 (1943) ◽  
pp. 20202934
Author(s):  
Jiaming Hu ◽  
Michael V. Westbury ◽  
Junxia Yuan ◽  
Zhen Zhang ◽  
Shungang Chen ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Mitochondrial Genomes ◽  
Effective Population ◽  
Wide Range ◽  
Two Samples ◽  
Spotted Hyenas ◽  
History Of ◽  
Close Relatives

Cave hyenas (genus Crocuta ) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta . Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta . Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62–2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.

scholarly journals Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Megan Phifer-Rixey ◽  
Bettina Harr ◽  
Jody Hey
Keyword(s):  
Gene Flow ◽  
Mus Musculus ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
House Mice ◽  
Mus Musculus Domesticus ◽  
Effective Population ◽  
Isolation With Migration ◽  
Mus Musculus Musculus ◽  
History Of

Abstract Background The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus, and Mus musculus musculus, are estimated to have diverged ~ 350-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here, we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange. Results Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus. In addition, we find evidence of gene flow between all pairs of subspecies, but that gene flow is most restricted from M. m. musculus into M. m. domesticus. Estimates of other key parameters are dependent on assumptions regarding generation time and mutation rate in house mice. Nevertheless, our results support previous findings that the effective population size, Ne, of M. m. castaneus is larger than that of the other two subspecies, that the three subspecies began diverging ~ 130 - 420KYA, and that the time between divergence events was short. Conclusions Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.

scholarly journals The evolutionary history of Neanderthal and Denisovan Y chromosomes

Science ◽  
2020 ◽  
Vol 369 (6511) ◽  
pp. 1653-1656 ◽  
Author(s):  
Martin Petr ◽  
Mateja Hajdinjak ◽  
Qiaomei Fu ◽  
Elena Essel ◽  
Hélène Rougier ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Evolutionary History ◽  
Genetic Load ◽  
Modern Human ◽  
Gene Pools ◽  
Chromosomal Gene ◽  
Human History ◽  
Effective Population ◽  
Y Chromosomes ◽  
History Of

Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.

scholarly journals A66 Tracing the evolutionary history of an emerging Salmonella 4,[5],12:i:- clone in the United States

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
E Elnekave ◽  
S Hong ◽  
A Taylor ◽  
D Boxrud ◽  
A Rovira ◽  
...  
Keyword(s):  
United States ◽  
Evolutionary History ◽  
The United States ◽  
Multidrug Resistant ◽  
Public Health Importance ◽  
Demographic Models ◽  
Salmonella Infections ◽  
The Usa ◽  
History Of ◽  
Different Sources

Abstract Salmonellosis is one of the leading causes of foodborne disease worldwide, with an estimated one million cases a year in the United States. Salmonella 4,[5],12: i:-, a monophasic variant of Salmonella typhimurium, is an emerging serovar that has been associated with multiple foodborne outbreaks throughout the world, mostly attributed to pig and pig products. Recently, we have demonstrated that two distinct groups of Salmonella 4,[5],12:i:- circulate in the USA and Europe, with the majority of isolates recovered during recent years belonging to an emerging multidrug-resistant clade (Elnekave et al. 2018). We applied Bayesian phylodynamic reconstruction to uncover the evolutionary history of this clade. We used a dataset of whole-genome sequences of 1446 4,[5],12:i:- isolates from different sources (livestock, human, food products, and others) from the USA (n = 752) and Europe (n = 694), collected between 2008 and 2017 and belonging to the Multilocus Subtype 34, which was predominant in the emerging clade (Elnekave et al. 2018). A subset (n = 110) of Salmonella 4,[5],12:i: isolates was then randomly selected after stratifying by location and year of isolation in order to achieve balanced sampling. Evidence of temporal signal was confirmed by looking at root-to-tip divergences using TempEst. Evolutionary hypotheses using strict and relaxed-clock models were tested using BEAST for a variety of demographic models and assuming a general time reversible substitution model. Model selection was performed by estimating Bayes Factors using path sampling and stepping-stone sampling. The selected model was then used for applying discrete trait models comparing different scenarios of transmission between locations (i.e. bidirectional symmetric/asymmetric or unidirectional). Our preliminary phylodynamic inference results indicate that the origin of this subtype was in Europe and dates back to 1990 (HPD 95%: 1984–2001). We report an exponential growth rate of 0.362 per year, which corresponds to a doubling time of 1.43 years. Our results suggest that this subtype was introduced to the US in the year 2000 (HPD 95%: 1994–2006). Phylodynamic analysis suggests that the recent increase in isolation of Salmonella 4,[5],12:i:- from different sources in the USA may be due to the exponential expansion of an emerging clone which originated in Europe and then expanded to the USA. The emergence and expansion of this serovar is of great public health importance due to the high prevalence of multidrug resistance traits found in USA isolates from this group and especially due to the presence of plasmid-mediated resistance genes for quinolones and extended spectrum cephalosporins, key antimicrobials used for the treatment of invasive Salmonella infections.

scholarly journals Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 266 ◽  
Author(s):  
Brian Park ◽  
John M. Burke
Keyword(s):  
Genetic Variation ◽  
Helianthus Annuus ◽  
Great Plains ◽  
Evolutionary History ◽  
Nucleotide Diversity ◽  
Secondary Development ◽  
Effective Population ◽  
Comprehensive Overview ◽  
Helianthus Annuus L ◽  
History Of

Patterns of genetic variation in crops are the result of selection and demographic changes that occurred during their domestication and improvement. In many cases, we have an incomplete picture of the origin of crops in the context of their wild progenitors, particularly with regard to the processes producing observed levels of standing genetic variation. Here, we analyzed sequence diversity in cultivated sunflower (Helianthus annuus L.) and its wild progenitor (common sunflower, also H. annuus) to reconstruct phylogeographic relationships and population genetic/demographic patterns across sunflower. In common sunflower, south-north patterns in the distribution of nucleotide diversity and lineage splitting indicate a history of rapid postglacial range expansion from southern refugia. Cultivated sunflower accessions formed a clade, nested among wild populations from the Great Plains, confirming a single domestication event in central North America. Furthermore, cultivated accessions sorted by market type (i.e., oilseed vs. confectionery) rather than breeding pool, recapitulating the secondary development of oil-rich cultivars during its breeding history. Across sunflower, estimates of nucleotide diversity and effective population sizes suggest that cultivated sunflower underwent significant population bottlenecks following its establishment ~5000 years ago. The patterns inferred here corroborate those from previous studies of sunflower domestication, and provide a comprehensive overview of its evolutionary history.

scholarly journals Bird size with dinosaur-level cancer defences: can evolutionary lags during miniaturisation explain cancer robustness in birds?

2020 ◽  
Author(s):  
E. Yagmur Erten ◽  
Marc Tollis ◽  
Hanna Kokko
Keyword(s):  
Body Size ◽  
Cancer Risk ◽  
Evolutionary History ◽  
Effective Population ◽  
Extrinsic Mortality ◽  
Cell Divisions ◽  
Large Size ◽  
History Of ◽  
Cancer Suppression ◽  
Gains And Losses

AbstractAn increased appreciation of the ubiquity of cancer risk across the tree of life means we also need to understand the more robust cancer defences some species seem to have. Peto’s paradox, the finding that large-bodied species do not suffer from more cancer even if their lives require far more cell divisions than those of small species, can be explained if large size selects for better cancer defences. Since birds live longer than non-flying mammals of an equivalent body size, and birds are descendants of moderate-sized dinosaurs, we ask whether ancestral cancer defence innovations are retained if body size shrinks in an evolutionary lineage. Our model derives selection coefficients and fixation events for gains and losses of cancer defence innovations over macroevolutionary time, based on known relationships between body size, intrinsic cancer risk, extrinsic mortality (modulated by flight ability) and effective population size. We show that evolutionary lags can, under certain assumptions, explain why birds, descendants of relatively large bodied dinosaurs, retain low cancer risk. Counterintuitively, it is possible for a bird to be ‘too robust’ for its own good: excessive cancer suppression can take away from reproductive success. On the other hand, an evolutionary history of good cancer defences may also enable birds to reap the lifespan-increasing benefits of other innovations such as flight.

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