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 diverse origins of New Zealand house mice

2008 ◽  
Vol 276 (1655) ◽  
pp. 209-217 ◽  
Author(s):  
Jeremy B Searle ◽  
Paul M Jamieson ◽  
İslam Gündüz ◽  
Mark I Stevens ◽  
Eleanor P Jones ◽  
...  
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Mus Musculus ◽  
Western Europe ◽  
Nuclear Dna ◽  
Morphological Characters ◽  
House Mice ◽  
Mus Musculus Domesticus ◽  
Mus Musculus Musculus ◽  
History Of

Molecular markers and morphological characters can help infer the colonization history of organisms. A combination of mitochondrial (mt) d -loop DNA sequences, nuclear DNA data, external measurements and skull characteristics shows that house mice ( Mus musculus ) in New Zealand and its outlying islands are descended from very diverse sources. The predominant genome is Mus musculus domesticus (from western Europe), but Mus musculus musculus (from central Europe) and Mus musculus castaneus (from southern Asia) are also represented genetically. These subspecies have hybridized to produce combinations of musculus and domesticus nuclear DNA coupled with domesticus mtDNA, and castaneus or musculus mtDNA with domesticus nuclear DNA. The majority of the mice with domesticus mtDNA that we sampled had d -loop sequences identical to two haplotypes common in Britain. This is consistent with long-term British–New Zealand cultural linkages. The origins of the castaneus mtDNA sequences widespread in New Zealand are less easy to identify.

scholarly journals Host subspecific viral strains in European house mice: Murine cytomegalovirus in the Eastern (Mus musculus musculus) and Western house mouse (Mus musculus domesticus)

Virology ◽  
2018 ◽  
Vol 521 ◽  
pp. 92-98 ◽  
Author(s):  
Dagmar Čížková ◽  
Stuart J.E. Baird ◽  
Jana Těšíková ◽  
Sebastian Voigt ◽  
Ďureje Ľudovít ◽  
...  
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Murine Cytomegalovirus ◽  
House Mice ◽  
Mus Musculus Domesticus ◽  
Mus Musculus Musculus

scholarly journals Genic differentiation and origin of Robertsonian populations of the house mouse (Mus musculus domesticus Rutty)

1989 ◽  
Vol 53 (1) ◽  
pp. 29-44 ◽  
Author(s):  
Janice Britton-Davidian ◽  
Joseph H. Nadeau ◽  
Henri Croset ◽  
Louis Thaler
Keyword(s):  
Gene Flow ◽  
House Mouse ◽  
Mus Musculus ◽  
Western Europe ◽  
Chromosomal Rearrangements ◽  
Nuclear Gene ◽  
Electrophoretic Analysis ◽  
Mus Musculus Domesticus ◽  
Effective Population ◽  
Chromosomal Races

SummaryThis paper examines the relation between chromosomal and nuclear-gene divergence in 28 wild populations of the house mouse semi-species, Mus musculus domesticus, in Western Europe and North Africa. Besides describing the karyotypes of 15 of these populations and comparing them to those of 13 populations for which such information was already known, it reports the results of an electrophoretic survey of proteins encoded by 34 nuclear loci in all 28 populations. Karyotypic variation in this taxon involves only centric (or Robertsonian) fusions which often differ in arm combination and number between chromosomal races. The electrophoretic analysis showed that the amount of genic variation within Robertsonian (Rb) populations was similar to that for all-acrocentric populations, i.e. bearing the standard karyotype. Moreover, divergence between the two types of populations was extremely low. These results imply that centric fusions in mice have not modified either the level or the nature of genic variability. The genetic similarity between Rb and all-acrocentric populations is not attributed to the persistence of gene flow, since multiple fusions cause marked reproductive isolation. Rather, we attribute this extreme similarity to the very recent origin of chromosomal races in Europe. Furthermore, genic diversity measures suggest that geographically separated Rb populations have in situ and independent origins. Thus, Rb translocations are probably not unique events, but originated repeatedly. Two models are presented to explain how the rapid fixation of a series of chromosomal rearrangements can occur in a population without lowering variability in the nuclear genes. The first model assumes that chromosomal mutation rates are between 10−3 and 10−4 and that populations underwent a series of transient bottlenecks in which the effective population size did not fall below 35. In the second model, genic variability is restored following severe bottlenecks, through gene flow and recombination.

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 Accounting for Gene Flow from Unsampled ‘Ghost’ Populations while Estimating Evolutionay History under the Isolation with Migration Model

2019 ◽  
Author(s):  
Arun Sethuraman ◽  
Melissa Lynch
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Population Genomics ◽  
Divergence Times ◽  
Effective Population ◽  
Migration Rates ◽  
Isolation With Migration ◽  
Population Sizes ◽  
And Migration ◽  
Erroneous Inferences

AbstractUnsampled or extinct ‘ghost’ populations leave signatures on the genomes of individuals from extant, sampled populations, especially if they have exchanged genes with them over evolutionary time. This gene flow from ‘ghost’ populations can introduce biases when estimating evolutionary history from genomic data, often leading to data misinterpretation and ambiguous results. Here we assess these biases while accounting, or not accounting for gene flow from ‘ghost’ populations under the Isolation with Migration (IM) model. We perform extensive simulations under five scenarios with no gene flow (Scenario A), to extensive gene flow to- and from- an unsampled ‘ghost’ population (Scenarios B, C, D, and E). Estimates of evolutionary history across all scenarios A-E (effective population sizes, divergence times, and migration rates) indicate consistent a) under-estimation of divergence times between sampled populations, (b) over-estimation of effective population sizes of sampled populations, and (c) under-estimation of migration rates between sampled populations, with increased gene flow from the unsampled ‘ghost’ population. Without accounting for an unsampled ‘ghost’, summary statistics like FST are under-estimated, and π is over-estimated with increased gene flow from the‘ghost’. To show this persistent issue in empirical data, we use a 355 locus dataset from African Hunter-Gatherer populations and discuss similar biases in estimating evolutionary history while not accounting for unsampled ‘ghosts’. Considering the large effects of gene flow from these ‘ghosts’, we propose a multi-pronged approach to account for the presence of unsampled ‘ghost’ populations in population genomics studies to reduce erroneous inferences.

scholarly journals Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

PeerJ ◽  
2015 ◽  
Vol 4 ◽  
pp. e1556 ◽  
Author(s):  
Rosa Alicia Jiménez ◽  
Juan Francisco Ornelas
Keyword(s):  
Gene Flow ◽  
Species Complex ◽  
Evolutionary History ◽  
Divergence Time ◽  
Haplotype Network ◽  
Genetic Admixture ◽  
Isolation With Migration ◽  
History Of ◽  
Isthmus Of Tehuantepec ◽  
Assignment Analysis

The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds,Amazilia beryllina,Amazilia cyanuraandAmazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the threeAmaziliaspecies, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of thisAmaziliaspecies complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1)A. beryllinapopulations located west of the Isthmus of Tehuantepec; (2)A. cyanurapopulations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3)A. saucerotteipopulations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers.

scholarly journals Genome-wide sequence data show no evidence of admixture and introgression among pollinator wasps associated with a community of Panamanian strangler figs

2020 ◽  
Author(s):  
Jordan D. Satler ◽  
Edward Allen Herre ◽  
Tracy A. Heath ◽  
Carlos A. Machado ◽  
Adalberto Gómez Zúñiga ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Genetic Admixture ◽  
Host Switching ◽  
Wasp Species ◽  
Pollinator Species ◽  
Genome Wide ◽  
History Of

AbstractInteractions between plants and their animal pollinators can shape processes of divergence and gene flow within associated lineages. For example, in the obligate mutualism between figs (Ficus) and fig pollinator wasps (family Agaonidae), each wasp species typically pollinates a single fig species, potentially reinforcing reproductive isolation among different wasp species. Multiple pollinator species, however, can sometimes reproduce in the same host fig species, potentially enabling hybridization and introgression between wasp species. In a community of Panamanian strangler figs (section Americana), we use genome-wide ultraconserved element (UCE) loci to estimate phylogenetic relationships and test for hybridization and gene flow among 19 pollinator species associated with 16 host fig species. Previous studies showing ongoing pollinator sharing and a history of pollinator host switching are consistent with documented genetic admixture in their host figs. Here we investigate if host sharing and a dynamic evolutionary history including host switching has also resulted in hybridization and gene flow between pollinator species. Phylogenetic analyses recover strong support for well-delimited wasp species coupled with high interspecific divergence. There is no evidence for ongoing hybridization or introgression, even among pairs of pollinator species currently reproducing within the same host. In contrast to work suggesting admixture among Panamanian host figs, we conclude hybridization and interspecific gene flow have not been important processes shaping the evolutionary history of their pollinating wasps.

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