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

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.

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

BMC Evolutionary Biology ◽

10.1186/s12862-020-01666-9 ◽

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.

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The Y-chromosome clarifies the evolutionary history of Sus scrofa by large-scale deep genome sequencing

10.1101/126060 ◽

2017 ◽

Author(s):

Huashui Ai ◽

Jun Ren ◽

Junwu Ma ◽

Zhiyan Zhang ◽

Wanbo Li ◽

...

Keyword(s):

Gene Flow ◽

Y Chromosome ◽

Sus Scrofa ◽

Evolutionary History ◽

Large Scale ◽

Divergence Time ◽

Chromosome Y ◽

Wild Boars ◽

History Of ◽

Ancient Gene

AbstractThe genetics and evolution of sex chromosomes are largely distinct from autosomes and mitochondrial DNA (mtDNA). The Y chromosome offers unique genetic perspective on male-line inheritance. Here, we uncover novel evolutionary history of Sus scrofa based on 205 high-quality genomes from worldwide-distributed different wild boars and domestic pig breeds. We find that only two haplotypes exist in the distal and proximal blocks of at least 7.7 Mb on chromosome Y in pigs across European and Asian continents. And the times of most recent common ancestors (TMRCA) within both haplotypes, approximately 0.14 and 0.10 million years, are far smaller than their divergence time of around 1.07 million years. What’s more, the relationship between Sumatran and Eurasian continent Sus scrofa is much closer than that we knew before. And surprisingly, European pigs share the same haplotype with many Chinese pigs, which is not consistent with their deep splitting status on autosome and mtDNA. Further analyses show that the haplotype in Chinese pigs was likely introduced from European wild boars via ancient gene flow before pig domestication about 24k years ago. Low mutation rates and no recombination in the distal and proximal blocks on chromosome Y help us detect this male-driven ancient gene flow. Taken together, our results update the knowledge of pig demography and evolution, and might shed insight into the genetics and evolution studies on chromosome Y in other mammals.

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

10.1101/2020.12.09.418376 ◽

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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Evolutionary history of a desert perennial Arnebia szechenyi (Boraginaceae): intraspecific divergence, regional expansion and asymmetric gene flow

Plant Diversity ◽

10.1016/j.pld.2021.04.002 ◽

2021 ◽

Author(s):

Meng-Jiao Fu ◽

Hai-Yang Wu ◽

Dong-Rui Jia ◽

Bin Tian

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

Intraspecific Divergence ◽

History Of

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Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽

10.1093/aobpla/plab017 ◽

2021 ◽

Author(s):

Min-Jie Li ◽

Huan-Xi Yu ◽

Xian-Lin Guo ◽

Xing-Jin He

Keyword(s):

Evolutionary History ◽

Divergence Time ◽

Time Estimation ◽

Adjacent Region ◽

Rapid Radiation ◽

Divergence Time Estimation ◽

Species Diversification ◽

The Third ◽

Evolutionary Line ◽

History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

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A new endemic family of New Zealand passerine birds: adding heat to a biodiversity hotspot

Australian Journal of Zoology ◽

10.1071/zo07007 ◽

2007 ◽

Vol 55 (2) ◽

pp. 73 ◽

Cited By ~ 33

Author(s):

Amy Driskell ◽

Les Christidis ◽

B. J. Gill ◽

Walter E. Boles ◽

F. Keith Barker ◽

...

Keyword(s):

New Zealand ◽

Evolutionary History ◽

Divergence Time ◽

Biodiversity Hotspot ◽

Passerine Birds ◽

New Family ◽

Close Relationship ◽

History Of ◽

Anthornis Melanura ◽

Notiomystis Cincta

The results of phylogenetic analysis of two molecular datasets sampling all three endemic New Zealand ‘honeyeaters’ (Prosthemadera novaeseelandiae, Anthornis melanura and Notiomystis cincta) are reported. The undisputed relatedness of the first two species to other honeyeaters (Meliphagidae), and a close relationship between them, are demonstrated. However, our results confirm that Notiomystis is not a honeyeater, but is instead most closely related to the Callaeidae (New Zealand wattlebirds) represented by Philesturnus carunculatus in our study. An estimated divergence time for Notiomystis and Philesturnus of 33.8 mya (Oligocene) suggests a very long evolutionary history of this clade in New Zealand. As a taxonomic interpretation of these data we place Notiomystis in a new family of its own which takes the name Notiomystidae. We expect this new phylogenetic and taxonomic information to assist policy decisions for the conservation of this rare bird.

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Historical divergence vs. contemporary gene flow: evolutionary history of the calcicoleRanunculus alpestrisgroup (Ranunculaceae) in the European Alps and the Carpathians

Molecular Ecology ◽

10.1111/j.1365-294x.2008.03908.x ◽

2008 ◽

Vol 17 (19) ◽

pp. 4263-4275 ◽

Cited By ~ 73

Author(s):

O. PAUN ◽

P. SCHÖNSWETTER ◽

M. WINKLER ◽

INTRABIODIV CONSORTIUM ◽

A. TRIBSCH

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

European Alps ◽

The Carpathians ◽

Contemporary Gene Flow ◽

History Of

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Chromosomal dynamics in space and time: evolutionary history of Mycetophylax ants across past climatic changes in the Brazilian Atlantic coast

Scientific Reports ◽

10.1038/s41598-019-55135-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Ricardo Micolino ◽

Maykon Passos Cristiano ◽

Natália Martins Travenzoli ◽

Denilce Meneses Lopes ◽

Danon Clemes Cardoso

Keyword(s):

Evolutionary History ◽

Chromosomal Rearrangements ◽

Atlantic Coast ◽

Ecological Impact ◽

Divergence Time ◽

Molecular Data ◽

Recent Common Ancestor ◽

Integrative Approach ◽

Most Recent Common Ancestor ◽

History Of

AbstractFungus-farming ants of the genus Mycetophylax exhibit intra and interspecific chromosome variability, which makes them suitable for testing hypotheses about possible chromosomal rearrangements that endure lineage diversification. We combined cytogenetic and molecular data from Mycetophylax populations from coastal environments to trace the evolutionary history of the clade in light of chromosomal changes under a historical and geographic context. Our cytogenetic analyses revealed chromosomal differences within and among species. M. morschi exhibited three distinct karyotypes and considerable variability in the localization of 45S rDNA clusters. The molecular phylogeny was congruent with our cytogenetic findings. Biogeographical and divergence time dating analyses estimated that the most recent common ancestor of Mycetophylax would have originated at about 30 Ma in an area including the Amazon and Southern Grasslands, and several dispersion and vicariance events may have occurred before the colonization of the Brazilian Atlantic coast. Diversification of the psammophilous Mycetophylax first took place in the Middle Miocene (ca. 18–10 Ma) in the South Atlantic coast, while “M. morschi” lineages diversified during the Pliocene-Pleistocene transition (ca. 3–2 Ma) through founder-event dispersal for the Northern coastal regions. Psammophilous Mycetophylax diversification fits into the major global climatic events that have had a direct impact on the changes in sea level as well as deep ecological impact throughout South America. We assume therefore that putative chromosomal rearrangements correlated with increased ecological stress during the past climatic transitions could have intensified and/or accompanied the divergence of the psammophilous Mycetophylax. We further reiterate that “M. morschi” comprises a complex of at least three well-defined lineages, and we emphasize the role of this integrative approach for the identification and delimitation of evolutionary lineages.

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Phylogeography of the widespread white-eared hummingbird (Hylocharis leucotis): pre-glacial expansion and genetic differentiation of populations separated by the Isthmus of Tehuantepec

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa043 ◽

2020 ◽

Vol 130 (2) ◽

pp. 247-267

Author(s):

Luz E Zamudio-Beltrán ◽

Yuyini Licona-Vera ◽

Blanca E Hernández-Baños ◽

John Klicka ◽

Juan Francisco Ornelas

Keyword(s):

Genetic Differentiation ◽

Haplotype Network ◽

Suitable Habitat ◽

Glacial Cycles ◽

Niche Modelling ◽

Climatic Fluctuations ◽

History Of ◽

Genetic Differentiation Of Populations ◽

Isthmus Of Tehuantepec ◽

Glacial Expansion

Abstract The Pleistocene glacial cycles had a strong influence on the demography and genetic structure of many species, particularly on northern-latitude taxa. Here we studied the phylogeography of the white-eared hummingbird (Hylocharis leucotis), a widely distributed species of the highlands of Mexico and Central America. Analysis of mitochondrial DNA (mtDNA) sequences was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. Analyses of 108 samples from 11 geographic locations revealed population structure and genetic differentiation among populations separated by the Isthmus of Tehuantepec (IT) and the Motagua-Polochic-Jocotán (MPJ) fault barriers. ENM predicted a widespread distribution of suitable habitat for H. leucotis since the Last Inter Glacial (LIG), but this habitat noticeably contracted and fragmented at the IT. Models for historical dispersal corridors based on population genetics data and ENM revealed the existence of corridors among populations west of the IT; however, the connectivity of populations across the IT has changed little since the LIG. The shallow geographic structure on either side of the isthmus and a star-like haplotype network, combined with the long-term persistence of populations across time based on genetic data and potential dispersal routes, support a scenario of divergence with migration and subsequent isolation and differentiation in Chiapas and south of the MPJ fault. Our findings corroborate the profound effects of Pleistocene climatic fluctuations on the evolutionary history of montane taxa but challenge the generality of expanded suitable habitat (pine-oak forests) during glacial cycles.

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