Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids

Abstract Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species.

Download Full-text

copia-, gypsy- and LINE-Like Retrotransposon Fragments in the Mitochondrial Genome of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/142.2.579 ◽

1996 ◽

Vol 142 (2) ◽

pp. 579-585 ◽

Cited By ~ 3

Author(s):

Volker Knoop ◽

Michael Unseld ◽

Joachim Marienfeld ◽

Petra Brandt ◽

Sabine Sünkel ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Mitochondrial Genome ◽

Evolutionary History ◽

Nuclear Genome ◽

Plant Mitochondrial Genome ◽

Gypsy Group ◽

History Of

Abstract Several retrotransposon fragments are integrated in the mitochondrial genome of Arabidopsis thaliana. These insertions are derived from all three classes of nuclear retrotransposons, the Tyl/copia, Ty3/gypsy- and non-LTR/LINE-families. Members of the Ty3/gypsy group of elements have not yet been identified in the nuclear genome of Arabidopsis. The varying degrees of similarity with nuclear elements and the dispersed locations of the sequences in the mitochondrial genome suggest numerous independent transfer-insertion events in the evolutionary history of this plant mitochondrial genome. Overall, we estimate remnants of retrotransposons to cover ≥5% of the mitochondrial genome in Arabidopsis.

Download Full-text

Morphological stasis in the first myxomycete from the Mesozoic, and the likely role of cryptobiosis

Scientific Reports ◽

10.1038/s41598-019-55622-9 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Jouko Rikkinen ◽

David A. Grimaldi ◽

Alexander R. Schmidt

Keyword(s):

Evolutionary History ◽

Molecular Data ◽

Fruiting Bodies ◽

Ecological Adaptations ◽

Environmental Selection ◽

Morphological Stasis ◽

Ancient Lineage ◽

History Of ◽

Spore Mass

AbstractMyxomycetes constitute a group within the Amoebozoa well known for their motile plasmodia and morphologically complex fruiting bodies. One obstacle hindering studies of myxomycete evolution is that their fossils are exceedingly rare, so evolutionary analyses of this supposedly ancient lineage of amoebozoans are restricted to extant taxa. Molecular data have significantly advanced myxomycete systematics, but the evolutionary history of individual lineages and their ecological adaptations remain unknown. Here, we report exquisitely preserved myxomycete sporocarps in amber from Myanmar, ca. 100 million years old, one of the few fossil myxomycetes, and the only definitive Mesozoic one. Six densely-arranged stalked sporocarps were engulfed in tree resin while young, with almost the entire spore mass still inside the sporotheca. All morphological features are indistinguishable from those of the modern, cosmopolitan genus Stemonitis, demonstrating that sporocarp morphology has been static since at least the mid-Cretaceous. The ability of myxomycetes to develop into dormant stages, which can last years, may account for the phenotypic stasis between living Stemonitis species and this fossil one, similar to the situation found in other organisms that have cryptobiosis. We also interpret Stemonitis morphological stasis as evidence of strong environmental selection favouring the maintenance of adaptations that promote wind dispersal.

Download Full-text

A transcriptome-based phylogenetic study of hard ticks (Ixodidae)

Scientific Reports ◽

10.1038/s41598-019-49641-9 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 6

Author(s):

N. Pierre Charrier ◽

Axelle Hermouet ◽

Caroline Hervet ◽

Albert Agoulon ◽

Stephen C. Barker ◽

...

Keyword(s):

Evolutionary History ◽

Nuclear Genome ◽

Single Copy ◽

Phylogenetic Study ◽

Data Sets ◽

Hard Tick ◽

Rna Seq ◽

Hard Ticks ◽

History Of ◽

Mitochondrial Sequences

Abstract Hard ticks are widely distributed across temperate regions, show strong variation in host associations, and are potential vectors of a diversity of medically important zoonoses, such as Lyme disease. To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for nine different Ixodes species. We combined this new data with 18 data sets obtained from public databases, both for Ixodes and non-Ixodes hard tick species, using soft ticks as an outgroup. We assembled transcriptomes (for 27 species in total), predicted coding sequences and identified single copy orthologues (SCO). Using Maximum-likelihood and Bayesian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome. We also obtained a mitochondrial DNA-based phylogeny using published genome sequences and mitochondrial sequences derived from the new transcriptomes. Our results confirm previous studies showing that the Ixodes genus is monophyletic and clarify the relationships among Ixodes sub-genera. This work provides a baseline for studying the evolutionary history of ticks: we indeed found an unexpected acceleration of substitutions for mitochondrial sequences of Prostriata, and for nuclear and mitochondrial genes of two species of Rhipicephalus, which we relate with patterns of genome architecture and changes of life-cycle, respectively.

Download Full-text

The unexpected survival of an ancient lineage of anseriform birds into the Neogene of Australia: the youngest record of Presbyornithidae

Royal Society Open Science ◽

10.1098/rsos.150635 ◽

2016 ◽

Vol 3 (2) ◽

pp. 150635 ◽

Cited By ~ 15

Author(s):

Vanesa L. De Pietri ◽

R. Paul Scofield ◽

Nikita Zelenkov ◽

Walter E. Boles ◽

Trevor H. Worthy

Keyword(s):

Evolutionary History ◽

South Australia ◽

First Record ◽

South American ◽

Crown Group ◽

Term Survival ◽

Skeletal Morphology ◽

Ancient Lineage ◽

History Of

Presbyornithids were the dominant birds in Palaeogene lacustrine assemblages, especially in the Northern Hemisphere, but are thought to have disappeared worldwide by the mid-Eocene. Now classified within Anseriformes (screamers, ducks, swans and geese), their relationships have long been obscured by their strange wader-like skeletal morphology. Reassessment of the late Oligocene South Australian material attributed to Wilaru tedfordi , long considered to be of a stone-curlew (Burhinidae, Charadriiformes), reveals that this taxon represents the first record of a presbyornithid in Australia. We also describe the larger Wilaru prideauxi sp. nov. from the early Miocene of South Australia, showing that presbyornithids survived in Australia at least until ca 22 Ma. Unlike on other continents, where presbyornithids were replaced by aquatic crown-group anatids (ducks, swans and geese), species of Wilaru lived alongside these waterfowl in Australia. The morphology of the tarsometatarsus of these species indicates that, contrary to other presbyornithids, they were predominantly terrestrial birds, which probably contributed to their long-term survival in Australia. The morphological similarity between species of Wilaru and the Eocene South American presbyornithid Telmabates antiquus supports our hypothesis of a Gondwanan radiation during the evolutionary history of the Presbyornithidae. Teviornis gobiensis from the Late Cretaceous of Mongolia is here also reassessed and confirmed as a presbyornithid. These findings underscore the temporal continuance of Australia’s vertebrates and provide a new context in which the phylogeny and evolutionary history of presbyornithids can be examined.

Download Full-text

Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two sexual species

10.1101/284950 ◽

2018 ◽

Author(s):

Robert D. Denton ◽

Ariadna E. Morales ◽

H. Lisle Gibbs

Keyword(s):

Genetic Variation ◽

Evolutionary History ◽

Parental Species ◽

Extended Period ◽

Reproductive Mode ◽

Mapping Method ◽

Genetic Introgression ◽

Sexual Species ◽

History Of ◽

Genomic Material

AbstractQuantifying genetic introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what factors drive the longevity of putatively asexual groups. However, the presence of multiple distinct subgenomes within a single lineage provides a significant logistical challenge to evaluating the origin of genetic variation in most polyploids. Here, we capitalize on three recent innovations—variation generated from ultraconserved elements (UCEs), bioinformatic techniques for assessing variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. We first analyzed variation from more than a thousand UCEs using a reference mapping method developed for polyploids to infer subgenome specific patterns of variation in the all-female lineage. We then used PHRAPL to choose between sets of historical models that reflected different patterns of introgression and divergence between the genomes of the parental species and the same genomes found within the polyploids. Our analyses support a scenario in which the genomes sampled in unisexuals salamanders were present in the lineage ∼3.4 million years ago, followed by an extended period of divergence from their parental species. Recent secondary introgression has occurred at different times between each sexual species and their representative genomes within the unisexuals during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage has been the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have also undergone long periods of divergence without introgression. Unlike other unisexual, sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could reveal the scenarios in which the influx of novel genomic material is favored and potentially explain why these salamanders are among the oldest described unisexual animals.

Download Full-text

EPAS1 Gain-of-Function Mutation Contributes to High-Altitude Adaptation in Tibetan Horses

Molecular Biology and Evolution ◽

10.1093/molbev/msz158 ◽

2019 ◽

Vol 36 (11) ◽

pp. 2591-2603 ◽

Cited By ~ 7

Author(s):

Xuexue Liu ◽

Yanli Zhang ◽

Yefang Li ◽

Jianfei Pan ◽

Dandan Wang ◽

...

Keyword(s):

High Altitude ◽

Extreme Environments ◽

Hypoxia Tolerance ◽

Missense Mutations ◽

Data Set ◽

Genetic Changes ◽

Genome Data ◽

Hypoxic Conditions ◽

Domestic Horses ◽

Altitude Adaptation

Abstract High altitude represents some of the most extreme environments worldwide. The genetic changes underlying adaptation to such environments have been recently identified in multiple animals but remain unknown in horses. Here, we sequence the complete genome of 138 domestic horses encompassing a whole altitudinal range across China to uncover the genetic basis for adaptation to high-altitude hypoxia. Our genome data set includes 65 lowland animals across ten Chinese native breeds, 61 horses living at least 3,300 m above sea level across seven locations along Qinghai-Tibetan Plateau, as well as 7 Thoroughbred and 5 Przewalski’s horses added for comparison. We find that Tibetan horses do not descend from Przewalski’s horses but were most likely introduced from a distinct horse lineage, following the emergence of pastoral nomadism in Northwestern China ∼3,700 years ago. We identify that the endothelial PAS domain protein 1 gene (EPAS1, also HIF2A) shows the strongest signature for positive selection in the Tibetan horse genome. Two missense mutations at this locus appear strongly associated with blood physiological parameters facilitating blood circulation as well as oxygen transportation and consumption in hypoxic conditions. Functional validation through protein mutagenesis shows that these mutations increase EPAS1 stability and its hetero dimerization affinity to ARNT (HIF1B). Our study demonstrates that missense mutations in the EPAS1 gene provided key evolutionary molecular adaptation to Tibetan horses living in high-altitude hypoxic environments. It reveals possible targets for genomic selection programs aimed at increasing hypoxia tolerance in livestock and provides a textbook example of evolutionary convergence across independent mammal lineages.

Download Full-text

A multi-decadal history of biomass burning plume heights identified using aerosol index measurements

Atmospheric Chemistry and Physics ◽

10.5194/acp-10-6461-2010 ◽

2010 ◽

Vol 10 (14) ◽

pp. 6461-6469 ◽

Cited By ~ 51

Author(s):

H. Guan ◽

R. Esswein ◽

J. Lopez ◽

R. Bergstrom ◽

A. Warnock ◽

...

Keyword(s):

High Altitude ◽

Biomass Burning ◽

Northeast Asia ◽

Time Interval ◽

Ozone Monitoring Instrument ◽

Fire Plume ◽

Data Set ◽

History Of ◽

Aerosol Index

Abstract. We have quantified the relationship between Aerosol Index (AI) measurements and plume height for young biomass burning plumes using coincident Ozone Monitoring Instrument (OMI) and Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) measurements. This linear relationship allows the determination of high-altitude plumes wherever AI data are available, and it provides a data set for validating global fire plume heights in chemistry transport models. We find that all plumes detected from June 2006 to February 2009 with an AI value ≥9 are located at altitudes higher than 5 km. Older high-altitude plumes have lower AI values than young plumes at similar altitudes. We have examined available AI data from the OMI and TOMS instruments (1978–2009) and find that large AI plumes occur more frequently over North America than over Australia or Russia/Northeast Asia. According to the derived relationship, during this time interval, 181 plumes, in various stages of their evolution, reached altitudes above 8 km.

Download Full-text

The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters

Diversity ◽

10.3390/d10030065 ◽

2018 ◽

Vol 10 (3) ◽

pp. 65 ◽

Cited By ~ 6

Author(s):

Thierry Grange ◽

Jean-Philip Brugal ◽

Laurence Flori ◽

Mathieu Gautier ◽

Antigone Uzunidis ◽

...

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

Nuclear Genome ◽

Population Diversity ◽

Ecological Niches ◽

Unified Framework ◽

Putative Gene ◽

Behavioral Studies ◽

History Of ◽

Genome Analyses

Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene in Eurasia. The produced data, however, were interpreted in contradicting manners. Here, we have gathered, reanalyzed and compared previously published or unpublished morphometric and genetic data that have not yet been integrated and that we synthesize in a unified framework. In particular, we re-estimate dates of divergence of mitogenome lineages based on an extended dataset comprising 81 complete ancient bison mitogenomes and we revisit putative gene flow between the Bos and Bison genera based on comparative analyses of ancient and modern bison genomes, thereby questioning published conclusions. Morphometric analyses taking into account sexual dimorphism invalidate a previous claim that Bison schoetensacki was present in France during the Late Pleistocene. Both morphometric and genome analyses reveal that Eurasian bison belonging to different Bison priscus and Bison bonasus lineages maintained parallel evolutionary paths with gene flow during a long period of incomplete speciation that ceased only upon the migration of B. priscus to the American continent establishing the American bison lineage. Our nuclear genome analysis of the evolutionary history of B. bonasus allows us to reject the previous hypothesis that it is a hybrid of B. priscus and Bos primigenius. Based on present-day behavioral studies of European and American bison, we propose that apparently conflicting lines of evidence can be reconciled by positing that female bison drove the specialization of bison populations to different ecological niches while male bison drove regular homogenizing genetic exchanges between populations.

Download Full-text

Evolutionary history of mitochondrial genomes in Discoba, including the extreme halophile Pleurostomum flabellatum (Heterolobosea)

Genome Biology and Evolution ◽

10.1093/gbe/evaa241 ◽

2020 ◽

Author(s):

Khaoula Ettahi ◽

Duck Hyun Lhee ◽

Ji Yeon Sung ◽

Alastair G B Simpson ◽

Jong Soo Park ◽

...

Keyword(s):

Evolutionary History ◽

Nuclear Genome ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Transport Chain ◽

Circular Molecule ◽

History Of ◽

Extreme Habitats ◽

Genome Information ◽

Naegleria Gruberi

Abstract Data from Discoba (Heterolobosea, Euglenozoa, Tsukubamonadida, and Jakobida) are essential to understand the evolution of mitochondrial genomes (mitogenomes), since this clade includes the most primitive-looking mitogenomes known, as well some extremely divergent genome information systems. Heterolobosea encompasses more than 150 described species, many of them from extreme habitats, but only six heterolobosean mitogenomes have been fully sequenced to date. Here we complete the mitogenome of the heterolobosean Pleurostomum flabellatum, which is extremely halophilic and reportedly also lacks classical mitochondrial cristae, hinting at reduction or loss of respiratory function. The mitogenome of P. flabellatum maps as a 57,829 bp long circular molecule, including 40 CDSs (19 tRNA, two rRNA, and 19 orfs). The gene content and gene arrangement are similar to Naegleria gruberi and N. fowleri, the closest relatives with sequenced mitogenomes. The P. flabellatum mitogenome contains genes that encode components of the electron transport chain similar to those of Naegleria mitogenomes. Homology searches against a draft nuclear genome showed that P. flabellatum has two homologs of the highly conserved Mic60 subunit of the MICOS complex, and likely lost Mic19 and Mic10. However, electron microscopy showed no cristae structures. We infer that P. flabellatum, which originates from high salinity (313‰) water where the dissolved-oxygen concentration is low, possesses a mitochondrion capable of aerobic respiration, but with reduced development of cristae structure reflecting limited use of this aerobic capacity (e.g., microaerophily).

Download Full-text

“Ghost Introgression” As a Cause of Deep Mitochondrial Divergence in a Bird Species Complex

Molecular Biology and Evolution ◽

10.1093/molbev/msz170 ◽

2019 ◽

Vol 36 (11) ◽

pp. 2375-2386 ◽

Cited By ~ 12

Author(s):

Dezhi Zhang ◽

Linfang Tang ◽

Yalin Cheng ◽

Yan Hao ◽

Ying Xiong ◽

...

Keyword(s):

Bird Species ◽

Nuclear Genome ◽

Distinct Species ◽

Comparative Genomic ◽

Genetic Introgression ◽

Effective Population ◽

Westward Expansion ◽

Whole Genomes ◽

Linked Selection ◽

Two Populations

Abstract In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by “speciation reversal” or by mitochondrial capture through genetic introgression. Here, we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological, and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of “ghost introgression” as the cause of DMD, and we suggest that “ghost introgression” may be a widely overlooked phenomenon in nature.

Download Full-text