Publications by authors named "Olga Kardailsky"

12 Publications

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Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America.

Hum Mol Genet 2021 Apr 15. Epub 2021 Apr 15.

Universidad Nacional de Córdoba, Facultad de Filosofía y Humanidades, Departamento de Antropología, Córdoba, Argentina.

The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina. Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared to a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of Central Argentina populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until present that stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to Central Argentina. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.
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http://dx.doi.org/10.1093/hmg/ddab105DOI Listing
April 2021

Hairpin-bisulfite sequencing of cells exposed to decitabine documents the process of DNA demethylation.

Epigenetics 2020 Dec 28:1-9. Epub 2020 Dec 28.

Department of Pathology, University of Otago, Dunedin, New Zealand.

Although the mechanism of DNA demethylating drugs has been understood for many years, the direct effect of these drugs on methylation of the complementary strands of DNA has not been formally demonstrated. By using hairpin-bisulphite sequencing, we describe the kinetics and pattern of DNA methylation following treatment of cells by the DNA methyltransferase 1 (DNMT1) inhibitor, decitabine. As expected, we demonstrate complete loss of methylation on the daughter strand following S-phase in selected densely methylated genes in synchronized Jurkat cells. Thereafter, cells showed a heterogeneous pattern of methylation reflecting replication of the unmethylated strand and restoration of methylation.
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http://dx.doi.org/10.1080/15592294.2020.1861169DOI Listing
December 2020

A tale of textiles: Genetic characterization of historical paper mulberry barkcloth from Oceania.

PLoS One 2020 18;15(5):e0233113. Epub 2020 May 18.

Escuela de Antropología, Facultad de Ciencias Sociales, Universidad Academia de Humanismo Cristiano, Santiago, Chile.

Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0233113PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233582PMC
August 2020

Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction.

Biol Lett 2019 09 4;15(9):20190491. Epub 2019 Sep 4.

Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden.

Human intervention, pre-human climate change (or a combination of both), as well as genetic effects, contribute to species extinctions. While many species from oceanic islands have gone extinct due to direct human impacts, the effects of pre-human climate change and human settlement on the genomic diversity of insular species and the role that loss of genomic diversity played in their extinctions remains largely unexplored. To address this question, we sequenced whole genomes of two extinct New Zealand passerines, the huia (Heteralocha acutirostris) and South Island kōkako (Callaeas cinereus). Both species showed similar demographic trajectories throughout the Pleistocene. However, the South Island kōkako continued to decline after the last glaciation, while the huia experienced some recovery. Moreover, there was no indication of inbreeding resulting from recent mating among closely related individuals in either species. This latter result indicates that population fragmentation associated with forest clearing by Maōri may not have been strong enough to lead to an increase in inbreeding and exposure to genomic erosion. While genomic erosion may not have directly contributed to their extinctions, further habitat fragmentation and the introduction of mammalian predators by Europeans may have been an important driver of extinction in huia and South Island kōkako.
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http://dx.doi.org/10.1098/rsbl.2019.0491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769136PMC
September 2019

Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change.

Sci Adv 2019 07 10;5(7):eaaw7006. Epub 2019 Jul 10.

Department of Anatomy, University of Otago, Dunedin, New Zealand.

Bluehead wrasses undergo dramatic, socially cued female-to-male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data suggest that the environmental stimulus is exerted via the stress axis and that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression and identifies notable sex-specific gene neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.
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http://dx.doi.org/10.1126/sciadv.aaw7006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6620101PMC
July 2019

Mitogenomic evidence of close relationships between New Zealand's extinct giant raptors and small-sized Australian sister-taxa.

Mol Phylogenet Evol 2019 05 10;134:122-128. Epub 2019 Feb 10.

Canterbury Museum, 8013 Christchurch, New Zealand.

Prior to human arrival in the 13th century, two large birds of prey were the top predators in New Zealand. In the absence of non-volant mammals, the extinct Haast's eagle (Hieraaetus moorei), the largest eagle in the world, and the extinct Eyles' harrier (Circus teauteensis) the largest harrier in the world, had filled ecological niches that are on other landmasses occupied by animals such as large cats or canines. The evolutionary and biogeographic history of these island giants has long been a mystery. Here we reconstruct the origin and evolution of New Zealand's giant raptors using complete mitochondrial genome data. We show that both Eyles' harrier and Haast's eagle diverged from much smaller, open land adapted Australasian relatives in the late Pliocene to early Pleistocene. These events coincided with the development of open habitat in the previously densely forested islands of New Zealand. Our study provides evidence of rapid evolution of island gigantism in New Zealand's extinct birds of prey. Early Pleistocene climate and environmental changes were likely to have triggered the establishment of Australian raptors into New Zealand. Our results shed light on the evolution of two of the most impressive cases of island gigantism in the world.
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http://dx.doi.org/10.1016/j.ympev.2019.01.026DOI Listing
May 2019

Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza.

Sci Rep 2018 12 4;8(1):17567. Epub 2018 Dec 4.

Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.

Ibiza was permanently settled around the 7 century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4 century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island's modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated.
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http://dx.doi.org/10.1038/s41598-018-35667-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279797PMC
December 2018

The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates.

F1000Res 2017 20;6:526. Epub 2017 Apr 20.

Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand.

Background: Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates.

Methods:  We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark . Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data.  Results: Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates.

Conclusions:  Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.
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http://dx.doi.org/10.12688/f1000research.11281.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437953PMC
April 2017

Ancient mitochondrial genomes clarify the evolutionary history of New Zealand's enigmatic acanthisittid wrens.

Mol Phylogenet Evol 2016 Sep 31;102:295-304. Epub 2016 May 31.

Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia.

The New Zealand acanthisittid wrens are the sister-taxon to all other "perching birds" (Passeriformes) and - including recently extinct species - represent the most diverse endemic passerine family in New Zealand. Consequently, they are important for understanding both the early evolution of Passeriformes and the New Zealand biota. However, five of the seven species have become extinct since the arrival of humans in New Zealand, complicating evolutionary analyses. The results of morphological analyses have been largely equivocal, and no comprehensive genetic analysis of Acanthisittidae has been undertaken. We present novel mitochondrial genome sequences from four acanthisittid species (three extinct, one extant), allowing us to resolve the phylogeny and revise the taxonomy of acanthisittids. Reanalysis of morphological data in light of our genetic results confirms a close relationship between the extant rifleman (Acanthisitta chloris) and an extinct Miocene wren (Kuiornis indicator), making Kuiornis a useful calibration point for molecular dating of passerines. Our molecular dating analyses reveal that the stout-legged wrens (Pachyplichas) diverged relatively recently from a more gracile (Xenicus-like) ancestor. Further, our results suggest a possible Early Oligocene origin of the basal Lyall's wren (Traversia) lineage, which would imply that Acanthisittidae survived the Oligocene marine inundation of New Zealand and therefore that the inundation was not complete.
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http://dx.doi.org/10.1016/j.ympev.2016.05.038DOI Listing
September 2016

A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa.

PLoS One 2016 25;11(5):e0155046. Epub 2016 May 25.

School of Medicine, Lebanese American University, Byblos, Lebanon.

While Phoenician culture and trade networks had a significant impact on Western civilizations, we know little about the Phoenicians themselves. In 1994, a Punic burial crypt was discovered on Byrsa Hill, near the entry to the National Museum of Carthage in Tunisia. Inside this crypt were the remains of a young man along with a range of burial goods, all dating to the late 6th century BCE. Here we describe the complete mitochondrial genome recovered from the Young Man of Byrsa and identify that he carried a rare European haplogroup, likely linking his maternal ancestry to Phoenician influenced locations somewhere on the North Mediterranean coast, the islands of the Mediterranean or the Iberian Peninsula. This result not only provides the first direct ancient DNA evidence of a Phoenician individual but the earliest evidence of a European mitochondrial haplogroup, U5b2c1, in North Africa.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155046PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880306PMC
July 2017

Bird evolution: testing the Metaves clade with six new mitochondrial genomes.

BMC Evol Biol 2008 Jan 23;8:20. Epub 2008 Jan 23.

Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.

Background: Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade.

Results: Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the beta-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved.

Conclusion: Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves.
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http://dx.doi.org/10.1186/1471-2148-8-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2259304PMC
January 2008

Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations.

Mol Biol Evol 2007 Jan 24;24(1):269-80. Epub 2006 Oct 24.

Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.

We improve the taxon sampling for avian phylogeny by analyzing 7 new mitochondrial genomes (a toucan, woodpecker, osprey, forest falcon, American kestrel, heron, and a pelican). This improves inference of the avian tree, and it supports 3 major conclusions. The first is that some birds (including a parrot, a toucan, and an osprey) exhibit a complete duplication of the control region (CR) meaning that there are at least 4 distinct gene orders within birds. However, it appears that there are regions of continued gene conversion between the duplicate CRs, resulting in duplications that can be stable for long evolutionary periods. Because of this stable duplicated state, gene order can eventually either revert to the original order or change to the new gene order. The existence of this stable duplicate state explains how an apparently unlikely event (finding the same novel gene order) can arise multiple times. Although rare genomic changes have theoretical advantages for tree reconstruction, they can be compromised if these apparently rare events have a stable intermediate state. Secondly, the toucan and woodpecker improve the resolution of the 6-way split within Neoaves that has been called an "explosive radiation." An explosive radiation implies that normal microevolutionary events are insufficient to explain the observed macroevolution. By showing the avian tree is, in principle, resolvable, we demonstrate that the radiation of birds is amenable to standard evolutionary analysis. Thirdly, and as expected from theory, additional taxa breaking up long branches stabilize the position of some problematic taxa (like the falcon). In addition, we report that within the birds of prey and allies, we did not find evidence pairing New World vultures with storks or accipitrids (hawks, eagles, and osprey) with Falconids.
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http://dx.doi.org/10.1093/molbev/msl158DOI Listing
January 2007