| 11. |
- Bergström, Anders, et al.
(author)
-
Grey wolf genomic history reveals a dual ancestry of dogs
- 2022
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 607:7918, s. 313-320
-
Journal article (peer-reviewed)abstract
- The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
|
|
| 12. |
- Brandariz-Fontes, Claudia, et al.
(author)
-
Y-Chromosome Analysis in Retuertas Horses
- 2013
-
In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:5, s. e64985-
-
Journal article (peer-reviewed)abstract
- Several studies based on a variety of genetic markers have attempted to establish the origins of horse domestication. Thus far a discrepancy between the results of mitochondrial DNA analysis, which show high levels of diversity, and results from the Y-chromosome, with almost no genetic variability, has been identified. Most previous work on the horse Y-chromosome has focused on widespread, popular breeds or local Asian breeds. It is possible that these breeds represent a reduced set of the genetic variation present in the species. Additional genetic variation may be present in local breeds and ancient feral populations, such as the Retuertas horse in Spain. In this study we analyzed the Y-chromosome of the Retuertas horse, a feral horse population on the Iberian Peninsula that is at least several hundred years old, and whose genetic diversity and morphology suggests that it has been reproductively isolated for a long time. Data from the Retuertas horse was compared to another 11 breeds from the region (Portugal, Spain and France) or likely of Iberian origin, and then to data from 15 more breeds from around the globe. We sequenced 31 introns, Zinc finger Y-chromosomal protein (ZFY) and anonymous Y-linked fragments and genotyped 6 microsatellite loci found on the Y-chromosome. We found no sequence variation among all individuals and all breeds studied. However, fifteen differences were discovered between our data set and reference sequences in GenBank. We show that these likely represent errors within the deposited sequences, and suggest that they should not be used as comparative data for future projects.
|
|
| 13. |
- Castroviejo-Fisher, Santiago, 1979-
(author)
-
Species Limits, and Evolutionary History of Glassfrogs
- 2009
-
Doctoral thesis (other academic/artistic)abstract
- Recognizing the mechanisms of speciation and the limits of species is essential to understand the origin of biodiversity and how to conserve it. The general aims of my investigations during my doctoral studies were two-fold: to study evolutionary patterns and processes, and to provide specific and superspecific taxonomic classifications that try to reflect evolutionary history. I have focused my research on anurans in their biodiversity hotspot, the American Tropics. I have used morphological, behavioral (mating calls), and genetic (DNA sequences) characters to study species boundaries between frogs of the genus Pristimantis and the family Centrolenidae (glassfrogs). The results show that the exclusive use of single lines of evidence or the application of arbitrary thresholds impair and bias our ability to recognize new species and limit the possibility to understand evolutionary processes. Only an integrative approach combining every source of evidence provides the necessary feedback to discover all species and test their identity by comparing independent sets of data. This approach further allows identifying those species that probably represent stable comparative units (well supported species hypotheses) and to flag taxa that require further assessment. Phylogenetic reconstructions based on seven nuclear and mitochondrial genes for about 100 species of glassfrogs revealed that previous hypotheses of relationships were mislead by rampant convergent evolution at the phenotypic level. None of the previously suggested classifications fit with the reconstructed evolutionary history. Consequently, we proposed a new classification consistent with this phylogeny. I also studied the tempo and mode of diversification among glassfrogs. Based on sequences from ten genes in 87 species, I estimated species divergence times, age-range correlation between sister species, and reconstructed ancestral areas and dispersal/vicariance events. The results revealed a complex model of diversification where geographical isolation seems to be the dominant scenario for speciation and only clades of altitudinal generalists have been able to spread across the Neotropical rainforests.
|
|
| 14. |
- Castroviejo-Fisher, Santiago, et al.
(author)
-
Vanishing Native American dog lineages
- 2011
-
In: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 73-
-
Journal article (peer-reviewed)abstract
- Background: Dogs were an important element in many native American cultures at the time Europeans arrived. Although previous ancient DNA studies revealed the existence of unique native American mitochondrial sequences, these have not been found in modern dogs, mainly purebred, studied so far. Results: We identified many previously undescribed mitochondrial control region sequences in 400 dogs from rural and isolated areas as well as street dogs from across the Americas. However, sequences of native American origin proved to be exceedingly rare, and we estimate that the native population contributed only a minor fraction of the gene pool that constitutes the modern population. Conclusions: The high number of previously unidentified haplotypes in our sample suggests that a lot of unsampled genetic variation exists in non-breed dogs. Our results also suggest that the arrival of European colonists to the Americas may have led to an extensive replacement of the native American dog population by the dogs of the invaders.
|
|
| 15. |
|
|
| 16. |
- den Tex, Robert-Jan, et al.
(author)
-
A molecular phylogeny of Asian barbets : Speciation and extinction in the tropics
- 2013
-
In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 68:1, s. 1-13
-
Journal article (peer-reviewed)abstract
- We reconstruct the phylogeny of all recognized species of the tropical forest associated Asian barbets based on mitochondrial and nuclear sequence data and test for the monophyly of species and genera. Tropical regions are well known for their extraordinarily high levels of biodiversity, but we still have a poor understanding of how this richness was generated and maintained through evolutionary time. Multiple theoretical frameworks have been developed to explain this diversity, including the Pleistocene pump hypothesis and the museum hypothesis. We use our phylogeny of the Asian barbets to test these hypotheses. Our data do not find an increase in speciation in the Pleistocene as predicted by the Pleistocene pump hypothesis. We do find evidence of extinctions, which apparently contradicts the museum hypothesis. However, the extinctions are only in a part of the phylogeny that is distributed mainly across Sundaland (the Malay peninsula and the islands off southeast Asia). The theory of island biogeography predicts a higher rate of extinction on islands than on mainland areas. The data from the part of the phylogeny primarily distributed on the mainland best fit a pure birth model of speciation, and thus supports the museum hypothesis.
|
|
| 17. |
|
|
| 18. |
- den Tex, Robert-Jan, et al.
(author)
-
Nuclear copies of mitochondrial genes : another problem for ancient DNA
- 2010
-
In: Genetica. - : Springer Science and Business Media LLC. - 0016-6707 .- 1573-6857. ; 138:9-10, s. 979-984
-
Journal article (peer-reviewed)abstract
- The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.
|
|
| 19. |
- den Tex, Robert-Jan, 1969-
(author)
-
Patterns and Processes of Evolution in Sundaland
- 2011
-
Doctoral thesis (other academic/artistic)abstract
- Biodiversity in the tropics is disproportionately high compared to other habitats, and also under disproportionate threat from human impact. It is necessary to understand how this diversity evolved and how it is partitioned across space in order to preserve it. In this thesis I construct phylogenies of tropical forest dependent vertebrates from Southeast Asia and the islands of the Sunda shelf, a region referred to as Sundaland. I focus on the tree squirrels (genus Sundasciurus) and Asian barbets (Aves: Family Megalaimidae), two taxa with similar ecological characteristics. I use these phylogenies to test hypotheses that have been put forward to explain high levels of tropical diversity including the Pleistocene pump and museum hypotheses. I also use phylogenies to elucidate phylogeographic patterns within the region. I find no evidence for an increase in speciation in the Pleistocene, but I do find within species structure that dates to this period. Common phylogeographic patterns were identified between many forest dependent vertebrates that suggest that populations on the island of Sumatra are generally more closely related to Malay Peninsula populations than to populations on Borneo. From a methodological viewpoint we propose careful usage of universal primers in ancient DNA studies because of our finding of increased risk of amplifying pseudogenes of the mtDNA.
|
|
| 20. |
|
|
