Biology subjects

Pacheco, G.

Publications and source records attributed to Pacheco, G..

6 recordsLinked to original sources

bioRxiv2023

Redefining rock doves, Columba livia, using historical whole genome sequences

The domestic pigeons exceptional phenotypic diversity was key in developing Darwins Theory of Evolution and establishing the concept of artificial selection in domestic species. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia, has received considerably less attention. Therefore, questions regarding their domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock dove samples representing all currently recognised subspecies and spanning the species original geographic distribution. Our dataset includes three specimens from Darwins collection and the type specimens of five different taxa. We characterised rock doves population structure, genomic diversity and gene-flow patterns. We show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons. Our results show gene-flow signals between the rock doves sister species C. rupestris and all rock doves except the West African populations. Our results led us to propose an evolutionary model for the rock dove considering the Pleistocene refugia theory. We propose that todays rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least one domestication event in the Levant region that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.

evolutionary biology↗

bioRxiv2022

Genomic differentiation among European perch in the western Baltic Sea reflects colonization history and local adaptation

Environmental variation across the distribution of wild species can lead to local adaptations. The Baltic Sea was formed when the Fenno-Scandian ice sheet retreated around 12 thousand years ago, creating a new brackish water habitat colonised by both marine and freshwater fish species. The European perch (Perca fluviatilis) is a predatory freshwater fish with a large geographical distribution across Eurasia, where it inhabits a wide range of environmental niches. In the Baltic Sea region it has even developed a specialised brackish water phenotype that can tolerate environmental salinity levels, which are lethal to the ancestral freshwater phenotype. However, very little is known about the colonisation history and underlying genomic mechanisms facilitating the colonisation and adaptation of perch to the Baltic Sea. Here, we use Genotyping-By-Sequencing data from six freshwater and six brackish water localities to disclose the evolutionary relationship between the freshwater and brackish water phenotype. Our results show that the brackish water perch phenotype occurs in multiple distinct genetic clusters. We find that gene flow between brackish water phenotypes with full access to the sea likely led to lower levels of differentiation and higher diversity than in freshwater phenotypes. Selection analyses suggest that genomic adaptation played a role in the colonisation of the Baltic Sea and that the top three regions under selection harbour salinity tolerance genes. We also find a link between the historic salinity of the Baltic Sea and the demographic history of the brackish water phenotypes and go on to discuss the implications of our findings for management of brackish water perch in the western Baltic sea. HighlightsO_LIGBS data from 12 perch populations, six with brackish and six with freshwater origin C_LIO_LIColonisation history and differentiated gene flow shaped the current population structure C_LIO_LIThe brackish water ecotype was found in all three major genetic clades C_LIO_LITop three regions under selection harboured salinity tolerance genes C_LIO_LISalinity influenced Ne during the formation of the Baltic Sea C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/516742v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@29e5dforg.highwire.dtl.DTLVardef@b2b35borg.highwire.dtl.DTLVardef@1d3457org.highwire.dtl.DTLVardef@1574e46_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Imaging Cuprizone-Induced Mitochondrial Dysfunction

Cuprizone is a copper chelator that induces mitochondrial dysfunction in myelin-producing oligodendrocytes and hepatic cells. Inhibition of oxidative phosphorylation has been proposed as a potential mechanism, but the exact relationship between shape changes and metabolic alterations is not well-understood. Here we explore how mitochondrial shape influences oxidative phosphorylation rates by performing simultaneous imaging and respiration measurements within intact cells. We observed that MO3.13 cells exposed to cuprizone undergo an initial increase in respiration followed by mitochondrial dysfunction and genetic dysregulation within 8 hours. Oxygen consumption was measured within 30 minutes of treatment and found to be elevated. This increase was followed by swelling of mitochondria over the first 8 hours, but preceded cell death by 24 hours. A transcriptomic analysis of early changes in cellular gene expression identified alterations within the electron transport chain, stress response pathways, and mitochondrial dynamics compared to control cells. These results suggest that pathological mitochondrial swelling is associated with increased oxygen consumption rates leading to transcriptional changes in respiratory complexes and ultimately mitochondrial failure.

biochemistry↗

bioRxiv2020

Additive and non-additive epigenetic signatures of hybridisation between fish species with different mating systems

Hybridisation is a major source of evolutionary innovation. However, several prezygotic and postzygotic factors influence its likelihood and evolutionary outcomes. Differences in mating systems can have a major effect on the extent and direction of hybridisation and introgression. In plants, epigenetic mechanisms help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the extent of a unique case of natural hybridisation between two genetically distant mangrove killifish species with different mating systems, Kryptolebias hermaphroditus (self-fertilising) and K. ocellatus (outcrossing), and the methylation patterns of their hybrids. Hybridisation rate between the species ranged between 14% and 26%. Although co-existing parental species displayed highly distinct genetic (microsatellites and SNPs) and methylation patterns (37,000 differentially methylated cytosines), our results indicate that F1 hybrids are viable and able to backcross with parental species. Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridisation between genetically distant species. Differentially methylated cytosines between hybrids and both parental species (5,800) suggest that introgressive hybridisation may play a role in generating novel genetic and epigenetic variation which could lead to species diversification. We also found a small percentage of non-additive epigenetic effects which might act as an evolutionary bet-hedging strategy and increase fitness under environmental change.

evolutionary biology↗

bioRxiv2020

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ca. 76X per individual, and estimated an average rate of 0.77 x 10-8 de novo mutations per site per generation (95 % CI: 0.69 x 10-8 - 0.85 x 10-8). By phasing 50 % of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed an average of 81 % of the de novo mutations, with a trend of an increasing male contribution for older fathers. About 3.5 % of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated based on the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecidae/Hominoidea molecular divergence dated at 52 Mya using our new estimate of the yearly mutation rate.

evolutionary biology↗

bioRxiv2019

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

evolutionary biology↗