Biology subjects

Ramos-Madrigal, J.

Publications and source records attributed to Ramos-Madrigal, J..

11 recordsLinked to original sources

bioRxiv2026

The population structure and genetic health of European wolves

Once nearly eradicated from Europe, grey wolves (Canis lupus) have recently undergone a remarkable demographic recovery, but their long-term survival remains precarious. By analyzing 1,001 genomes, we uncover a mosaic of distinct evolutionary lineages, not a single recovering population. Northern populations exhibit Asian wolf ancestry, while southern populations preserve ancient Holocene lineages, with dog introgression varying by region. Isolated wolves from the Scandinavian, Italian, and Iberian peninsulas harbored particularly high levels of inbreeding and fixed deleterious mutations. Signatures of genome erosion were widespread across Europe, with many populations falling well short of the minimum size recommended for long-term survival. Our study reveals the complex tapestry of wolf ancestry and variation across Europe, which calls for nuanced, regional conservation plans founded in genetic monitoring.

genomics↗

bioRxiv2024

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management and no estimates of Ne have been obtained. In this study, we use countrys range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10-15,000 years ago. After that, a change in connectivity, a real decrease in size or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: [~]10,000 decreasing to 1,000-6,000 individuals), possibly indicating a fragmentation into coastal and inner subpopulations. In the most recent past, contemporary Ne is below or close to 500 (GONE: 116-580, NeEstimator: 107-549), suggesting a high risk of extinction. The populations at coastal Parks may have been small or isolated for several generations whereas the Boe Park one exhibit higher long-term Ne estimates and can be considered a stronghold of chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we try to overcome the limitations of obtaining high quality DNA sampling from wild threatened populations and estimate Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

genomics↗

bioRxiv2024

A 20+ Ma old enamel proteome from Canada's High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

In the past decade, ancient protein sequences have emerged as a valuable source of data for deep-time phylogenetic inference. Still, the recovery of protein sequences providing novel phylogenetic insights does not exceed 3.7 Ma (Pliocene). Here, we push this boundary back to 21-24 Ma (early Miocene), by retrieving enamel protein sequences of an early-diverging rhinocerotid (Epiaceratherium sp. - CMNF-59632) from the Canadian High Arctic. We recover partial sequences of seven enamel proteins (AHSG, ALB, AMBN, AMELX, AMTN, ENAM, MMP20) and over 1000 peptide-spectrum matches, spanning over at least 251 amino acids. Authentic endogeneity of these sequences is supported by indicators of protein damage, including several spontaneous and irreversible post-translational modifications accumulated during prolonged diagenesis and reaching near-complete occupancy at many sites. Bayesian tip-dating, across 15 extant and extinct perissodactyl taxa, places the divergence time of CMNF-59632 in the middle Eocene-Oligocene, and identifies a later divergence time for Elasmotheriinae in the Oligocene. The finding weakens alternative models suggesting a deep basal split between Elasmotheriinae and Rhinocerotinae. This divergence time of CMNF-59632 coincides with a phase of high diversification of rhinocerotids, and supports a Eurasian origin of this clade in the late Eocene or Oligocene. The findings are consistent with previous hypotheses on the origin of the enigmatic fauna of the Haughton crater, which, in spite of their considerable degree of endemism, also display similarity to distant Eurasian faunas. Our findings demonstrate the potential of palaeoproteomics in obtaining phylogenetic information from a specimen that is ten times older than any sample from which endogenous DNA has been obtained.

paleontology↗

bioRxiv2023

Whole mitogenome analysis highlights demographic history and shared connections among distal Indigenous groups of Mexico Complete mitogenome sequencing from 60 Mexican Native American groups

The study of mitochondrial DNA is a valuable tool to delve into the demographic history of human populations. Particularly in the Americas, five widespread Native American specific mitochondrial lineages have been identified. Here we included the complete mitogenome sequencing of 572 Indigenous individuals belonging to 60 populations spanning the Mexican territory. Our results show a great diversity of matrilineages widespread across the country, revealing shared mtDNA haplogroups in populations from distant regions. We identified all the five main Native American haplogroups clades, including 83 different subhaplogroups, from which nine are novel. The most frequent of the novel haplogroups was A2+64. A phylogenetic inference suggests that A2+64 comes from an ancestral maternal lineage that spread into the Caribbean islands. Additionally, a demographic reconstruction from whole mitogenomes showed an exponential increase in female Ne around 10 Ka ago in all the tested regions. All these findings suggest a genetic persistence through Mexico and possibly the Americas, in agreement with the model of the Mesoamerican-related expansion into the Caribbean and South America.

genetics↗

bioRxiv2023

Enamel proteins reveal biological sex and genetic variability within southern African Paranthropus

The evolutionary relationships among extinct African hominin taxa are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. For Paranthropus robustus, a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa 1,2 and the nature of intraspecific variation 3-6 are still disputed. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from four ca. 2 million year (Ma) old dental specimens attributed morphologically to P. robustus, from the site of Swartkrans. The identification of AMELY-specific peptides and semi-quantitative MS data analysis enabled us to determine the biological sex of all the specimens. Our combined molecular and morphometric data also provide compelling evidence of a significant degree of variation within southern African Paranthropus, as previously suggested based on morphology alone 6. Finally, the molecular data also confirm the taxonomic placement of Paranthropus within the hominin clade. This study demonstrates the feasibility of recovering informative Early Pleistocene hominin enamel proteins from Africa. Crucially, it also shows how the analysis of these proteins can contribute to understanding whether hominin morphological variation is due to sexual dimorphism or to taxonomic differences. We anticipate that this approach can be widely applied to geologically-comparable sites within South Africa, and possibly more broadly across the continent.

evolutionary biology↗

bioRxiv2023

Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf genetic affiliations and their taxonomic implications, we sequenced and analysed the genomes of a historical Korean wolf dated to the beginning of the 20th century, and a captive wolf originally located at the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find the Korean wolf has similar diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is more genetically similar to wolves from the Tibetan Plateau, hence, Korean wolf conservation programs might not benefit from the inclusion of this specimen.

evolutionary biology↗

bioRxiv2022

PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

Ancient proteins from fossilized or semi-fossilized remains can yield phylogenetic information at broad temporal horizons, in some cases even millions of years into the past. In recent years, peptides extracted from archaic hominins and long-extinct mega-fauna have enabled unprecedented insights into their evolutionary history. In contrast to the field of ancient DNA - where several computational methods exist to process and analyze sequencing data - few tools exist for handling ancient protein sequence data. Instead, most studies rely on loosely combined custom scripts, which makes it difficult to reproduce results or share methodologies across research groups. Here, we present PaleoProPhyler: a new fully reproducible pipeline for aligning ancient peptide data and subsequently performing phylogenetic analyses. The pipeline can not only process various forms of proteomic data, but also easily harness genetic data in different formats (CRAM, BAM, VCF) and translate it, allowing the user to create reference panels for phyloproteomic analyses. We describe the various steps of the pipeline and its many functionalities, and provide some examples of how to use it. PaleoProPhyler allows researchers with little bioinformatics experience to efficiently analyze palaeoproteomic sequences, so as to derive insights from this valuable source of evolutionary data.

bioinformatics↗

bioRxiv2022

Genomes of the extinct Sicilian wolf reveal a complex history of isolation and admixture with ancient dogs

The Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1-7. Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9, until human persecutions led them to extinction 1-7. There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspecies Canis lupus cristaldii 10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8x-11.6x) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM 11, around 17 kya, we explored the possibility that the Sicilian wolf retained ancestry from ancient wolf and dog lineages. Additionally, we explored whether the long-term isolation might have affected the genomic diversity, inbreeding levels and genetic load of the Sicilian wolf. Our findings show that the Sicilian wolves shared most ancestry with the modern Italian wolf population but are better modelled as admixed with European dog breeds, and shared traces of Eneolithic and Bronze age European dogs. We also find signatures of severe inbreeding and low genomic diversity at population and individual levels due to long-term isolation and drift, suggesting also low effective population size.

genomics↗

bioRxiv2022

The Rhizosphere Bacterial Communities Differ Among Domesticated Maize Landraces - An Experimental Confirmation

O_LIThe plant-associated microbiome has been shown to vary considerably between species and across environmental gradients. The effects of genomic variation on the microbiome within single species are less clearly understood, with results often confounded by the larger effects of climatic and edaphic variation. C_LIO_LIIn this study, the effect of genomic variation on the rhizosphere bacterial communities of maize was investigated by comparing different genotypes grown within controlled environments. Rhizosphere bacterial communities were profiled by metabarcoding the universal bacterial 16S rRNA v3-v4 region. Initially, plants from the inbred B73 line and the Ancho - More 10 landrace were grown for 12- weeks and compared. The experiment was then repeated with an additional four Mexican landraces (Apachito - Chih 172, Tehua - Chis 204, Serrano - Pueb 180 and Hairnoso de Ocho) that were grown alongside additional B73 and Ancho - More 10 genotypes. C_LIO_LIIn both experiments there were significant genotypic differences in the rhizosphere bacteria. Additionally, the bacterial communities were significantly correlated with genomic distance between genotypes, with the more closely related landraces being more similar in rhizosphere bacterial communities. C_LIO_LIDespite limited sampling numbers, here we confirm that genomic variation in maize landraces is associated with differences in the rhizosphere bacterial communities. Further studies that go beyond correlations to identify the mechanisms that determine the genotypic variation of the rhizosphere microbiome are required. C_LI

microbiology↗

bioRxiv2020

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable population reduction in the last 150 years due to human activities. The two white rhinoceros subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly after the onset of the decline, while the SWR recovered after a severe bottleneck. Such demographic events are predicted to have an erosive effect at the genomic level, in connection with the extirpation of diversity, and increased genetic drift and inbreeding. However there is currently little empirical data available that allows us to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore to assess these effects, we generated a whole-genome, temporal dataset consisting of 52 re-sequenced white rhinoceros genomes, that represents both subspecies at two time windows: before and during/after the bottleneck. Our data not only reveals previously unknown population substructure within both subspecies, but allowed us to quantify the genomic erosion undergone by both, with post-bottleneck white rhinoceroses harbouring significantly fewer heterozygous sites, and showing higher inbreeding coefficients than pre-bottleneck individuals. Moreover, the effective population size suffered a decrease of two and three orders of magnitude in the NWR and SWR respectively, due to the recent bottleneck. Our data therefore provides much needed empirical support for theoretical predictions about the genomic consequences of shrinking populations, information that is relevant for understanding the process of population extinction. Furthermore, our findings have the potential to inform management approaches for the conservation of the remaining white rhinoceroses.

evolutionary biology↗

bioRxiv2019

The genetic origins of Saint Helena’s liberated Africans

Between the early 16th and late 19th centuries, an estimated 12 million Africans were transported to the Americas as part of the transatlantic slave trade. Following Britains abolition of slave trade in 1807, the Royal Navy patrolled the Atlantic and intercepted slave ships that continued to operate. During this period, the island of St Helena in the middle of the South Atlantic served as a depot for \"liberated\" Africans. Between 1840 and 1867, approximately 27,000 Africans were disembarked on the island. To investigate their origins, we generated genome-wide ancient DNA data for 20 individuals recovered from St Helena. The genetic data indicate that they came from West Central Africa, possibly the area of present-day Gabon and Angola. The data further suggest that they did not belong to a single population, confirming historical reports of cultural heterogeneity among the islands African community. Our results shed new light on the origins of enslaved Africans during the final stages of the slave trade and illustrate how genetic data can be used to complement and validate existing historical sources.

genomics↗