The role of hybridization in shaping evolutionary divergence

Dissertação de Mestrado em Antropologia, apresentada ao Departamento de Ciências da Vida da Faculdade de Ciências e Tecnologia da Universidade de Coimbra.O Adro da Igreja Velha de S. Pedro da Sobreira (Paredes) funcionou como cemitério entre o séc. XIII e os finais do Século XIX. Durante as intervenções arqueológicas realizadas em 2007 e 2008, foram identificadas oitenta sepulturas, de várias tipologias (de forma oval e escavadas no solo, sepulturas formadas por lajes de xisto verticalizadas e caixões incluídos em sepulturas de lajes de xisto, que terão sito reaproveitadas), das quais trinta e duas continham material osteológico, correspondente a um número mínimo de noventa indivíduos (oitenta e três adultos e sete não-adultos). Dos quarenta e um esqueletos, foi possível diagnosticar o sexo para vinte e sete indivíduos, sendo onze do sexo feminino e dezasseis do sexo masculino. Os objetivos do presente estudo relacionam-se com a reconstrução do modus vivendi dos indivíduos exumados do Adro da Igreja Velha de S. Pedro da Sobreira., através da construção do perfil demográfico. No que concerne aos marcadores de stress fisiológico verificou-se uma elevada frequência de hipoplasias do esmalte dentário (151/221 – 68,3%), e percentagens elevadas para os marcadores específicos de stress: vinte e sete crânios (de cinquenta e um observados) apresentam hiperostose porótica (52,9%); e treze órbitas, de vinte e três, exibem cribra orbitalia (56,5%). Também a patologia infeciosa apresenta uma frequência elevada nesta população, com duzentos e noventa ossos – de setecentos e trinta e cinco observados – a mostrarem algum tipo de lesão devida a patologia infeciosa (39,5%). O estado nutricional dos indivíduos e as condições de patologia infeciosa podem ter comprometido a sua qualidade de vida. A patologia neoplásica inclui a presença de um fibroma não ossificante no fémur esquerdo de um indivíduo do sexo masculino, com uma idade à morte superior a quarenta anos. É ainda relevante a presença de um indivíduo adulto jovem, do sexo masculino, que desenvolveu um mieloma múltiplo. Finalmente, a patologia oral apresenta frequências elevadas, o que deverá ser devido ao tipo de alimentação consumida (dieta baseada em produtos vegetais), à falta de tratamento dentário e à pobre higiene oral. O estudo desenvolvido na amostra exumada no Adro da Igreja Velha de S. Pedro da Sobreira (século XIII a finais do século XIX) permitiu a caracterização do modo de vida destes indivíduos e proporcionou dados que podem contribuir para um conhecimento mais alargado do perfil das populações que viveram durante a Idade Média em Portugal.The churchyard of the Old Church of S. Pedro da Sobreira (Paredes) worked as a cemetery between the 13th century and the end 19th century. During the archaeological excavations carried out in 2007 and 2008, eighty graves were identified, of which thirty two contained osteological material, corresponding to a minimum of ninety individuals (eighty-three adults and seven subadults). Of the forty-one skeletons, it was possible to diagnose the sex into twenty-seven subjects (eleven females and sixteen males). The objectives of the study are related to the reconstruction of the modus vivendi of individuals exhumed from the churchyard of the Old Church of S. Pedro da Sobreira, through the construction of demographic profile. With regard to physiological stress markers, there was a high frequency of dental enamel hypoplasias (151/221 - 68.3%), and high percentages for specific markers of stress: twenty-seven skulls (in fifty-one observed) present porotic hyperostosis (52.9%), and thirteen orbits, of the twenty-three, display cribra orbitalia (56.5%). Infectious disease also presents a high frequency in this population, with two hundred and ninety bones - of seven hundred thirty-five observed - to show some kind of injury due to infectious disease (39.5%). The nutritional status of individuals and conditions of infectious disease may have compromised their quality of life. The neoplastic pathology includes the presence of a non-ossifying fibroma in the left femur of a male individual with an age at death over forty years. It is significant the presence of an adult young male who developed multiple myeloma. Finally, oral pathology presents high frequencies, which should be due to the type of food consumed (diet based on plant products), lack of dental care and poor oral hygiene. The study conducted in individuals exhumed in Churchyard of Old Church of S. Pedro da Sobreira (13th century and the end 19th century) allowed the characterization of the lifestyle of this individuals and provided data that may contribute to a broader understanding of the profile of the people who lived during the Middle Ages in Portugal

Genetic modification of the ant Lasius niger using CRISPR-Cas9 technology

Abstract CRISPR-Cas9 has become one of the most prominent gene editing tools available and it has been utilized in various organisms from bacteria to fungi, plants, and animals. In this study, we developed a CRISPR-Cas9 protocol for the black garden ant Lasius niger, a common and easily available study species for lab and field experiments. To create indel mutations using CRISPR-Cas9 in L. niger, we targeted three different locations in a well-studied eye pigmentation gene cinnabar, generating several mutations that disrupt the ommochrome biosynthesis pathway and result in the lack of the pigment and therefore, abnormal eye coloration in adult workers. We also developed a protocol to collect L. niger eggs, inject them with CRISPR-Cas9 construct, and rear the eggs into mature adult workers with the assistance of nursing workers. We demonstrated for the first time in L. niger that CRISPR-Cas9 is an excellent tool to create targeted mutations for this species. Our protocol can be referred to when developing similar studies for other species of ants and eusocial insects.CRISPR-Cas9 has become one of the most prominent gene editing tools available and it has been utilized in various organisms from bacteria to fungi, plants, and animals. In this study, we developed a CRISPR-Cas9 protocol for the black garden ant Lasius niger, a common and easily available study species for lab and field experiments. To create indel mutations using CRISPR-Cas9 in L. niger, we targeted three different locations in a well-studied eye pigmentation gene cinnabar, generating several mutations that disrupt the ommochrome biosynthesis pathway and result in the lack of the pigment and therefore, abnormal eye coloration in adult workers. We also developed a protocol to collect L. niger eggs, inject them with CRISPR-Cas9 construct, and rear the eggs into mature adult workers with the assistance of nursing workers. We demonstrated for the first time in L. niger that CRISPR-Cas9 is an excellent tool to create targeted mutations for this species. Our protocol can be referred to when developing similar studies for other species of ants and eusocial insects.Peer reviewe

Assembly of a Hybrid Formica aquilonia × F. polyctena Ant Genome From a Haploid Male

Publisher Copyright: © 2022 The American Genetic Association..Formica red wood ants are a keystone species of boreal forest ecosystems and an emerging model system in the study of speciation and hybridization. Here, we performed a standard DNA extraction from a single, field-collected Formica aquilonia × Formica polyctena haploid male and assembled its genome using ~60× of PacBio long reads. After polishing and contaminant removal, the final assembly was 272 Mb (4687 contigs, N50 = 1.16 Mb). Our reference genome contains 98.5% of the core Hymenopteran BUSCOs and was pseudo-scaffolded using the assembly of a related species, F. selysi (28 scaffolds, N50 = 8.49 Mb). Around one-third of the genome consists of repeats, and 17 426 gene models were annotated using both protein and RNAseq data (97.4% BUSCO completeness). This resource is of comparable quality to the few other single individual insect genomes assembled to date and paves the way to genomic studies of admixture in natural populations and comparative genomic approaches in Formica wood ants.Peer reviewe

Insights into the Evolution of the CSP Gene Family through the Integration of Evolutionary Analysis and Comparative Protein Modeling

Peer reviewe

Genome organization and molecular characterization of the three Formica exsecta viruses—FeV1, FeV2 and FeV4

We present the genome organization and molecular characterization of the three Formica exsecta viruses, along with ORF predictions, and functional annotation of genes. The Formica exsecta virus-4 (FeV4; GenBank ID: MF287670) is a newly discovered negative-sense single-stranded RNA virus representing the first identified member of order Mononegavirales in ants, whereas the Formica exsecta virus-1 (FeV1; GenBank ID: KF500001), and the Formica exsecta virus-2 (FeV2; GenBank ID: KF500002) are positive single-stranded RNA viruses initially identified (but not characterized) in our earlier study. The new virus FeV4 was found by re-analyzing data from a study published earlier. The Formica exsecta virus-4 genome is 9,866 bp in size, with an overall G + C content of 44.92%, and containing five predicted open reading frames (ORFs). Our bioinformatics analysis indicates that gaps are absent and the ORFs are complete, which based on our comparative genomics analysis suggests that the genomes are complete. Following the characterization, we validate virus infection for FeV1, FeV2 and FeV4 for the first time in field-collected worker ants. Some colonies were infected by multiple viruses, and the viruses were observed to infect all castes, and multiple life stages of workers and queens. Finally, highly similar viruses were expressed in adult workers and queens of six other Formica species: F. fusca, F. pressilabris, F. pratensis, F. aquilonia, F. truncorum and F. cinerea. This research indicates that viruses can be shared between ant species, but further studies on viral transmission are needed to understand viral infection pathways.Peer reviewe

Differences in Thermal Tolerance between Parental Species Could Fuel Thermal Adaptation in Hybrid Wood Ants

Genetic variability is essential for adaptation and could be acquired via hybridization with a closely related lineage. We use ants to investigate thermal adaptation and the link between temperature and genetic variation arising from hybridization. We test for differences in cold and heat tolerance between Finnish Formica polyctena and Formica aquilonia wood ants and their naturally occurring hybrids. Using workers, we find that the parental individuals differ in both cold and heat tolerances and express thermal limits that reflect their global distributions. Hybrids, however, cannot combine thermal tolerance of parental species as they have the same heat tolerance as F. polyctena but not the same cold tolerance as F. aquilonia. We then focus on a single hybrid population to investigate the relationship between temperature variation and genetic variation across 16 years using reproductive individuals. On the basis of the thermal tolerance results, we expected the frequency of putative F. polyctena alleles to increase in warm years and F. aquilonia alleles to increase in cold years. We find support for this in hybrid males but not in hybrid females. These results contribute to understanding the outcomes of hybridization, which may be sex specific or depend on the environment. Furthermore, genetic variability resulting from hybridization could help hybrid wood ants cope with changing thermal conditions.Peer reviewe

Rapid and predictable genome evolution across three hybrid ant populations

Funding Information: This work was supported by Academy of Finland (www.aka.fi) no. 328961 and HiLIFE (www2.helsinki.fi/en/helsinki-institute-of-lifescience) grants to JK. SHM was supported by a Royal Society University Research Fellowship URF \R1\180682 (www.royalsociety.org). VCS was supported by Fundação Ciência e Tecnologia CEECINST/00032/2018/CP1523/CT0008 and UIDB/00329/2020 grants (www.fct.pt). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank G. Barroso for assistance with iSMC, the SpecIAnt group for feedback, and CSC–IT Center for Science, Finland, for computational resources. This work was performed under the Global Ant Genomics Alliance. Publisher Copyright: Copyright: © 2022 Nouhaud et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Hybridization is frequent in the wild but it is unclear when admixture events lead to predictable outcomes and if so, at what timescale. We show that selection led to correlated sorting of genetic variation rapidly after admixture in 3 hybrid Formica aquilonia × F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.Peer reviewe