Pronounced Fixation, Strong Population Differentiation and Complex Population History in the Canary Islands Blue Tit Subspecies Complex

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible

Memories, museum artefacts and excavations in resolving the history of maternal lineages in the Finnhorse

We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Finnhorses, estimated the effective population sizes, and searched for both temporal and geographic population genetic structure. We observed high maternal haplotype and nucleotide diversity at the time during the foundation of the breed, and a decrease in both measures during 1931-1970. In addition, we observed losses of some haplotypes present in the early stages of the breed. There was only slight evidence of geographical or temporal population structure. This study is, to our knowledge, the first to use such temporal sampling to reveal the history of a specific animal breed.Peer reviewe

Memories, museum artefacts and excavations in resolving the history of maternal lineages in the Finnhorse

We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Finnhorses, estimated the effective population sizes, and searched for both temporal and geographic population genetic structure. We observed high maternal haplotype and nucleotide diversity at the time during the foundation of the breed, and a decrease in both measures during 1931-1970. In addition, we observed losses of some haplotypes present in the early stages of the breed. There was only slight evidence of geographical or temporal population structure. This study is, to our knowledge, the first to use such temporal sampling to reveal the history of a specific animal breed.Peer reviewe

Genetic differentiation between insular and continental populations of migratory and resident warblers, the Great Reed Warbler Acrocephalus arundinaceus and the Cetti's Warbler Cettia cetti Journal of Ornithology

[EN] Island populations are frequently smaller than continental populations, have lower genetic diversity, are more inbred and show genetic differentiation from the mainland ones. However, sufficient numbers of immigrants may reduce the differentiation of insular populations and moderate the effects of genetic drift. In this study, we compared insular and continental populations of Cetti¿s Warbler Cettia cetti and Great Reed Warbler Acrocephalus arundinaceus. We assessed the degree of genetic differentiation between insular and continental birds, their demographic history and genetic diversity. We compared the results, taking into account the differences in migration strategy and morphology of the two warblers. We found slightly lower genetic diversity in the insular populations than in the continental birds, possibly because of the lower population size or reduced immigration. The genetic differentiation between island and mainland birds was low, but higher in Cetti¿s Warbler than in the Great Reed Warbler, suggesting differences in the species¿ capability of crossing the sea. We found evidence for a past bottleneck in both the insular and continental populations of Cetti¿s Warbler, while for the Great Reed Warbler we found no signs of past population reductions. A high dispersal capability of the Great Reed Warbler may have allowed high gene flow, which may explain the observed interspecific differences in the demographic history of the Great Reed Warbler and Cetti¿s Warbler.We acknowledge M. Rebassa, H. Rguibi-Idrissi, M. Marin, J. Gomez, Santi, Luis, Kames and family and many others, who have helped us with the fieldwork. We would also like to thank the authorities of the Marjal de Pego-Oliva Natural Park, the S'Albufera de Mallorca Natural Park, the Consejeria de medio Ambiente y Desarrollo Rural de Castilla-La Mancha, the Servei de Conservacio de la Biodiversitat de la Generalitat Valenciana and the Haut Commissariat aux Eaux et Forets et a la lutte contre la desertification de Rabat, Morocco for providing the facilities to work in protected areas and for the relevant permits. We are grateful to M. Serra and the researchers and Ph.D. students of the Laboratory of Evolutionary Ecology (Institute Cavanilles of Biodiversity and Evolutionary Biology University of Valencia), for providing a laboratory for DNA extraction. This study has been partly financed by projects CGL2005-02041/BOS and CGL201021933-0O2-02 of the Spanish Ministry of Science and Innovation and by the University of Oulu. F. Ceresa was supported by an Atraent talent grant from the University of Valencia.Ceresa, F.; Belda, E.; Kvist, L.; Kajanus, M.; Monrós González, JS. (2018). Genetic differentiation between insular and continental populations of migratory and resident warblers, the Great Reed Warbler Acrocephalus arundinaceus and the Cetti's Warbler Cettia cetti Journal of Ornithology. Journal of Ornithology (Online). 159(3):703-712. https://doi.org/10.1007/s10336-018-1543-2S703712159

Does fragmentation of wetlands affect gene flow in sympatric Acrocephalus warblers with different migration strategies?

Wetlands are naturally patchy habitats, but patchiness has been accentuated by the extensive wetlands loss due to human activities. In such a fragmented habitat, dispersal ability is especially important to maintain gene flow between populations. Here we studied population structure, genetic diversity and demographic history of Iberian and North African populations of two wetland passerines, the Eurasian reed warbler Acrocephalus scirpaceus and the moustached warbler Acrocephalus melanopogon. These species are closely related and sympatric in our study sites, but the reed warbler is a long-distance migrant and widespread bird while the moustached warbler is resident or migrates over short distances, and breeds across a more discontinuous range. Using microsatellites and mtDNA data, we found higher population differentiation in moustached than in reed warbler, indicating higher dispersal capability of the latter species. Our results also suggest that the sea limits dispersal in the moustached warbler. For both species, we found evidence of gene flow between study sites, indicating the capability of compensating for habitat fragmentation. However, in most cases gene flow was restricted, possibly because of the large distances between study sites (from c. 290 to 960 km) or breeding site fidelity. Haplotype diversity was higher for the reed warbler, possibly because of a more important contribution of dispersal from different populations and the higher population size. Studying demographic history, we obtained signs of postglacial population growth for both species, and evidences of a recent colonization or re-colonization of the Mallorca Island by the moustached warblerWe acknowledge M. Rebassa, M. Marin, J. Gomez, Santi, Luis, Kames and family and many others, who have helped us with the field work. We would also like to thank the authorities of the Marjal de Pego-Oliva Natural Park, the S'Albufera de Mallorca Natural Park, 'Consejeria de medio Ambiente y Desarrollo Rural de Castilla-La Mancha', the 'Servei de Conservacio de la Biodiversitat de la Generalitat Valenciana' and the 'Haut Commissariat aux Eaux et Forets et a la lutte contre la desertification de Rabat, Morocco' for providing the facilities to work in protected areas and for the relevant permits. The people in these areas were always kind and have greatly helped us in sampling reed and moustached warblers. We are grateful to M. Serra and the researchers and PhD students of the Laboratory of Evolutionary Ecology (Inst. Cavanilles of Biodiversity and Evolutionary Biology - Univ. of Valencia), for providing the laboratory and useful advices for DNA extraction. This study has been funded by Projects CGL2005-02041/BOS and CGL2010-21933-C02-02 of the Spanish Ministry of Science and Innovation. FC was supported by an 'Atraent talent' grant from the Univ. of Valencia.Ceresa, F.; Belda, E.; Kvist, L.; Rguibi-Idrissi, H.; Monrós González, JS. (2015). Does fragmentation of wetlands affect gene flow in sympatric Acrocephalus warblers with different migration strategies?. Journal of Avian Biology. 46(6):577-588. doi:10.1111/jav.00589S57758846

Using genomic information for management planning of an endangered perennial, Viola uliginosa

Species occupying habitats subjected to frequent natural and/or anthropogenic changes are a challenge for conservation management. We studied one such species, Viola uliginosa, an endangered perennial wetland species typically inhabiting sporadically flooded meadows alongside rivers/lakes. In order to estimate genomic diversity, population structure, and history, we sampled five sites in Finland, three in Estonia, and one each in Slovenia, Belarus, and Poland using genomic SNP data with double-digest restriction site-associated DNA sequencing (ddRAD-seq). We found monophyletic populations, high levels of inbreeding (mean population F-SNP = 0.407-0.945), low effective population sizes (N-e = 0.8-50.9), indications of past demographic expansion, and rare long-distance dispersal. Our results are important in implementing conservation strategies for V. uliginosa, which should include founding of seed banks, ex situ cultivations, and reintroductions with individuals of proper origin, combined with continuous population monitoring and habitat management.Peer reviewe

Endangered subspecies of the reed bunting (Emberiza schoeniclus witherbyi and E. s. lusitanica) in Iberian Peninsula have different genetic structures

In the Iberian Peninsula, populations of two subspecies of the Reed Bunting Emberiza schoeniclus have become increasingly fragmented during the last decades when suitable habitats have been lost and/or the populations have gone extinct. Presently, both subspecies are endangered. We estimated the amount of genetic variation and population structure in order to define conservation units and management practices for these populations. We found that the subspecies lusitanica has clearly reduced genetic variation in nuclear and mitochondrial markers, has a drastically small effective population size and no genetic differentiation between populations. In contrast, the subspecies witherbyi is significantly structured, but the populations still hold large amounts of variation even though the effective population sizes are smaller than in the non-endangered subspecies schoeniclus. We suggest several management units for the Iberian populations. One unit includes subspecies lusitanica as a whole; the other three units are based on genetically differentiated populations of witherbyi. The most important genetic conservation measure in the case of lusitanica is to preserve the remaining habitats in order to at least maintain the present levels of gene flow. In the case of the three management units within witherbyi, the most urgent conservation measure is to improve the habitat quality to increase the population sizes.This project would not have been possible without the help of many people, among them A. Rodriguez, D. Bigas, P. Vicens, J. Segura, M. Suarez, J. L. Martinez, V. Urios, M. Rebassa, C. Torralvo, J. L. Hernandez, M. Carregal, P. Alcazar, J. L. Canto, J. Ramirez,, D. Alonso, J. Arizaga, F. Arcos, H. Rguibi, Acciona-Trasnmediterranea, and many others who helped us with the difficult task of sampling Reed Buntings and who sent us their samples. We apologize if we have forgotten someone. "Arcea Xestion de Recursos Naturais S. L." was of inestimable value in obtaining most of the samples from Galicia in 2008, in getting funding from the "Xunta de Galicia", and in helping us with the discussion of the results. We would like to thank the authorities of Daimiel National Park, Marjal Pego-Oliva Natural Park, S'Albufera de Mallorca Natural Park, Delta de L'Ebre Natural Park, "Consejeria de Medio Ambiente y Desarrollo Rural de Castilla La Mancha", "Servicio de Conservacion de la Diversidad del Gobierno de Navarra", "Direccion Xeral de Conservacion da Natureza de la Xunta Galicia and "Servei de Conservacio de la Biodiversitat de la Generalitat Valenciana" for the facilities to work in protected areas and for the appropriate permits to obtain the samples. The people from these protected areas were always very nice and helped us with the fieldwork. This study was funded by projects CGL2005-02041/BOS of the "Ministerio de Educacion y Ciencia" of Spain, and SC000207, Orden 14-12-2005 of the "Consejeria de Medio Ambiente y Desarrollo Rural de la Junta de Castilla La Mancha", Spain, through the "Ayudas para la realizacion de actuaciones de apoyo a la conservacion de las areas y recursos naturales protegidos, Orden 14-12-2005". The "Direccion Xeral de Conservacion da Natureza de la Xunta de Galicia", Spain, funded part of the fieldwork in NW Iberian Peninsula during the development of the Recovery plan for Emberiza schoeniclus lusitanica in Galicia. The experiments comply the current laws of the countries (Spain, Portugal and Finland) where they were done.Kvist, L.; Ponnikas, S.; Belda Perez, EJ.; Encabo, I.; Martinez, E.; Onrubia, A.; Hernandez, JM.... (2011). Endangered subspecies of the reed bunting (Emberiza schoeniclus witherbyi and E. s. lusitanica) in Iberian Peninsula have different genetic structures. 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Genetic differentiation in an endangered and strongly philopatric, migrant shorebird

Background Populations living in fragmented habitats may suffer from loss of genetic variation and reduced between-patch dispersal, which are processes that can result in genetic differentiation. This occurs frequently in species with reduced mobility, whereas genetic differentiation is less common among mobile species such as migratory birds. The high dispersal capacity in the latter species usually allows for gene flow even in fragmented landscapes. However, strongly philopatric behaviour can reinforce relative isolation and the degree of genetic differentiation. The Southern Dunlin (Calidris alpina schinzii) is a philopatric, long-distance migratory shorebird and shows reduced dispersal between isolated breeding patches. The endangered population of the Southern Dunlin breeding at the Baltic Sea has suffered from habitat deterioration and fragmentation of coastal meadows. We sampled DNA across the entire population and used 12 polymorphic microsatellite loci to examine whether the environmental changes have resulted in genetic structuring and loss of variation. Results We found a pattern of isolation-by-distance across the whole Baltic population and genetic differentiation between local populations, even within the southern Baltic. Observed heterozygosity was lower than expected throughout the range and internal relatedness values were positive indicating inbreeding. Conclusions Our results provide long-term, empirical evidence for the theoretically expected links between habitat fragmentation, population subdivision, and gene flow. They also demonstrate a rare case of genetic differentiation between populations of a long-distance migratory species. The Baltic Southern Dunlin differs from many related shorebird species that show near panmixia, reflecting its philopatric life history and the reduced connectivity of its breeding patches. The results have important implications as they suggest that reduced connectivity of breeding habitats can threaten even long-distance migrants if they show strong philopatry during breeding. The Baltic Southern Dunlin warrants urgent conservation efforts that increase functional connectivity and gene flow between breeding areas.Peer reviewe

CRISPR activation enables high-fidelity reprogramming into human pluripotent stem cells

Conventional reprogramming methods rely on the ectopic expression of transcription factors to reprogram somatic cells into induced pluripotent stem cells (iPSCs). The forced expression of transcription factors may lead to off-target gene activation and heterogeneous reprogramming, resulting in the emergence of alternative cell types and aberrant iPSCs. Activation of endogenous pluripotency factors by CRISPR activation (CRISPRa) can reduce this heterogeneity. Here, we describe a high-efficiency reprogramming of human somatic cells into iPSCs using optimized CRISPRa. Efficient reprogramming was dependent on the additional targeting of the embryo genome activation-enriched Alu-motif and the miR-302/367 locus. Single-cell transcriptome analysis revealed that the optimized CRISPRa reprogrammed cells more directly and specifically into the pluripotent state when compared to the conventional reprogramming method. These findings support the use of CRISPRa for high-quality pluripotent reprogramming of human cells.Peer reviewe