BUSCADOR RECOLECTA

This study was mainly supported by European Union project LIFE14 NAT/ES/000077 and the Conservation Program for
the blue chaffinch implemented by the Cabildo de Gran Canaria. Frank Hailer and two anonymous reviewers made
valuable and constructive comments on the manuscript. JCI was funded by a research grant from the Spanish Ministry of
Science, Innovation and Universities, and the European Regional Development Fund (PGC2018-097575-B-I00;
PID2022-140091NB-I00) and a regional GRUPIN grant from the Regional Government of Asturias (AYUD/2021/51261).
The content of the paper is a contribution to the post-LIFE “LifePinzon” (http://lifepinzon.org/). We are very grateful to
Felipe Rodríguez, Ángel Cruz Moreno, Dolores Estévez and Ruth de O~nate for the help provided during the field-work in Inagua. Claire Jasinski improved the English of the manuscript. The Canarian Regional Government and the Cabildo of Gran Canaria provided the permits for ringing and taking biological samples from the Gran Canaria blue chaffinch (Ref.: 269/2017, 334/2018, 155/2020, 16/2020, 242/2021) and working within the natural protected areas of Gran Canaria (Ref.: 10588/2017, 16669/2020, 839/2021), some of them lasting two years.

Oceanic archipelagos are excellent systems for studying speciation, yet inference of evolutionary process requires that the colonization history of island organisms be known with accuracy. Here, we used phylogenomics and patterns of genetic diversity to infer the sequence and timing of colonization of Macaronesia by mainland common chaffinches (Fringilla coelebs), and assessed whether colonization of the different archipelagos has resulted in a species-level radiation. To reconstruct the evolutionary history of the complex we generated a molecular phylogeny based on genome-wide SNP loci obtained from genotyping-by-sequencing, we ran ancestral range biogeographic analyses, and assessed fine-scale genetic structure between and within archipelagos using admixture analysis. To test for a species-level radiation, we applied a probabilistic tree-based species delimitation method (mPTP) and an integrative taxonomy approach including phenotypic differences. Results revealed a circuitous colonization pathway in Macaronesia, from the mainland to the Azores, followed by Madeira, and finally the Canary Islands. The Azores showed surprisingly high genetic diversity, similar to that found on the mainland, and the other archipelagos showed the expected sequential loss of genetic diversity. Species delimitation methods supported the existence of several species within the complex. We conclude that the common chaffinch underwent a rapid radiation across Macaronesia that was driven by the sequential colonization of the different archipelagos, resulting in phenotypically and genetically distinct, independent evolutionary lineages. We recommend a taxonomic revision of the complex that takes into account its genetic and phenotypic diversity., The research was funded by Spain’s Ministry of Science grants CGL2015-66381P, PGC-2018-098897-B-I00, and PGC2018-097575-B-I00. MR was supported by a doctoral fellowship from the Spanish Ministry of Education, Culture, and Sport (FPU16/05724), and JCI was funded by a GRUPIN research grant from the Regional Government of Asturias (Ref.: IDI/2018/000151)., We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI)., Peer reviewed

G. Cardoso, R. Lopes, & P.G. Mota (Eds.) - Chapter one, Macaronesia is a biogeographic region comprising five oceanic archipelagos (Azores, Madeira, Selvagens, Canary Islands and Cabo Verde) with more than 30 principal volcanic islands (i.e. larger than 3 km2) showing a variable degree of erosion, and located in the northeastern Atlantic Ocean (Fig. 1.1). They show many floral and faunal affinities among archipelagos and with the European and African mainland wildlife. The different geographical positions of each archipelago in relation with the mainland (less than 100 km away from the mainland for the Canary Islands and more than 1300 km from the Azores), the huge variation of geological ages (0.035–25.7 million years (my)), altitudes (122–3.718 m above sea level) and latitudes (from 39°N to 15°N) provide a diverse collection of ecological conditions and unique biotas (Florencio et al., 2021)., Juan Carlos Illera was funded by two research grants from the Spanish Ministry of Science, Innovation and Universities, and the European Regional Development Fund (PGC2018-097575-B-I00; PID2022-140091NB-I00), and by a regional GRUPIN grant from the Regional Government of Asturias (AYUD/2021/51261)., Peer reviewed

Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequencing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome., This work was supported by the Max Planck Society (Max Planck Research Group grant MFFALIMN0001 to M.L.), the DFG (project Z02 and Nav05 within SFB 1372—Magnetoreception and Navigation in Vertebrates (project 395940726) to M.L.), and DFG Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). A.R. was supported by the Intramural Research Program of the NHGRI, NIH (1ZIAHG200398). J.C.I. was funded by two research grants from the Spanish Ministry of Science, Innovation and Universities, and the European Regional Development Fund (PGC2018-097575-B-I00; PID2022-140091NB-I00)., Peer reviewed

Human activities have been reshaping the natural world for tens of thousands of years, leading to the extinction of hundreds of bird species. Past research has provided evidence of extinction selectivity towards certain groups of species, but trait information is lacking for the majority of clades, especially for prehistoric extinctions identified only through subfossil remains. This incomplete knowledge potentially obscures the structure of natural communities, undermining our ability to infer changes in biodiversity across space and time. Biases in currently available trait data also limit our ability to identify drivers and processes of extinction. Here we present AVOTREX, an open-access database of species traits for all birds known to have gone extinct in the last 130,000 years. This database provides detailed morphological information for 610 extinct species.

For each extinct bird species, we provide information on the taxonomy, geographic location, and period of extinction. We also present data on island endemicity, flight ability and body mass, as well as standard measurements of external (matching the AVONET database of extant birds) and skeletal morphology from museum specimens where available. To ensure comprehensive morphological data coverage, we estimate all missing morphological measurements using a data imputation technique based on machine learning. This method can integrate measurements from different sources (i.e. skeletal and skin material), together with taxonomic information, and allows us to provide complete information on standard morphological traits of all known extinct birds., “la Caixa” Foundation: LCF/BQ/PI23/11970019, Junior Leader program; Ministerio de Ciencia, Innovación y Universidades: PGC2018-097575-B-I00; Ministerio de Ciencia, Innovación y Universidades: PID2022-140091NB-I00, Peer reviewed

Determining the effectiveness of conservation actions is a priority in conservationbiology, especially in island ecosystems which can host large numbers of endemicand often threatened species. In this study, we have brought together a genetic,body condition and breeding success assessment with the aim of evaluating theviability of a newly founded population of the endangered Gran Canaria blue chaf-finch (Fringilla polatzeki), the forest passerine species with the most restricted dis-tribution in the Western Palearctic. The species occurs exclusively in the Canarypine forests (Pinus canariensis) of the island of Gran Canaria, with the Inaguanature reserve harbouring the highest number individuals. In 2010, a translocationprogram was initiated within the same island in the nearby pine forests of La Cum-bre with the goal of establishing a viable breeding population. Genetic resultsrevealed that La Cumbre shows genetic parameters (diversity, inbreeding, and relat-edness) similar to the core source of Inagua, which contrasts with the reducedgenetic diversity expected due to the small size of the newly founded population.The biometric and body condition results (wing and tarsus length, body mass, andlength asymmetry of the tail feathers), together with the breeding success (nest sur-vival and number of fledglings per successful breeding attempt), were also similarin both populations. Overall, these findings suggest that the translocation programhas been successful and provide insights on the effectiveness of the actions per-formed. Our evaluation also delivers future avenues for the conservation planningin other upland forest endangered avian species inhabiting island ecosystems, espe-cially those threatened by the effects of global warming., This study was mainly supported by European Union project LIFE14 NAT/ES/000077 and the Conservation Program for the blue chaffinch implemented by the Cabildo de Gran Canaria. Frank Hailer and two anonymous reviewers madevaluable and constructive comments on the manuscript. JCI was funded by a research grant from the Spanish Ministry of Science, Innovation and Universities, and the European Regional Development Fund (PGC2018-097575-B-I00; PID2022-140091NB-I00) and a regional GRUPIN grant fromthe Regional Government of Asturias (AYUD/2021/51261)., Peer reviewed

We present the first synthesis of all known terrestrial endemic species extinctions in the biogeographical region of Macaronesia, covering all archipelagos (Azores, Madeira, Selvagens, the Canaries, and Cabo Verde) and multiple taxa (arthropods, birds, bryophytes, fungi, land molluscs, lichens, mammals, reptiles, and vascular plants). This list also includes information on the original distribution of extinct species, extinction chronologies, and likely causes of extinction, as reported by the original works' authors. Our survey identified 220 extinction records, with the highest numbers observed among land snails (111 species), arthropods (55), birds (27), and reptiles (15). The proportional impact of extinction was greatest among vertebrates: birds (50% of the original endemics lost), mammals (43%), and reptiles (28%). Very few extinctions were recorded in vascular plants or bryophytes, and none in fungi or lichens. However, these low levels of loss may partly reflect the scarcity of historical and fossil records for these taxa. Exactly half of the recorded endemic species losses (including nearly all vertebrates, as well as the arthropods and vascular plants) have extinction chronologies matching with the human occupation of the islands, providing a minimum estimate of the number of extinction events that may be directly or indirectly attributed to human activities., J.C.I. and J.C.R. were funded by two research grants from the Spanish Ministry of Science, Innovation and Universities and the European Regional Development Fund (PGC2018-097575-B-I00 and PID2022-140091NB-I00). J.P. was supported by the Spanish Ministry of Science and Innovation (MICINN) projects (PID2019-110538GA-I00 funded by MCIN/AEI /10.13039/501100011033 and PID2023-147122NB-I00 funded by MICIU/AEI /10.13039/501100011033 and FEDER, UE). E.F.-P. received financial support through a FPU grant (FPU2019-02379) from the Spanish Ministry of Science, Innovation and Universities., Peer reviewed

Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequencing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.