Mitochondrial DNA control region diversity in the endangered blue chaffinch, Fringilla teydea

Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review

A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10336-021-01893-x.

Habitat suitability-density relationship in an endangered woodland species: the case of the Blue Chaffinch (Fringilla polatzeki)

BACKGROUND

Understanding constraints to the distribution of threatened species may help to ascertain whether there are other suitable sectors for reducing the risks associated with species that are recorded in only one protected locality, and to inform about the suitability of other areas for reintroduction or translocation programs.

METHODS

We studied the Gran Canaria blue chaffinch (Fringilla polatzeki), a habitat specialist endemic of the Canary Islands restricted to the pine forest of Inagua, the only area where the species has been naturally present as a regular breeder in the last 25 years. A suitability distribution model using occurrences with demographic relevance (i.e., nest locations of successful breeding attempts analysed using boosted classification trees) was built considering orographic, climatic and habitat structure predictors. By means of a standardized survey program we monitored the yearly abundance of the species in 100 sectors since the declaration of Inagua as a Strict Nature Reserve in 1994.

RESULTS

The variables with the highest relative importance in blue chaffinch habitat preferences were pine height, tree cover, altitude, and rainfall during the driest trimester (July-September). The observed local abundance of the blue chaffinch in Inagua (survey data) was significantly correlated with habitat suitability derived from modelling the location of successful nesting attempts (using linear and quantile regressions). The outcomes of the habitat suitability model were used to quantify the suitability of other natural, historic, pine forests of Gran Canaria. Tamadaba is the forest with most suitable woodland patches for the species. We estimated a population size of 195-430 blue chaffinches in Inagua since 2011 (95% CI), the smallest population size of a woodland passerine in the Western Palearctic.

DISCUSSION

Habitat suitability obtained from modelling the location of successful breeding attempts is a good surrogate of the observed local abundance during the reproductive season. The outcomes of these models can be used for the identification of potential areas for the reintroduction of the species in other suitable pine forests and to inform forest management practices.

Population history of Berthelot's pipit: colonization, gene flow and morphological divergence in Macaronesia

The fauna of oceanic islands provide exceptional models with which to examine patterns of dispersal, isolation and diversification, from incipient speciation to species level radiations. Here, we investigate recent differentiation and microevolutionary change in Berthelot's pipit (Anthus berthelotii), an endemic bird species inhabiting three Atlantic archipelagos. Mitochondrial DNA sequence data and microsatellite markers were used to deduce probable colonization pathway, genetic differentiation, and gene flow among the 12 island populations. Phenotypic differentiation was investigated based on eight biologically important morphological traits. We found little mitochondrial DNA variability, with only one and four haplotypes for the control region and cytochrome b, respectively. However, microsatellite data indicated moderate population differentiation (FST=0.069) between the three archipelagos that were identified as genetically distinct units with limited gene flow. Both results, combined with the estimated time of divergence (2.5 millions years ago) from the Anthus campestris (the sister species), suggest that this species has only recently dispersed throughout these islands. The genetic relationships, patterns of allelic richness and exclusive alleles among populations suggest the species originally colonized the Canary Islands and only later spread from there to the Madeiran archipelago and Selvagen Islands. Differentiation has also occurred within archipelagos, although to a lesser degree. Gene flow was observed more among the eastern and central islands of the Canaries than between these and the western islands or the Madeiran Islands. Morphological differences were also more important between than within archipelagos. Concordance between morphological and genetic differentiation provided ambiguous results suggesting that genetic drift alone was not sufficient to explain phenotypic differentiation. The observed genetic and morphological differences may therefore be the result of differing patterns of selection pressures between populations, with Berthelot's pipit undergoing a process of incipient differentiation.

An application of control region sequence as a matrilineage marker for Elliot's pheasant of a zoo population

Control region sequence, an mtDNA marker, was usually used in phylogenesis analysis in species level or genetic structure study among populations. In this study, enlightened by its character of maternal heredity in vertebrates, we used control region sequence as a matrilineage marker for Elliot's pheasant (Syrmaticus ellioti) of Ningbo Zoo population. In Ningbo Zoo, 36 individuals of Elliot's pheasant were descendants from three female founders introduced in 1988. Three control region haplotypes (Ha, Hb, Hc) were identified by six variable nucleotide positions among the control region sequences over 36 individuals. The number of haplotypes was accorded with the number of female founders. Total 20 individuals (C04, C06, C08-11, C14, C20, C21, C23-29, C32, C34-36) shared haplotype a, while 12 individuals (C01, C05, C07, C12, C13, C16-19, C22, C30, C33) shared haplotype b and 4 individuals (C02, C03, C15, C31) shared haplotype c. Those individuals sharing the same haplotype were offspring from one female founder. In other words, there were three maternal lineages and the simple relationship among individuals was indicated. As a result, it seemed that the control region sequence was a useful marker for identification of matrilineage in this study. Meanwhile, the matrilineage information may be compensatory data if there were no any pedigree records in captive species for breeding management.

Colonisation and diversification of the blue tits (Parus caeruleus teneriffae-group) in the Canary Islands

The blue tit (Parus caeruleus teneriffae group) is proposed to have colonised the Canary Islands from North Africa according to an east-to-west stepping stone model, and today, the species group is divided into four subspecies, differing in morphological, acoustic, and ecological characters. This colonisation hypothesis was tested and the population structure between and within the islands studied using mitochondrial DNA sequences of the non-coding and relatively fast evolving control region. Our results suggest that one of the central islands, Tenerife, was colonised first and the other islands from there. Three of the presently recognised four subspecies are monophyletic, exception being the subspecies teneriffae, which consists of two monophyletic groups, the one including birds of Tenerife and La Gomera and the other birds of Gran Canaria. The Gran Canarian birds are well differentiated from birds of the other islands and should be given a subspecies status. In addition, the teneriffae subspecies group is clearly distinct from the European caeruleus group, and therefore the blue tit assemblage should be divided into two species.

Phylogeography of pipistrelle-like bats within the Canary Islands, based on mtDNA sequences

Evolution of three Canary Island Vespertilionid bat species, Pipistrellus kuhlii, Pipistrellus maderensis, and Hypsugo savii was studied by comparison of approximately 1 kbp of mtDNA (from cytochrome b and 16S rRNA genes) between islands. mtDNA reveals that both P. kuhlii and P. maderensis exist in sympatry on Tenerife (and possibly other islands). Their morphological similarity explains why their co-occurrence had not been detected previously. Levels of sequence divergence are quite low within P. maderensis. Haplotypes were either identical or separated by </=2 mutational steps on two of the islands (La Gomera and El Hierro). However there is sufficient between-island divergence between haplotypes from Tenerife, La Palma, and La Gomera/El Hierro to suggest that they could represent three evolutionary significant units (ESU). H. savii has an overlapping island distribution but a contrasting phylogeographical pattern. Most significantly, sequence divergence is greatest between La Gomera and El Hierro (>/=12 mutational steps) indicating colonization of the latter from the former sometime during the last approximately 1.2 Ma, with low subsequent gene flow. Unlike P. maderensis the El Hierro population alone appears to represent an ESU. The H. savii haplotypes detected in Gran Canaria and Tenerife are identical or separated by 1 mutational step.

Mitochondrial pseudo-control region in old world eagles (genus Aquila)

The mitochondrial pseudo-control region was analysed in five species of Aquila eagles. Indels caused great length differences in the nonrepetitive part of the region, whereas tandem repeat units were highly conserved among the genus. In a reconstructed phylogenetic tree, the clade formed by A. clanga and A. pomarina showed approximately the same distance to A. chrysaetos as did the clade A. heliaca/nipalensis. In Estonian subpopulations, 12 haplotypes were found among 51 A. pomarina individuals and 7 haplotypes among 8 A. clanga individuals. Nucleotide diversity in A. clanga was greater, and may be caused by decreased breeding density or by gene flow from other subpopulations.