Variabilidade genética e estruturação populacional do Bicudinho-do-brejo-paulista, Formicivora paludicola (aves: Thamnophilidae): uma espécie criticamente ameaçada do estado de São Paulo

Small populations are more susceptible to genetic drift and inbreeding effects which, generally, can be associated to loss of genetic variability. Low levels of genetic diversity can result in severe effects in the individuals, as fertility alterations and capability of adaption to environmental changes. Although these factors can, in turn, increase the risk of extinction, gene flow may balance these effects, maintaining the genetic variability and reducing genetic divergences among populations. Therefore, it is essential to understand intra and inter population genetic data, in order to conserve threatened species. Molecular markers, such as microsatellites and SNPs (Single Nucleotide Polymorphisms), are reliable tools for assessing levels of genetic variability and patterns of gene flow in populations and have been widely used to analyze target species on conservation programs. The São Paulo marsh antwren (Formicivora paludicola) is a small bird restricted to marshes of Atlantic Forest that was recently described in the metropolitan region of São Paulo city. It occurs in 15 isolated localities spread on High Tietê and Paraíba do Sul River basins and, especially due to its habitat destruction, it is already considered as Critically Endangered in São Paulo State. Priorities actions for this species' conservation include genetic studies to establish the monitoring and management of natural populations. Therefore, the present study aimed to evaluate the genetic variability levels and the gene flow patterns of two populations of F. paludicola in order to support future conservation strategies for the species. As so, we analyzed 9 species-specific microsatellite loci and 8 additional heterologous loci, and also 1.227 SNPs loci that were developed by a RAD-seq (Restriction-site Associated DNA sequencing) approach. A total of 44 animals were collected in two marsh areas near Mogi das Cruzes city (MC) (N = 26) and Salesópolis city (SL) ...Populações pequenas são mais susceptíveis aos efeitos causados por deriva genética e endocruzamento o que, geralmente, está associado à perda de variabilidade genética. Baixos níveis de diversidade genética podem resultar em drásticas consequências nos indivíduos, como alterações nas taxas de fertilidade e capacidade de se adaptar a mudanças ambientais. Embora estes fatores possam elevar o risco de extinção, o fluxo gênico pode balancear estes efeitos, mantendo a variabilidade genética e diminuindo a divergência entre populações. Deste modo, conhecer as características genéticas intra e interpopulacionais é essencial quando se trata da conservação de espécies ameaçadas. Marcadores moleculares, como microssatélites e SNPs (Single Nucleotide Polymorphisms), são importantes ferramentas para acessar níveis de variabilidade genética e padrões de fluxo gênico em populações e vêm sendo amplamente utilizados em espécies alvo de programas de conservação. O bicudinho-do-brejo-paulista (Formicivora paludicola) é uma pequena ave restrita a brejos da Mata Atlântica que foi recentemente descrita na região metropolitana da cidade de São Paulo. Ocorre em 15 localidades isoladas situadas nas bacias do Alto Tietê e do rio Paraíba do Sul e, especialmente devido à destruição do seu hábitat, já está classificada como “Criticamente em Perigo” no estado de São Paulo. Ações prioritárias para a conservação da espécie incluem estudos genéticos para estabelecer o monitoramento e o manejo das populações naturais. Visto isso, o presente trabalho teve como objetivo avaliar os níveis de variabilidade genética e os padrões de fluxo gênico de duas populações de bicudinho-do-brejo-paulista, visando fornecer subsídios para futuras estratégias de conservação a serem desenvolvidas para a espécie. Para tanto, foram analisados 9 loci de microssatélites espécie-específicos e ...Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Marshes as “Mountain Tops”: Genetic Analyses of the Critically Endangered São Paulo Marsh Antwren (Aves: Thamnophilidae)

<div><p>Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The São Paulo Marsh Antwren (<i>Formicivora paludicola</i>) is a recently-described and critically endangered bird from São Paulo State (Brazil) whose total estimated population is around 250–300 individuals, distributed in only 15 isolated marshes around São Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall <i>F</i>_ST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8–99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants.</p></div

Novel and cross-amplified microsatellite loci for the critically endangered São Paulo marsh antwren Formicivora paludicola (Aves: Thamnophilidae)

The So Paulo marsh antwren (Formicivora paludicola) is a critically endangered bird endemic to marshes in the metropolitan region of So Paulo city, Brazil. The total population is estimated to be around 300 individuals, distributed among 15 small (&lt; 50 ha) fragments, suggesting that loss of genetic variability may affect the long-term viability of this species. To develop genetic tools for gaining information on effective population sizes, inbreeding and gene flow between populations, we describe nine polymorphic microsatellite loci isolated from a F. paludicola library using next-generation sequencing. We report on levels of variation in these novel microsatellites and eight additional heterologous loci in these birds. Expected (H (E)) and observed (H (O)) heterozygosities averaged 0.72 and 0.70, respectively, and the number of alleles per locus ranged from 3 to 10. These loci will permit evaluation of whether artificial translocations are necessary for long-term viability of this rare bird.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

<i>F</i>_ST and <i>F′</i>_ST (in parentheses) values between pairs of studied populations (above diagonal), and <i>R</i>_ST values (bellow diagonal).

<p>The overall <i>F</i>_ST, <i>F′</i>_ST, and <i>R</i>_ST values across all populations were 0.103, 0.344, and 0.097, respectively. All P values are < 0.01.</p

Number of analyzed individuals (<i>N</i>), average number of alleles per loci (<i>N</i>_A), allelic richness (<i>A</i>_R), observed (<i>H</i>_O) and expected (<i>H</i>_E) heterozygosities, inbreeding coefficient (<i>F</i>_IS), and its probability of being different from zero (<i>P</i>), across 17 microsatellite loci, found in three populations of the São Paulo Marsh Antwren.

<p>The critical P value after Bonferroni correction was 0.001. (SD: Standard Deviation).</p

Population structure and first generation migrants.

<p><b>(A)</b> Proportional membership (<i>Q</i>) of each São Paulo Marsh Antwren in the genetic clusters inferred by Structure (<i>K</i> = 3). This graphic represents each individual as a bar, and its membership probability in each cluster. Individuals <b>1</b> to <b>26</b>: Mogi das Cruzes population; Individuals <b>27</b> to <b>43</b>: Salesópolis population, and individuals <b>44</b> to <b>57:</b> São José dos Campos. Black arrows identify individuals indicated as first generation migrants. <b>(B)</b> Output graphics from Structure Harvester, indicating the higher value of <i>Ln P</i>(<i>K</i>) (left), and Δ<i>K</i> (right).</p

Probabilities of recent population decline obtained in BOTTLENECK for the three main populations of São Paulo Marsh Antwren across a range of variance values (4, 9, 16, and 25) used to parameterize the distribution of multi-step microsatellite mutations.

<p>Probabilities of recent population decline obtained in BOTTLENECK for the three main populations of São Paulo Marsh Antwren across a range of variance values (4, 9, 16, and 25) used to parameterize the distribution of multi-step microsatellite mutations.</p

Recovering the Genetic Identity of an Extinct-in-the-Wild Species: The Puzzling Case of the Alagoas Curassow

<div><p>The conservation of many endangered taxa relies on hybrid identification, and when hybrids become morphologically indistinguishable from the parental species, the use of molecular markers can assign individual admixture levels. Here, we present the puzzling case of the extinct in the wild Alagoas Curassow (<i>Pauxi mitu</i>), whose captive population descends from only three individuals. Hybridization with the Razor-billed Curassow (<i>P</i>. <i>tuberosa</i>) began more than eight generations ago, and admixture uncertainty affects the whole population. We applied an analysis framework that combined morphological diagnostic traits, Bayesian clustering analyses using 14 microsatellite loci, and mtDNA haplotypes to assess the ancestry of all individuals that were alive from 2008 to 2012. Simulated data revealed that our microsatellites could accurately assign an individual a hybrid origin until the second backcross generation, which permitted us to identify a pure group among the older, but still reproductive animals. No wild species has ever survived such a severe bottleneck, followed by hybridization, and studying the recovery capability of the selected pure Alagoas Curassow group might provide valuable insights into biological conservation theory.</p></div

Diagnostic morphological characteristics of Alagoas Curassow.

<p>Pure Alagoas Curassow (A1 and A2), hybrid (B1 and B2), and Razor-billed Curassow (C1 and C2).</p