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

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

<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

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

Median Joining network based on 311 bp of the mtDNA control region for 11 Razor-billed Curassows (left circle), and for 72 animals assigned to Alagoas Curassow based on the stringent analyses and Structure analyses using 98% threshold (right circle), with circle sizes reflecting the numbers of individuals.

<p>Green and red colors represent Alagoas and Razor-billed Curassow haplotypes, respectively, indicating Razor-billed maternal ancestry for six individuals assigned to Alagoas Curassow based on morphology and microsatellites. Hatches represent unobserved haplotypes.</p

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

Proportional membership of potential Alagoas Curassows (<i>Pauxi mitu</i>), and Razor-billed Curassows (<i>P</i>. <i>tuberosa</i>) obtained with 14 microsatellite loci.

<p><b>(A)</b> First stringent analysis performed in NewHybrids. <b>(B)</b> First stringent analysis performed in Structure.</p

Factorial Correspondence Analysis using 14 microsatellite loci.

<p>General overview of the genetic relationships among Razor-billed Curassows (red); individuals assigned to Alagoas Curassow based on morphology, microsatellites, and mtDNA (green); individuals assigned to Alagoas Curassow based on morphology and microsatellites, but excluded by mtDNA analysis (purple); individuals pointed out as admixted by microsatellites, using Structure 98% threshold (yellow), and individuals assigned as hybrids based on morphology (blue).</p