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

<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

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