Population Genomics of the Critically Endangered Brazilian Merganser

Abstract

The Brazilian merganser (Mergus octosetaceus) is one of the most endangered bird species in South America and comprises less than 250 mature individuals in wild environments. This is a species extremely sensitive to environmental disturbances and restricted to a few "pristine" freshwater habitats in Brazil, and it has been classified as Critically Endangered on the IUCN Red List since 1994. Thus, biological conservation studies are vital to promote adequate management strategies and to avoid the decline of merganser populations. In this context, to understand the evolutionary dynamics and the current genetic diversity of remaining Brazilian merganser populations, we used the "Genotyping by Sequencing" approach to genotype 923 SNPs in 30 individuals from all known areas of occurrence. These populations revealed a low genetic diversity and high inbreeding levels, likely due to the recent population decline associated with habitat loss. Furthermore, it showed a moderate level of genetic differentiation between all populations located in four separated areas of the highly threatened Cerrado biome. The results indicate that urgent actions for the conservation of the species should be accompanied by careful genetic monitoring to allow appropriate in situ and ex situ management to increase the long-term species' survival in its natural environment.

Keywords: Brazilian Cerrado; anseriformes; conservation genetics; endangered species; neotropical bird; neotropics.

Figure 1

Historical and current population distribution of Mergus octosetaceus. The red area highlights the historical geographic occurrence of M. octosetaceus across Brazil, Argentina, and Paraguay (left map). The black dots represent the collection sites of samples from all four remaining populations in central Brazil (right map in detail): Canastra—Serra da Canastra National Park; Jalapão—Jalapão State Park; Veadeiros—Chapada dos Veadeiros National Park; Paranaíba—Alto Paranaíba region.

Figure 2

Heatmap depicting kinship indices, corrected by Pearson’s correlation matrix among individuals from Canastra (CAN). Paranaíba (PAR), Veadeiros (VEA) and Jalapão (JAL). The values on the map range from −1 (negative correlation, represented in blue) to 1 (positive correlation, represented in red).

Figure 3

Inbreeding coefficients of 30 Mergus octosetaceus individuals from the four remaining populations (CAN—Canastra, PAR—Paranaíba, VEA—Veadeiros, and JAL—Jalapão). Positive inbreeding coefficients appear in blue (above) and negative ones in brown (below). The samples are in descending order of inbreeding coefficients.

Figure 4

PCA analysis using 923 SNPs for 22 unrelated individuals. Green—individuals from Canastra (CAN); blue—individuals from the Jalapão (JAL); orange—individuals from the Paranaíba (PAR); pink—individuals from Veadeiros (VEA).

Figure 5

DAPC analysis using 923 SNPs for 22 unrelated individuals. Green—individuals from Canastra; blue—individuals from the Jalapão; orange—individuals from the Paranaíba; pink—individuals from Veadeiros.

Figure 6

Population attribution analyses. (A) Graphic representation of the probability of every individual to belong to a determined “genetic population” (four assigned populations, k = 4) using adegenet/compoplot tool. (B) Structure result using the uncorrelated model and k = 2, excluding 1st-degree related individuals. Red—common alleles in the Canastra/Paranaíba cluster; Green—common alleles in the group formed by Veadeiros and Jalapão. (C) Geneland graphic showing the spatial distribution of three genetic clusters formed by Mergus octosetaceus individuals. Green—population of the Jalapão; White—population of Veadeiros; Yellow—populations of Canastra and Paranaíba. Geographic coordinates for samples/localities are shown as black dots (see Table S1), and at right it is shown a graphic with the associated probabilities to the estimated number of clusters.

Figure 7

Phylogenetic tree (maximum clade credibility tree) using a Bayesian Inference with 923 SNPs from Mergus octosetaceus individuals. Posterior probabilities (PP) are depicted on each node. There is no outgroup assigned.