Recent Changes in Genetic Diversity, Structure, and Gene Flow in a Passerine Experiencing a Rapid Population Decline, the Dupont’s Lark (Chersophilus duponti)

Abstract

Monitoring temporal dynamics in genetic diversity is of great importance for conservation, especially for threatened species that are suffering a rapid population decline and increased fragmentation. Here, we investigate temporal variation in genetic diversity, structure, and gene flow in the Dupont’s lark (Chersophilus duponti) across most of its range. This species shows increasing levels of population fragmentation, substantial population declines, and severe range contraction, so temporal losses of genetic diversity, increasing differentiation, and decreasing gene flow are expected when comparing present day data with previous situations. To address this, we resampled sites (nine regions in two countries) after 12–15 years (five-to-seven generations) and assessed changes in genetic parameters using 11 microsatellite markers. We found no substantial loss in genetic diversity over time at the species level, but we detected considerable variation among regions in the amount of allelic diversity and heterozygosity lost over time. Temporal variation in allele frequencies (common, rare, and private alleles), and changes in genetic differentiation and gene flow over time suggest a major role of connectivity for the stability of the overall metapopulation. Our results agree with the hypothesis that connectivity rescues genetic diversity via immigration and gene flow. However, evidence of recent genetic bottleneck and the substantial changes detected in some regions are clear signs of genetic erosion and may be signalling a rapid decline of the populations. Urgent actions must be carried out to stop and reverse human impacts on this threatened lark and its habitat.

DNA metabarcoding revealed how time and space do matter -sex does not- in the dietary variation of the endangered Dupont’s Lark

“…In Spain, sampling was conducted in spring, during the Dupont’s Lark breeding seasons (March-June) of 2017-2019 and in autumn, during the non-breeding season (September-November) of 2017. We collected fecal samples in 11 study sites distributed over five broad geographic regions throughout the range (see regions description in [41]) (Table 1, Fig 2): Northern Plateau (NP), Ebro Valley (EV), Iberian Range (IR), Southern Plateau (SP), and Southern Spain (SS). IR and EV regions are the main core areas of Dupont’s Lark, where the largest patches of continuous typical habitat of the species in Spain are found, whereas the rest are isolated and highly fragmented areas [42].…”

Landscape features influencing gene flow and connectivity of an endangered passerine

“…In the present study, we used the microsatellite loci genotypes obtained by Bustillo‐de la Rosa et al. ( 2022 ) where the DNA extraction protocol and PCR conditions are explained. Briefly, DNA was extracted from blood samples which were genotyped at 12 polymorphic microsatellite loci isolated in C. duponti (Méndez, Prats, et al., 2011 ).…”

“…Briefly, DNA was extracted from blood samples which were genotyped at 12 polymorphic microsatellite loci isolated in C. duponti (Méndez, Prats, et al., 2011 ). One locus showed no polymorphism and was removed from further analyses (Bustillo‐de la Rosa et al., 2022 ). Amplifications were performed in one multiplex panel using four dyes (FAM, PET, NED, VIC) in a 10 μL total volume containing: 25–50 ng of template DNA, 1× QIAGEN Multiplex PCR Master Mix and 0.1 μM of each forward and reverse primers.…”

“…Less than 1% of pairs exhibited a first‐order relationship (full‐sibling, parent‐offspring), thus all individuals were kept for analyses. Genetic population structure of Dupont's lark has been previously addressed with different genetic markers (Bustillo‐de la Rosa et al., 2022 ; García et al., 2008 ; Méndez, Tella, & Godoy, 2011 ), showing that there are both unique and shared clusters in Spain with some degree of gene flow among them. Thus, landscape genetic analyses were performed at the individual level, calculating genetic distance between all pairs of individuals, increasing the likelihood to find genetic differences at finer scales and to detect novel barriers to gene flow (Mulvaney et al., 2021 ; Pavlacky Jr. et al., 2009 ).…”

“…Less than 1% of pairs exhibited a first-order relationship (full-sibling, parent-offspring), thus all individuals were kept for analyses. Genetic population structure of Dupont's lark has been previously addressed with different genetic markers (Bustillo-de la Rosa et al, 2022;García et al, 2008;,…”