The use of microsatellite loci for accurate hybrid detection in a recent contact zone between an endangered and a recently-arrived hummingbird

Abstract

Interspecies hybridisation frequently occurs when the distributional ranges of two closely-related species overlap after a period of geographic isolation. From a conservation perspective, such hybridisation events can incur detrimental effects on the viability of each species involved, especially for species which are already threatened by other ecological processes, such as humaninduced declines in population size. The early and accurate detection of hybrids within recent contact zones is therefore of crucial importance for conservation strategies. A recent contact zone occurs in the north of Chile between the endangered Chilean Woodstar (Eulidia yarrellii) and the non-native and recently-arrived Peruvian Sheartail (Thaumastura cora), which expanded its range from Peru into Chile during the 1970s. Several factors suggest that these species may be hybridising. We here describe a set of microsatellite loci which prove to be a powerful tool in detecting F1 hybrids and backcrosses between the two species. These loci will be an invaluable tool for future research to ascertain the degree of hybridisation that is occurring between the two species and to devise appropriate conservation strategies.

Comparative Assessment of Genetic and Morphological Variation at an Extensive Hybrid Zone between Two Wild Cats in Southern Brazil

“…The use of a more conservative threshold (0.8) led to an underestimation of hybrids in the population due to the larger overlap of values found for pure animals and backcrosses. Such a problem has also been reported in other studies that used simulated genotypes in hybrid analyses [10] , [11] , [34] , [35] .…”

Decline of unionid mussels enhances hybridisation of native and introduced bitterling fish species through competition for breeding substrate

“…We used a threshold value for the posterior probability of q = 0.5 with assignment to the aforementioned categories following van Dongen et al. (2012). Parameters used in NewHybrids were set as follows: without individual or allele frequency prior information; Jeffreys‐like prior for both mixing proportions and allele frequencies; 25,000 sweeps of burn‐in; and 100,000 iterations of the Markov chain Monte Carlo.…”

“…The optimum K value was two ( Figure S2) calculated by Structure Harvester version 0.6.94 (Earl & vonHoldt, 2012). We used a threshold q-value of 0.20 and defined hybrids as those with more than 20% of their genetic contents matching both purebred types (Vähä & Primmer, 2006). Using NewHybrids (Anderson & Thompson, 2002) we further assigned each individual to one of six genotypic classes based on the posterior probabilities: the two parental species (P 0 , P 1 ), first-generation hybrid (F 1 ), secondgeneration hybrid (F 2 ), backcross of F 1 with P 0 , and backcross of F 1 with P 1 .…”

Hybridization between an endangered freshwater fish and an introduced congeneric species and consequent genetic introgression

“…We used NewHybrids [45] to assign each individual to one of six genotypic classes based on the posterior probabilities: the two parental species (P0, P1), first-generation hybrid (F1), second-generation hybrid (F2), backcross of F1 with P0, and backcross of F1 with P1. We used 0.5 as a threshold value for the posterior probability ( q ) with their assignment following [46]. Parameters of NewHybrids were set as follows: without individual or allele frequency prior information; Jeffreys-like prior for both mixing proportions and allele frequencies; 25,000 sweeps of burn-in; and 100,000 iterations of the Markov chain Monte Carlo.…”