Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus)

Abstract

Genetic analyses of bird subspecies designated as conservation units can address whether they represent units with independent evolutionary histories and provide insights into the evolutionary processes that determine the degree to which they are genetically distinct. Here we use mitochondrial DNA control region sequence and six microsatellite DNA loci to examine phylogeographical structure and genetic differentiation among five North American grasshopper sparrow (Ammodramus savannarum) populations representing three subspecies, including a population of the endangered Florida subspecies (A. s. floridanus). This federally listed taxon is of particular interest because it differs phenotypically from other subspecies in plumage and behaviour and has also undergone a drastic decline in population size over the past century. Despite this designation, we observed no phylogeographical structure among populations in either marker: mtDNA haplotypes and microsatellite genotypes from floridanus samples did not form clades that were phylogenetically distinct from variants found in other subspecies. However, there was low but significant differentiation between Florida and all other populations combined in both mtDNA (FST = 0.069) and in one measure of microsatellite differentiation (theta = 0.016), while the non-Florida populations were not different from each other. Based on analyses of mtDNA variation using a coalescent-based model, the effective sizes of these populations are large (approximately 80,000 females) and they have only recently diverged from each other (< 26,000 ybp). These populations are probably far from genetic equilibrium and therefore the lack of phylogenetic distinctiveness of the floridanus subspecies and minimal genetic differentiation is due most probably to retained ancestral polymorphism. Finally, levels of variation in Florida were similar to other populations supporting the idea that the drastic reduction in population size which has occurred within the last 100 years has not yet had an impact on levels of variation in floridanus. We argue that despite the lack of phylogenetic distinctiveness of floridanus genotypes the observed genetic differentiation and previously documented phenotypic differences justify continued designation of this subspecies as a protected population segment.

Concordant and Discordant Signals Between Genetic Data and Described Subspecies of Pacific Coast Song Sparrows

“…We strongly agree with other researchers that the use of a combination of characters (genetic, morphological, and behavioral) will determine whether groups differ enough to be considered unique units in taxonomy or conservation (Crandall et al 2000, Bulgin et al 2003, Remsen 2005, Spaulding et al 2006Winker et al 2007). Song Sparrows on Mandarte Island provide a good example of why a single-criterion approach can be misleading and why such data must be considered in the context of biologically meaningful patterns.…”

The function of seasonal song in a tropical resident species, the Red-throated Ant-tanager (Habia fuscicauda)

“…To determine genetic parentage, we used microsatellite analysis at three loci, two isolated from Cherrie's Tanager (loci: Rcaat11 and Rcaaag406, Ramphocelus costaricensis; Krueger and Williams 2006) and one from Grasshopper Sparrow (locus Asu18, Ammodramus savannarum; Bulgin et al 2003).…”

Fine-scale population structure and asymmetrical dispersal in an obligate salt-marsh passerine, the Saltmarsh Sparrow(Ammodramus caudacutus)

“…Four 15-to 25-lL multiplexed polymerase chain reactions were performed containing 2 lL of eluted genomic DNA, 0.1-0.7 lM of each dye-labeled primer, 2.0 mM MgCl 2 , 1X PCR buffer (Promega, Madison, Wisconsin, USA), 0.12 mM of deoxyribonucleotides, and 1 unit of Taq DNA polymerase (Promega). Cycling conditions for the Hanotte et al (1994), Bulgin et al (2003), and Hill et al (2008) primers followed Walsh et al (2012). Cycling conditions for the Ammo primers were as follows: 25 cycles of 948C for 30 s, 56-608C for 45 s, 728C for 1 min, and a final extension step at 728C for 5 min.…”