1 2013 Vol: 1. DOI: 10.7717/peerj.64

Conservation genetics of extremely isolated urban populations of the northern dusky salamander (Desmognathus fuscus) in New York City

Urbanization is a major cause of amphibian decline. Stream-dwelling plethodontid salamanders are particularly susceptible to urbanization due to declining water quality and hydrological changes, but few studies have examined these taxa in cities. The northern dusky salamander (Desmognathus fuscus) was once common in the New York City metropolitan area, but has substantially declined throughout the region in recent decades. We used five tetranucleotide microsatellite loci to examine population differentiation, genetic variation, and bottlenecks among five remnant urban populations of dusky salamanders in NYC. These genetic measures provide information on isolation, prevalence of inbreeding, long-term prospects for population persistence, and potential for evolutionary responses to future environmental change. All populations were genetically differentiated from each other, and the most isolated populations in Manhattan have maintained very little genetic variation (i.e. <20% heterozygosity). A majority of the populations also exhibited evidence of genetic bottlenecks. These findings contrast with published estimates of high genetic variation within and lack of structure between populations of other desmognathine salamanders sampled over similar or larger spatial scales. Declines in genetic variation likely resulted from population extirpations and the degradation of stream and terrestrial paths for dispersal in NYC. Loss of genetic variability in populations isolated by human development may be an underappreciated cause and/or consequence of the decline of this species in urbanized areas of the northeast USA.

Mentions
Figures
Figure 1: Map of study sites.Map of study sites in relation to urbanization in the NYC metropolitan area. Areas colored in shades of red and purple denote landscape areas with increasingly greater percentages of impervious surfaces as measured by the 2006 National Landcover Database (Homer et al., 2004). Figure 2: Results of evolutionary clustering analyses.A) bar plots from STRUCTURE analysis for estimated number of clusters K = 2 (top) and K = 6 (bottom). Sample sizes, N, appear on top of each sampling site. (B) Results of spatial clustering of groups in BAPS for K = 5. The X and Y axes represent geographic coordinates of the sampling sites. WR = Watchung Reservation (purple), CPW = Corson’s Brook Woods (blue), RB = Reed’s Basket Willow (yellow), HPS = South Highbridge Park (green), HPN = North Highbridge Park (red).
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    • . . . Other studies of small passerine birds have also reported weak to moderate genetic structure among urban populations, but without evidence of severe loss of genetic variation (Bjorklund, Ruiz & Senar, 2010; Vangestel et al., 2011; Unfried, Hauser & Marzluff, 2013). . . .
  58. DB Wake What salamanders have taught us about evolution Annual Review of Ecology and Systematics 40, 333-352 (2009) .
    • . . . Many salamanders including D. fuscus have large genomes (Wake, 2009), and more than five unlinked, genome-wide markers will be needed to estimate the timing of demographic events in urban populations with precision and accuracy . . .
  59. CJ Walsh; AH Roy; JW Feminella; PD Cottingham; PM Groffman; RP Morgan The urban stream syndrome: current knowledge and the search for a cure Journal of the North American Benthological Society 24, 706-723 (2005) .
    • . . . Population stability may be realized when salamanders disperse through multiple pathways in stream networks (Campbell Grant et al., 2010), but both streams (Walsh et al., 2005) and overland corridors (Munshi-South, 2012) are typically degraded in urban environments . . .
  60. HH Welsh; S Droege A case for using plethodontid salamanders for monitoring biodiversity and ecosystem integrity of North American forests Conservation Biology 15, 558-569 (2001) .
    • . . . Lungless salamanders (Family: Plethodontidae) are particularly understudied, despite their potential as bioindicators of habitat quality (Welsh & Droege, 2001) . . .
  61. J Willson; M Dorcas Effects of habitat disturbance on stream salamanders: implications for buffer zones and watershed management Conservation Biology 17, 763-771 (2003) .
    • . . . Furthermore, riparian buffer zones provide little protection in urbanized watersheds (Willson & Dorcas, 2003) . . .
  62. JA Wooten; CD Camp; LJ Rissler Genetic diversity in a narrowly endemic, recently described dusky salamander, Desmognathus folkertsi, from the southern Appalachian Mountains Conservation Genetics 11, 835-854 (2010) .
    • . . . An Appalachian endemic with a highly restricted range, D. folkertsi, also exhibited very little genetic structure across river drainages, although this result may be partly explained by human transport of these salamanders between sites (Wooten et al., 2010) . . .
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