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

Abstract

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.

The spatial genetic structure of the yellow-necked mouse in an urban environment – a recent invader vs. a closely related permanent inhabitant

“…Such a pattern has been suggested for many other species, including rodents (e.g. Gardner-Santana et al 2009;Munshi-South and Kharchenko 2010;Munshi-South et al 2013;Gortat et al 2013Gortat et al , 2015a. However, given the very recent colonization of Warsaw by A. flavicollis, a clearly pronounced genetic structure was rather unexpected.…”

“…Seeking a better understanding of how an urban environment can affect population processes in various species, molecular genetics methods have long been applied to analyse gene flow within urbanized landscapes and among urban landscapes and surrounding rural areas, as well as to estimate genetic variability in urban populations of wild species (e.g. Noël et al 2007;Gardner-Santana et al 2009;Gortat et al 2013Gortat et al , 2015aMunshi-South et al 2013). …”

“…amphibians), often related to a specific environment, such as water bodies, exhibit decreased genetic variability due to isolation and intensified genetic drift (Hitchings and Beebee 1998;Noël et al 2007;Noël and Lapointe 2010;Mikulič and Pišút 2012;Munshi-South et al 2013;Zak and Pehek 2013, but see also Saarikivi et al 2013); (ii) mobile species able to cross environmental barriers seem to maintain a high level of genetic variability, probably avoiding complete isolation between patches of habitat within the city as well as between urban and rural areas (Desender et al 2005;Gardner-Santana et al 2009;Rutkowski et al 2009;Bj rklund et al 2010;Munshi-South and Kharchenko 2010); (iii) urban populations, usually fragmented into local subpopulations inhabiting small patches of suitable habitats (e.g. green spaces), exhibit pronounced genetic structure (Rubin et al 2001;Wood and Pullin 2002;Wandeler et al 2003;Desender et al 2005;Gardner-Santana et al 2009;Bj rklund et al 2010;Delaney et al 2010;Munshi-South and Kharchenko 2010;Vangestel et al 2011;Gortat et al 2013Gortat et al , 2015aMunshi-South et al 2013;Unfried et al 2013).…”

Anthropopressure gradients and the population genetic structure of Apodemus agrarius

“…The process of fragmentation and isolation, followed by subsequent genetic drift and increased relatedness among individuals, has been confirmed not only in the case of animals of low mobility (e.g. Noël et al 2007;Noël and Lapointe 2010;Mikulič and Pišút 2012;Munshi-South et al 2013), but also for mobile ''active colonizers'' (Wandeler et al 2003;Rasner et al 2004;Evans et al 2009). However, there are many other examples including small mammals (Mossman and Waser 2001;Gardner-Santana et al 2009;Munshi-South and Kharchenko 2010), which suggest that genetic variability within an urban environment may not necessarily be decreased in comparison with ex-urban populations.…”

Ecological Characteristics of Two Closely Related Rodent Species in Urban Environment—Permanent Inhabitant vs Newcomer

“…Different abiotic conditions in cities and the spatial structure supporting the isolation of small patches of the environment frequently lead to greater genetic differentiation between isolated local populations within cities and in comparison to natural populations [2] [12]. Additionally, within isolated local populations, genetic variability is frequently reduced and the degree of relatedness between individuals is increased [13] [14], in particular in species with a limited mobility [15] [16] for whom crossing anthropogenic barriers is difficult or impossible.…”