Date: 26 September, 2021

Dataset Title: Dataset of genetic (microsatellite) and associated habitat data of salamanders (coastal giant salamanders; Dicamptodon tenebrosus) in Oregon, USA

Dataset Creators: Giorgia G. Auteri, L. Lacey Knowles, Raquel M. Marchán-Rivadeneira, and Deanna H. Olson 

Dataset Contact: Giorgia G. Auteri gauteri@umich.edu

Key Points:
- We consider genetic data (five microsatellite) from 318 individual salamanders (coastal giant salamanders; Dicamptodon tenebrosus) from Oregon, USA
- Salamanders were sampled from 23 different headwater sites within the state, permitting population and landscape genetics comparisons
- The primary genetic signature was that populations in the north had lower genetic diversity. This is likely because those sites were more recently colonized 
(or recolonized) following the post-Pleistocene glacial retreat
- Accompanying genetic signatures indicate locally fluctuating population sizes


Research overview

Determining the consequences of both historical and contemporary events can clarify the effects of the environment on population connectivity and inform 
conservation decisions. Historical events (like glaciations) and contemporary factors (like logging) can disrupt gene flow with potentially negative consequences. 
This is especially true among species with specialized ecological requirements and low dispersal ability, like amphibians. We test for the genetic consequences of 
historical and contemporary disturbances in the coastal giant salamander (Dicamptodon tenebrosus) in the Pacific Northwest of the United States. We consider 
predictions based on the contemporary landscape (habitat connectivity, logging, forest fires, and topography), in addition to relatively ancient isolation 
associated with post-Pleistocene range expansion (following the last glacial retreat). With a sampling design to assess regional and local genetic variation using 
five microsatellite markers, we found evidence of (i) historical regional isolation, with decreased genetic diversity among more recently colonized northern sites, 
as well as (ii) high levels of inbreeding and loss of heterozygosity at local scales, despite relatively low population differentiation (FST) or strong evidence for 
population bottlenecks. Moreover,  genetic diversity was not associated with contemporary disturbances (logging or fire), and contemporary landscape features 
(habitat fragmentation and topography) did not have detectable effects on genetic connectivity. Multiple explanations might be applied to explain any single 
genetic test or summary statistic, but joint consideration of the findings point to a population dynamic of instability of conservation concern in D. tenebrosus. 
That is, even in species with potentially higher levels of gene flow, their locally fluctuating population sizes may make them subject to high inbreeding and 
reduced heterozygosity, potentially masking any potential association with particular disturbance factors. Moreover, lower genetic diversity may persist at sites 
in northern compared to southern regions, despite gene flow among regions. As such, conservation plans should recognize that population connectivity itself may not 
be sufficient to override the detrimental effects of inbreeding and loss of heterozygosity that make species vulnerable. 


Methodology:
Salamanders were sampled July through September 2010. The five microsatellites considered were D6, D14, D17 (markers previously developed by Steele et al. 2008) and 
Dte 11 and Dte 14 (Curtis and Taylor 2009). 

	Steele CA, Baumsteiger J, Storfer A. Polymorphic tetranucleotide microsatellites for Cope’s giant salamander (Dicamptodon copei) and Pacific giant salamander 
(Dicamptodon tenebrosus). Molecular Ecology Resources. 2008;8(5):1071–3. 
	Curtis JM, Taylor EB. Isolation and characterization of microsatellite loci in the Pacific giant salamander Dicamptodon tenebrosus. Molecular Ecology. 
2000;9(1):116–8. 


Instrument and/or Software specifications: NA

Files contained here:

- DicamptodonDatabase.csv: 
	-Each row is data for an individual salamander (including the individual's original Sample ID). 
	-There are also columns denoting which of the five geographic sampling regions from within Oregon the sample was collected (Region; see published manuscript), and 
	-which of the separate drainage basins the individual was found in (Drainage). 
	-There following column denotes which of the 23 populations the salamander was sampled from (Population). 
	-The remaining columns denote how many microsatellite repeats each of the five sampled loci had. The species is diploid, therefore each marker has two values.
	 (There is one allele per column)

- PairwisePopData.csv: This file summarizes data based on population comparisons. 
	-Each row represents a comparison between two populations (1-23). 
	-The first two columns indicate which populations are being compared. 
	-This file includes data output from FSTAT (v. 2.9.3; FST values) and calculated in QGIS (distance and direction of populations from each other). 
		-Specifically, the FST column is a measure of genetic differentiation between the two populations. 
		-The Distance_km column is a measure of geographic distance between the populations as measured in kilometers. 
		-The Angle_CCW column is the direction of the second population from the first (measured in degrees counter-clock wise).
	-General Direction is provided in the final column (N for North, NW for northwest, etc.) as a confirmation to the Angle_CCW data.