DOI: 10.5061/dryad.np5hqc048
title: Data from: Characterizing population structure and documenting rapid loss of genetic diversity in Chiricahua Leopard Frogs (Lithobates chiricahuensis) with high throughput microsatellite genotyping

description: The use of molecular markers to assess genetic diversity has become a
 common component of recovery action plans for threatened and endangered
 species. In this study, we use an unusually large number of microsatellite
 markers (N = 91) to characterize the genetic variation of Chiricahua
 Leopard Frogs (Lithobates chiricahuensis) across their range in order to
 understand their distribution of genetic variation, identify genetic
 bottlenecks, and measure genetic changes over time in a single,
 highly-managed population. Populations were best divided into three
 genetically distinct clusters, with the southeastern Arizona and New
 Mexico populations forming distinct genetic clusters. While there is
 moderate genetic variation distributed across the sampled populations,
 each population on its own shows relatively low allelic diversity. Most
 populations displayed strong genetic signals of recent population
 bottlenecks or a deficiency of heterozygous genotypes that is typically
 associated with frequent inbreeding. Populations that have a history of no
 management through translocations harbored the greatest number of unique
 alleles and overall allelic richness, especially in a subset of the
 Mexican populations. Finally, long-term cohort sampling at one specific
 site (the Southwestern Research Station in Portal, Arizona) allowed us to
 demonstrate how rapidly genetic diversity can decrease across a matter of
 years in a population with few founders. This work shows how
 microsatellite markers can provide important context for conservation
 agencies, but even a large suite of markers beyond what is typical may not
 be enough for populations that are extremely bottlenecked and have low
 levels of standing genetic diversity.
description: # Characterizing population structure and documenting rapid loss of
 genetic diversity in Chiricahua Leopard Frogs (Lithobates chiricahuensis)
 with high throughput microsatellite genotyping
 [https://doi.org/10.5061/dryad.np5hqc048](https://doi.org/10.5061/dryad.np5hqc048) ## Description of the data and file structure "Frog_R_matrix_24Nov20.txt" - This file is the raw genotypes file sent from Cornell University following the completion of multiplex microsatellite sequencing "RACH_broad_management_genepop.txt" - This file contains sample genotypes in the genepop format, grouped by management assignment "RACH_broad_metapopulation_genepop.txt" - This file contains sample genotypes in the genepop format, grouped by metapopulation assignment ### Files and variables #### File: Frog\_R\_matrix\_24Nov20.txt **Description:** Raw genotypes file  ##### Variables * Locus name, i.e. "Rchi[#]" * Individual name, i.e. "LC# * Diploid microsatellite repeat genotypes, i.e. "3/4" #### File: RACH\_broad\_management\_genepop.txt **Description:** Genepop format for microsatellite genotypes, organized by management category ##### Variables * Management categories as described below: **Management Category and** **Definition** No Management: No history of management through translocations or isolated site with no known population origin. Emigration and immigration occur or presumed to occur across a functioning metapopulation Unmanaged/Declining: Population has had no translocations, but is small, isolated, or declining Minimally Managed: Multiple wild to wild translocations have occurred and emigration and immigration occur or are likely to occur within metapopulation Captive Propagation: Metapopulation is augmented with offspring of breeders from captive facility; emigration and immigration occur within management area Heavily Managed: Wild to wild translocations and/or captive propagation releases have occurred within population; natural metapopulation functioning unlikely Refugia Site: Genetic stock represented in an isolated population following wild population extirpation Few Founders: Population initially started with few, closely related individuals #### File: RACH\_broad\_metapopulation\_genepop.txt **Description:** Genepop format for microsatellite genotypes, organized by population assignments ##### Variables | Lab # | Recovery Unit | Metapopulation | Management Category | Locality | PitTag#/Other specimen# | Sex | Date Collected | Lat | Long | | :---- | :------------ | :--------------------------- | :------------------- | :------------------------------------------------------------------- | :----------------------------- | :-- | :------------- | :---------- | :----------- | | LC001 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 900118000102105 | F | 8/3/2013 | 31.882962 | -109.208247 | | LC004 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 900118000102188 | M | 8/3/2013 | 31.882962 | -109.208247 | | LC007 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 981098102384607 | F | 8/3/2013 | 31.882962 | -109.208247 | | LC008 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 900118000102156 (2011 PIT tag) | M | 8/3/2013 | 31.882962 | -109.208247 | | LC010 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 900118000102171 | M | 8/3/2013 | 31.882962 | -109.208247 | | LC012 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 900118000102180 | F | 8/3/2013 | 31.882962 | -109.208247 | | LC013 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 113663271A (2011 PIT tag) | M | 8/3/2013 | 31.882962 | -109.208247 | | LC014 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 113663272A (2011 PIT tag) | M | 8/3/2013 | 31.882962 | -109.208247 | | LC016 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 900118000102134 | M | 8/3/2013 | 31.882962 | -109.208247 | | LC020 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | J | 8/3/2013 | 31.882962 | -109.208247 | | LC033 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | J | 8/3/2013 | 31.882962 | -109.208247 | | LC049 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | J | 8/3/2013 | 31.882962 | -109.208247 | | LC050 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 900118000102148 | F | 8/3/2013 | 31.882962 | -109.208247 | | LC052 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 900118000102177 | M | 8/3/2013 | 31.882962 | -109.208247 | | LC053 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | 113556224A (2011 PIT tag) | M | 8/3/2013 | 31.882962 | -109.208247 | | LC061 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | J | 8/3/2013 | 31.882962 | -109.208247 | | LC066 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | F | 7/28/2018 | 31.882962 | -109.208247 | | LC067 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | J | 7/28/2018 | 31.882962 | -109.208247 | | LC068 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | M | 7/28/2018 | 31.882962 | -109.208247 | | LC069 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | M | 7/28/2018 | 31.882962 | -109.208247 | | LC070 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | M | 7/28/2018 | 31.882962 | -109.208247 | | LC071 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | M | 7/28/2018 | 31.882962 | -109.208247 | | LC073 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | M | 7/28/2018 | 31.882962 | -109.208247 | | LC075 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | M | 7/28/2018 | 31.882962 | -109.208247 | | LC078 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | J | 7/28/2018 | 31.882962 | -109.208247 | | LC079 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | J | 7/28/2018 | 31.882962 | -109.208247 | | LC081 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | F | 7/28/2018 | 31.882962 | -109.208247 | | LC085 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station | --- | M | 7/28/2018 | 31.882962 | -109.208247 | | LC090 | 1 | Altar\_Valley | Unmanaged | Altar Valley, Pima Co. | --- | --- | --- | 31.574338 | -111.626326 | | LC095 | 2 | Huachuca\_M | managed\_heavy | Mud Spring Pond | --- | --- | 8/20/2018 | 31.394819 | -110.387933 | | LC096 | 2 | Huachuca\_M | managed\_heavy | Unnamed Tank (=House Pond) | --- | --- | 8/19/2014 | 31.474186 | -110.297727 | | LC097 | 2 | Huachuca\_M | refugia\_site | Glendale Community College | --- | --- | 4/18/2011 | 31.415937 | -110.27651 | | LC098 | 2 | Huachuca\_M | refugia\_site | Glendale Community College | --- | --- | 4/18/2011 | 31.415937 | -110.27651 | | LC099 | 2 | Huachuca\_M | refugia\_site | Unmarked Pond (Beatty NW Corner Pond) | --- | --- | 6/9/2014 | 31.416474 | -110.277379 | | LC100 | 2 | Santa\_Ritas | managed\_minimal | Gardner Canyon | --- | --- | 10/27/2014 | 31.710943 | -110.758207 | | LC101 | 3 | S\_MX\_CLF | Unmanaged | Chihuahua, MX: Maquarichic | --- | --- | --- | 27.915991 | -107.904671 | | LC102 | 3 | N\_Chihuahua\_CLF | Unmanaged | Chihuahua, MX: Rio San Miguel at Puente Ulfano, \~2.2 NW I. Zaragosa | --- | --- | 2006 | 29.671512 | -107.783425 | | LC104 | 4 | Dragoons | Unmanaged | Unmarked Flooded Mine Shaft (=Quarry)-Middlemarch Canyon | --- | --- | 7/3/2019 | 31.881577 | -109.953487 | | LC105 | 5 | Gentry\_Buckskin | managed\_heavy | Sycamore basin tank (reared at Phoenix Zoo) | --- | --- | 2010 | 34.481377 | -111.641693 | | LC106 | 5 | Gentry\_Buckskin | captive\_propagation | Carroll Spring | --- | --- | 10/24/2017 | 34.134119 | -110.837152 | | LC107 | 5 | Gentry\_Buckskin | managed\_heavy | Sycamore Basin Tank | --- | --- | 5/24/2010 | 34.481377 | -111.641693 | | LC110 | 5 | Gentry\_Buckskin | captive\_propagation | Unmarked Tank | --- | --- | 8/14/2018 | 34.20562 | -110.818496 | | LC112 | 6 | Deep\_Creek\_Divide | natural | Catron County, NM: Long Mesa | --- | --- | --- | 33.551655 | -108.68684 | | LC113 | 6 | San\_Francisco | natural | Catron County, NM: San Francisco | --- | --- | --- | 33.454531 | -108.910978 | | LC114 | 6 | E\_Fork\_Gila\_R | natural | Catron County, NM: Beaver Creek | --- | --- | --- | 33.37453779 | -108.1180017 | | LC123 | 8 | E\_Slope\_Black\_Range\_CNWS | natural | Sierra County, NM: Ladder Ranch Cuchillo Negro Warm Spring + creek | --- | --- | 2004 | 33.273797 | -107.562416 | | LC124 | 8 | E\_Slope\_Black\_Range\_Seco | natural | Sierra County, NM: Ladder Ranch - S.F. Palomas Creek | --- | --- | 2003 | 33.164636 | -107.715041 | | LC125 | 8 | E\_Slope\_Black\_Range\_Seco | natural | Sierra County, NM: N Seco Well | --- | --- | --- | 33.011998 | -107.272805 | | LC126 | 1 | Sierritas | natural/unknown | FMI Sierrita | PVT-0494 | F | 7/5/2017 | 31.894679 | -111.145448 | | LC127 | 1 | Sierritas | natural/unknown | FMI Sierrita | PVT-0494 | F | 7/5/2017 | 31.894679 | -111.145448 | | LC128 | 1 | Sierritas | natural/unknown | FMI Sierrita | PVT-0494 | F | 7/5/2017 | 31.894679 | -111.145448 | | LC129 | 1 | Sierritas | natural/unknown | FMI Sierrita | PVT-0494 | F | 7/5/2017 | 31.894679 | -111.145448 | | LC130 | 1 | Sierritas | natural/unknown | FMI Sierrita | PVT-0494 | F | 7/5/2017 | 31.894679 | -111.145448 | | LC131 | 1 | Sierritas | natural/unknown | FMI Sierrita | PVT-0494 | F | 7/5/2017 | 31.894679 | -111.145448 | | LC132 | 2 | Santa\_Ritas | managed\_minimal | West Tank | COR-0423 | --- | 2/14/2014 | 31.788004 | -110.760151 | | LC133 | 2 | Santa\_Ritas | managed\_minimal | West Tank | COR-0423 | --- | 2/14/2014 | 31.788004 | -110.760151 | | LC134 | 2 | Santa\_Ritas | managed\_minimal | Gardner Canyon | COR-0422 | --- | 10/27/2014 | 31.710943 | -110.758207 | | LC135 | 2 | Santa\_Ritas | managed\_minimal | Unnamed Tank (=Greaterville Tank) | COR-0329 | --- | 10/27/2014 | 31.767505 | -110.759391 | | LC136 | 2 | Santa\_Ritas | managed\_minimal | Unnamed Tank (=Milo Tank) | COR-0445 | M | 6/2/2015 | 31.698246 | -110.738539 | | LC137 | 2 | Santa\_Ritas | managed\_minimal | Apache Springs Pond | SHA-0001 | F | 6/2/2015 | 31.720034 | -110.747586 | | LC138 | 3 | Verde | unmanaged | Chihuahua, MX: Rio Papigochic | ESP 8593 | --- | 2005 | 28.28324 | -107.394911 | | LC139 | 3 | Verde | unmanaged | Chihuahua, MX: Rio Papigochic | ESP 8594 | --- | 2005 | 28.28324 | -107.394911 | | LC140 | 3 | Verde | unmanaged | Chihuahua, MX: Rio Verde at MX 16 | ESP 8607 | --- | 2005 | 28.392313 | -107.755097 | | LC141 | 3 | Verde | unmanaged | Chihuahua, MX: Rio Verde at MX 16 | ESP 8608 | --- | 2005 | 28.392313 | -107.755097 | | LC148 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station (stock originated from Leslie Creek) | PVT-0148 | --- | 2011 | 31.882962 | -109.208247 | | LC149 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station (stock originated from Leslie Creek) | PVT-0148 | --- | 2011 | 31.882962 | -109.208247 | | LC150 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station (stock originated from Leslie Creek) | PVT-0148 | --- | 2011 | 31.882962 | -109.208247 | | LC151 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station (stock originated from Leslie Creek) | PVT-0148 | --- | 2011 | 31.882962 | -109.208247 | | LC152 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station (stock originated from Leslie Creek) | PVT-0148 | --- | 2011 | 31.882962 | -109.208247 | | LC153 | 3 | N\_Chiricahuas | few\_founders | Southwestern Research Station (stock originated from Leslie Creek) | PVT-0148 | --- | 2011 | 31.882962 | -109.208247 | | LC155 | 4 | Dragoons | unmanaged | Unmarked Flooded Mine Shaft (=Quarry)-Middlemarch Canyon | COR-0155 | --- | 7/3/2019 | 31.881577 | -109.953487 | | LC156 | 4 | Dragoons | unmanaged | Unmarked Flooded Mine Shaft (=Quarry)-Middlemarch Canyon | COR-0155 | --- | 7/3/2019 | 31.881577 | -109.953487 | | LC157 | 6 | Three\_Forks | refugia\_site | Sundt Pond | SHA-0047 | --- | 6/5/2017 | 33.85299 | -109.315727 | | LC158 | 6 | Three\_Forks | refugia\_site | Sundt Pond | SHA-0047 | --- | 6/5/2017 | 33.85299 | -109.315727 | | LC159 | 6 | Three\_Forks | refugia\_site | Sundt Pond | SHA-0047 | --- | 6/5/2017 | 33.85299 | -109.315727 | | LC160 | 6 | Three\_Forks | refugia\_site | Sundt Pond | SHA-0047 | --- | 6/5/2017 | 33.85299 | -109.315727 | | LC161 | 6 | Three\_Forks | refugia\_site | Sundt Pond | SHA-0047 | --- | 6/5/2017 | 33.85299 | -109.315727 | | LC162 | 6 | Three\_Forks | refugia\_site | Sundt Pond | SHA-0047 | --- | 6/5/2017 | 33.85299 | -109.315727 | | LC163 | 6 | Apache\_Tularosa\_R | unmanaged\_declining | Catron County, NM: Whiskey Creek | Rach1 | --- | 2013 | 33.93900165 | -108.6638628 | | LC164 | 6 | Apache\_Tularosa\_R | unmanaged\_declining | Catron County, NM: Whiskey Creek | Rach4 | --- | 2013 | 33.93900165 | -108.6638628 | | LC165 | 6 | Apache\_Tularosa\_R | unmanaged\_declining | Catron County, NM: Whiskey Creek | Rach5 | --- | 2013 | 33.93900165 | -108.6638628 | | LC166 | 6 | Apache\_Tularosa\_R | unmanaged\_declining | Catron County, NM: Whiskey Creek | Rach6 | --- | 2013 | 33.93900165 | -108.6638628 | | LC167 | 6 | Apache\_Tularosa\_R | unmanaged\_declining | Catron County, NM: Whiskey Creek | Rach7 | --- | 2013 | 33.93900165 | -108.6638628 | | LC168 | 6 | Apache\_Tularosa\_R | unmanaged\_declining | Catron County, NM: Whiskey Creek | Rach8 | --- | 2013 | 33.93900165 | -108.6638628 | | LC169 | 7 | Lower\_Gila\_R | unmanaged\_declining | Grant County, NM: Allen Spring 12S 0746700/3641515 (+/- 5) | F55 | --- | 2014 | 32.88403605 | -108.36295 | | LC170 | 7 | Lower\_Gila\_R | unmanaged\_declining | Grant County, NM: Allen Spring 12S 0746700/3641515 (+/- 5) | F66 | --- | 2014 | 32.88403605 | -108.36295 | | LC171 | 7 | Lower\_Gila\_R | unmanaged\_declining | Grant County, NM: Allen Spring 12S 0746700/3641515 (+/- 5) | M57 | --- | 2014 | 32.88403605 | -108.36295 | | LC172 | 7 | Lower\_Gila\_R | unmanaged\_declining | Grant County, NM: Allen Spring 12S 0746700/3641515 (+/- 5) | M57A | --- | 2014 | 32.88403605 | -108.36295 | | LC173 | 7 | Lower\_Gila\_R | unmanaged\_declining | Grant County, NM: Allen Spring 12S 0746700/3641515 (+/- 5) | T1 | --- | 2014 | 32.88403605 | -108.36295 | | LC174 | 7 | Lower\_Gila\_R | unmanaged\_declining | Grant County, NM: Allen Spring 12S 0746700/3641515 (+/- 5) | F61 | --- | 2014 | 32.88403605 | -108.36295 | | LC175 | 8 | Seco | unmanaged\_declining | Sierra County, NM: N Seco Well | F2 | --- | 2001 | 33.011998 | -107.272805 | | LC176 | 8 | Seco | unmanaged\_declining | Sierra County, NM: N Seco Well | F4 | --- | 2001 | 33.011998 | -107.272805 | | LC177 | 8 | Seco | unmanaged\_declining | Sierra County, NM: N Seco Well | M2 | --- | 2001 | 33.011998 | -107.272805 | | LC178 | 8 | Seco | unmanaged\_declining | Sierra County, NM: N Seco Well | M3 | --- | 2001 | 33.011998 | -107.272805 | | LC179 | 8 | Seco | unmanaged\_declining | Sierra County, NM: N Seco Well | unknown | --- | --- | 33.011998 | -107.272805 | | LC180 | 8 | Seco | unmanaged\_declining | Sierra County, NM: N Seco Well | unknown | --- | --- | 33.011998 | -107.272805 |