Data from: Characterizing population structure and documenting rapid loss of genetic diversity in Chiricahua Leopard Frogs (Lithobates chiricahuensis) with high throughput microsatellite genotyping
Data files
Jan 07, 2025 version files 161.44 KB
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Frog_R_matrix_24Nov20.txt
40.91 KB
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RACH_broad_management_genepop.txt
47.56 KB
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RACH_broad_metapopulation_genepop.txt
47.46 KB
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README.md
25.51 KB
Abstract
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.
README: 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
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 |