Phylogenomics reveals conservation challenges and opportunities for cryptic endangered species in a rapidly disappearing desert ecosystem

Daniel Rubinoff; J. Bradley Reil; Kendall H. Osborne; Christopher J. Gregory; Scott M. Geib; Julian R. Dupuis

doi:10.1007/s10531-020-01968-w

Phylogenomics reveals conservation challenges and opportunities for cryptic endangered species in a rapidly disappearing desert ecosystem

Daniel Rubinoff, J. Bradley Reil, Kendall H. Osborne, Christopher J. Gregory, Scott M. Geib, Julian R. Dupuis

Entomology

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

There is growing evidence for the decline of cryptic species across the planet as a result of human activities. Accurate data regarding patterns of poorly known or hard-to-find species diversity is essential for the recognition and conservation of threatened species and ecosystems. Casey’s June beetle Dinacoma caseyi is a federally listed endangered species restricted to the Coachella Valley in southern California, where rapid development is leading to habitat fragmentation. This fragmentation may be disproportionately impacting a wide-range of poorly-dispersing, cryptic species, including Casey’s June beetle, which has flightless females. We characterized 1876 single nucleotide polymorphisms from across the genome along with 1480 bp of mitochondrial DNA of all confirmed extant Dinacoma populations. We found that Dinacoma is isolated into three distinct species, including evidence for a previously undescribed species revealed during this study. Each is restricted to a small part of the inland desert region. Our results suggest unappreciated and fine scale diversity, which may be reflected in the other cryptic species of the region. Patterns of diversity in non-vagile species should guide ongoing conservation planning in the region. These results show that genetic exchange within the one remaining island of beetle habitat (Palm Canyon Wash) is not limited. However, non-vagile species, such as Casey’s June beetle, may not colonize suitable but fragmented habitat islands which presents risks to the species due to habitat loss and periodic natural events that may put the single population at risk of extirpation.

Original language	English
Pages (from-to)	2185-2200
Number of pages	16
Journal	Biodiversity and Conservation
Volume	29
Issue number	7
DOIs	https://doi.org/10.1007/s10531-020-01968-w
State	Published - Jun 1 2020

Bibliographical note

Funding Information:
We dedicate this paper to the memory of Chris Gregory, USFWS, who tirelessly advocated for the thorough investigation and protection of all threatened species, and without whom this project would have never been completed. Noelle Ronan (USFWS) provided valuable feedback, comments and support. ddRAD library construction was performed with the support of Angela Kauwe (USDA-ARS). HiSeq 4000 sequencing was provided by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. This research was funded by the United States Fish and Wildlife Service, with additional funding provided by The College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa; USDA Cooperative State Research, Education and Extension (CSREES), Grant/Award Number: HAW00942-H. USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.

Funding Information:
We dedicate this paper to the memory of Chris Gregory, USFWS, who tirelessly advocated for the thorough investigation and protection of all threatened species, and without whom this project would have never been completed. Noelle Ronan (USFWS) provided valuable feedback, comments and support. ddRAD library construction was performed with the support of Angela Kauwe (USDA-ARS). HiSeq 4000 sequencing was provided by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. This research was funded by the United States Fish and Wildlife Service, with additional funding provided by The College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa; USDA Cooperative State Research, Education and Extension (CSREES), Grant/Award Number: HAW00942-H. USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.

Publisher Copyright:
© 2020, Springer Nature B.V.

Keywords

Coachella valley
DNA barcodes
DdRAD phylogenomics
Dinacoma
MtDNA
Southern California

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Ecology
Nature and Landscape Conservation

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1007/s10531-020-01968-w

Cite this

@article{48259add297e4f2bb7f6c357180c0d70,

title = "Phylogenomics reveals conservation challenges and opportunities for cryptic endangered species in a rapidly disappearing desert ecosystem",

abstract = "There is growing evidence for the decline of cryptic species across the planet as a result of human activities. Accurate data regarding patterns of poorly known or hard-to-find species diversity is essential for the recognition and conservation of threatened species and ecosystems. Casey{\textquoteright}s June beetle Dinacoma caseyi is a federally listed endangered species restricted to the Coachella Valley in southern California, where rapid development is leading to habitat fragmentation. This fragmentation may be disproportionately impacting a wide-range of poorly-dispersing, cryptic species, including Casey{\textquoteright}s June beetle, which has flightless females. We characterized 1876 single nucleotide polymorphisms from across the genome along with 1480 bp of mitochondrial DNA of all confirmed extant Dinacoma populations. We found that Dinacoma is isolated into three distinct species, including evidence for a previously undescribed species revealed during this study. Each is restricted to a small part of the inland desert region. Our results suggest unappreciated and fine scale diversity, which may be reflected in the other cryptic species of the region. Patterns of diversity in non-vagile species should guide ongoing conservation planning in the region. These results show that genetic exchange within the one remaining island of beetle habitat (Palm Canyon Wash) is not limited. However, non-vagile species, such as Casey{\textquoteright}s June beetle, may not colonize suitable but fragmented habitat islands which presents risks to the species due to habitat loss and periodic natural events that may put the single population at risk of extirpation.",

keywords = "Coachella valley, DNA barcodes, DdRAD phylogenomics, Dinacoma, MtDNA, Southern California",

author = "Daniel Rubinoff and Reil, {J. Bradley} and Osborne, {Kendall H.} and Gregory, {Christopher J.} and Geib, {Scott M.} and Dupuis, {Julian R.}",

note = "Funding Information: We dedicate this paper to the memory of Chris Gregory, USFWS, who tirelessly advocated for the thorough investigation and protection of all threatened species, and without whom this project would have never been completed. Noelle Ronan (USFWS) provided valuable feedback, comments and support. ddRAD library construction was performed with the support of Angela Kauwe (USDA-ARS). HiSeq 4000 sequencing was provided by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. This research was funded by the United States Fish and Wildlife Service, with additional funding provided by The College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa; USDA Cooperative State Research, Education and Extension (CSREES), Grant/Award Number: HAW00942-H. USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. Funding Information: We dedicate this paper to the memory of Chris Gregory, USFWS, who tirelessly advocated for the thorough investigation and protection of all threatened species, and without whom this project would have never been completed. Noelle Ronan (USFWS) provided valuable feedback, comments and support. ddRAD library construction was performed with the support of Angela Kauwe (USDA-ARS). HiSeq 4000 sequencing was provided by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. This research was funded by the United States Fish and Wildlife Service, with additional funding provided by The College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa; USDA Cooperative State Research, Education and Extension (CSREES), Grant/Award Number: HAW00942-H. USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. Publisher Copyright: {\textcopyright} 2020, Springer Nature B.V.",

year = "2020",

month = jun,

day = "1",

doi = "10.1007/s10531-020-01968-w",

language = "English",

volume = "29",

pages = "2185--2200",

number = "7",

}

TY - JOUR

T1 - Phylogenomics reveals conservation challenges and opportunities for cryptic endangered species in a rapidly disappearing desert ecosystem

AU - Rubinoff, Daniel

AU - Reil, J. Bradley

AU - Osborne, Kendall H.

AU - Gregory, Christopher J.

AU - Geib, Scott M.

AU - Dupuis, Julian R.

N1 - Funding Information: We dedicate this paper to the memory of Chris Gregory, USFWS, who tirelessly advocated for the thorough investigation and protection of all threatened species, and without whom this project would have never been completed. Noelle Ronan (USFWS) provided valuable feedback, comments and support. ddRAD library construction was performed with the support of Angela Kauwe (USDA-ARS). HiSeq 4000 sequencing was provided by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. This research was funded by the United States Fish and Wildlife Service, with additional funding provided by The College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa; USDA Cooperative State Research, Education and Extension (CSREES), Grant/Award Number: HAW00942-H. USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. Funding Information: We dedicate this paper to the memory of Chris Gregory, USFWS, who tirelessly advocated for the thorough investigation and protection of all threatened species, and without whom this project would have never been completed. Noelle Ronan (USFWS) provided valuable feedback, comments and support. ddRAD library construction was performed with the support of Angela Kauwe (USDA-ARS). HiSeq 4000 sequencing was provided by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. This research was funded by the United States Fish and Wildlife Service, with additional funding provided by The College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa; USDA Cooperative State Research, Education and Extension (CSREES), Grant/Award Number: HAW00942-H. USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. Publisher Copyright: © 2020, Springer Nature B.V.

PY - 2020/6/1

Y1 - 2020/6/1

N2 - There is growing evidence for the decline of cryptic species across the planet as a result of human activities. Accurate data regarding patterns of poorly known or hard-to-find species diversity is essential for the recognition and conservation of threatened species and ecosystems. Casey’s June beetle Dinacoma caseyi is a federally listed endangered species restricted to the Coachella Valley in southern California, where rapid development is leading to habitat fragmentation. This fragmentation may be disproportionately impacting a wide-range of poorly-dispersing, cryptic species, including Casey’s June beetle, which has flightless females. We characterized 1876 single nucleotide polymorphisms from across the genome along with 1480 bp of mitochondrial DNA of all confirmed extant Dinacoma populations. We found that Dinacoma is isolated into three distinct species, including evidence for a previously undescribed species revealed during this study. Each is restricted to a small part of the inland desert region. Our results suggest unappreciated and fine scale diversity, which may be reflected in the other cryptic species of the region. Patterns of diversity in non-vagile species should guide ongoing conservation planning in the region. These results show that genetic exchange within the one remaining island of beetle habitat (Palm Canyon Wash) is not limited. However, non-vagile species, such as Casey’s June beetle, may not colonize suitable but fragmented habitat islands which presents risks to the species due to habitat loss and periodic natural events that may put the single population at risk of extirpation.

AB - There is growing evidence for the decline of cryptic species across the planet as a result of human activities. Accurate data regarding patterns of poorly known or hard-to-find species diversity is essential for the recognition and conservation of threatened species and ecosystems. Casey’s June beetle Dinacoma caseyi is a federally listed endangered species restricted to the Coachella Valley in southern California, where rapid development is leading to habitat fragmentation. This fragmentation may be disproportionately impacting a wide-range of poorly-dispersing, cryptic species, including Casey’s June beetle, which has flightless females. We characterized 1876 single nucleotide polymorphisms from across the genome along with 1480 bp of mitochondrial DNA of all confirmed extant Dinacoma populations. We found that Dinacoma is isolated into three distinct species, including evidence for a previously undescribed species revealed during this study. Each is restricted to a small part of the inland desert region. Our results suggest unappreciated and fine scale diversity, which may be reflected in the other cryptic species of the region. Patterns of diversity in non-vagile species should guide ongoing conservation planning in the region. These results show that genetic exchange within the one remaining island of beetle habitat (Palm Canyon Wash) is not limited. However, non-vagile species, such as Casey’s June beetle, may not colonize suitable but fragmented habitat islands which presents risks to the species due to habitat loss and periodic natural events that may put the single population at risk of extirpation.

KW - Coachella valley

KW - DNA barcodes

KW - DdRAD phylogenomics

KW - Dinacoma

KW - MtDNA

KW - Southern California

UR - http://www.scopus.com/inward/record.url?scp=85083801155&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85083801155&partnerID=8YFLogxK

U2 - 10.1007/s10531-020-01968-w

DO - 10.1007/s10531-020-01968-w

M3 - Article

AN - SCOPUS:85083801155

SN - 0960-3115

VL - 29

SP - 2185

EP - 2200

JO - Biodiversity and Conservation

JF - Biodiversity and Conservation

IS - 7

ER -

Phylogenomics reveals conservation challenges and opportunities for cryptic endangered species in a rapidly disappearing desert ecosystem

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this