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de Souza Oliveira L, de Araújo Bitencourt J, Galdino JH, Sampaio I, Souza Carneiro PL, Antunes de Mello Affonso PR. Genetic Diversity in Natural Populations of the Near-Threatened Species Lignobrycon myersi (Characiformes, Triportheidae): Implications for Species Conservation. Zebrafish 2023; 20:271-279. [PMID: 38011710 DOI: 10.1089/zeb.2023.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
The river basins of Brazil contain a highly diverse ichthyofauna of remarkable endemism, including several threatened species. Accordingly, Lignobrycon myersi is a fish species distributed only in a few rivers from the state of Bahia, northeastern Brazil. Since this species is classified as Near Threatened and is poorly studied, efforts to understand the genetic structure of populations and putative cryptic forms should help define efficient strategies of management and conservation. Herein, the molecular identification and the population genetic diversity of specimens of L. myersi across their range (Almada, Contas, and Cachoeira river basins) were assessed using mitochondrial markers (16S rDNA and D-Loop, respectively). The inferences based on phylogenetics, genetic distance, and species delimitation methods invariably identified all samples as L. myersi. In addition, sequencing of D-loop fragments revealed significant haplotype diversity and a considerable level of population genetic structure. Despite their geographic isolation, these data suggested that populations from Almada and Contas rivers represent a single evolutionary lineage that could be managed as a whole. In contrast, the population from Cachoeira River was highly differentiated from the others and should be managed separately as a unique and endemic unit, particularly focused on the conservation of native habitats.
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Affiliation(s)
| | | | - José Henrique Galdino
- Department of Biological Sciences, State University of Southwestern Bahia, Jequié, Brazil
| | - Iracilda Sampaio
- Department of Coastal Studies, Federal University of Pará, Bragança, Brazil
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Chen J, Zhang L, Gao L, Wei Z, Dang D, Yang L. Population Structure and Genetic Diversity of Yunling Cattle Determined by Whole-Genome Resequencing. Genes (Basel) 2023; 14:2141. [PMID: 38136963 PMCID: PMC10742670 DOI: 10.3390/genes14122141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
The Yunling cattle breed, a three-breed crossbreed, which comprises 50% Brahman cattle, 25% Murray Grey cattle and 25% Yunnan Yellow cattle, has several advantageous traits, including rapid growth, superior meat quality, ability to improve tolerance in hot and humid climates, tick resistance and rough feed. It can be rightfully stated that Yunling cattle serve as vital genetic repositories of the local Yunnan cattle. Gaining insights into the genetic information of Yunling cattle plays a significant role in the formulation of sound breeding strategies for this breed, safeguarding genetic resources and mitigating the risks associated with inbreeding depression. In this study, we constructed the Yunling cattle standard reference genome and aligned the whole genomes of 129 Yunling cattle individuals to the constructed reference genome to estimate the current genetic status of Yunling cattle in Yunnan Province, China. The average alignment rate and the average percentage of properly paired are both 99.72%. The average nucleotide diversity in Yunling cattle is 0.000166, which indicates a lower level of diversity. Population structure analysis classified Yunling cattle into two subgroups. Inbreeding analysis revealed that inbreeding events did occur in the Yunling cattle, which may have contributed to the low genetic diversity observed. This study presents a comprehensive assessment of the genetic structure and diversity among the Yunling cattle and provides a theoretical foundation for the preservation and exploitation of these precious germplasm resources.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
| | - Lilian Zhang
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
| | - Lutao Gao
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
| | - Zaichao Wei
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
- School of Data Science, Baoshan University, Baoshan 678000, China
| | - Dong Dang
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
| | - Linnan Yang
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
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Lange JJ, Angelo CL, Revuelta E, Possley J. Population Assessments of Federally Threatened Everglades Bully in Big Cypress National Preserve, Florida, USA, Using Habitat Suitability Modeling and Micromorphology. PLANTS (BASEL, SWITZERLAND) 2023; 12:1430. [PMID: 37050055 PMCID: PMC10097282 DOI: 10.3390/plants12071430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
In Big Cypress National Preserve, the federally threatened Everglades bully (Sideroxylon reclinatum subsp. austrofloridense) is sympatric with its conspecific, more widespread relative, the Florida bully (Sideroxylon reclinatum subsp. reclinatum). In this area of overlap, the only reliable characters to distinguish the two are cryptic, micromorphological traits of the abaxial laminar surface. In order to better understand the distribution of the federally threatened taxon, we used a combination of habitat suitability modeling (HSM), field surveys, and microscopy. Using models to inform initial surveys, we collected leaf material of 96 individuals in the field, 86 of which we were able to identify to subspecies. Of these, 73 (85%) were identified as the threatened taxon, expanding both the known range and population size within Big Cypress. We used these 73 new occurrences to rerun HSMs to create a more accurate picture of where the taxon is likely to occur. A total of 15,015 hectares were predicted to be suitable habitat within Big Cypress, with 34,069 hectares across the entire study area. These model results could be used to inform the critical habitat designation for this taxon. For at-risk, cryptic taxa, such as the Everglades bully, multiple approaches are needed to inform management and conservation priorities, including the consideration of a hybridization zone.
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Affiliation(s)
- James J. Lange
- Smart-Sciences, Inc., 330 SW 27th Ave STE 504, Miami, FL 33135, USA;
- Fairchild Tropical Botanic Garden, 10901 Old Cutler Rd., Miami, FL 33156, USA
| | - Courtney L. Angelo
- Big Cypress National Preserve, 33100 Tamiami Trail E, Ochopee, FL 34141, USA
| | - Erick Revuelta
- Fairchild Tropical Botanic Garden, 10901 Old Cutler Rd., Miami, FL 33156, USA
- St. John’s River Water Management District, 4049 Reid Street, Palatka, FL 32177, USA
| | - Jennifer Possley
- Fairchild Tropical Botanic Garden, 10901 Old Cutler Rd., Miami, FL 33156, USA
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Edwards CE, Bassüner B, Williams BR. Population Genetic Analysis of the Threatened Plant Leavenworthia exigua var. laciniata (Brassicaceae) Reveals Virtually No Genetic Diversity and a Unique Mating System. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.831085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Leavenworthia (Brassicaceae) has served as a model group for investigating the evolution of mating systems in plants, yet several Leavenworthia species remain understudied. One such taxon is Leavenworthia exigua var. laciniata, one of three varieties of L. exigua, a winter-annual plant endemic to the central United States. Because L. exigua var. laciniata occupies a narrow geographic range and is experiencing major habitat loss, it was recently listed as threatened; however, little is known about its genetic diversity and implications for conservation. We conducted a range-wide population genetic study of L. exigua var. laciniata and L. exigua var. exigua to understand: (1) levels of genetic diversity within and among populations, (2) whether L. exigua var. laciniata is genetically distinct from L. exigua var. exigua, and (3) implications for conservation. L. exigua var. laciniata showed identical genotypes at all 16 microsatellite loci across most of its range, fixed heterozygosity at some loci, and significant heterozygote excesses, consistent with a lack of recombination associated with an asexual mating system, which has not been documented previously in Leavenworthia. Because L. exigua var. laciniata is an annual and the same genotype occurs across multiple populations, asexuality may be caused by apomixis, asexual reproduction via seed. In contrast, most populations of L. exigua var. exigua demonstrated population genetic patterns consistent with a self-compatible mating system. Because L. exigua var. laciniata is morphologically, geographically, and genetically distinct, it should be recognized as an evolutionarily significant unit for conservation. We recommend maintaining large population sizes to conserve evolutionary potential in L. exigua var. laciniata, as the likelihood that facultative sexual reproduction may occur may be greater in larger populations. Additional research in L. exigua var. laciniata is needed to confirm the occurrence of asexuality and apomixis, clarify its reproductive isolation from other taxa, and to understand whether it exhibits residual sexual reproduction, epigenetic variation, or phenotypic plasticity to help it persist in response to environmental variation. In the future, L. exigua var. laciniata may serve as an important model in which to investigate the conservation of threatened plant species with little genetic variation in a changing climate.
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Linan AG, Lowry Ii PP, Miller AJ, Schatz GE, Sevathian JC, Edwards CE. Interspecific hybridization and island colonization history, not rarity, most strongly affect the genetic diversity in a clade of Mascarene-endemic trees. J Hered 2022; 113:336-352. [PMID: 35192705 DOI: 10.1093/jhered/esac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/21/2022] [Indexed: 11/14/2022] Open
Abstract
Many factors shape the genetic diversity of island-endemic trees, with important implications for conservation. Oceanic island-endemic lineages undergo an initial founding bottleneck during the colonization process and subsequently accumulate diversity following colonization. Moreover, many island endemics occur in small populations and are further threatened by anthropogenic factors that cause population declines, making them susceptible to losses in genetic diversity through genetic drift, inbreeding, and bottlenecks. However, life-history traits commonly found in trees, such as outcrossing mechanisms, long lifespans, and a propensity for interspecific hybridization, may help buffer against losses of genetic variation. To assess the relative importance of colonization history, rarity, and distribution in shaping genetic diversity of island-endemic trees, we conducted a comparative population genomic analysis of 13 species of Diospyros (Ebenaceae) endemic to the Mascarene Islands that differ in island colonization history, distribution, population size, and IUCN threat status. We genotyped 328 individuals across the islands using 2b-RADseq, compared genetic diversity both among and within species, and assessed patterns of genetic structure. Genetic diversity did not vary significantly by IUCN status, but we found that species that co-occur with others on the same intermediate-aged island (Mauritius) had much greater genetic diversity than those that occur solitarily on an island (Réunion and Rodrigues), likely because of greater interspecific hybridization among species with overlapping distributions and processes related to time since island colonization. Results presented here were used to determine priority localities for in situ and ex situ conservation efforts to maximize the genetic diversity of each Mascarene Diospyros species.
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Affiliation(s)
- Alexander G Linan
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA.,Department of Biology, Saint Louis University, Macelwane Hall, 3507 Laclede Avenue, St. Louis, MO 63103, USA
| | - Porter P Lowry Ii
- Africa and Madagascar Program, Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA.,Institut de Systématique, Évolution et Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, C.P. 39, 57 rue Cuvier, 75005 Paris, France
| | - Allison J Miller
- Department of Biology, Saint Louis University, Macelwane Hall, 3507 Laclede Avenue, St. Louis, MO 63103, USA.,Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
| | - George E Schatz
- Africa and Madagascar Program, Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA
| | - Jean Claude Sevathian
- Botanist, Sustainability Consultant and Landscape Care and Maintenance Service, 20 Bis Morcellement La Confiance, Beau Bassin 71504, Mauritius
| | - Christine E Edwards
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA
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Portella RO, Cordeiro EMG, Marques APS, Ming LC, Zucchi MI, Lima MP, Martins ER, Hantao LW, Sawaya ACHF, Semir J, Pinheiro JB, Marques MOM. Evidence of altitudinal gradient modifying genomic and chemical diversity in populations of Lychnophora pinaster Mart. PHYTOCHEMISTRY 2021; 192:112898. [PMID: 34492545 DOI: 10.1016/j.phytochem.2021.112898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/27/2021] [Accepted: 08/03/2021] [Indexed: 05/28/2023]
Abstract
Lychnophora pinaster Mart. (Asteraceae) is endemic to the Brazilian Cerrado. It is distributed along the altitudinal gradient of the mountainous ranges of the state of Minas Gerais. This study aimed to evaluate the influence of altitude on the genetic diversity of L. pinaster populations and the effects of altitude and climatic factors on essential oil chemical composition. Essential oils from L. pinaster populations from the north (North 01, North 02, and North 03, 700-859 m) and the Metropolitan region of Belo Horizonte (MhBH 01 and MrBH 02, 1366-1498 m) were analyzed. SNP markers from L. pinaster in these regions and Campos das Vertentes (CV 01, CV 02, and CV 03, 1055-1292 m) were also analyzed. The main compounds in essential oils were 14-hydroxy-α-humulene (North 01 and North 03), cedr-8(15)-en-9-α-ol (North 02), 14-acetoxy-α-humulene (MrBH 01), and 4-oxo-15-nor-eudesman-11-ene (MrBH 02). Hierarchical cluster and heatmap analyses showed that the North and MrBH populations included five different groups, indicating the chemical composition of essential oils is distinct in each population. Furthermore, principal component analysis showed that higher altitudes (1366 m and 1498 m) in the MrBH influence the chemical composition of essential oils, and climatic factors determine the chemical composition in North region. The genetic diversity showed that most alleles are in Hardy-Weinberg equilibrium and imply high genetic variation and genetic polymorphisms between populations. Furthermore, the results of Mantel tests (R = 0.3861517; p = 0.04709529; R = 0.9423121; p = 0.02739726) also showed that higher altitude (>1360 m) shapes the genetic diversity at the MrBH. The genetic structure showed that higher altitudes (>1360 m) contribute to the structure of the MrBH populations, but not to North and CV populations. Therefore, the altitudinal ranges of Minas Gerais mountainous ranges determine the higher genetic and chemical diversity of L. pinaster populations.
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Affiliation(s)
- Roberto O Portella
- Universidade de Taubaté, Av. Tiradentes, 500, Bom Conselho, CEP: 12030-180, Taubaté, SP, Brazil; Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua Prof. Dr. Antônio Celso Wagner Zanin, 250 - Distrito de Rubião Junior, CEP: 18618-689, Botucatu, SP, Brazil
| | - Erick M G Cordeiro
- Agência Paulista de Tecnologia dos Agronegócios, Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Caixa Postal 28, CEP: 13400-970, Piracicaba, SP, Brazil
| | - Ana Paula S Marques
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua Prof. Dr. Antônio Celso Wagner Zanin, 250 - Distrito de Rubião Junior, CEP: 18618-689, Botucatu, SP, Brazil
| | - Lin C Ming
- Departamento de Horticultura, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua José Barbosa de Barros, 1780, CEP: 18610-307, Botucatu, SP, Brazil
| | - Maria I Zucchi
- Agência Paulista de Tecnologia dos Agronegócios, Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Caixa Postal 28, CEP: 13400-970, Piracicaba, SP, Brazil
| | - Maria P Lima
- Coordenação de Inovação Tecnológica, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Aleixo, CEP: 69011-970, Manaus, AM, Brazil
| | - Ernane R Martins
- Instituto de Ciências Agrárias, Universidade Federal de Minas Gerais, Av. Universitária, 1000, Universitário, CEP: 39404-547, Montes Claros, MG, Brazil
| | - Leandro W Hantao
- Instituto de Química, Universidade Estadual de Campinas, Rua Monteiro Lobato, 270, CEP: 13083-862, Campinas, SP, Brazil
| | - Alexandra C H F Sawaya
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200, Cidade Universitária, CEP: 13083-871, Campinas, SP, Brazil
| | - João Semir
- Departamento de Botânica, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, Barão Geraldo, CEP: 13083-862, Campinas, SP, Brazil
| | - José B Pinheiro
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, CEP: 13418-900, Piracicaba, SP, Brazil
| | - Marcia O M Marques
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico, Avenida Barão de Itapura, 1481, Botafogo, CEP: 13020-902, Campinas, SP, Brazil.
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Borokini IT, Klingler KB, Peacock MM. Life in the desert: The impact of geographic and environmental gradients on genetic diversity and population structure of Ivesia webberi. Ecol Evol 2021; 11:17537-17556. [PMID: 34938528 PMCID: PMC8668734 DOI: 10.1002/ece3.8389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 11/11/2022] Open
Abstract
For range-restricted species with disjunct populations, it is critical to characterize population genetic structure, gene flow, and factors that influence functional connectivity among populations in order to design effective conservation programs. In this study, we genotyped 314 individuals from 16 extant populations of Ivesia webberi, a United States federally threatened Great Basin Desert using six microsatellite loci. We assessed the effects of Euclidean distance, landscape features, and ecological dissimilarity on the pairwise genetic distance of the sampled populations, while also testing for a potential relationship between I. webberi genetic diversity and diversity in the vegetative communities. The results show low levels of genetic diversity overall (H e = 0.200-0.441; H o = 0.192-0.605) and high genetic differentiation among populations. Genetic diversity was structured along a geographic gradient, congruent with patterns of isolation by distance. Populations near the species' range core have relatively high genetic diversity, supporting in part a central-marginal pattern, while also showing some evidence for a metapopulation dynamic. Peripheral populations have lower genetic diversity, significantly higher genetic distances, and higher relatedness. Genotype cluster admixture results suggest a complex dispersal pattern among populations with dispersal direction and distance varying on the landscape. Pairwise genetic distance strongly correlates with elevation, actual evapotranspiration, and summer seasonal precipitation, indicating a role for isolation by environment, which the observed phenological mismatches among the populations also support. The significant correlation between pairwise genetic distance and floristic dissimilarity in the germinated soil seed bank suggests that annual regeneration in the plant communities contribute to the maintenance of genetic diversity in I. webberi.
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Affiliation(s)
- Israel T. Borokini
- Ecology, Evolution and Conservation Biology Graduate ProgramDepartment of BiologyUniversity of Nevada, RenoRenoNevadaUSA
- University and Jepson HerbariaDepartment of Integrative BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Kelly B. Klingler
- Department of Environmental ConservationUniversity of MassachusettsAmherstMassachusettsUSA
| | - Mary M. Peacock
- Ecology, Evolution and Conservation Biology Graduate ProgramDepartment of BiologyUniversity of Nevada, RenoRenoNevadaUSA
- Department of BiologyUniversity of Nevada, RenoRenoNevadaUSA
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Teixeira TM, Nazareno AG. One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species. FRONTIERS IN PLANT SCIENCE 2021; 12:730258. [PMID: 34630476 PMCID: PMC8496504 DOI: 10.3389/fpls.2021.730258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Intraspecific genetic variation plays a fundamental role in maintaining the evolutionary potential of wild populations. Hence, the assessment of genetic diversity patterns becomes essential to guide biodiversity conservation policies, particularly for threatened species. To inform management strategies for conservation of Mimosa catharinensis - a narrow endemic, critically endangered plant species - we identified 1,497 unlinked SNP markers derived from a reduced representation sequencing method (i.e., double digest restriction site associated DNA sequencing, or ddRADseq). This set of molecular markers was employed to assess intrapopulation genetic parameters and the demographic history of one extremely small population of M. catharinensis (N=33) located in the Brazilian Atlantic Forest. Contrary to what is expected for narrow endemic and threatened species with small population sizes, we observed a moderate level of genetic diversity for M. catharinensis [uH E(0%missing data)=0.205, 95% CI (0.160, 0.250); uH E(30%missing data)=0.233, 95% CI (0.174, 0.292)]. Interestingly, M. catharinensis, which is a lianescent shrub with no indication of seed production for at least two decades, presented high levels of outcrossing [t (0%missing data)=0.883, SE±0.0483; t (30%missing data)=0.909, SE±0.011] and an apparent absence of inbreeding [F (0%missing data)=-0.145, 95% CI (-0.189, -0.101); F (30%missing data)=-0.105, 95% CI (-0.199, -0.011)]. However, the reconstruction of demographic history of M. catharinensis indicated that the population should be suffered a recent bottleneck. Our population genomic study tackles a central issue in evolution and conservation biology and we expect that it will be useful to help safeguard the remaining genetic diversity reported for this unique genetic resource.
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Affiliation(s)
- Thais M. Teixeira
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alison G. Nazareno
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
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Blyth C, Christmas MJ, Bickerton DC, Breed MF, Foster NR, Guerin GR, Mason ARG, Lowe AJ. Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy. Life (Basel) 2021; 11:553. [PMID: 34208381 PMCID: PMC8231295 DOI: 10.3390/life11060553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/01/2022] Open
Abstract
Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population diversity and divergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. Samples identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other samples and likely form a separate, range-restricted species. Remaining samples formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic diversity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations.
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Affiliation(s)
- Colette Blyth
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | | | - Martin F. Breed
- College of Science and Engineering, Flinders University, Bedford Park 5042, Australia;
| | - Nicole R. Foster
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
- College of Science and Engineering, Flinders University, Bedford Park 5042, Australia;
| | - Greg R. Guerin
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
- Terrestrial Ecosystem Research Network (TERN), University of Adelaide, Adelaide 5005, Australia
| | - Alex R. G. Mason
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
| | - Andrew J. Lowe
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
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