Abstract
The identification of closely related species with partially overlapping distributions is fundamental for effective conservation. Here we analyzed 28 sequenced microsatellites, mtDNA sequences, and morphological data, to describe the connectivity, genetic relationship, and distribution of Percilia gillissi and Percilia irwini, two endangered species inhabiting two contiguous watersheds in Chile (Itata and Biobío). We provide evidence of discordance in the spatial distribution of the two genomes (nuclear and mitochondrial). Three large clusters were identified with microsatellites, with one cluster straddling both watersheds. Three clusters were also evident in mtDNA with one cluster straddling both watersheds and the other two restricted to the Itata watershed’s northern reaches. Analyses of both microsatellite and mtDNA identified P. gillissi in the Itata watershed northern reaches and P. irwini in the Biobío watershed. Fish were detected in the Itata watershed that carried mtDNA characteristic of P. irwini but nuclear microsatellite profiles of P. gillissi suggesting an incomplete reproductive barrier between the species and connectivity between the watersheds. Additionally, fish were identified in the Itata northern reaches carrying mtDNA haplotypes sufficiently distinct from those of P. gillissi and P. irwini to suggest the existence of higher mtDNA diversity within P. gillissi than previously recognized. Finally, there was limited support for taxonomical classification based on morphological and meristic traits in this region.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data Availability
Data have been deposited in DRYAD and are available for peer review. https://datadryad.org/stash/share/QB86ISKvlO8u4E4FTnVP2kc2QO21hWonM6PCB9U9h_w
Code availability
Not applicable.
References
Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229. https://doi.org/10.1175/1520-0442(1992)0052.0.CO;2
Arratia G (1982) A Review of freshwater percoids from South America (Pisces, Osteichthyes, Perciformes, Percichthyidae, and Peciliidae). Abh Senckenb Naturforsch Ges 15:1–52
Arratia G, Quezada-Romegialli C (2019) The South American and Australian percichthyids and perciliids. What is new about them? Neotrop Ichthyol. https://doi.org/10.1590/1982-0224-20180102
Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48. https://doi.org/10.1093/oxfordjournals.molbev.a026036
Barreto SB, Knowles LL, de Affonso PRA (2020) Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish. J Evol Biol 33:1530–1542. https://doi.org/10.1111/jeb.13689
Barrett RDH, Hebert PDN (2005) Identifying spiders through DNA barcodes. Can J Zool 83:481–491. https://doi.org/10.1139/z05-024
Barton NH, Gale KS (1993) Genetic Analysis of Hybrid Zones. In: Harrison RG (ed) Hybrid Zones and the Evolutionary Process. Oxford University Press Inc, New York, p 364
Barton NH, Hewitt GM (1985) Analysis of hybrid zones. Annu Rev Ecol Syst 16:113–148. https://doi.org/10.1146/annurev.es.16.110185.000553
Carrea C, Barriga JP, Cussac VE, Ruzzante DE (2012) Genetic and phenotypic differentiation among Galaxias maculatus populations in a Patagonian postglacial lake system. Biol J Linn Soc 107:368–382. https://doi.org/10.1111/j.1095-8312.2012.01939.x
Carvalho Gomes L, Pessali TC, Sales NG et al (2015) Integrative taxonomy detects cryptic and overlooked fish species in a neotropical river basin. Genetica 143:581–588. https://doi.org/10.1007/s10709-015-9856-z
Chan WY, Hoffmann AA, van Oppen MJH (2019) Hybridization as a conservation management tool. Conserv Lett 12:1–11. https://doi.org/10.1111/conl.12652
Coissac E, Hollingsworth PM, Lavergne S, Taberlet P (2016) From barcodes to genomes: extending the concept of DNA barcoding. Mol Ecol 25:1423–1428. https://doi.org/10.1111/mec.13549
Cox AJ, Hebert PDN (2001) Colonization, extinction, and phylogeographic patterning in a freshwater crustacean. Mol Ecol 10:371–386. https://doi.org/10.1046/j.1365-294X.2001.01188.x
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772–772. https://doi.org/10.1038/nmeth.2109
Dayrat B (2005) Towards integrative taxonomy. Biol J Linn Soc 85:407–415. https://doi.org/10.1111/j.1095-8312.2005.00503.x
Dirección General de Aguas (2004) Diagnostico y Clasificación de los cursos y cuerpos de agua segun objetivos de calidad: Cuenca del río Itata. Gob Chile, Minist obras públicas y Dir obras Hidraúlicas 1–127
Dyer B (2000) Systematic review and biogeography of the freshwater fishes of chile revision sistematicay biogeografica de los peces dulceacuicolas De Chile. Estud Ocean 19:77–98. https://doi.org/10.4067/S0717-65382006000100016
Earl DA, vonHoldt BM (2012) Structure harvester: a website and program for visualizing structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361. https://doi.org/10.1007/s12686-011-9548-7
Elphinstone MS, Hinten GN, Anderson MJ, Nock CJ (2003) An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies. Mol Ecol Notes 3:317–320. https://doi.org/10.1046/j.1471-8286.2003.00397.x
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Folmer O, Black M, Hoeh W et al (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–299. https://doi.org/10.1071/ZO9660275
Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst 34:397–423. https://doi.org/10.1146/annurev.ecolsys.34.011802.132421
Genovart M (2009) Natural hybridization and conservation. Biodivers Conserv 18:1435–1439. https://doi.org/10.1007/s10531-008-9550-x
Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Updated from Goudet J. (1995) FSTAT Version 1.2: A computer program to calculate F-statistics. J Hered 86:485–486
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704. https://doi.org/10.1080/10635150390235520
Habit E, Bertrán C, Arévalo S, Victoriano P (1998) Benthonic fauna of the Itata river and irrigation canals (Chile). Irrig Sci 18:91–99. https://doi.org/10.1007/s002710050049
Habit E, Parra O (2001) Impacto ambiental de los canales de riego sobre la fauna de peces. Ambient y Desarro XVII: 50–58
Harrison RG (1990) Hybrid zones: windows on evolutionary process. Oxford Surv Evol Biol 7:69–128
Hata H, Uemura Y, Ouchi K, Matsuba H (2019) Hybridization between an endangered freshwater fish and an introduced congeneric species and consequent genetic introgression. PLoS ONE 14:1–16. https://doi.org/10.1371/journal.pone.0212452
Hebert PDN, Cywinska A, Ball SL, Dewaard JR (2003a) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321. https://doi.org/10.1098/rspb.2002.2218
Hebert PDN, Penton EH, Burns JM et al (2004a) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci U S A 101:14812–14817. https://doi.org/10.1073/pnas.0406166101
Hebert PDN, Ratnasingham S, Dewaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B. https://doi.org/10.1098/rsbl.2003.0025
Hebert PDN, Ratnasingham S, Zakharov EV et al (2016) Counting animal species with DNA barcodes: Canadian insects. Philos Trans R Soc B Biol Sci. https://doi.org/10.1098/rstb.2015.0333
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004b) Identification of birds through DNA barcodes. PLoS Biol. https://doi.org/10.1371/journal.pbio.0020312
Hendry AP, Lohmann LG, Conti E et al (2010) Evolutionary biology in biodiversity science, conservation, and policy: A call to action. Evolution (n Y) 64:1517–1528. https://doi.org/10.1111/j.1558-5646.2010.00947.x
Hewitt GM (1988) Hybrid zones-natural laboratories for evolutionary studies. Trends Ecol Evol 3:158–167. https://doi.org/10.1016/0169-5347(88)90033-X
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Yang and Rannala 17:754–755
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806. https://doi.org/10.1093/bioinformatics/btm233
Lavoué S, Nakayama K, Jerry DR et al (2014) Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): Comparison with recent nuclear gene-based studies and simultaneous analysis. Gene 549:46–57. https://doi.org/10.1016/j.gene.2014.07.033
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452. https://doi.org/10.1093/bioinformatics/btp187
Martinsen GD, Whitham TG, Turek RJ, Keim P (2001) Hybrid populations selectively filter gene introgression between species. Evolution (n Y) 55:1325–1335. https://doi.org/10.1111/j.0014-3820.2001.tb00655.x
Milne DJ, Jackling FC, Sidhu M, Appleton BR (2009) Shedding new light on old species identifications: Morphological and genetic evidence suggest a need for conservation status review of the critically endangered bat, Saccolaimus saccolaimus. Wildl Res 36:496–508. https://doi.org/10.1071/WR08165
Mimura M, Yahara T, Faith DP et al (2017) Understanding and monitoring the consequences of human impacts on intraspecific variation. Evol Appl 10:121–139. https://doi.org/10.1111/eva.12436
Muñoz-Ramírez CP, Habit E, Unmack PJ et al (2016) Low genetic diversity in Diplomystes camposensis, an endemic and endangered catfish from South Chile. Zool Stud 55:1–14. https://doi.org/10.6620/ZS.2016.55-16
Peakall R, Smouse PE (2006) genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
Porter TM, Hajibabaei M (2018) Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Mol Ecol 27:313–338. https://doi.org/10.1111/mec.14478
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Raja HA, Miller AN, Pearce CJ, Oberlies NH (2017) Fungal identification using molecular tools: a primer for the natural products research community. J Nat Prod 80:756–770. https://doi.org/10.1021/acs.jnatprod.6b01085
Rambaut A (2006) FigTree: tree figure drawing tool version 1.4.4.
Rosenberg NA (2004) DISTRUCT: A program for the graphical display of population structure. Mol Ecol Notes 4:137–138. https://doi.org/10.1046/j.1471-8286.2003.00566.x
Ruiz VH, Marchant M (2004) Ictiofauna de aguas continentales Chilenas. Universidad de Concepción, Chile, Concepción
Ruzzante DE, Simons AP, McCracken GR et al (2020) Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites: Drainage reversals revealed by genomics. Proc R Soc B Biol Sci 287:1–10. https://doi.org/10.1098/rspb.2020.0468rspb20200468
Ruzzante DE, Walde SJ, Cussac VE et al (2006) Phylogeography of the Percichthyidae (Pisces) in Patagonia: roles of orogeny, glaciation, and volcanism. Mol Ecol 15:2949–2968. https://doi.org/10.1111/j.1365-294X.2006.03010.x
Ruzzante DE, Walde SJ, Gosse JC et al (2008) Climate control on ancestral population dynamics: Insight from Patagonian fish phylogeography. Mol Ecol 17:2234–2244. https://doi.org/10.1111/j.1365-294X.2008.03738.x
Ruzzante DE, Walde SJ, Macchi PJ et al (2011) Phylogeography and phenotypic diversification in the Patagonian fish Percichthys trucha: The roles of Quaternary glacial cycles and natural selection. Biol J Linn Soc 103:514–529. https://doi.org/10.1111/j.1095-8312.2011.01682.x
Seehausen O, Takimoto G, Roy D, Jokela J (2008) Speciation reversal and biodiversity dynamics with hybridization in changing environments. Mol Ecol 17:30–44. https://doi.org/10.1111/j.1365-294X.2007.03529.x
Taylor HR, Harris WE (2012) An emergent science on the brink of irrelevance: a review of the past 8years of DNA barcoding. Mol Ecol Resour 12:377–388. https://doi.org/10.1111/j.1755-0998.2012.03119.x
Thiele R, Moreno H, Elgueta S et al (1998) Evolución geológico-geomorfológica cuaternaria del tramo superior del valle del río Laja. Rev Geológica Chile 25:229–253. https://doi.org/10.4067/S0716-02081998000200007
Toews DPL, Brelsford A (2012) The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol 21:3907–3930. https://doi.org/10.1111/j.1365-294X.2012.05664.x
Valenzuela-Aguayo F, McCracken GR, Manosalva A et al (2019) Human-induced habitat fragmentation effects on connectivity, diversity, and population persistence of an endemic fish, Percilia irwini, in the Biobío River basin (Chile). Evol Appl 13:1–14. https://doi.org/10.1111/eva.12901
Vanhaecke D, de Leaniz CG, Gajardo G et al (2012) DNA barcoding and microsatellites help species delimitation and hybrid identification in endangered galaxiid fishes. PLoS ONE 7:1–10. https://doi.org/10.1371/journal.pone.0032939
Vera-Escalona I, Habit E, Ruzzante DE (2015) Echoes of a distant time: Effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia. Mol Ecol 24:4112–4128. https://doi.org/10.1111/mec.13303
Ward RD (2009) DNA barcode divergence among species and genera of birds and fishes. Mol Ecol Resour 9:1077–1085. https://doi.org/10.1111/j.1755-0998.2009.02541.x
Wilson KH (1995) Molecular biology as a tool for taxonomy. Clin Infect Dis 20:S117–S121. https://doi.org/10.1093/clinids/20.Supplement_2.S117
Yu D, Ding X, Zhang Z et al (2018) Microsatellite records for volume 10, issue 2. Conserv Genet Resour 10:269–276. https://doi.org/10.1007/s12686-018-1046-8
Yu D, Ding X, Zhang Z et al (2020) Correction to: Microsatellite records for volume 10, issue 2 (Conservation Genetics Resources, (2018), 10, 2, (269–276), DOI: 10.1007/s12686-018-1046-8). Conserv Genet Resour 12:155–156
Zemlak TS, Walde SJ, Habit EM, Ruzzante DE (2011) Climate-induced changes to the ancestral population size of two Patagonian galaxiids: The influence of glacial cycling. Mol Ecol 20:5280–5294. https://doi.org/10.1111/j.1365-294X.2011.05352.x
Zhan L, Paterson IG, Fraser BA et al (2017) megasat : automated inference of microsatellite genotypes from sequence data. Mol Ecol Resour 17:247–256. https://doi.org/10.1111/1755-0998.12561
Acknowledgements
We thank three anonymous reviewers for their insightful comments that improved the clarity and quality of this manuscript. FVA thanks Sarah Salisbury and Ivan Vera-Escalona in the Ruzzante lab for feedback and comments on earlier versions of the manuscript. The research was supported by a FONDECYT Grant 1150154 to EH and collaborators and an NSERC Discovery Grant to DER. FV-A was supported by Beca CONICYT Nacional Folio 21160882 and a Canada Department of Foreign Affairs, Trade and Development (DFATD) Emerginf Leaders of Amerricas Program (ELAP) scholarship.
Funding
This research was supported by a FONDECYT Grant 1150154 to EH and collaborators and an NSERC Discovery Grant to DER. FVA was supported by Beca CONICYT Nacional Folio 21160882 and a Canada Department of Foreign Affairs, Trade and Development (DFATD) Emerging Leaders of Americas Program (ELAP) scholarship.
Author information
Authors and Affiliations
Contributions
This study is part of FVA Doctoral thesis at Universidad de Concepción, Chile under the co-supervision of EH and DER. The study was conceived and designed by EH, DER and FVA. FVA, GD, and AM, EH and DER participated in the fieldwork. GRM developed the microsatellite markers and GRM and FVA generated the molecular data. FVA conducted all population genetics analyses with assistance from DER and GRM. GD conducted the morphometric analysis. FVA wrote the first draft of the MS with assistance from DER and EH.
Corresponding authors
Ethics declarations
Conflict of interest
The authors have no conflicts of interest to declare that are relevant to the content of this article.
Ethical approval
The sampling was carried out based on the ethics and biosafety rules and procedures specified in Law 18.755 of the Agricultural and Livestock Service of Chile and the Ethics Committee of Universidad de Concepción.
Consent to participate
The authors give their consent to participate.
Consent for publication
The authors give their consent to publish.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Valenzuela-Aguayo, F., McCracken, G.R., Diaz, G. et al. Connectivity, diversity, and hybridization between two endemic fish species (Percilia spp.) in a complex temperate landscape. Conserv Genet 23, 23–33 (2022). https://doi.org/10.1007/s10592-021-01400-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10592-021-01400-y