Conservation Genetics

, Volume 18, Issue 1, pp 211–223 | Cite as

Cryptic genetic diversity and spatial patterns of admixture within Belizean marine reserves

  • C. C. D’Aloia
  • S. M. Bogdanowicz
  • R. G. Harrison
  • P. M. Buston
Research Article


Despite the potential for long-distance gene flow in the sea, there is growing evidence of cryptic genetic diversity in many marine taxa. Understanding the geographic distribution of cryptic lineages, as well as the spatial patterns of admixture among them, can have important implications for conservation planning. Here, we explore patterns of divergence in a coral reef fish, the neon goby Elacatinus lori, across the species’ range. First, we use targeted amplicon sequencing to describe the spatial pattern of genetic divergence using two marker types (57 anonymous ddRAD-derived loci and mtDNA cytb). Second, we quantify the degree of admixture and hybridization between two previously-unidentified divergent lineages within Belize. Third, we assess whether the existing group of marine protected areas (MPAs) in Belize protects this cryptic genetic diversity. The results provide strong evidence for two divergent genetic lineages of E. lori within Belize, separated geographically by only 30 km of low-suitability habitat. There is a sharp genetic cline across these 30 km, and evidence of admixture and introgression at the boundary regions of the habitat break. We also show that the broadly-distributed arrangement of MPAs within Belize protects both major lineages as well as subtle structure within-lineages, and therefore may confer protection to co-distributed species that exhibit similar spatial patterns of divergence.


Marine Evolution Hybridization Cryptic species Mesoamerican reef Marine protected area 



We are grateful to Diana Acosta, Alben David, Philip Schmiege, and Derek Scolaro for assistance in the field, and to Carrie Bow Caye Field Station, ReefCI, Glover’s Reef Research Station, Itza Lodge, and St. George’s Caye Resort for hosting our team in the field. We also thank José Andrés and the Harrison Lab for constructive feedback on lab work; Erica Larson for thoughtful advice on data analysis; and Benjamin Victor for providing Honduran tissue samples. We thank Einar Eg Nielsen, Amy McCune, and one anonymous reviewer for comments that improved this manuscript. All work complied with Boston University IACUC (#13-008) and Belize Fisheries. CCD was supported by an NSF GRF (DGE-1247312) and an NSERC Strategic Grant (#430706-12); research was supported by an NSF Ocean Sciences grant (OCE-1260424).

Supplementary material

10592_2016_895_MOESM1_ESM.docx (1 mb)
Supplement 1 Contains supplementary tables and figures related to primers; within-site tests of HWE and LD; and additional population structure analyses. Supplementary material 1 (DOCX 1067 kb)
10592_2016_895_MOESM2_ESM.docx (19 kb)
Supplement 2 Contains additional simulation and Structure runs to explore analytical thresholds for the admixture and genomic cline analyses. Supplementary material 2 (DOCX 18 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • C. C. D’Aloia
    • 1
    • 4
  • S. M. Bogdanowicz
    • 2
  • R. G. Harrison
    • 2
  • P. M. Buston
    • 3
  1. 1.Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoCanada
  2. 2.Department of Ecology and Evolutionary BiologyCornell UniversityIthacaUSA
  3. 3.Department of Biology and Marine ProgramBoston UniversityBostonUSA
  4. 4.Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleUSA

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