Conservation biology and genetics of the largest living rays: manta rays

Kashiwagi, Tsutomu (2014). Conservation biology and genetics of the largest living rays: manta rays PhD Thesis, School of Biomedical Sciences, The University of Queensland.

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Author Kashiwagi, Tsutomu
Thesis Title Conservation biology and genetics of the largest living rays: manta rays
School, Centre or Institute School of Biomedical Sciences
Institution The University of Queensland
Publication date 2014-09-12
Thesis type PhD Thesis
Supervisor Michael Bennett
Jennifer Ovenden
Total pages 182
Total colour pages 13
Total black and white pages 169
Language eng
Subjects 0604 Genetics
0602 Ecology
0603 Evolutionary Biology
Formatted abstract
Conservation biology and genetics study on manta rays Manta spp. was conducted. To elucidate the degree of habitat segregation between Manta alfredi and M. birostis, photographic records (n=3328) from 20 localities and 91 sites were examined. Manta alfredi and M. birostis were found to exhibit habitat segregation between near-shore and offshore environments, respectively, and mosaic habitat occupancy within their large overlapping distribution range in the world ocean. To identify the degree and patterns of genetic differentiation, DNA analyses were conducted. Analyses using CO1 and ND5 region of mitochondrial DNA and RAG1 gene of nuclear DNA showed a signature of recent speciation with an estimated divergence time within 1Ma.

The two species reach the northern limit of their range in Japanese water in the West Pacific. To update the knowledge of the distribution of the two species in this region, photographic records sourced from published record, web-based information, museums, aquariums, fisheries research stations, dive shops, photographers, universities and others were examined. Northernmost occurrence record was Yomogita, Aomori (40° 59´N 140° 41´E) for M. birostris and Iburi, Kochi (32° 48´ N 132° 58´ E) for M. alfredi. However, year-round aggregation site were found only in Yaeyama Islands (24° 20´ N 124° 00´ E, n = 305 M. alfredi individuals identified during a 1987- 2009 study) and Ogasawara Islands (26°40´ N 142° 10´ E, n = 42 M. birostris individuals identified during a 1995-1998 study).

To gain robust empirical knowledge on reproductive ecology, vital rates, and demographic processes, a focused study on the logbook record of M. alfredi in Yaeyama Islands was conducted. Photographically identified M. alfredi individuals have been the subjects of diver observation since the mid 1970s. Logbook record between 1987 and 2009 contained 11,111 sighting records of 305 individuals. The maximum disc width (DW) was 4.2 m for females and 3.6 m for males. The minimum size was 1.3m DW. Maturity of females, based on first reproduction, occurred at 3.8 – 4.0m DW and 9 -16 years of age. Maturity of males, based on clasper development, occurred at 2.8 – 3.0 m DW and 4 – 9 years of age. Longevity may be closed to 40 years. A maximum reproductive span of at least 27 years was observed. A maximum of number of pregnancies for any individual was 9 at a rate of 0.41 year -1. The average birth interval among female with pregnancy record was 3.61 – 3.93 years.

Series of capture-mark-recapture (CMR) analyses determined the juvenile and adult survival rate as 0.63 and 0.95, respectively. Annual population size increased from minimum 36 (35-37, 95% CI) to 159 (154 – 165) with population growth rate (λG) 1.056 (0.976 – 1.143). Decadal population size increased from 181 (169-194) to 245 (237 – 253) with λG of 1.023 (1.009-1.036). Empirically obtained demographic rates, population growth rates and abundance estimate were evaluated with integrated analyses that included matrix population projection model, AgeNe model and genetic estimates of effective population size (Ne) calculated from genotypic data of 10 microsatellite loci. Analyses found that the size of the observed aggregation population (estimated by CMR) is actually the majority of the size of the total population (NT calculated by AgeNe model) (81.6%) and there are not many unmarked but demographically connected individuals outside of the aggregation site. Effective population size Ne = 89 based on the estimate using microsatellite data, upper confidence limit of N = 165 for aggregation site by CMR analyses and the estimated maximum of 202 for the total population size by AgeNe model indicated that this population belongs to “very small wild subpopulation” category in CITES guideline.

Analyses integrating Ne should be applicable to other studies facing typical and critical challenges of studying highly mobile marine species. CMR analyses can provide useful measurement on vital rates and population size that is statistically available for capture. If researchers aim to infer total population size, however, the research project needs auxiliary information, such as Ne and abundance information in neighbouring habitat. This study highlighted that the genetic monitoring should be incorporated to all monitoring and assessment program in light of the expected trajectory of depleted marine populations becoming smaller and more fragmented.
Keyword speciation
mark and recapture
effective population size
Linkage Disequilibrium
multi state open robust design
Matrix population models
Mitochondrial - DNA

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Created: Fri, 12 Sep 2014, 14:47:12 EST by Mr Tsutomu Kashiwagi on behalf of Scholarly Communication and Digitisation Service