Strong genetic differentiation among populations of the freshwater shrimp Caridina cantonensis in Hong Kong: implications for conservation of freshwater fauna in urban areas
Ling Ming Tsang A , Kwok Ho Tsoi B , Simon Kin-Fung Chan C , Tony King-Tung Chan C and Ka Hou Chu D E
+ Author Affiliations
- Author Affiliations
A Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan.
B Department of Science and Environmental Studies, Hong Kong Institute of Education, Tai Po, Hong Kong.
C Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong.
D Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
E Corresponding author. Email: kahouchu@cuhk.edu.hk
Marine and Freshwater Research 68(1) 187-194 https://doi.org/10.1071/MF15377
Submitted: 8 January 2015 Accepted: 9 December 2015 Published: 21 March 2016
Abstract
Freshwater organisms generally exhibit strong genetic structuring. Although understanding the level and spatial distribution of genetic diversity is crucial for conservation management planning, such information has received little attention until recently in highly developed cities where local extinction attributed to habitat destruction and urbanisation is intense. We compared the genetic divergence in mitochondrial COI of the freshwater shrimp Caridina cantonensis collected from 32 sites in Hong Kong, to determine the connectivity among populations and the levels of genetic diversity of the shrimp. We found that shrimp from different streams are genetically highly differentiated and each stream always has its own unique haplotype groups, even though some of the streams are separated only by a few kilometres, indicating very limited gene flow across streams. Moreover, genetic diversity within each stream is very low, usually with a single haplotype dominating the entire population, and genetic differentiation was observed among tributaries from the same drainage. The high genetic diversity of these species over short distances has significant conservation implications because a substantial amount of biodiversity may have already been lost as a result of past development. Careful conservation planning is essential for future development in Hong Kong and other cities.
Additional keywords: conservation genetics, genetic diversity, population genetics.
References
Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions on Automatic Control 19, 716–723.| A new look at the statistical model identification.Crossref | GoogleScholarGoogle Scholar |
Bilton, D. T., Freeland, J. R., and Okamura, B. (2001). Dispersal in freshwater invertebrates. Annual Review of Ecology and Systematics 32, 159–181.
| Dispersal in freshwater invertebrates.Crossref | GoogleScholarGoogle Scholar |
Bohonak, A. J. (1999). Dispersal, gene flow, and population structure. The Quarterly Review of Biology 74, 21–45.
| Dispersal, gene flow, and population structure.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DyaK1M7otFKltw%3D%3D&md5=2e37c964afbb9b9208f9c1a567812dc0CAS | 10081813PubMed |
Bohonak, A. J., and Jenkins, D. G. (2003). Ecological and evolutionary significance of dispersal by freshwater invertebrates. Ecology Letters 6, 783–796.
| Ecological and evolutionary significance of dispersal by freshwater invertebrates.Crossref | GoogleScholarGoogle Scholar |
Bunn, S. E., and Hughes, J. M. (1997). Dispersal and recruitment in streams: evidence from genetic studies. Journal of the North American Benthological Society 16, 338–346.
| Dispersal and recruitment in streams: evidence from genetic studies.Crossref | GoogleScholarGoogle Scholar |
Cai, Y. (1996). A revision of the genus Neocaridina (Crustacea: Decapoda: Atyidae). Dong Wu Fen Lei Xue Bao 21, 129–160.
Cai, Y., and Ng, N. K. (1999). A revision of Caridina serrata species group, with descriptions of five new species (Crustacea: Decapoda: Caridea: Atyidae). Journal of Natural History 33, 1603–1638.
| A revision of Caridina serrata species group, with descriptions of five new species (Crustacea: Decapoda: Caridea: Atyidae).Crossref | GoogleScholarGoogle Scholar |
Clement, M., Posada, D., and Crandall, K. A. (2000). TCS: a computer program to estimate gene genealogies. Molecular Ecology 9, 1657–1660.
| TCS: a computer program to estimate gene genealogies.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3cXnvV2gtbw%3D&md5=f37ae8fc8622c7f1c48a796e5faa350dCAS | 11050560PubMed |
Cook, B. D., Baker, A. M., Page, T. J., Grant, S. C., Hurwood, D. A., and Hughes, J. M. (2006). Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): the role life transition in phylogeographic diversification. Molecular Ecology 15, 1083–1093.
| Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): the role life transition in phylogeographic diversification.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XjslWms74%3D&md5=22ad1ebad2d138e19070546466040cb1CAS | 16599968PubMed |
De Grave, S., and Fransen, C. H. J. M. (2011). Carideorum catalogus: the recent species of the dendrobranchiata, stenopodidean, procarididean and caridean shrimps (Crustacea: Decapoda). Zoölogische Mededeelingen 85, 195–589.
Dudgeon, D. (2000). The ecology of tropical Asian rivers and streams in relation to biodiversity conservation. Annual Review of Ecology and Systematics 31, 239–263.
| The ecology of tropical Asian rivers and streams in relation to biodiversity conservation.Crossref | GoogleScholarGoogle Scholar |
Dudgeon, D. (2011). Asian river fishes in the Anthropocene: threats and conservation challenges in an era of rapid environmental change. Journal of Fish Biology 79, 1487–1524.
| Asian river fishes in the Anthropocene: threats and conservation challenges in an era of rapid environmental change.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC38%2FkslWrsQ%3D%3D&md5=abe17affefeb095311736d6074acadcdCAS | 22136237PubMed |
Dudgeon, D., Arthington, A. H., Gessner, M. O., Kawabata, Z., Knowler, D., Lévêque, C., Naiman, R. J., Prieur-Richard, A.-H., Soto, D., Stiassny, M. L. J., and Sullivan, C. A. (2006). Freshwater biodiversity: importance, threats, status and conservation challenges. Biological Reviews of the Cambridge Philosophical Society 81, 163–182.
| Freshwater biodiversity: importance, threats, status and conservation challenges.Crossref | GoogleScholarGoogle Scholar | 16336747PubMed |
Dupanloup, I., Schneider, S., and Exocffier, L. (2002). A simulated annealing approach to define the genetic structure of populations. Molecular Ecology 11, 2571–2581.
| A simulated annealing approach to define the genetic structure of populations.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD38nptlaksw%3D%3D&md5=7906998ecd3f35a65a1b914e383f75feCAS | 12453240PubMed |
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792–1797.
| MUSCLE: multiple sequence alignment with high accuracy and high throughput.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXisF2ks7w%3D&md5=eed91ec94ed694f3c3a3eaa725d81f9eCAS | 15034147PubMed |
Excoffier, L., Smouse, P. E., and Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 86, 991–1000.
Excoffier, L., Laval, L. G., and Schneider, S. (2005). Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1, 47–50.
| 1:CAS:528:DC%2BD28XjsFSltg%3D%3D&md5=3cb5eea1ce5fab9d714560774e9d8a2aCAS |
Folmer, O., Black, M., Hoeh, W., Lutz, R. A., and Vrijenhoek, R. C. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3, 294–299.
| 1:CAS:528:DyaK2MXjt12gtLs%3D&md5=a3486685be3507eb76e89c84375ae16bCAS | 7881515PubMed |
Fu, Y.-X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Genetics 147, 915–925.
| 1:STN:280:DyaK2svns1egtQ%3D%3D&md5=a890b625dc5d990e91c11fe1c782ac6bCAS | 9335623PubMed |
Hau, B. C. H., Dudgeon, D., and Corlett, R. T. (2005). Beyond Singapore: Hong Kong and Asian biodiversity. Trends in Ecology & Evolution 20, 281–282.
| Beyond Singapore: Hong Kong and Asian biodiversity.Crossref | GoogleScholarGoogle Scholar |
Hughes, J. M. (2007). Constraints on recovery: using molecular methods to study connectivity of aquatic biota in rivers and streams. Freshwater Biology 52, 616–631.
| Constraints on recovery: using molecular methods to study connectivity of aquatic biota in rivers and streams.Crossref | GoogleScholarGoogle Scholar |
Hughes, J. M., Real, K. M., Marshall, J. C., and Schmidt, D. J. (2012). Extreme genetic structure in a small-bodied freshwater fish, the purple spotted gudgeon, Mogurnda adspersa (Eleotridae). PLoS One 7, e40546.
| Extreme genetic structure in a small-bodied freshwater fish, the purple spotted gudgeon, Mogurnda adspersa (Eleotridae).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhtVOnsL3M&md5=e683c59431dc92a790f02fadb2a63919CAS | 22808190PubMed |
Hurwood, D. A., and Hughes, J. M. (2001). Nested clade analysis of the freshwater shrimp, Caridina zebra (Decapoda: Atyidae), from north-eastern Australia. Molecular Ecology 10, 113–125.
| Nested clade analysis of the freshwater shrimp, Caridina zebra (Decapoda: Atyidae), from north-eastern Australia.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3MXjs1ejtLk%3D&md5=ee281debd91f9ba93e02a343e32a079dCAS | 11251792PubMed |
Klotz, W., and von Rintelen, T. (2014). To ‘bee’ or not to be: on some ornamental shrimp from Guangdong Province, southern China and Hong Kong SAR, with descriptions of three new species. Zootaxa 3889, 151–184.
| To ‘bee’ or not to be: on some ornamental shrimp from Guangdong Province, southern China and Hong Kong SAR, with descriptions of three new species.Crossref | GoogleScholarGoogle Scholar | 25544138PubMed |
Liang, X.-Q., and Yan, S.-L. (1977). New species and subspecies of Caridina (Decapoda, Caridea) from Fukien, China. Acta Hydrobiologia Sinica 6, 219–225.
Milne Edwards, H. (1837). ‘Histoire naturelle des Crustaceés, Comprenant l’Anatomie, la Physiologie et la Classification de ces Animaux, Vol. 2’. (Libraire Encyclopedique de Roret: Paris.)
Myers, M. J., Meyer, C. P., and Resh, V. H. (2000). Neritid and thiarid gastropods from French Polynesian streams: how reproduction (sexual, parthenogenetic) and dispersal (active, passive) affect population structure. Freshwater Biology 44, 535–545.
| Neritid and thiarid gastropods from French Polynesian streams: how reproduction (sexual, parthenogenetic) and dispersal (active, passive) affect population structure.Crossref | GoogleScholarGoogle Scholar |
Page, T. J., and Hughes, J. M. (2007). Radically different scales of phylogeographic structuring within cryptic species of freshwater shrimp (Atyidae: Caridina). Limnology and Oceanography 52, 1055–1066.
| Radically different scales of phylogeographic structuring within cryptic species of freshwater shrimp (Atyidae: Caridina).Crossref | GoogleScholarGoogle Scholar |
Poff, N. L. (1997). Landscape filters and species traits: towards mechanistic understanding and prediction in stream ecology. Journal of the North American Benthological Society 16, 391–409.
| Landscape filters and species traits: towards mechanistic understanding and prediction in stream ecology.Crossref | GoogleScholarGoogle Scholar |
Posada, D. (2008). jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25, 1253–1256.
| jModelTest: phylogenetic model averaging.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXotlKgsb4%3D&md5=8566c781e6b63325ced17a8591ad98d9CAS | 18397919PubMed |
Roy, A. H., Purcell, A. H., Walsh, C. J., and Wenger, S. J. (2009). Urbanization and stream ecology: five years later. Journal of the North American Benthological Society 28, 908–910.
| Urbanization and stream ecology: five years later.Crossref | GoogleScholarGoogle Scholar |
Sodhi, N. S., Koh, L. P., Brook, B. W., and Ng, P. K. L. (2004). Southeast Asian biodiversity: an impending disaster. Trends in Ecology & Evolution 19, 654–660.
| Southeast Asian biodiversity: an impending disaster.Crossref | GoogleScholarGoogle Scholar |
Stimpson, W. (1860). Prodromus descriptionis animalium evertebratorum, quae in Expeditione ad Oceanum Pacificum Septemtrionalem, a Republica Federata missa, C. Ringgold et J. Rodgers, observavit et descriptsit. Proceedings of National Academy of Sciences, Philadelphia 8, 97–116.
Strayer, D. L., and Dudgeon, D. (2010). Freshwater biodiversity conservation: recent progress and future challenges. Journal of the North American Benthological Society 29, 344–358.
| Freshwater biodiversity conservation: recent progress and future challenges.Crossref | GoogleScholarGoogle Scholar |
Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.
| 1:CAS:528:DyaK3cXhslentA%3D%3D&md5=7a22257071f5a361e4623d3f4031cf24CAS | 2513255PubMed |
Tong, J. G., Chan, T. Y., and Chu, K. H. (2000). A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda: Penaeidae) based on mitochondrial DNA sequences of selected species from the Indo-West Pacific. Journal of Crustacean Biology 20, 541–549.
| A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda: Penaeidae) based on mitochondrial DNA sequences of selected species from the Indo-West Pacific.Crossref | GoogleScholarGoogle Scholar |
von Rintelen, K. (2011). Intraspecific geographic differentiation and patterns of endemism in freshwater shrimp species flocks in ancient lakes of Sulawesi. In ‘Crustacean Issues 19. Phylogeography and Population Genetics in Crustacea’. (Eds C. Held, S. Koenemann and C. D. Schubart.) pp. 257–271. (CRC Press: Baton Raton, FL.)
Vörösmarty, C., McIntyre, P. B., Gessner, M. O., Dudgeon, D., Prusevich, A., Green, P., Glidden, S., Bunn, S. E., Sullivan, C. A., Reidy Liermann, C., and Davies, P. M. (2010). Global threats to human water security and river biodiversity. Nature 467, 555–561.
| Global threats to human water security and river biodiversity.Crossref | GoogleScholarGoogle Scholar | 20882010PubMed |
Walsh, C. J., Roy, A. H., Feminella, J. W., Cottingham, P. D., Groffman, P. M., and Morgan, R. P. (2005). The urban stream syndrome: current knowledge and the search for a cure. Journal of the North American Benthological Society 24, 706–723.
| The urban stream syndrome: current knowledge and the search for a cure.Crossref | GoogleScholarGoogle Scholar |
Yam, R. S. W., and Cai, Y. (2003). Caridina trifasciata, a new species of freshwater shrimp (Decapoda: Atyidae) from Hong Kong. The Raffles Bulletin of Zoology 51, 277–282.
Yam, R. S. W., and Dudgeon, D. (2005a). Stable isotope investigation of food use by Caridina spp. (Decapoda: Atyidae) in Hong Kong streams. Journal of the North American Benthological Society 24, 68–81.
| Stable isotope investigation of food use by Caridina spp. (Decapoda: Atyidae) in Hong Kong streams.Crossref | GoogleScholarGoogle Scholar |
Yam, R. S. W., and Dudgeon, D. (2005b). Genetic differentiation of Caridina spp. (Decapoda: Atyidae) in Hong Kong streams. Journal of the North American Benthological Society 24, 845–857.
| Genetic differentiation of Caridina spp. (Decapoda: Atyidae) in Hong Kong streams.Crossref | GoogleScholarGoogle Scholar |
Yu, S. C. (1936). Report on the macrurous Crustacea collected during the ‘Hainan Biological Expedition’ in 1934. Chinese Journal of Zoology 2, 85–99.
Yu, S. C. (1938). Study on Chinese Caridina with descriptions of five species. Bulletin of the Fan Memorial of the Institute of Biology – Zoology Series 8, 271–310.
