Abbott, R. J. (2017). Plant speciation across environmental gradients
and the occurrence and nature of hybrid zones. Journal of
Systematics and Evolution, 55(4), 238–258. doi:
10.1111/jse.12267
Abbott, R. J., Albach, D., Ansell, S., Arntzen, J. W., Baird, S. J. E.,
Bierne, N., … Zinner, D. (2013). Hybridization and speciation.Journal of Evolutionary Biology, 26(2), 229–246. doi:
10.1111/j.1420-9101.2012.02599.x
Andrews, S. (2010). FASTQC: a quality control tool for high
throughput sequence data.
Beaumont, M. A., Zhang, W., & Balding, D. J. (2002). Approximate
Bayesian computation in population genetics. Genetics,162(4), 2025–2035.
Bilmes, J. A. (1998). A gentle tutorial of the EM algorithm and its
application to parameter estimation for gaussian mixture and hidden
markov models. ReCALL, 4(510), 126. doi:
10.1080/0042098032000136147
Binks, R. M., Byrne, M., Mcmahon, K., Pitt, G., Murray, K., & Evans, R.
D. (2019). Habitat discontinuities form strong barriers to gene flow
among mangrove populations, despite the capacity for long-distance
dispersal. Diversity and Distributions, 25(2), 298–309.
doi: 10.1111/ddi.12851
Brandvain, Y., Kenney, A. M., Flagel, L., Coop, G., & Sweigart, A. L.
(2014). Speciation and Introgression between Mimulus nasutus andMimulus guttatus. Plos Genetics, 10(6), e1004410.
doi: 10.1371/journal.pgen.1004410
Chen, Y., Shen, Y., Lin, P., Tong, D., Zhao, Y., Allesina, S., …
Wu, C. I. (2019). Gene regulatory network stabilized by pervasive weak
repressions: MicroRNA functions revealed by the May-Wigner theory.National Science Review, 6(6), 1176–1188. doi:
10.1093/nsr/nwz076
Clarke, P. J., Kerrigan, R. A., & Westphal, C. J. (2001). Dispersal
potential and early growth in 14 tropical mangroves: Do early life
history traits correlate with patterns of adult distribution?Journal of Ecology, 89(4), 648–659. doi:
10.1046/j.0022-0477.2001.00584.x
Clarkson, C. S., Weetman, D., Essandoh, J., Yawson, A. E., Maslen, G.,
Manske, M., … Donnelly, M. J. (2014). Adaptive introgression
between Anopheles sibling species eliminates a major genomic
island but not reproductive isolation. Nature Communications,5(May). doi: 10.1038/ncomms5248
Cruickshank, T. E., & Hahn, M. W. (2014). Reanalysis suggests that
genomic islands of speciation are due to reduced diversity, not reduced
gene flow. Molecular Ecology, 23(13), 3133–3157. doi:
10.1111/mec.12796
Csilléry, K., François, O., & Blum, M. G. B. (2012). Abc: An R package
for approximate Bayesian computation (ABC). Methods in Ecology and
Evolution, 3(3), 475–479. doi: 10.1111/j.2041-210X.2011.00179.x
Dempster, A. P., Laird, N. M., & Rubin, D. B. (1977). Maximum
Likelihood from Incomplete Data Via the EM Algorithm.Journal of the Royal Statistical Society: Series B
(Methodological), 39(1), 1–22. doi:
10.1111/j.2517-6161.1977.tb01600.x
Doyle, J. J., & Doyle, J. L. (1987). A rapid DNA isolation procedure
for small quantities of fresh leaf tissue. Phytochemical
Bulletin, (19), 11–15.
Duke, N. C. (1991). A systematic revision of the mangrove genusAvicennia (Avicenniaceae) in Australasia. Australian
Systematic Botany, 4(2), 299. doi: 10.1071/SB9910299
Duke, N. C. (2006). Australia’s mangroves: the authoritative guide
to Australia’s mangrove plants. MER.
Duke, N. C., Benzie, J. A. H., Goodall, J. A., & Ballment, E. R.
(1998). Genetic Structure and Evolution of Species in the Mangrove GenusAvicennia (Avicenniaceae) in the Indo-West Pacific.Evolution, 52(6), 1612–1626.
Durrant, S. D. (1955). In Defense of the Subspecies. Systematic
Zoology, 4(4), 186–190.
Feder, J. L., Egan, S. P., & Nosil, P. (2012). The genomics of
speciation-with-gene-flow. Trends in Genetics, 28(7),
342–350. doi: 10.1016/J.TIG.2012.03.009
Feder, J. L., Flaxman, S. M., Egan, S. P., Comeault, A. A., & Nosil, P.
(2013). Geographic Mode of Speciation and Genomic Divergence.Annual Review of Ecology, Evolution, and Systematics,44(1), 73–97. doi: 10.1146/annurev-ecolsys-110512-135825
Ganachaud, A., Kessler, W., Wijffels, S., Ridgway, K., Cai, W.,
Holbrook, N., … Aung, T. (2007). Southwest Pacific Ocean
Circulation and Climate Experiment (SPICE). Seattle, WA.
Gilman, E. L., Ellison, J., Duke, N. C., & Field, C. (2008). Threats to
mangroves from climate change and adaptation options: A review.Aquatic Botany, 89(2), 237–250. doi:
10.1016/j.aquabot.2007.12.009
Gordon, A. L. (2005). Oceanography of the Indonesian seas and their
throughflow. Oceanography, 18(4), 14–27.
Guo, Z., Li, X., He, Z., Yang, Y., Wang, W., Zhong, C., … Shi, S.
(2018). Extremely low genetic diversity across mangrove taxa reflects
past sea level changes and hints at poor future responses. Global
Change Biology, 24(4). doi: 10.1111/gcb.13968
Guo, Z, Guo, W., Wu, H., Fang, X., Ng, W. L., Shi, X., … Huang,
Y. (2018). Differing phylogeographic patterns within the Indo-West
Pacific mangrove genus Xylocarpus (Meliaceae). Journal of
Biogeography, 45(3), 676–689. doi: 10.1111/jbi.13151
Guo, Z, Huang, Y., Chen, Y., Duke, N. C., Zhong, C., & Shi, S. (2016).
Genetic discontinuities in a dominant mangrove Rhizophora
apiculata (Rhizophoraceae) in the Indo-Malesian region. Journal
of Biogeography, 43, 1856–1868. doi: 10.1111/jbi.12770
Hall, R. (2009). Southeast Asia’s changing palaeogeography. Blumea
- Biodiversity, Evolution and Biogeography of Plants, 54(1),
148–161. doi: 10.3767/000651909X475941
Harr, B. (2006). Genomic islands of differentiation between house mouse
subspecies. Genome Research, 16(6), 730–737. doi:
10.1101/gr.5045006
Hawlitschek, O., Nagy, Z. T., & Glaw, F. (2012). Island evolution and
systematic revision of comoran snakes: Why and when subspecies still
make sense. PLoS ONE, 7(8). doi:
10.1371/journal.pone.0042970
He, Z., Li, X., Ling, S., Fu, Y.-X., Hungate, E., Shi, S., & Wu, C.-I.
(2013). Estimating DNA polymorphism from next generation sequencing data
with high error rate by dual sequencing applications. BMC
Genomics, 14(1), 535. doi: 10.1186/1471-2164-14-535
He, Z., Li, X., Yang, M., Wang, X., Zhong, C., Duke, N. C., …
Shi, S. (2019). Speciation with gene flow via cycles of isolation and
migration : insights from multiple mangrove taxa. National
Science Review, 6(2), 275–288. doi: 10.1093/nsr/nwy078
He, Z., Xu, S., Zhang, Z., Guo, W., Lyu, H., Zhong, C., … Shi, S.
(2020). Convergent adaptation of the genomes of woody plants at the
land-sea interface. National Science Review.
Huang, J., Lu, X., Zhang, W., Huang, R., Chen, S., & Zheng, Y. (2014).
Transcriptome Sequencing and Analysis of Leaf Tissue of Avicennia
marina Using the Illumina Platform. PLoS ONE, 9(9),
e108785. doi: 10.1371/journal.pone.0108785
Hudson, R. R. (2002). Generating samples under a Wright-Fisher neutral
model of genetic variation. Bioinformatics, 18(2),
337–338. doi: 10.1093/bioinformatics/18.2.337
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular
Evolutionary Genetics Analysis version 7.0 for bigger datasets.Molecular Biology and Evolution, 33(7), msw054. doi:
10.1093/molbev/msw054
Li, H., Ruan, J., & Durbin, R. (2008). Mapping short DNA sequencing
reads and calling variants using mapping quality scores. Genome
Research, 1851–1858. doi: 10.1101/gr.078212.108.
Li, J., Yang, Y., Chen, Q., Fang, L., He, Z., Guo, W., … Shi, S.
(2016). Pronounced genetic differentiation and recent secondary contact
in the mangrove tree Lumnitzera racemosa revealed by population
genomic analyses. Scientific Reports, 6(July), 1–12. doi:
10.1038/srep29486
Li, X., Duke, N. C., Yang, Y., Huang, L., Zhu, Y., Zhang, Z., …
Shi, S. (2016). Re-evaluation of phylogenetic relationships among
species of the mangrove genus Avicennia from Indo-West Pacific
based on multilocus analyses. PLoS ONE, 11(10), 1–14.
doi: 10.1371/journal.pone.0164453
Maguire, T., Peakall, R., Saenger, P., & Maguire, L. (2002).
Comparative analysis of genetic diversity in the mangrove speciesAvicennia marina (Forsk.) Vierh.(Avicenniaceae) detected by AFLPs
and SSRs. TAG Theoretical and Applied Genetics, 104(2),
388–398.
Maguire, T., Saenger, P., Baverstock, P., & Henry, R. (2000).
Microsatellite analysis of genetic structure in the mangrove speciesAvicennia marina (Forsk.) Vierh.(Avicenniaceae). Molecular
Ecology, 9(11), 1853–1862.
Manni, F., Gue, E., & Heyer, E. (2004). Variation : how barriers can
be detected by using monmonier’s algorithm. Human Biology,76(2), 173–190.
Mayr, E. (1940). Speciation phenomena in birds. The American
Naturalist, 74, 249–278.
Mayr, E. (1963). Animal Species and Evolution. Cambridge, MA:
Harvard University Press.
Mayr, E. (1982). Commentary Forum : Avian Subspecies in the 1980 ’ S of
What Use Are Subspecies ? The Auk, 99(3), 593–595.
Moritz, C. (1994). Defining ‘Evolutionarily Significant Units’ for
conservation. Tree, 9(10), 373–375. doi:
10.1016/0169-5347(94)90057-4
Nadeau, N. J., Martin, S. H., Kozak, K. M., Salazar, C., Dasmahapatra,
K. K., Davey, J. W., … Mark, L. (2013). Genome-wide patterns of
divergence and gene flow across a butterfly radiation. Molecular
Ecology, 22, 814–826. doi: 10.1111/j.1365-294X.2012.05730.x
Nei, M. (1987). Molecular evolutionary genetics. New York:
Columbia University Press.
Nei, M., & Li, W.-H. (1979). Mathematical model for studying genetic
variation in terms of restriction endonucleases. Proceedings of
the National Academy of Sciences of the United States of America,76(10), 5269–5273. doi: 10.1073/pnas.76.10.5269
Nei, M., & Miller, J. C. (1990). A simple method for estimating average
number of nucleotide substitutions within and between populations from
restriction data. Genetics, 125(4), 873–879.
O’Brien, S. J., & Mayr, E. (1991). Bureaucratic mischief: Recognizing
endangered species and subspecies. Science, 251(4998),
1187–1188. doi: 10.1126/science.251.4998.1187
Patten, M. A. (2015). Subspecies and the philosophy of science.The Auk, 132(2), 481–485. doi: 10.1642/auk-15-1.1
Phillimore, A. B., & Owens, I. P. F. (2006). Are subspecies useful in
evolutionary and conservation biology? Proceedings of the Royal
Society B: Biological Sciences, 273(1590), 1049–1053. doi:
10.1098/rspb.2005.3425
Pickrell, J. K., & Pritchard, J. K. (2012). Inference of Population
Splits and Mixtures from Genome-Wide Allele Frequency Data. PLoS
Genetics, 8(11). doi: 10.1371/journal.pgen.1002967
Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Baglione,
V., … Wolf, J. B. W. (2014). The genomic landscape underlying
phenotypic integrity in the face of gene flow in crows. Science,344(6190), 1410–1414.
Polzin, T., & Daneshmand, S. V. (2003). On Steiner trees and minimum
spanning trees in hypergraphs. Operations Research Letters,31(1), 12–20. doi: 10.1016/S0167-6377(02)00185-2
Schiller, A., Oke, P. R., Brassington, G., Entel, M., Fiedler, R.,
Griffin, D. A., & Mansbridge, J. V. (2008). Eddy-resolving ocean
circulation in the Asian–Australian region inferred from an ocean
reanalysis effort. Progress in Oceanography, 76(3),
334–365. doi: 10.1016/j.pocean.2008.01.003
Seehausen, O., Butlin, R. K., Keller, I., Wagner, C. E., Boughman, J.
W., Hohenlohe, P. A., … Widmer, A. (2014). Genomics and the
origin of species. Nature Reviews Genetics, 15(3),
176–192. doi: 10.1038/nrg3644
Steinke, T. D., & Ward, C. J. (2003). Use of plastic drift cards as
indicators of possible dispersal of propagules of the mangroveAvicennia marina by ocean currents. African Journal of
Marine Science, 25(1), 169–176. doi: 10.2989/18142320309504007
Tan, F., Huang, Y., Ge, X., Su, G., Ni, X., & Shi, S. (2005).
Population genetic structure and conservation implications ofCeriops decandra in Malay Peninsula and North Australia.Aquatic Botany, 81(2), 175–188. doi:
10.1016/j.aquabot.2004.11.004
Tomlinson, P. B. (2016). The Botany of Mangrovess (Second Edi).
Cambridge, UK: Cambridge University Press.
Torstrom, S. M., Pangle, K. L., & Swanson, B. J. (2014). Shedding
subspecies: The influence of genetics on reptile subspecies taxonomy.Molecular Phylogenetics and Evolution, 76(1), 134–143.
doi: 10.1016/j.ympev.2014.03.011
Van der Stocken, T., Carroll, D., Menemenlis, D., Simard, M., & Koedam,
N. (2019). Global-scale dispersal and connectivity in mangroves.Proceedings of the National Academy of Sciences of the United
States of America, 116(3), 915–922. doi:
10.1073/pnas.1812470116
Venables, W. N., & Ripley, B. D. (2002). Modern applied statistics with
S Springer-Verlag. New York.
Wang, X., He, Z., Shi, S., & Wu, C.-I. (2020). Genes and speciation –
Is it time to abandon the Biological Species Concept? National
Science Review. doi: 10.1093/nsr/nwz220
Watterson, G. A. (1977). Heterosis or Neutrality? Genetics,85(4), 789–814.
Wee, A. K. S., Takayama, K., Chua, J. L., Asakawa, T.,
Meenakshisundaram, S. H., Onrizal, … Kajita, T. (2015). Genetic
differentiation and phylogeography of partially sympatric species
complex Rhizophora mucronata Lam. and R. stylosa Griff.
using SSR markers. BMC Evolutionary Biology, 15(1), 57.
doi: 10.1186/s12862-015-0331-3
Willing, E. M., Dreyer, C., & van Oosterhout, C. (2012). Estimates of
genetic differentiation measured by fst do not necessarily require large
sample sizes when using many snp markers. PLoS ONE, 7(8),
1–7. doi: 10.1371/journal.pone.0042649
Wilson, E. O., & Brown, W. L. (1953). The subspecies concept and its
taxonomic application. Systematic Zoology, 2(3), 97–111.
doi: 10.2307/2411818
Wu, C.-I. (2001). The genic view of the process of speciation.Journal of Evolutionary Biology, 14(September), 851–865.
Wu, C.-I., & Ting, C. T. (2004). Genes and speciation. Nature
Reviews Genetics, 5(2), 114–122. doi: 10.1038/nrg1269
Yan, F., Lü, J., Zhang, B., Yuan, Z., Zhao, H., Huang, S., … Che,
J. (2018, May 21). The Chinese giant salamander exemplifies the hidden
extinction of cryptic species. Current Biology, Vol. 28, pp.
R590–R592. doi: 10.1016/j.cub.2018.04.004
Yang, Y., Li, J., Yang, S., Li, X., Fang, L., Zhong, C., … Shi,
S. (2017). Effects of Pleistocene sea-level fluctuations on mangrove
population dynamics: a lesson from Sonneratia alba. BMC
Evolutionary Biology, 17(1), 1–14. doi:
10.1186/s12862-016-0849-z
Zachos, F. E. (2016). An Annotated List of Species Concepts. InSpecies Concepts in Biology:Historical Development, Theoretical
Foundations and Practical Relevance (pp. 77–96). doi:
10.1007/978-3-319-44966-1A