References
Auton, A., Abecasis, G. R., Altshuler, D. M., Durbin, R. M., Abecasis,
G. R., Bentley, D. R., . . . National Eye Institute, N. I. H. (2015). A
global reference for human genetic variation. Nature, 526 (7571),
68-74. doi:10.1038/nature15393
Aykanat, T., Lindqvist, M., Pritchard, V. L., & Primmer, C. R. (2016).
From population genomics to conservation and management: a workflow for
targeted analysis of markers identified using genome-wide approaches in
Atlantic salmon Salmo salar. Journal of Fish Biology, 89 (6),
2658-2679. doi:10.1111/jfb.13149
Baffoni, L., Stenico, V., Strahsburger, E., Gaggìa, F., Di Gioia, D.,
Modesto, M., . . . Biavati, B. (2013). Identification of species
belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60
gene fragment. BMC Microbiology, 13 (1), 149.
doi:10.1186/1471-2180-13-149
Barlow, G. W., & Munsey, J. W. (1976). The red devil-Midas-arrow
cichlid species complex in Nicaragua.
Barluenga, M., Stölting, K. N., Salzburger, W., Muschick, M., & Meyer,
A. (2006). Sympatric speciation in Nicaraguan crater lake cichlid fish.Nature, 439 (7077), 719-723. doi:10.1038/nature04325
Campbell, M. R., Vu, N. V., LaGrange, A. P., Hardy, R. S., Ross, T. J.,
& Narum, S. R. (2019). Development and Application of Single-Nucleotide
Polymorphism (SNP) Genetic Markers for Conservation Monitoring of Burbot
Populations. Transactions of the American Fisheries Society,
148 (3), 661-670. doi:10.1002/tafs.10157
Clark, A. G., Hubisz, M. J., Bustamante, C. D., Williamson, S. H., &
Nielsen, R. (2005). Ascertainment bias in studies of human genome-wide
polymorphism. Genome research, 15 (11), 1496-1502.
doi:10.1101/gr.4107905
Clusa, L., Ardura, A., Fernández, S., Roca, A. A., & García-Vázquez, E.
(2017). An extremely sensitive nested PCR-RFLP mitochondrial marker for
detection and identification of salmonids in eDNA from water samples.PeerJ, 5 , e3045. doi:10.7717/peerj.3045
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E.,
DePristo, M. A., . . . Group, G. P. A. (2011). The variant call format
and VCFtools. Bioinformatics, 27 (15), 2156-2158.
doi:10.1093/bioinformatics/btr330
Elmer, K. R., Fan, S., Kusche, H., Spreitzer, M. L., Kautt, A. F.,
Franchini, P., & Meyer, A. (2014). Parallel evolution of Nicaraguan
crater lake cichlid fishes via non-parallel routes. Nat Commun,
5 , 5168. doi:10.1038/ncomms6168
Elmer, K. R., Kusche, H., Lehtonen, T. K., & Meyer, A. (2010). Local
variation and parallel evolution: morphological and genetic diversity
across a species complex of neotropical crater lake cichlid fishes.Philosophical Transactions of the Royal Society B: Biological
Sciences, 365 (1547), 1763-1782. doi:doi:10.1098/rstb.2009.0271
Elmer, K. R., Lehtonen, T. K., Fan, S., & Meyer, A. (2013). Crater Lake
Colonization by Neotropical Cichlid Fishes. Evolution, 67 (1),
281-288. doi:https://doi.org/10.1111/j.1558-5646.2012.01755.x
Elmer, K. R., Lehtonen, T. K., & Meyer, A. (2009). Color assortative
mating contributes to sympatric divergence of neotropical cichlid fish.Evolution, 63 (10), 2750-2757.
Fennessy, J., Bidon, T., Reuss, F., Kumar, V., Elkan, P., Nilsson, M.
A., . . . Janke, A. (2016). Multi-locus analyses reveal four giraffe
species instead of one. Current Biology, 26 (18), 2543-2549.
Geiger, M. F., McCrary, J. K., & Stauffer Jr, J. R. (2010). Description
of two new species of the Midas cichlid complex (Teleostei: Cichlidae)
from Lake Apoyo, Nicaragua. Proceedings of the Biological Society
of Washington, 123 (2), 159-173.
Kato, H., Gomez, E. A., Seki, C., Furumoto, H., Martini-Robles, L.,
Muzzio, J., . . . Hashiguchi, Y. (2019). PCR-RFLP analyses of Leishmania
species causing cutaneous and mucocutaneous leishmaniasis revealed
distribution of genetically complex strains with hybrid and mito-nuclear
discordance in Ecuador. PLOS Neglected Tropical Diseases, 13 (5),
e0007403. doi:10.1371/journal.pntd.0007403
Kautt, A. F., Kratochwil, C. F., Nater, A., Machado-Schiaffino, G.,
Olave, M., Henning, F., . . . Meyer, A. (2020). Contrasting signatures
of genomic divergence during sympatric speciation. Nature, 588 ,
106–111. doi:10.1038/s41586-020-2845-0
Kautt, A. F., Machado-Schiaffino, G., & Meyer, A. (2016). Multispecies
Outcomes of Sympatric Speciation after Admixture with the Source
Population in Two Radiations of Nicaraguan Crater Lake Cichlids.PLoS Genet, 12 (6), e1006157. doi:10.1371/journal.pgen.1006157
Kautt, A. F., Machado-Schiaffino, G., & Meyer, A. (2018). Lessons from
a natural experiment: Allopatric morphological divergence and sympatric
diversification in the Midas cichlid species complex are largely
influenced by ecology in a deterministic way. Evol Lett, 2 (4),
323-340. doi:10.1002/evl3.64
Knaus, B. J., Grunwald, N. J., Anderson, E. C., Winter, D. J., Kamvar,
Z. N., & Tabima, J. F. (2020). R Package ‘vcfR’ v.1.10.0. Cran
R .
Kratochwil, C. F., & Rijli, F. M. (2014). The Cre/Lox system to assess
the development of the mouse brain. Methods Mol Biol, 1082 ,
295-313. doi:10.1007/978-1-62703-655-9_20
Larraín, M. A., González, P., Pérez, C., & Araneda, C. (2019).
Comparison between single and multi-locus approaches for specimen
identification in Mytilus mussels. Scientific reports, 9 (1),
19714. doi:10.1038/s41598-019-55855-8
Lozano-Duque, Y., Richlen, M. L., Smith, T. B., Anderson, D. M., &
Erdner, D. L. (2018). Development and validation of PCR-RFLP assay for
identification of Gambierdiscus species in the Greater Caribbean Region.Journal of Applied Phycology, 30 (6), 3529-3540.
doi:10.1007/s10811-018-1491-5
Machado-Schiaffino, G., Kautt, A. F., Torres-Dowdall, J., Baumgarten,
L., Henning, F., & Meyer, A. (2017). Incipient speciation driven by
hypertrophied lips in Midas cichlid fishes? Mol Ecol, 26 (8),
2348-2362. doi:10.1111/mec.14029
McKeown, N. J., Robin, J.-P., & Shaw, P. W. (2015). Species-specific
PCR-RFLP for identification of early life history stages of squid and
other applications to fisheries research. Fisheries Research,
167 , 207-209.
Mukherjee, S., Cn, A., Home, C., & Ramakrishnan, U. (2010). An
evaluation of the PCR-RFLP technique to aid molecular-based monitoring
of felids and canids in India. BMC Research Notes, 3 (1), 159.
doi:10.1186/1756-0500-3-159
Nater, A., Mattle-Greminger, M. P., Nurcahyo, A., Nowak, M. G., De
Manuel, M., Desai, T., . . . Roos, C. (2017). Morphometric, behavioral,
and genomic evidence for a new orangutan species. Current Biology,
27 (22), 3487-3498. e3410.
Ota, M., Fukushima, H., Kulski, J. K., & Inoko, H. (2007). Single
nucleotide polymorphism detection by polymerase chain
reaction-restriction fragment length polymorphism. Nature
protocols, 2 (11), 2857-2864. doi:10.1038/nprot.2007.407
Pegg, E., Doyle, K., Clark, E. L., Jatau, I. D., Tomley, F. M., &
Blake, D. P. (2016). Application of a new PCR-RFLP panel suggests a
restricted population structure for Eimeria tenella in UK and Irish
chickens. Veterinary Parasitology, 229 , 60-67.
doi:https://doi.org/10.1016/j.vetpar.2016.09.018
Piertney, S. B. (2016). High-Throughput DNA Sequencing and the Next
Generation of Molecular Markers in Wildlife Research. In R. Mateo, B.
Arroyo, & J. T. Garcia (Eds.), Current Trends in Wildlife
Research (pp. 201-223). Cham: Springer International Publishing.
R Development Core Team. (2019). R: A language and environment for
statistical computing. R Foundation for Statistical Computing . Vienna,
Austria.
Recknagel, H., Kusche, H., Elmer, K. R., & Meyer, A. (2013). Two new
endemic species in the Midas cichlid species complex from Nicaraguan
crater lakes: Amphilophus tolteca and Amphilophus viridis (Perciformes,
Cichlidae). aqua, 19 (4).
Shafer, A. B. A., Wolf, J. B. W., Alves, P. C., Bergström, L., Bruford,
M. W., Brännström, I., . . . Zieliński, P. (2015). Genomics and the
challenging translation into conservation practice. Trends in
ecology & evolution, 30 (2), 78-87.
doi:https://doi.org/10.1016/j.tree.2014.11.009
Stauffer Jr, J. R., McCrary, J. K., & Black, K. E. (2008). Three new
species of cichlid fishes (Teleostei: Cichlidae) from Lake Apoyo,
Nicaragua. Proceedings of the Biological Society of Washington,
121 (1), 117-129.
Stauffer Jr, J. R., & McKaye, K. (2002). Descriptions of three new
species of cichlid fishes (Teleostei: Cichlidae) from Lake Xiloá,
Nicaragua. Cuadernos de Investigación de la UCA, 12 , 1-18.
Torres-Dowdall, J., & Meyer, A. (in press). Sympatric and allopatric
diversification in the adaptive radiation of Midas cichlids in
Nicaraguan lakes. In M. E. Abate & D. L. G. Noakes (Eds.), The
Behavior, Ecology and Evolution of Cichlid Fishes: A Contemporary Modern
Synthesis (Vol. 40): Springer Netherlands.