References
Ahrens, D. (2023) Species diagnosis and DNA taxonomy. In: Desalle, R.
(ed) DNA Barcoding: Methods and protocols. Preprint
DOI:10.5281/zenodo.8079017
Ahrens, D., Fujisawa, T., Krammer, H.-J., Eberle, J., Fabrizi, S., &
Vogler, A.P. (2016). Rarity and incomplete sampling in DNA-based species
delimitation. Systematic Biology , 65 (3), 478-494.
Ahrens, D., Ahyong, S. T., Ballerio, A., Barclay, M. V. L., Eberle, J.,
Espeland, M., Huber, B.A., Mengual, X., Pacheco, T.L., Peters, R. S.,
Rulik, B., Vaz-de-Mello, F., Wesener, T., & Krell, F.-T. (2021). Is it
time to describe new species without diagnoses? – A comment on Sharkey
et al. (2021). Zootaxa , 5027 (2), 151–159.
Arnheim, N., Calabrese, P., & Tiemann-Boege, I. (2007). Mammalian
meiotic recombination hot spots. Annual Review of Genetics , 41,
369–399.
Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L.,
Lewis, Z. A., Selker, E. U., Cresko, W. A., & Johnson, E. A. (2008).
Rapid SNP discovery and genetic mapping using sequenced RAD markers.PloS One , 3, e337.
Ballard, J. W., & Whitlock M. C. (2004). The incomplete natural history
of mitochondria. Molecular Ecolology , 13, 729–744.
Baudat, F., Buard, J., Grey C., Fledel-Alon, A., Ober, C., Przeworski,
M., Coop G., & de Massy, B. (2010). PRDM9 is a major determinant of
meiotic recombination hotspots in humans and mice. Science ,
327(5967), 836–840.
Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J.,
Mattick, J. S., & Haussler, D. (2004). Ultraconserved elements in the
human genome. Science , 304, 1321–1325.
Blankers, T., Oh, K.P., Bombarely, A., & Shaw, K.L. (2018). The genomic
architecture of a rapid island radiation: Recombination rate variation,
chromosome structure, and genome assembly of the Hawaiian cricketLaupala . Genetics , 209(4), 1329–1344.
Bryant, D., & Hahn, M. W. (2020). The concatenation question. In:
Scornavacca C., Delsuc F., Galtier N. Phylogenetics in the genomic era.
No commercial publisher | Authors open access book,
pp.3.4:1–3.4:23. Hal-02535651
Chambers, E.A., & Hillis, D. M. (2020). The multispecies coalescent
over-splits species in the case of geographically widespread taxa.Systematic Biology , 69, 184-193.
Chan, A. H., Jenkins, P.A., & Song Y. S. (2012). Genome-wide fine-scale
recombination rate variation in Drosophila melanogaster .PloS Genetics , 8(12), e1003090.
Chen, C.-S., Huang, C.-T., & Hseu, R.-S. (2017). Evidence for two types
of nrDNA existing in Chinese medicinal fungus Ophiocordyceps
sinensis . AIMS Genetics , 4, 192–201.
Dietz, L., Eberle, J., Mayer, C., Kukowka, S., Bohacz, C., Baur, H.,
Espeland, M., Huber, B. A., Hutter, C., Mengual, X., Peters, R. S.,
Vences, M., Wesener, T., Willmott, K., Misof, B., Niehuis, O., &
Ahrens, D. (2023) Standardized nuclear markers improve and homogenize
species delimitation in Metazoa. Methods in Ecology and
Evolution , 14, 543-555.
Eberle, J., Ahrens, D., Mayer, C., Niehuis, O., & Misof, B. (2020). A
plea for standardized nuclear markers in metazoan DNA taxonomy.Trends in Ecology and Evolution , 35, 336–345.
Edelman, N. B., Frandsen, P. B., Miyagi, M., Clavijo, B., Davey, J.,
Dikow, R. B., García-Accinelli, G., Belleghem, S. M. V., Patterson, N.,
Neafsey, D. E., Challis, R., Kumar, S., Moreira, G. R. P., Salazar, C.,
Chouteau, M., Counterman, B. A., Papa, R., Blaxter, M., Reed, R. D.,
Dasmahapatra, K. K., Kronforst, M., Joron, M., Jiggins, C.D., McMillan,
W. O., Palma, F. D., Blumberg, A. J., Wakeley, J., Jaffe, D., Mallet,
J., 2019. Genomic architecture and introgression shape a butterfly
radiation. Science , 366, 594–599.https://doi.org/10.1126/science.aaw2090
Edwards, D. L., & Knowles, L. L. (2014). Species detection and
individual assignment in species delimitation: can integrative data
increase efficacy? Proceedings of the Royal Society B: Biological
Sciences , 281, 20132765.
Edwards, S. V., Xi, Z., Janke, A., Faircloth, B. C., McCormack, J. E.,
Glenn, T. C., Zhong, B., Wu, S., Lemmon, E. M., Lemmon, A. R., Leaché,
A. D., Liu, L., & Davis, C. C. (2016). Implementing and testing the
multispecies coalescent model: A valuable paradigm for phylogenomics.Molecular Phylogenetics and Evolution , 94, 447–462.
Erickson, K. L., Pentico, A., Quattrini, A. M., & McFadden, C. S.
(2021). New approaches to species delimitation and population structure
of anthozoans: Two case studies of octocorals using ultraconserved
elements and exons. Molecular Ecology Resources , 21, 78–92.https://doi.org/10.1111/1755-0998.13241
Esselstyn, J. A., Oliveros, C. H., Swanson, M. T., & Faircloth, B. C.
(2017). Investigating difficult nodes in the placental mammal tree with
expanded taxon sampling and thousands of ultraconserved elements.Genome Biology and Evolution , 9, 2308-2321.
Faircloth, B. C., McCormack, J. E., Crawford, N. G., Harvey, M. G.,
Brumfield ,R. T., Glenn, T. C. (2012). Ultraconserved elements anchor
thousands of genetic markers spanning multiple evolutionary timescales.Systematic Biology , 61, 717–726.
Fernández, R., Kallal, R.J., Dimitrov, D., Ballesteros, J.A., Arnedo,
M.A., Giribet, G., & Hormiga, G. (2018). Phylogenomics, diversification
dynamics, and comparative transcriptomics across the spider tree of
life. Current Biology , 28, 1489-1497.e5.
Fontaine, M. C., Pease, J. B., Steele, A., Waterhouse, R. M., Neafsey,
D. E., Sharakhov, I. V., Jiang, X., Hall, A. B., Catteruccia, F.,
Kakani, E., Mitchell, S. N., Wu, Y. C., Smith, H. A., Love, R. R.,
Lawniczak, M. K., Slotman, M. A., Emrich, S. J., Hahn, M. W., &
Besansky, N. J. (2015). Extensive introgression in a malaria vector
species complex revealed by phylogenomics. Science , 347, 1258524.
Fontaneto, D., Flot, J. F., & Tang, C. Q. (2015). Guidelines for DNA
taxonomy, with a focus on the meiofauna. Marine Biodiversity , 45,
433–451.https://doi.org/10.1007/s12526-015-0319-7
Fujisawa T., Aswad A., & Barraclough T.G. (2016). A rapid and scalable
method for multilocus species delimitation using Bayesian model
comparison and rooted triplets. Systematic Biology , 65, 759-71.
Funk, D. J., & Omland, K. E. (2003). Species-level paraphyly and
polyphyly: frequency, causes, and consequences, with insights from
animal mitochondrial DNA. Annual Review of Ecology, Evolution, and
Systematics , 34, 397–423.
Gatesy, J., & Springer, M. S. (2014). Phylogenetic analysis at deep
timescales: Unreliable gene trees, bypassed hidden support, and the
coalescence/concatalescence conundrum. Molecular Phylogenetics and
Evolution , 80, 231–266.
Grant, P. R., & Grant, B. R. (2016). Introgressive hybridization and
natural selection in Darwin’s finches. Biological Journal of the
Linnean Society , 117, 812-822.
Gueuning, M., Frey, J. E., & Praz, C. (2020). Ultraconserved yet
informative for species delimitation: Ultraconserved elements resolve
long-standing systematic enigma in Central European bees.Molecular Ecology , 29, 4203–4220.
Hammer, Ø., Harper, D. A. T., & Ryan, P. D. (2001). PAST:
Paleontological Statistics Software Package for Education and Data
Analysis. Palaeontologia Electronica , 4, 1–9.
Hebert, P. D. N., Cywinska, A., Ball, S. L., & DeWaard, J. R. (2003).
Biological identifications through DNA barcodes. Proceedings of
the Royal Society B: Biological Sciences , 270, 313–321.
Heip, C. H. R., Herman, P. M. J., & Soetaert, K. (1998). Indices of
diversity and evenness. Océanis , 24(4), 61–87.
Herrera, S., & Shank, T. M. (2016). RAD sequencing enables
unprecedented phylogenetic resolution and objective species delimitation
in recalcitrant divergent taxa. Molecular Phylogenetics and
Evolution , 100, 70–79.
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L.
S. (2018). UFBoot2: Improving the ultrafast bootstrap approximation.Molecular Biology and Evolution , 35, 518–522.
International Chicken Genome Sequencing Consortium. (2004). Sequence and
comparative analysis of the chicken genome provide unique perspectives
on vertebrate evolution. Nature , 432, 695–716.
Irisarri, I., Baurain, D., Brinkmann, H., Delsuc, F., Sire, J.-Y.,
Kupfer, A., Petersen, J., Jarek, M., Meyer, A., Vences, M., & Philippe,
H. (2017). Phylotranscriptomic consolidation of the jawed vertebrate
timetree. Nature Ecology & Evolution , 1, 1370–1378.
Jeffreys, A. J., Kauppi, L., & Neumann, R. (2001). Intensely punctate
meiotic recombination in the class II region of the major
histocompatibility complex. Nature Genetics , 29(2), 217–222.
Ješovnik, A., Sosa-Calvo, J., Lloyd, M. W., Branstetter, M. G.,
Fernández, F., & Schultz, T. R. (2017). Phylogenomic species
delimitation and host-symbiont coevolution in the fungus-farming ant
genus Sericomyrmex Mayr (Hymenoptera: Formicidae): ultraconserved
elements (UCEs) resolve a recent a recent radiation. Systematic
Entomology , 42, 523–542.
Joshi, C. J., Ke, W., Drangowska-Way, A., O’Rourke, E. J., & Lewis, N.
E. (2022). What are housekeeping genes? PloS Computational
Biology , 18(7), e1010295. Doi: 10.1371/journal.pcbi.1010295.
Joshi, M., Espeland, M., Huemer, P., deWaard, J., Mutanen, M. (2023).
Species delimitation under allopatry: genomic divergences within and
across continents in Lepidoptera. bioRxiv 2023.03.06.531242; doi:
https://doi.org/10.1101/2023.03.06.531242
Junier, T., & Zdobnov, E.M. (2010). The Newick Utilities:
High-throughput phylogenetic tree processing in the UNIX shell.Bioinformatics , 26, 1669-1670.
Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A., &
Jermiin, L.S. (2017). ModelFinder: Fast model selection for accurate
phylogenetic estimates. Nature Methods , 14, 587–589.
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment
software version 7: improvements in performance and usability.Molecular Biology and Evolution , 30, 772–780.
Kauppi, L., Jeffreys, A. J., & Keeney, S. (2004). Where the crossovers
are: recombination distributions in mammals. Nature Reviews
Genetics , 5(6), 413–424.
Kawakami, T., Mugal, C. F., Suh, A., Nater, A., Burri, R., Smeds, L., &
Ellegren, H. (2017). Whole-genome patterns of linkage disequilibrium
across flycatcher populations clarify the causes and consequences of
fine-scale recombination rate variation in birds. Molecular
Ecology , 26(16), 4158–4172.
Krehenwinkel, H., Pomerantz, A., Henderson, J. B., Kennedy, S. R., Lim,
J. Y., Swamy, V., Shoobridge, J. D., Graham, N., Patel, N. H.,
Gillespie, R. G., & Prost, S. (2019). Nanopore sequencing of long
ribosomal DNA amplicons enables portable and simple biodiversity
assessments with high phylogenetic resolution across broad taxonomic
scale. Gigascience , 8, 1–16.
Kriventseva, E. V., Kuznetsov, D., Tegenfeldt, F., Manni, M., Dias, R.,
Simão, F. A., & Zdobnov, E. M. (2019). OrthoDB v10: sampling the
diversity of animal, plant, fungal, protist, bacterial and viral genomes
for evolutionary and functional annotations of orthologs. Nucleic
Acids Research , 47(D1), D807–D811.
Kück, P., Meusemann, K., Dambach, J., Thormann, B., von Reumont, B. M.,
Wägele, J. W., & Misof, B. (2010). Parametric and non-parametric
masking of randomness in sequence alignments can be improved and leads
to better resolved trees. Frontiers in Zoology , 7, 10.
Kuznetsov, D., Tegenfeldt, F., Manni, M., Seppey, M., Berkeley, M.,
Kriventseva, E. V., & Zdobnov, E. M. (2023). OrthoDB v11: annotation of
orthologs in the widest sampling of organismal diversity. Nucleic
Acids Research , 51(D1), D445-D451.
Lamichhaney, S., Berglund, J., Almén, M. S., Maqbool, K., Grabherr, M.,
Martinez-Barrio, A., Promerová, M., Rubin, C. J., Wang, C., Zamani, N.,
Grant, B. R., Grant, P. R, Webster, M. T., & Andersson, L. 2015.
Evolution of Darwin’s finches and their beaks revealed by genome
sequencing. Nature , 518, 371-375.
Lamichhaney, S., Han, F., Berglund, J., Wang, C., Almén, M. S., Webster,
M. T., Grant, B. R., Grant, P. R., & Andersson, L. (2016). A beak size
locus in Darwin’s finches facilitated character displacement during a
drought. Science , 352, 470–474.
Lamichhaney, S., Han, F., Webster, M. T., Andersson, L., Grant, B. R.,
& Grant, P. R. (2018). Rapid hybrid speciation in Darwin’s finches.Science , 359, 224–228.
Lanier, H. C., & Knowles, L. L. (2012). Is recombination a problem for
species-tree analyses? Systematic Biology , 61(4), 691–701.
Larsson, A. (2014). AliView: a fast and lightweight alignment viewer and
editor for large data sets. Bioinformatics , 30(22), 3276–3278.
Laumer, C. E., Fernández, R., Lemer, S., Combosch, D., Kocot, K. M.,
Riesgo, A., Andrade, S. C. S., Sterrer, W., Sørensen, M. V., & Giribet,
G. (2019). Revisiting metazoan phylogeny with genomic sampling of all
phyla. Proceedings of the Royal Society B: Biological Sciences ,
286, 20190831.
Lebonah, D. E., Dileep, A., Chandrasekhar, K., Sreevani, S., Sreedevi,
B., & Pramoda Kumari, J. (2014). DNA barcoding on bacteria: A review.Advances in Biology , 2014, 541787.
https://doi.org/10.1155/2014/541787
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment
with Burrows-Wheeler Transform. Bioinformatics , 25, 1754–60.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N.,
Marth, G., Abecasis, G., & Durbin, R. (2009). 1000 genome project data
processing subgroup. The sequence alignment/map (SAM) format and
SAMtools. Bioinformatics , 25, 2078–2079.
Maddison, W. P., & Maddison, D.R. (2018). Mesquite: a modular system
for evolutionary analysis. Version 3.51http://www.mesquiteproject.org
Mai, D., Nalley, M.J., & Bachtrog, D. (2019). Patterns of genomic
differentiation in the Drosophila nasuta species complex.Molecular Biology and Evolution , 37, 208–220.
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M.
(2021). BUSCO Update: novel and streamlined workflows along with broader
and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic,
and viral genomes. Molecular Biology and Evolution , 38(10),
4647–4654.
Martin, S. H., Dasmahapatra, K. K., Nadeau, N. J., Salazar, C., Walters,
J. R., Simpson, F., Blaxter, M., Manica, A., Mallet, J., & Jiggins, C.
D. (2013). Genome-wide evidence for speciation with gene flow inHeliconius butterflies. Genome Reserach , 23, 1817–1828.
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M.
D., von Haeseler, A., & Lanfear, R. (2020). IQ-TREE 2: New models and
efficient methods for phylogenetic inference in the genomic era.Molecular Biology and Evolution , 37, 1530–1534.
Miralles, A., Bruy, T., Wolcott, K., Scherz, M.D., Begerow, D.,
Beszteri, B., Bonkowski, M., Felden, J., Gemeinholzer, B., Glaw, F.,
Glöckner, F. O., Hawlitschek, O., Kostadinov, I., Nattkemper, T. W.,
Printzen, C., Renz, J., Rybalka, N., Stadler, M., Weibulat, T., Wilke,
T., Renner, S. S., & Vences, M. (2020). Repositories for taxonomic
data: where we are and what is missing. Systematic Biology ,
69(6),1231–1253
Misof, B., & Misof, K. (2009). A Monte Carlo approach successfully
identifies randomness in multiple sequence alignments: a more objective
means of data exclusion. Systematic Biology , 2009: 58.
Myers, S., Bottolo, L., Freeman, C., McVean, G., & Donnelly, P. (2005).
A fine-scale map of recombination rates and hotspots across the human
genome. Science , 310, 321–324.
Niehuis, O., Gibson, J. D., Rosenberg, M. S., Pannebakker, B. A.,
Koevoets, T., Judson, A. K., Desjardins, C. A., Kennedy, K., Duggan, D.,
Beukeboom, L. W., van de Zande, L., Shuker, D. M., Werren, J. H., &
Gadau, J. (2010). Recombination and its impact on the genome of the
haplodiploid parasitoid wasp Nasonia . PloS One , 5, e8597.
Nosil, P., & Schluter, D. (2011). The genes underlying the process of
speciation. Trends in Ecology & Evolution , 26(4), 160–7.
O’Leary, N.A., Wright, M.W., Brister, J.R., Ciufo, S., Haddad, D.,
McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D.,
et al. (2016). Reference sequence (RefSeq) database at NCBI: current
status, taxonomic expansion, and functional annotation. Nucleic
Acids Research , 44(D1), D733-745.
Orr, H. A., Masly, J. P., & Presgraves, D. C. (2004). Speciation genes.Current Opinion in Genetics & Development , 14(6), 675-9.
Page, A. J., Taylor, B., Delaney, A. J., Soares, J., Seemann, T., Keane,
J. A., & Harris, S. R. (2016). SNP-sites: rapid efficient extraction of
SNPs from multi-FASTA alignments. Microbial Genomics , 2(4),
e000056.
Pante, E., Abdelkrim, J., Viricel, A., Gey, D., France, S. C.,
Boisselier, M. C., & Samadi, S. (2015). Use of RAD sequencing for
delimiting species. Heredity , 114, 450–459.
Penalba, J. V., & Wolf, J. B. W. (2020). From molecules to populations:
appreciating and estimating recombination rate variation. Nature
Reviews Genetics , 21(8), 476–492.
Petersen, M., Meusemann, K., Donath, A., Dowling, D., Liu, S., Peters,
R. S., Podsiadlowski, L., Vasilikopoulos, A., Zhou, X., Misof, B., &
Niehuis, O. (2017). Orthograph: a versatile tool for mapping coding
nucleotide sequences to clusters of orthologous genes. BMC
Bioinformatics , 18, 111.
Pierce, M. P. (2019). Filling in the gaps: adopting ultraconserved
elements alongside COI to strengthen metabarcoding studies.Frontiers in Ecology and Evolution , 7(469), 1–6.
Prebus, M. M. (2021). Phylogenomic species delimitation in the ants of
the Temnothorax salvini group (Hymenoptera: Formicidae): an
integrative approach. Systematic Entomology , 46, 307–326.
Pritchard, J. K., Stephens, M., & Donnelly, P. J. (2000). Inference of
population structure using multilocus genotype data. Genetics ,
155, 945–959.
Rabiee M., & Mirarab S. (2020). SODA: Multi-locus species delimitation
using quartet frequencies. Bioinformatics , 36, 5623–5631.
Sahbou, A.-E., Iraqi, D., Mentag, R., & Khayi, S. (2022). BuscoPhylo: A
webserver for Busco-based phylogenomic analysis for non-specialists.Scientific Reports , 12, 17352
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., &
Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation
completeness with single-copy orthologs. Bioinformatics , 31,
3210–2.
Springer, M. S., & Gatesy, J. (2016). The gene tree delusion.Molecular Phylogenetics and Evolution , 94A, 1–33.
Springer, M. S., & Gatesy, J. (2018). Delimiting coalescence genes
(C-Genes) in phylogenomic data sets. Genes , 9(3), 123.
Solís-Lemus, C., Yang, M., Ané, C. (2016). Inconsistency of species tree
methods under gene flow. Systematic Biology , 65(5), 843–851,
https://doi.org/10.1093/sysbio/syw030
Stanke, M., & Waack S. (2003). Gene prediction with a hidden Markov
model and a new intron submodel. Bioinformatics , 19 (suppl 2),
ii215–ii225, https://doi.org/10.1093/bioinformatics/btg1080
Stanke, M., Tzvetkova, A., & Morgenstern, B. (2006). AUGUSTUS at EGASP:
using EST, protein and genomic alignments for improved gene prediction
in the human genome. Genome Biology , 7 (Suppl 1), S11 (2006).
https://doi.org/10.1186/gb-2006-7-s1-s11
Stolle, E., Pracana, R., López-Osorio, F. et al. (2022). Recurring
adaptive introgression of a supergene variant that determines social
organization. Nature Communications , 13, 1180https://doi.org/10.1038/s41467-022-28806-7
Sukumaran, J., & Knowles, L. L. (2017). Multispecies coalescent
delimits structure, not species. Proceedings of the National
Academy of Sciences , 114, 1607–1612.
Suvorov, A., Kim, B. Y., Wang, J., Armstrong, E. E., Peede, D.,
D’Agostino, E. R. R., Price, D. K., Waddell, P. J., Lang, M.,
Courtier-Orgogozo, V., David, J. R., Petrov, D., Matute, D. R.,
Schrider, D. R., & Comeault, A. A. (2022). Widespread introgression
across a phylogeny of 155 Drosophila genomes. Current
Biology , 32(1), 111-123.e5,https://doi.org/10.1016/j.cub.2021.10.052.
Suyama, M., Torrents, D., & Bork, P. (2006). PAL2NAL: robust conversion
of protein sequence alignments into the corresponding codon alignments.Nucleic Acids Research , 34, W609-W612.
Thawornwattana, Y., Dalquen, D., & Yang, Z. (2018). Coalescent analysis
of phylogenomic data confidently resolves the species relationships in
the Anopheles gambiae species complex. Molecular
Biology and Evolution , 35, 2512–2527.
Vicente, J. L., Clarkson, C. S., Caputo, B., Gomes, B., Pombi, M.,
Sousa, C. A., Antao, T., Dinis, J., Bottà, G., Mancini, E., Petrarca,
V., Mead, D., Drury, E., Stalker, J., Miles, A., Kwiatkowski, D. P.,
Donnelly, M. J., Rodrigues, A., della Torre, A., Weetman, D., & Pinto,
J. (2017). Massive introgression drives species radiation at the range
limit of Anopheles gambiae . Scientific Reports , 7,
46451.
Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P.,
Klioutchnikov, G., Kriventseva, E. V., & Zdobnov, E. M. (2018). BUSCO
applications from quality assessments to gene prediction and
phylogenomics. Molecular Biology and Evolution , 35, 543–548.
Waters, P. D., Patel, H. R., Ruiz-Herrera, A., & Marshall Graves, J. A.
(2021). Microchromosomes are building blocks of bird, reptile, and
mammal chromosomes. Proceedings of the National Academy of
Sciences , 118(45), e2112494118.
Wu, C.-I. (2001). The genic view of the process of speciation.Journal of Evolutionary Biology , 14: 851–865.
Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C., & Ding,
Z. (2012). Biodiversity soup: metabarcoding of arthropods for rapid
biodiversity assessment and biomonitoring. Methods in Ecology and
Evolution , 3, 613–623.
Zarza, E., Connors, E. M., Maley, J. M., Tsai, W. L. E., Heimes, P.,
Kaplan, M., & McCormack, J. E. (2018). Combining ultraconserved
elements and mtDNA data to uncover lineage diversity in a Mexican
highland frog (Sarcohyla ; Hylidae). PeerJ , 6, e6045.
Zdobnov, E. M., Tegenfeldt, F., Kuznetsov, D., Waterhouse, R. M., Simão,
F. A., Ioannidis, P., Seppey, M., Loetscher, A., Kriventseva, E. V.
(2017). OrthoDB v9.1: cataloging evolutionary and functional annotations
for animal, fungal, plant, archaeal, bacterial and viral orthologs.Nucleic Acids Research , 45(D1), D744–D749.
Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018). ASTRAL-III:
polynomial time species tree reconstruction from partially resolved gene
trees. BMC Bioinformatics , 19, 153.
Zhang, F., Ding, Y., Zhu, C.D., Zhou, X., Orr, M.C., Scheu, S., & Luan,
Y.X. (2019). Phylogenomics from low-coverage whole-genome sequencing.Methods in Ecology and Evolution , 10, 507–517.
Zhu, T., Flouri, T., & Yang, Z. (2022). A simulation study to examine
the impact of recombination on phylogenomic inferences under the
multispecies coalescent model. Molecular Ecology , 31, 2814–2829.
Zink, R. M., & Vázquez-Miranda, H. (2019). Species limits and
phylogenomic relationships of Darwin’s finches remain unresolved:
potential consequences of a volatile ecological setting.Systematic Biology , 68, 347–357.