Hagen, O. et al. gen3sis: a general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity. PLoS Biol. 19, e3001340 (2021).
Google Scholar
Urban, M. C. et al. Evolutionary origins for ecological patterns in space. Proc. Natl Acad. Sci. USA 117, 17482–17490 (2020).
Google Scholar
Hubbell, S. P. The Unified Neutral Theory of Biodiversity and Biogeography (MPB-32) (Princeton Univ. Press, 2001).
Volkov, I., Banavar, J. R., Hubbell, S. P. & Maritan, A. Neutral theory and relative species abundance in ecology. Nature 424, 1035–1037 (2003).
Google Scholar
McGill, B. J. et al. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecol. Lett. 10, 995–1015 (2007).
Google Scholar
de Aguiar, M. A. M., Baranger, M., Baptestini, E. M., Kaufman, L. & Bar-Yam, Y. Global patterns of speciation and diversity. Nature 460, 384 (2009).
Google Scholar
O’Dwyer, J. P. & Green, J. L. Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity. Ecol. Lett. 13, 87–95 (2010).
Google Scholar
Chisholm, R. A. & Pacala, S. W. Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities. Proc. Natl Acad. Sci. USA 107, 15821–15825 (2010).
Google Scholar
Mutshinda, C. M., O’Hara, R. B. & Woiwod, I. P. What drives community dynamics? Proc. R. Soc. B 276, 2923–2929 (2009).
Google Scholar
Rosindell, J., Cornell, S. J., Hubbell, S. P. & Etienne, R. S. Protracted speciation revitalizes the neutral theory of biodiversity. Ecol. Lett. 13, 716–727 (2010).
Google Scholar
Chisholm, R. A. & O’Dwyer, J. P. Species ages in neutral biodiversity models. Theor. Popul. Biol. 93, 85–94 (2014).
Google Scholar
Nee, S. The neutral theory of biodiversity: do the numbers add up? Funct. Ecol. 19, 173–176 (2005).
Google Scholar
Ricklefs, R. E. A comment on Hubbell’s zero-sum ecological drift model. Oikos 100, 185–192 (2003).
Google Scholar
Etienne, R. S., Apol, M. E. F., Olff, H. & Weissing, F. J. Modes of speciation and the neutral theory of biodiversity. Oikos 116, 241–258 (2007).
Google Scholar
Davies, T. J., Allen, A. P., Borda-de Água, L., Regetz, J. & Melián, C. J. Neutral biodiversity theory can explain the imbalance of phylogenetic trees but not the tempo of their diversification. Evolution 65, 1841–1850 (2011).
Google Scholar
Higgs, P. G. & Derrida, B. Stochastic models for species formation in evolving populations. J. Phys. A 24, L985 (1991).
Google Scholar
Gavrilets, S., Li, H. & Vose, M. D. Rapid parapatric speciation on holey adaptive landscapes. Proc. R. Soc. B 265, 1483–1489 (1998).
Google Scholar
Dieckmann, U. & Doebeli, M. On the origin of species by sympatric speciation. Nature 400, 354 (1999).
Google Scholar
Gavrilets, S. & Vose, A. Dynamic patterns of adaptive radiation. Proc. Natl Acad. Sci. USA 102, 18040–18045 (2005).
Google Scholar
Nosil, P. Ecological Speciation (Oxford Univ. Press, 2012).
Gavrilets, S., Acton, R. & Gravner, J. Dynamics of speciation and diversification in a metapopulation. Evolution 54, 1493–1501 (2000).
Google Scholar
Costa, C. L. N. et al. Signatures of microevolutionary processes in phylogenetic patterns. Syst. Biol. 68, 131–144 (2018).
Li, J., Huang, J.-P., Sukumaran, J. & Knowles, L. L. Microevolutionary processes impact macroevolutionary patterns. BMC Evol. Biol. 18, 123 (2018).
Google Scholar
Melián, C. J., Alonso, D., Allesina, S., Condit, R. S. & Etienne, R. S. Does sex speed up evolutionary rate and increase biodiversity? PLoS Comput. Biol. 8, e1002414 (2012).
Google Scholar
Rangel, T. F. et al. Modeling the ecology and evolution of biodiversity: biogeographical cradles, museums, and graves. Science 361, eaar5452 (2018).
Pontarp, M. et al. The latitudinal diversity gradient: novel understanding through mechanistic eco-evolutionary models. Trends Ecol. Evol. 34, 211–223 (2019).
Google Scholar
de Alencar, L. R. V. & Quental, T. B. Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale. Ecol. Evol. 11, 5828–5843 (2021).
Google Scholar
Hurlbert, A. H. & Stegen, J. C. When should species richness be energy limited, and how would we know? Ecol. Lett. 17, 401–413 (2014).
Google Scholar
Morlon, H. Phylogenetic approaches for studying diversification. Ecol. Lett. 17, 508–525 (2014).
Google Scholar
Rosindell, J., Harmon, L. J. & Etienne, R. S. Unifying ecology and macroevolution with individual-based theory. Ecol. Lett. 18, 472–482 (2015).
Google Scholar
Rosindell, J. & Harmon, L. J. A unified model of species immigration, extinction and abundance on islands. J. Biogeogr. 40, 1107–1118 (2013).
Google Scholar
Etienne, R. S. & Rosindell, J. Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification. Syst. Biol. 61, 204–213 (2012).
Google Scholar
Rabosky, D. L. & Matute, D. R. Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds. Proc. Natl Acad. Sci. USA 110, 15354–15359 (2013).
Google Scholar
Louca, S. & Pennell, M. W. Extant timetrees are consistent with a myriad of diversification histories. Nature 580, 502–505 (2020).
Google Scholar
Princepe, D. & De Aguiar, M. A. M. Modeling mito-nuclear compatibility and its role in species identification. Syst. Biol. 70, 133–144 (2021).
Google Scholar
Bar-Yaacov, D., Blumberg, A. & Mishmar, D. Mitochondrial-nuclear co-evolution and its effects on OXPHOS activity and regulation. Biochim. Biophys. Acta 1819, 1107–1111 (2012).
Google Scholar
Sunnucks, P., Morales, H. E., Lamb, A. M., Pavlova, A. & Greening, C. Integrative approaches for studying mitochondrial and nuclear genome co-evolution in oxidative phosphorylation. Front. Genet. 8, 25 (2017).
Google Scholar
Hill, G. E. The mitonuclear compatibility species concept. Auk 134, 393–409 (2017).
Google Scholar
Lima, T. G., Burton, R. S. & Willett, C. S. Genomic scans reveal multiple mito-nuclear incompatibilities in population crosses of the copepod Tigriopus californicus. Evolution 73, 609–620 (2019).
Barreto, F. S. & Burton, R. S. Elevated oxidative damage is correlated with reduced fitness in interpopulation hybrids of a marine copepod. Proc. R. Soc. B https://doi.org/10.1098/rspb.2013.1521 (2013).
Hill, G. E. Mitonuclear compensatory coevolution. Trends Genet. 36, 403–414 (2020).
Google Scholar
Gershoni, M., Templeton, A. R. & Mishmar, D. Mitochondrial bioenergetics as a major motive force of speciation. BioEssays 31, 642–650 (2009).
Google Scholar
Hill, G. E. Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap. Ecol. Evol. 6, 5831–5842 (2016).
Google Scholar
Tobler, M., Barts, N. & Greenway, R. Mitochondria and the origin of species: bridging genetic and ecological perspectives on speciation processes. Integr. Comp. Biol. 59, 900–911 (2019).
Google Scholar
Burton, R. S. & Barreto, F. S. A disproportionate role for mtDNA in Dobzhansky–Muller incompatibilities? Mol. Ecol. 21, 4942–4957 (2012).
Google Scholar
Telschow, A., Gadau, J., Werren, J. H. & Kobayashi, Y. Genetic incompatibilities between mitochondria and nuclear genes: effect on gene flow and speciation. Front. Genet. 10, 62 (2019).
Google Scholar
Lane, N. Biodiversity: on the origin of bar codes. Nature 462, 272–274 (2009).
Google Scholar
Hill, G. E Mitonuclear Ecology (Oxford Univ. Press, 2019).
Wolff, J. N., Ladoukakis, E. D., Enríquez, J. A. & Dowling, D. K. Mitonuclear interactions: evolutionary consequences over multiple biological scales. Philos. Trans. R. Soc. B 369, 20130443 (2014).
Google Scholar
Koch, R. E. et al. Integrating mitochondrial aerobic metabolism into ecology and evolution. Trends Ecol. Evol. 36, 321–332 (2021).
Google Scholar
Weir, J. T. & Schluter, D. The latitudinal gradient in recent speciation and extinction rates of birds and mammals. Science 315, 1574–1576 (2007).
Google Scholar
Botero, C. A., Dor, R., McCain, C. M. & Safran, R. J. Environmental harshness is positively correlated with intraspecific divergence in mammals and birds. Mol. Ecol. 23, 259–268 (2014).
Google Scholar
Weir, J. T. Environmental harshness, latitude and incipient speciation. Mol. Ecol. 23, 251–253 (2014).
Google Scholar
Schluter, D. & Pennell, M. W. Speciation gradients and the distribution of biodiversity. Nature 546, 48–55 (2017).
Google Scholar
Harvey, M. G. et al. The evolution of a tropical biodiversity hotspot. Science 370, 1343–1348 (2020).
Google Scholar
Rabosky, D. L. et al. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559, 392–395 (2018).
Google Scholar
Rabosky, D. L. & Hurlbert, A. H. Species richness at continental scales is dominated by ecological limits. Am. Nat. 185, 572–583 (2015).
Google Scholar
Sugihara, G. Minimal community structure: an explanation of species abundance patterns. Am. Nat. 116, 770–787 (1980).
Google Scholar
Zhang, F. & Broughton, R. E. Mitochondrial–nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes? Genome Biol. Evol. 5, 1781–1791 (2013).
Google Scholar
Piccinini, G. et al. Mitonuclear coevolution, but not nuclear compensation, drives evolution of OXPHOS complexes in bivalves. Mol. Biol. Evol. 38, 2597–2614 (2021).
Google Scholar
Barreto, F. S. et al. Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus. Nat. Ecol. Evol. 2, 1250–1257 (2018).
Google Scholar
Kennedy, J. D. et al. Into and out of the tropics: the generation of the latitudinal gradient among New World passerine birds. J. Biogeogr. 41, 1746–1757 (2014).
Google Scholar
Etienne, R. S. et al. A minimal model for the latitudinal diversity gradient suggests a dominant role for ecological limits. Am. Nat. 194, E122–E133 (2019).
Google Scholar
Mittelbach, G. G. et al. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol. Lett. 10, 315–331 (2007).
Google Scholar
Hillebrand, H. On the generality of the latitudinal diversity gradient. Am. Nat. 163, 192–211 (2004).
Google Scholar
Evans, K. L. & Gaston, K. J. Can the evolutionary-rates hypothesis explain species–energy relationships? Funct. Ecol. 19, 899–915 (2005).
Google Scholar
Allen, A. P. & Gillooly, J. F. Assessing latitudinal gradients in speciation rates and biodiversity at the global scale. Ecol. Lett. 9, 947–954 (2006).
Google Scholar
Cutter, A. D. & Gray, J. C. Ephemeral ecological speciation and the latitudinal biodiversity gradient. Evolution 70, 2171–2185 (2016).
Google Scholar
Dowling, D. K., Abiega, K. C. & Arnqvist, G. Temperature-specific outcomes of cytoplasmic–nuclear interactions on egg-to-adult development time in seed beetles. Evolution 61, 194–201 (2007).
Google Scholar
Smith, B. T., Seeholzer, G. F., Harvey, M. G., Cuervo, A. M. & Brumfield, R. T. A latitudinal phylogeographic diversity gradient in birds. PLoS Biol. 15, e2001073 (2017).
Google Scholar
Freeman, B. G., Weeks, T., Schluter, D. & Tobias, J. A. The latitudinal gradient in rates of evolution for bird beaks, a species interaction trait. Ecol. Lett. 25, 635–646 (2022).
Google Scholar
Vellend, M. Species diversity and genetic diversity: parallel processes and correlated patterns. Am. Nat. 166, 199–215 (2005).
Google Scholar
Pontarp, M. & Wiens, J. J. The origin of species richness patterns along environmental gradients: uniting explanations based on time, diversification rate and carrying capacity. J. Biogeogr. 44, 722–735 (2017).
Google Scholar
Harvey, M. G. et al. Positive association between population genetic differentiation and speciation rates in New World birds. Proc. Natl Acad. Sci. USA 114, 6328–6333 (2017).
Google Scholar
Araújo, M. S. & Costa-Pereira, R. Latitudinal gradients in intraspecific ecological diversity. Biol. Lett. 9, 20130778 (2013).
Derrida, B. & Peliti, L. Evolution in a flat fitness landscape. Bull. Math. Biol. 53, 355–382 (1991).
Google Scholar
de Aguiar, M. A. M. Speciation in the Derrida–Higgs model with finite genomes and spatial populations. J. Phys. A 50, 85602 (2017).
Google Scholar
Thibert-Plante, X. & Gavrilets, S. Evolution of mate choice and the so-called magic traits in ecological speciation. Ecol. Lett. 16, 1004–1013 (2013).
Google Scholar
Seehausen, O. Hybridization and adaptive radiation. Trends Ecol. Evol. 19, 198–207 (2004).
Google Scholar
Kearns, A. M. et al. Genomic evidence of speciation reversal in ravens. Nat. Commun. 9, 906 (2018).
Google Scholar
Gray, J. S., Bjørgesæter, A. & Ugland, K. I. On plotting species abundance distributions. J. Anim. Ecol. 75, 752–756 (2006).
Google Scholar
Source: Ecology - nature.com