References
Aiello-Lammens, M. E., Boria, R. A., Radosavljevic, A., Vilela, B., &
Anderson, R. P. (2015). spThin: An R package for spatial thinning of
species occurrence records for use in ecological niche models.Ecography, 38 , 541–545.
Akani, G. C., Barieenee, I. F., & Luiselli, L. (1998). Observations on
habitat, reproduction and feeding of Boiga blandingii(Colubridae) in south-eastern Nigeria. Amphibia-Reptilia, 19,430–436.
Allen, A. P., & Gillooly, J. F. (2006). Assessing latitudinal gradients
in speciation rates and biodiversity at the global scale. Ecology
Letters , 9 , 947–954.
Allen, K. E., N. Tapondjou, W. P., Greenbaum, E., Welton, L. J., &
Bauer, A. M. (2019). High levels of hidden phylogenetic structure within
Central and West African Trachylepis skinks. Salamandra ,55 , 231–234.
Amorim, D. D. S. (1991). Refuge model simulations: Testing the theory.Revista Brasileira de Entomologia , 35 , 803–812.
Anderson, R. P., Lew, D., & Peterson, A. T. (2003). Evaluating
predictive models of species’ distributions: Criteria for selecting
optimal models. Ecological Modelling , 162 , 211–232.
Anthony, N. M., Johnson-Bawe, M., Jeffrey, K., Clifford, S. L.,
Abernethy, K. A., Tutin, C. E., … Bruford, M. W. (2007). The role of
Pleistocene refugia and rivers in shaping gorilla genetic diversity in
Central Africa. Proceedings of the National Academy of Sciences ,USA , 104 , 20432–20436.
Avise, J. C. (2000). Phylogeography: The history and formation of
species . Cambridge, MA: Harvard University Press.
Ayres, J.M.C. & Clutton-Brock, T.H. (1992). River boundaries and
species range size in Amazonian primates. American Naturalist ,140 , 531– 537.
Barej, M. F., Schmitz, A., Menegon, M., Hillers, A., Hinkel, H., Boehme,
W., & Rödel, M.‐O. (2011). Dusted off–the African Amietophrynus
superciliaris species complex of giant toads. Zootaxa ,2772 , 1–32.
Bates, H.W. (1863). The Naturalist on the River Amazon. London,
UK: John Murray.
Bell, R. C., Parra, J. L., Badjedjea, G., Barej, M. F., Blackburn, D.
C., Burger, M., … Zamudio, K. R. (2017). Idiosyncratic responses
to climate‐driven forest fragmentation and marine incursions in reed
frogs from Central Africa and the Gulf of Guinea Islands.Molecular Ecology , 26 , 5223–5244.
Blackburn, D. C. (2008). Biogeography and evolution of body size and
life history of African frogs: Phylogeny of squeakers
(Arthroleptis ) and long-fingered frogs (Cardioglossa )
estimated from mitochondrial data. Molecular Phylogenetics and
Evolution , 49 , 806–826.
Born, C., Alvarez, N., McKey, D., Ossari, S., Wickings, E. J.,
Hossaert-McKey, M., & Chevallier, M.-H. (2011). Insights into the
biogeographical history of the Lower Guinea Forest Domain: Evidence for
the role of refugia in the intraspecific differentiation ofAucoumea klaineana . Molecular Ecology , 20 ,
131–142.
Bohoussou, K. H., Cornette, R., Akpatou, B., Colyn, M., Peterhans, J.
K., Kennis, J., .. . Nicolas, V. (2015). The phylogeography of the
rodent genus Malacomys suggests multiple Afrotropical Pleistocene
lowland forest refugia. Journal of Biogeography , 42 ,
2049–2061.
Bonnefille, R. & Riollet, G. (1988). The Kashiru pollen sequence
(Burundi): Paleoclimatic implications for the last 40,000 yr BP in
tropical Africa. Quaternary Research , 30 , 19–35.
Bouckaert, R., Vaughan, T.G., Barido-Sottani, J., Duchêne, S., Fourment,
M., Gavryushkina, A., … Matschiner, M. (2019). BEAST 2.5: An
advanced software platform for Bayesian evolutionary analysis.PLoS Computational Biology , 15 , e1006650.
Brenac, P. (1988). Evolution de la végétation et du climat dans l’Ouest
Cameroun entre 25.000 et 11.000 ans BP. Actes Xème Symposium Ass.
Palynologues Langue Franwise. Travaux de la Section des Sciences
& Techniques de l’Institut Français de Pondichéry , 25 , 91–103.
Buckley, L. B., Davies, T. J., Ackerly, D. D., Kraft, N. J., Harrison,
S. P., Anacker, B. L., … McCain, C. M. (2010). Phylogeny, niche
conservatism and the latitudinal diversity gradient in
mammals. Proceedings of the Royal Society B: Biological
Sciences , 277 , 2131–2138.
Budde, K. B., González-Martínez, S. C., Hardy, O. J., & Heuertz, M.
(2013). The ancient tropical rainforest tree Symphonia
globulifera L. f. (Clusiaceae) was not restricted to postulated
Pleistocene refugia in Atlantic Equatorial Africa. Heredity ,111 , 66–76.
Burbrink, F. T., Lawson, R., & Slowinski, J. B. (2000). Mitochondrial
DNA phylogeography of the polytypic North American Rat Snake
(Elaphe obsoleta ): A critique of the subspecies concept.Evolution , 54 , 2107–2118.
Cardillo, M., Orme, C. D. L. & Owens, I. P. F. (2005). Testing for
latitudinal bias in diversification rates: An example using New World
birds. Ecology , 86 , 2278–2287.
Carstens, B. C., & Richards, C. L. (2007). Integrating coalescent and
ecological niche modeling in comparative
phylogeography. Evolution: International Journal of Organic
Evolution , 61 , 1439–1454.
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A.
(2013). Stacks: An analysis tool set for population genomics.Molecular Ecology , 22 , 3124–3140.
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S.
M., & Lee, J. J. (2015). Second-generation PLINK: Rising to the
challenge of larger and richer data sets. Gigascience , 4 ,
7.
Charles, K. L., Bell, R. C., Blackburn, D. C., Burger, M., Fujita, M.
K., Gvoždík, V., … Portik, D. M. (2018). Sky, sea, and forest
islands: Diversification in the African leaf‐folding frogAfrixalus paradorsalis (Anura: Hyperoliidae) of the Lower
Guineo‐Congolian rainforest. Journal of Biogeography , 45 ,
1781–1794.
Chifman, J., & Kubatko, L. (2014). Quartet inference from SNP data
under the coalescent model. Bioinformatics , 30 ,
3317–3324.
Clifford, S. L., Anthony, N. M., Bawe‐Johnson, M., Abernethy, K. A.,
Tutin, C. E., White, L. J., … Wickings, E. J. (2004).
Mitochondrial DNA phylogeography of western lowland gorillas
(Gorilla gorilla gorilla ). Molecular Ecology , 13,1551–1565.
Chippaux, J. P., & Jackson, K. (2019). Snakes of Central and
Western Africa . Baltimore, MD: John Hopkins University Press.
Cobos, M. E., Peterson, A. T., Barve, N., & Osorio-Olvera, L. (2019).
Kuenm: An R package for detailed development of ecological niche models
using Maxent. PeerJ , 7 , e6281.
Colinvaux, P. A., De Oliveira, P. E., Moreno, J. E., Miller, M. C., &
Bush, M. B. (1996). A long pollen record from lowland Amazonia: Forest
and cooling in glacial times. Science , 274 , 85–88.
Colinvaux, P. A., Irion, G., Räsänen, M. E., Bush, M. B., & De Mello,
J. N. (2001). A paradigm to be discarded: Geological and paleoecological
data falsify the Haffer & Prance refuge hypothesis of Amazonian
speciation. Amazoniana , 16 , 609–646.
Colyn, M. M. (1987). Les Primates des forêts ombrophiles de la cuvette
du Zaïre: Interprétations zoogéographiques des modèles de distribution.Revue de Zoologie Africaine, Tervuren, 101 , 183–96.
Colyn, M. M. (1991). L’importance zoogéographique du bassin du fleuve
Zaïre pour la spéciation: Le cas des Primates Siens. Annales Musée
Royal de I; Afrique Centrale, Section Zoologie, Tervuren, 264 ,
1– 250.
Colyn, M., Gautier-Hion, A. & Verheyen, W. (1991). A re-appraisal of
palaeoenvironmental history in Central Africa: Evidence for a major
fluvial refuge in the Zaire Basin. Journal of Biogeography ,18 , 403–407.
Cracraft, J. (1985). Historical biogeography and patterns of
differentiation within the South American avifauna: Areas of
endemism. Ornithological Monographs , 36 , 49–84.
Daïnou, K., Bizoux, J.-P., Doucet, J.-L., Mahy, G., Hardy, O. J., &
Heuertz, M. (2010). Forest refugia revisited: NSSRs and cpDNA sequences
support historical isolation in a wide-spread African tree with high
colonization capacity, Milicia excels (Moracea). Molecular
Ecology , 19 , 4462–4477.
Darlington, P. J., Jr. (1957). Zoogeography and the Geographical
Distribution of Animals . New York, NY: John Wiley & Sons, Inc.
Darwin, C.R. (1859). The Origin of Species by Means of Natural
Selection, or the Preservation of Favoured Races in the Struggle for
Life . London, UK: John Murray.
Dauby, G., Duminil, J., Heuertz, M., & Hardy, O. J. (2010). Chloroplast
DNA polymorphism and phylogeography of a Central African tree species
widespread in mature rainforest: Greenwayodendron suaveolens(Annonaceae). Tropical Plant Biology , 3 , 4–13.
Dauby, G., Duminil, J., Heuertz, M., Koffi, G. K., Stévart, T., &
Hardy, O. J. (2014). Congruent phylogeographical patterns of eight tree
species in Atlantic Central Africa provide insights into the past
dynamics of forest cover. Molecular Ecology , 23 ,
2299–2312.
Debout, G. D. C., Doucet, J.-L., & Hardy, O. J. (2011). Population
history and gene dispersal inferred from spatial genetic structure of a
Central African timber tree, Distemonanthus benthamianus(Caesalpinioideae). Heredity , 106 , 88–99.
DeMenocal, P. B. (2004). African climate change and faunal evolution
during the Pliocene–Pleistocene. Earth and Planetary Science
Letters , 220 , 3–24.
Devitt, T. J., Devitt, S. E., Hollingsworth, B. D., McGuire, J. A., &
Moritz, C. (2013). Montane refugia predict population genetic structure
in the Large-blotched Ensatina salamander. Molecular
Ecology , 22 , 1650–1665.
Duminil, J., Mona, S., Mardulyn, P., Doumenge, C., Walmacq, F., Doucet,
J.‐L., & Hardy, O. J. (2015). Late Pleistocene molecular dating of past
population fragmentation and demographic changes in African rain forest
tree species supports the forest refuge hypothesis. Journal of
Biogeography , 42 , 1443–1454.
Ellegren, H. (2014). Genome sequencing and population genomics in
non-model organisms. Trends in Ecology & Evolution , 29 ,
51–63.
Escobar, L. E., Lira-Noriega, A., Medina-Vogel, G., & Peterson, A.T.
(2014). Potential for spread of the white-nose fungus
(Pseudogymnoascus destructans ) in the Americas: Use of Maxent and
Niche A to assure strict model transference. Geospatial Health ,9 , 221–229.
Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of
clusters of individuals using the software STRUCTURE: A simulation
study. Molecular Ecology , 14 , 2611–2620.
Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V.C., & Foll,
M. (2013). Robust demographic inference from genomic and SNP data.PLOS Genetics , 9 , e1003905.
Falush, D., Stephens, M., & Pritchard, J. K. (2003). Inference of
population structure using multilocus genotype data: Linked loci and
correlated allele frequencies. Genetics , 164 , 1567–1587.
Fagny, M. F., Nkouandou, O. F., Temdjim, R., Bardintzeff, J. M.,
Guillou, H., Stumbea, D., & Boutale, A. (2016). New K–Ar ages of
Tchabal Mbabo alkaline volcano massif, Cameroon Volcanic Line and
Adamawa plateau (Central Africa). International Journal of
Advanced Geosciences , 4 , 62–71.
Faye, A., Deblauwe, V., Mariac, C., Richard, D., Sonké, B., Vigouroux,
Y., & Couvreur, T. (2016). Phylogeography of the genusPodococcus (Palmae/Arecaceae) in Central African rain forests:
Climate stability predicts unique genetic diversity. Molecular
Phylogenetics and Evolution , 105 , 126–138.
Fine, P.V.A. & Ree, R.H. (2006). Evidence for a time‐integrated
species‐area effect on the latitudinal gradient in tree diversity.The American Naturalist , 168 , 796–804.
Fjeldså, J. (1994). Geographical patterns for relict and young species
of birds in Africa and South America and implications for conservation
priorities. Biodiversity & Conservation , 3 , 207–226.
Fjeldså, J., & Bowie, R. C. (2008). New perspectives on the origin and
diversification of Africa’s forest avifauna. African Journal of
Ecology , 46 , 235–247.
Fjeldså, J., & Lovett, J. C. (1997). Geographical patterns of old and
young species in African forest biota: The significance of specific
montane areas as evolutionary centres. Biodiversity &
Conservation, 6 , 325–346.
Flügel, T. J., Eckardt, F. D., & Cotterill, F. P. (2015). The present
day drainage patterns of the Congo river system and their Neogene
evolution. In De Wit, M. J., Guillocheau, F., & De Wit, M. C. (Eds.)Geology and Resource Potential of the Congo Basin . (pp.
315–337). Berlin, Germany: Springer.
Francis, R. M. (2017). Pophelper: An R package and web app to analyze
and visualize population structure. Molecular Ecology
Resources , 17 , 27–32.
François, O. (2016). Running structure‐like population genetic analyses
with R. R tutorials in Population Genetics, U. Grenoble‐Alpes ,
1–9.
Frichot, E., & François, O. (2015). LEA: An R package for landscape and
ecological association studies. Methods in Ecology and
Evolution , 6 , 925–929.
Frichot, E., Mathieu, F., Trouillon, T., Bouchard, G. & François, O.
(2014). Fast and efficient estimation of individual ancestry
coefficients. Genetics , 196 , 973–983.
Gascon, C., Malcolm, J. R., Patton, J. L., da Silva, M. N., Bogart, J.
P., Lougheed, S. C., … Boag, P. T. (2000). Riverine barriers and the
geographic distribution of Amazonian species. Proceedings of the
National Academy of Sciences, USA , 97 , 13672–13677.
Gaubert, P., Njiokou, F., Ngua, G., Afiademanyo, K., Dufour, S.,
Malekani, J., … Antunes, A. (2016). Phylogeography of the heavily
poached African common pangolin (Pholidota, Manis tricuspis )
reveals six cryptic lineages as traceable signatures of Pleistocene
diversification. Molecular Ecology , 25 , 5975–5993.
Girese, P., Maley, J. & Brenac, P. (1994). Late Quaternary
palaeoenvironments in the Lake Barombi Mbo (Cameroon) deduced from
pollen and carbon isotopes of organic matter. Palaeogeography,
Palaeoclimatology, Palaeoecology, 107 , 65–78.
Gomez, C., Dussert, S., Hamon, P., Hamon, S., de Kochko, A., & Poncet,
V. (2009). Current genetic differentiation of Coffea canephoraPierre ex. A. Froehn in Guineo-Congolian African zone: Cumulative impact
of ancient climatic changes and recent human activities. BMC
Evolutionary Biology , 9 , 167.
Gonder, M. K., Locatelli, S., Ghobrial, L., Mitchell, M. W., Kujawski,
J. T., Lankester, F. J., … Tishkoff, S. A. (2011). Evidence from
Cameroon reveals differences in the genetic structure and histories of
chimpanzee populations. Proceedings of the National Academy of
Sciences, USA , 108 , 4766–4771.
Goudie, A. S. (2005). The drainage of Africa since the Cretaceous.Geomorphology , 67 , 437–456.
Greenbaum E. (2017). Emerald Labyrinth: A Scientist’s Adventures
in the Jungles of the Congo . Lebanon, NH: University Press of New
England.
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante,
C. D. (2009). Inferring the joint demographic history of multiple
populations from multidimensional SNP frequency data. PLoS
Genetics , 5 , e1000695.
Haffer, J. R. (1969). Speciation in Amazonian forest birds.Science , 165 , 131–137.
Haffer, J. R. (1974). Avian speciation in tropical South
America. Publications of the Nuttall Ornithological Club, 14 ,
1–390.
Haffer, J. R. (1982). General aspects of the refuge theory. In Prance,
G. T. (Ed.) Biological Diversification in the Tropics . (pp.
6–24). New York, NY: Columbia University Press.
Haffer, J. R. (1992). On the “river effect” in some forest birds of
southern Amazonia. Boletim do Museu Paraense Emílio Goeldi. Nova
série. Zoologia , 8 , 217–245.
Haffer, J. R. (1993). Time’s cycle and time’s arrow in the history of
Amazonia. Compte Rendu des Séances de la Société de
Biogéographie , 69 , 15–45.
Haffer, J. R. (1997). Alternative models of vertebrate speciation in
Amazonia: An overview. Biodiversity and Conservation , 6 ,
451–476.
Haffer J. R. (2008). Hypotheses to explain the origin of species in
Amazonia. Brazilian Journal of Biology , 68 , 917– 947.
Hampe, A., & Jump, A. S. (2011). Climate relicts: Past, present,
future. Annual Review of Ecology, Evolution, and
Systematics , 42 , 313–333.
Harcourt, A. H., & Wood, M. A. (2012). Rivers as barriers to primate
distributions in Africa. International Journal of
Primatology , 33 , 168–183.
Hardy, O. J., Born, C., Budde, K., Daïnou, K., Dauby, G., Duminil, J.,
… Poncet, V. (2013). Comparative phylogeography of African rain
forest trees: A review of genetic signatures of vegetation history in
the Guineo-Congolian region. Comptes Rendus Geoscience ,345 , 284–296.
Harrison, S., & Noss, R. (2017). Endemism hotspots are linked to stable
climatic refugia. Annals of Botany , 119 , 207–214.
Haus, T., Akom, E., Agwanda, B., Hofreiter, M., Roos, C., & Zinner, D.
(2013). Mitochondrial diversity and distribution of African green
monkeys (Chlorocebus Gray, 1870). American Journal of
Primatology , 75 , 350–360.
Hawkins, B. A., Diniz-Filho, J. A. F., Jaramillo, C. A., & Soeller, S.
A. (2007). Climate, niche conservatism, and the global bird diversity
gradient. The American Naturalist , 170 , S16–S27.
Hawkins, B. A., Porter, E. E., Diniz-Filho, F., & Alexandre, J. (2003).
Productivity and history as predictors of the latitudinal diversity
gradient of terrestrial birds. Ecology , 84 , 1608–1623.
Head, J. J., Mahlow, K., & Müller, J. (2016). Fossil calibration dates
for molecular phylogenetic analysis of snakes 2: Caenophidia,
Colubroidea, Elapoidea, Colubridae. Palaeontologia
Electronica , 19 , 1–21.
Herbert, T. D., Lawrence, K. T., Tzanova, A., Peterson, L. C.,
Caballero-Gill, R., & Kelly, C. S. (2016). Late Miocene global cooling
and the rise of modern ecosystems. Nature Geoscience , 9 ,
843–847.
Hershkovitz, P. (1977). Living New World Monkeys (Platyrrhini).Chicago, IL: University of Chicago Press.
Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G., & Jarvis,
A. (2005). Very high-resolution interpolated climate surfaces for global
land areas. International Journal of Climatology , 25 ,
1965–1978.
Hime, P. M., Briggler, J. T., Reece, J. S., & Weisrock, D. W. (2019).
Genomic data reveal conserved female heterogamety in giant salamanders
with gigantic nuclear genomes. G3: Genes | Genomes
| Genetics , 9 , 3467–3476.
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.
Hofer, U., Bersier, L.-F., & Borcard, D. (1999). Spatial organization
of a herpetofauna on an elevational gradient revealed by null model
tests. Ecology, 80 , 976–988.
Hofer, U., Bersier, L.-F., & Borcard, D. (2000). Ecotones and gradient
as determinants of herpetofaunal community structure in the primary
forest of Mount Kupe, Cameroon. Journal of Tropical Ecology ,16 , 517–533.
Hrdina, A., & Romportl, D. (2017). Evaluating global biodiversity
hotspots–Very rich and even more endangered. Journal of Landscape
Ecology , 10 , 108–115.
Hughes, D. F., Kusamba, C., Behangana, M., & Greenbaum, E. (2017).
Integrative taxonomy of the Central African forest chameleon,Kinyongia adolfifriderici (Sauria: Chamaeleonidae), reveals
underestimated species diversity in the Albertine Rift. Zoological
Journal of the Linnean Society , 181 , 400–438.
Huntley, J. W., Harvey, J. A., Pavia, M., Boano, G., & Voelker, G.
(2018). The systematics and biogeography of the Bearded Greenbuls (Aves:
Criniger) reveals the impact of Plio-Pleistocene forest fragmentation on
Afro-tropical avian diversity. Zoological Journal of the Linnean
Society , 183 , 672–686.
Huntley, J. W., Keith, K. D., Castellanos, A. A., Musher, L. J., &
Voelker, G. (2019). Underestimated and cryptic diversification patterns
across Afro‐tropical lowland forests. Journal of
Biogeography , 46 , 381–391.
Hutchinson, G. E. (1959). Homage to Santa Rosalia or why are there so
many kinds of animals? The American Naturalist , 93 ,
145–159.
Jablonski, D., Roy, K. & Valentine, J.W. (2006). Out of the tropics:
evolutionary dynamics of the latitudinal diversity gradient.
Science , 314 , 102–106.
Jacobs, B.F. (2004). Paleobotanical studies from Tropical Africa:
Relevance to the evolution of forest, woodland and savannah biomes.Philosophical Transactions of the Royal Society B ., 359 ,
1573–1583.
Jacquet, F., Nicolas, V., Colyn, M., Kadjo, B., Hutterer, R., Decher,
J., … Denys, C. (2014). Forest refugia and riverine barriers promote
diversification in the West African pygmy shrew (Crocidura
obscurior complex, Soricomorpha). Zoologica Scripta , 43 ,
131–148.
Jacquet, F., Denys, C., Verheyen, E., Bryja, J., Hutterer, R., Kerbis
Peterhans, J. C., .. . Nicolas, V. (2015). Phylogeography and
evolutionary history of the Crocidura olivieri complex (Mammalia,
Soricomorpha): From a forest origin to broad ecological expansion across
Africa. BMC Evolutionary Biology , 15 , 71.
Jansson, R., & Dynesius, M. (2002). The fate of clades in a world of
recurrent climatic change: Milankovitch oscillations and
evolution. Annual Review of Ecology and Systematics , 33 ,
741–777.
Janzen, D. H. (1967). Why mountain passes are higher in the
tropics. The American Naturalist , 101 , 233–249.
Jetz, W., & Fine, P. V. (2012). Global gradients in vertebrate
diversity predicted by historical area-productivity dynamics and
contemporary environment. PLoS Biology , 10 , e1001292.
Jombart, T., & Ahmed, I. (2011). Adegenet 1.3-1: New tools for the
analysis of genome-wide SNP data. Bioinformatics , 27 ,
3070–3071.
Jongsma, G. F. M., Barej, M. F., Barratt, C. D., Burger, M., Conradie,
W., Ernst, R., … Blackburn, D. C. (2018). Diversity and
biogeography of frogs in the genus Amnirana (Anura: Ranidae)
across sub‐Saharan Africa. Molecular Phylogenetics and Evolution ,120 , 274–285.
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K., von Haeseler, A., &
Jermiin, L. S. (2017). ModelFinder: Fast model selection for accurate
phylogenetic estimates. Nature Methods , 14 , 587.
Katoh, M., & Kuma, M. (2002). MAFFT: A novel method for rapid multiple
sequence alignment based on fast Fourier transform. Nucleic Acids
Research , 30 , 3059–3066.
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M.,
Sturrock, S., … Thierer, T. (2012). Geneious Basic: An integrated and
extendable desktop software platform for the organization and analysis
of sequence data. Bioinformatics , 28 , 1647–1649.
Knowles, L. L. (2009). Statistical phylogeography. Annual Review
of Ecology, Evolution, and Systematics , 40 , 593–612.
Knowles, L. L., & Maddison, W. P. (2002). Statistical
phylogeography. Molecular Ecology , 11 , 2623–2635.
Lamanna, C., Blonder, B., Violle, C., Kraft, N. J., Sandel, B., Šímová,
I., … & Buzzard, V. (2014). Functional trait space and the
latitudinal diversity gradient. Proceedings of the National
Academy of Sciences, USA , 111 , 13745–13750.
Larson, T. R., Castro, D., Behangana, M., & Greenbaum, E. (2016).
Evolutionary history of the river frog genus Amietia (Anura:
Pyxicephalidae) reveals extensive diversification in Central African
highlands. Molecular Phylogenetics and Evolution , 99 ,
168–181.
Lawson, R., Slowinski, J.B., Crother, B.I., & Burbrink, F.T. (2005).
Phylogeny of the Colubroidea (Serpentes): New evidence from
mitochondrial and nuclear genes. Molecular Phylogenetics and
Evolution , 37 , 581–601.
Leaché, A. D., & Fujita, M. K. (2010). Bayesian species delimitation in
West African forest geckos (Hemidactylus fasciatus ).Proceedings of the Royal Society of London B: Biological
Sciences , 277, 3071–3077.
Leaché, A. D., Grummer, J. A., Miller, M., Krishnan, S., Fujita, M. K.,
Böhme, W., … Ofori-Boateng, C. (2017). Bayesian inference of species
diffusion in the West African Agama agama species group
(Reptilia, Agamidae). Systematics and Biodiversity , 15 ,
192–203.
Leaché, A. D., Harris, R. B., Rannala, B., & Yang, Z. (2014). The
influence of gene flow on species tree estimation: A simulation study.Systematic Biology , 63 , 17–30.
Leaché, A. D., Portik, D. M., Rivera, D., Rödel, M.-O., Penner, J.,
Gvoždík, V., …Fujita, M.K. (2019). Exploring rain forest
diversification using demographic model testing in the African foam‐nest
treefrog Chiromantis rufescens . Journal of Biogeography ,46 , 2706–2721.
Levinsky, I., Araújo, M. B., Nogués‐Bravo, D., Haywood, A. M., Valdes,
P. J., & Rahbek, C. (2013). Climate envelope models suggest
spatio‐temporal co‐occurrence of refugia of African birds and
mammals. Global Ecology and Biogeography , 22 , 351–363.
Ley, A. C., Dauby, G., Köhler, J., Wypior, C., Röser, M., & Hardy, O.
J. (2014). Comparative phylogeography of eight herbs and lianas
(Marantaceae) in central African rainforests. Frontiers in
Genetics , 5 , 403.
Ley, A. C., Heuertz, M., & Hardy, O. J. (2016). The evolutionary
history of Central African rain forest plants: Phylogeographical
insights from sister species in the climber genus Haumania(Marantaceae). Journal of Biogeography , 44 , 308–321.
Lowe, A. J., Harris, D., Dormontt, E., & Dawson, I. K. (2010). Testing
putative African tropical forest refugia using chloroplast and nuclear
DNA phylogeography. Tropical Plant Biology , 3 , 50–58.
Luikart, G., England, P. R., Tallmon, D., Jordan, S., & Taberlet, P.
(2003). The power and promise of population genomics: from genotyping to
genome typing. Nature Reviews Genetics , 4 , 981–994.
Maley, J. (1987). Fragmentation de la forêt dense humide africaine et
extension des biotopes montagnards au Quatemaire récent: Nouvelles
données polliniques et chronologiques. Implications paléo-climatiques et
biogéographiques. Palaeoecology of Africa , 18 , 307–334.
Maley, J. (1989). Late Quaternary climatic changes in the African rain
forest: Forest refugia and the major role of sea surface temperature
variations. In Leinen, M. & Sarnthein, M. (Eds.) Paleoclimatology
and Paleometeorology: Modern and Past Patterns of Global Atmospheric
Transport (pp. 585–616). Dordrecht, Netherlands: Springer.
Maley, J. (1991). The African rain forest vegetation and
palaeoenvironments during late Quaternary. Climatic Change ,19 , 79–98.
Maley, J. (1996). The African rain forest–main characteristics of
changes in vegetation and climate from the Upper Cretaceous to the
Quaternary. Proceedings of the Royal Society of Edinburgh ,104 , 31–73.
Maley, J., & Brénac, P. (1987). Analyses polliniques préliminaires du
Quaternaire récent de l’Ouest Cameroun: Mise en évidence de refuges
forestiers et discussion des problèmes paléoclimatiques. Mémoires
et Travaux de l’Institut de Montpellier , 17 , 129–142.
Maley, J., & Brenac, P. (1998). Vegetation dynamics, palaeoenvironments
and climatic changes in the forests of western Cameroon during the last
28,000 years BP. Review of Palaeobotany and Palynology ,99 , 157–187.
Maley, J., & Livingstone, D. A. (1983). Extension d’un élément
montagnard dans le Sud du Ghana (Afrique de l’Ouest) au Pléistocène
supérieur et à l’Holocène inférieur: Premières données polliniques.Comptes Rendus de l’Académie des Sciences , Paris ,296 , 1287–1292.
Marks, B. D. (2010). Are lowland rainforests really evolutionary
museums? Phylogeography of the green hylia (Hylia prasina ) in the
Afrotropics. Molecular Phylogenetics and Evolution , 55 ,
178–184.
Mayr, E. (1942). Systematics and the Origin of Species from the
Viewpoint of a Zoologist. New York, NY: Columbia University Press.
Mayr, E., & O’Hara, R. J. (1986). The biogeographic evidence supporting
the Pleistocene forest refuge hypothesis. Evolution , 40 ,
55–67.
Menegon, M., Loader, S. P., Marsden, S. J., Branch, W. R., Davenport, T.
R. B., & Ursenbacher, S. (2014). The genus Atheris (Serpentes:
Viperidae) in East Africa: Phylogeny and the role of rifting and climate
in shaping the current pattern of species diversity. Molecular
Phylogenetics and Evolution , 79 , 12–22.
Mitchell, M. W., Locatelli, S., Ghobrial, L., Pokempner, A. A., Clee, P.
R. S., Abwe, E. E., … & Fotso, R. (2015). The population genetics of
wild chimpanzees in Cameroon and Nigeria suggests a positive role for
selection in the evolution of chimpanzee subspecies. BMC
Evolutionary Biology , 15 , 3.
Mittermeier, R. A., Myers, N., & Mittermeier, C. G. (2000).Hotspots: Earth’s Biologically Richest and Most Endangered
Terrestrial Ecoregions. Chicago, IL: University of Chicago Press.
Mittermeier, R. A., Turner, W. R., Larsen, F. W., Brooks, T. M.,
& Gascon, C. (2011). Global biodiversity conservation: The critical
role of hotspots. In Zachos, F. E. & Habel, J.
C. (Eds.), Biodiversity Hotspots – Distribution and Protection of
Conservation Priority Areas . (pp. 3–22). Berlin, Germany: Springer.
Myers, N. (1988). Threatened biotas: ”Hot spots” in tropical
forests. Environmentalist , 8 , 187–208.
Nagy, Z. T., Kusamba, Z. C., Tungaluma, G. G., Lokasola, A. L., Kolby,
J., & Kielgast, J. (2011). Foraging acrobatics of Toxicodryas
blandingii in the Democratic Republic of the Congo. Herpetology
Notes , 4 , 91–92.
Nicolas, V., Missoup, A. D., Denys, C., Kerbis Peterhans, J., Katuala,
P., Couloux, A., & Colyn, M. (2011). The roles of rivers and
Pleistocene refugia in shaping genetic diversity in Praomys
misonnei in tropical Africa. Journal of Biogeography , 38 ,
191–207.
Nicolas, V., Missoup, A. D., Colyn, M., Cruaud, C., & Denys, C. (2012).
West-Central African Pleistocene lowland forest evolution revealed by
the phylogeography of Misonne’s soft-furred mouse. African
Zoology , 47 , 100–112.
Nguyen, L. T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2014).
IQ-TREE: A fast and effective stochastic algorithm for estimating
maximum-likelihood phylogenies. Molecular Biology and Evolution ,32 , 268–274.
Paris, J. R., Stevens, J. R., & Catchen, J. M. (2017). Lost in
parameter space: A road map for stacks. Methods in Ecology and
Evolution , 8 , 1360–1373.
Patton, J. L., & Silva, M. F. (2005). The history of Amazonian mammals:
Mechanisms and timing of diversification. In Bermingham, E., Dick, C.W.,
& Moritz, C. (Eds.) Tropical rainforests: Past, present and
future. (pp. 107–126). Chicago, IL: The University of Chicago Press.
Penner, J., Wegmann, M., Hillers, A., Schmidt, M., & Rödel, M.-O.
(2011). A hotspot revisited - a biogeographical analysis of West African
amphibians. Diversity and Distribution, 17 , 1077–1088.
Penner, J. Augustin, M., & Rödel, M.-O. (2019) Modelling the spatial
baseline for amphibian conservation in West Africa. Acta
Oecologica, 84 , 31–40.
Prance, G.T. (1982). Biological Diversification in the Tropics .
New York, NY: Columbia University Press.
Richardson, J. E., Pennington, R. T., Pennington, T. D., &
Hollingsworth, P. M. (2001). Recent and rapid diversification of a
species-rich genus of Neotropical trees. Science , 293 ,
2242–2245.
Peterson, A.T., Papes, ̵̧ M., & Soberón, J. (2008). Rethinking receiver
operating characteristic analysis applications in ecological niche
modeling. Ecological Modelling , 213 , 63–72.
Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra,
H. E. (2012). Double digest RADseq: An inexpensive method for de
novo discovery and genotyping in model and non-model species.PLoS ONE , 7 , e37135.
Petkova, D., Novembre, J., & Stephens, M. (2016). Visualizing spatial
population structure with estimated effective migration surfaces.Nature Genetics , 48 , 94–100.
Phillips, S. J., Anderson, R. P., & Schapire, R. E. (2006). Maximum
entropy modeling of species geographic distributions. Ecological
Modelling , 190 , 231–259.
Pianka, E. R. (1966). Latitudinal gradients in species diversity: A
review of concepts. American Naturalist , 100 , 33–46.
Plana, V. (2004). Mechanisms and tempo of evolution in the African
Guineo–Congolian rainforest. Philosophical Transactions of the
Royal Society of London. Series B: Biological Sciences , 359 ,
1585–1594.
Porras-Hurtado, L., Ruiz, Y., Santos, C., Phillips, C., Carracedo, Á.,
& Lareu, M. (2013). An overview of STRUCTURE: applications, parameter
settings, and supporting software. Frontiers in
Genetics , 4 , 98.
Portik, D. M., Leaché, A. D., Rivera, D., Barej, M. F., Burger, M.,
Hirschfeld, M., … Fujita, M. K. (2017). Evaluating mechanisms of
diversification in a Guineo‐Congolian tropical forest frog using
demographic model selection. Molecular Ecology , 26 , 5245–
5263.
Portillo, F., Stanley, E. L., Branch, W. R., Conradie, W., Rödel, M.-O.,
Penner, J., … Eli Greenbaum (2019). Evolutionary history of burrowing
asps (Lamprophiidae: Atractaspidinae) with emphasis on fang evolution
and prey selection. PloS ONE , 14 , e0214889.
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of
population structure using multilocus genotype data. Genetics ,155 , 945–959.
Provan, J., & Bennett, K. D. (2008). Phylogeographic insights into
cryptic glacial refugia. Trends in Ecology &
Evolution , 23 , 564–571.
Pudlo, P., Marin, J. M., Estoup, A., Cornuet, J. M., Gautier, M., &
Robert, C. P. (2015). Reliable ABC model choice via random
forests. Bioinformatics , 32 , 859–866.
Puechmaille, S. J. (2016). The program structure does not reliably
recover the correct population structure when sampling is uneven:
Subsampling and new estimators alleviate the problem. Molecular
Ecology Resources , 16 , 608–627.
Pyron, R. A., Burbrink, F. T., & Wiens, J. J. (2013). A phylogeny and
revised classification of Squamata, including 4161 species of lizards
and snakes. BMC Evolutionary Biology , 13 , 93.
QGIS Development Team (2020). QGIS Geographic Information System. Open
Source Geospatial Foundation Project. http://qgis.osgeo.org.
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A.
(2018). Posterior summarization in Bayesian phylogenetics using Tracer
1.7. Systematic Biology , 67 , 901–904.
Richards, P. W. (1963). Ecological notes on West African vegetation. II.
Lowland forest of the southern Bakundu Forest Reserve. Journal of
Ecology , 51 , 123–149.
Ricklefs, R. E. (2006). Global variation in the diversification rate of
passerine birds. Ecology , 87 , 2468–2478.
Ricklefs, R. E., & Schluter, D. (1993). Species diversity: Regional and
historical influences. In Ricklefs, R. E. & Schluter, D. (Eds.)Species Diversity in Ecological Communities: Historical and
Geographical Perspectives . (pp. 350–363). Chicago, IL: University of
Chicago Press.
Rietkerk, M., Ketner, P., & De Wilde, J. (1995). Caesalpinioideae and
the study of forest refuges in Gabon: Preliminary results.Bulletin du Museum National d‘Histoire Naturelle, Paris,
Adansonia , 17 , 95–105.
Robbrecht, E. (1996). Geography of African Rubiaceae with reference to
glacial rain forest refuges. In van der Maesen, L. J. G., van der Burgt,
X. M. & van Medenbach de Rooy, J.M. (Eds.), The Biodiversity of
African Plants . (pp. 564–581). Dordrecht, Netherlands: Kluwer.
Rödel, M.-O., Emmrich, M., Penner, J., Schmitz, A., & Barej, M. F.
(2014). The taxonomic status of two West African Leptopelisspecies: L. macrotis Schiøtz, 1967 and L. spiritusnoctisRödel, 2007 (Amphibia: Anura: Arthroleptidae). Zoosystematics and
Evolution , 90 , 21–31.
Rohde, K. (1992). Latitudinal gradients in species diversity: The search
for the primary cause. Oikos , 65 , 514–527.
Rosenzweig, M. L. (1995). Species Diversity in Space and Time .
Cambridge, UK: Cambridge University Press.
Schmidt, K. P. (1923). Contributions to the herpetology of the Belgian
Congo based on the collection of the American Museum Congo Expedition,
1909–1915. Part II. Snakes, with field notes by Herbert Lang and James
P. Chapin. Bulletin of the American Museum of Natural History,49, 1–146
Schunke, A. C., & Hutterer, R. (2005). The variance of variation:
Geographic patterns of coat colouration in Anomalurops andAnomalurus (Mammalia, Rodentia, Anomaluridae). Bonner
Zoologische Beiträge , 53 , 169–185.
Shafer, A. B., Peart, C. R., Tusso, S., Maayan, I., Brelsford, A.,
Wheat, C. W., & Wolf, J. B. (2017). Bioinformatic processing of RAD‐seq
data dramatically impacts downstream population genetic
inference. Methods in Ecology and Evolution , 8 , 907–917.
Sick, H. (1967). Rios e enchentes na Amazônia como obstáculo para a
avifauna. Atas do Simpósio Sobre a Biota Amazônica , 5 ,
495–520.
Siddig, A. A. (2019). Why is biodiversity data-deficiency an ongoing
conservation dilemma in Africa? Journal for Nature
Conservation , 50 , 125719.
Smith, B. T., Seeholzer, G. F., Harvey, M. G., Cuervo, A. M., &
Brumfield, R. T. (2017). A latitudinal phylogeographic diversity
gradient in birds. PLoS Biology , 15 , e2001073.
Smith, M. L., & Carstens, B. C. (2020). Process‐based species
delimitation leads to identification of more biologically relevant
species. Evolution , 74 , 216–229.
Smith, M. L., Ruffley, M., Tank, D. C., Sullivan, J., & Carstens, B. C.
(2017). Demographic model selection using random forests and the site
frequency spectrum. Molecular Ecology , 26 , 4562–4573.
Soberón, J., & Peterson, A. T. (2005). Interpretation of models of
fundamental ecological niches and species’ distributional areas.Biodiversity Informatics , 2 , 1–10.
Sosef, M. S. M. (1991). New species of Begonia in Africa and
their relevance to the study of glacial rain forest refuges.Wageningen Agricultural University Papers , 91 , 120–151.
Sowunmi, M. A. (1991). Late Quaternary environments in equatorial
Africa: Palynological evidence. Palaeoecology of Africa ,22 , 213–238.
Spawls, S., Howell, K., Hinkel, H., & Menegon, M. (2018). Field
guide to East African reptiles . New York, NY: Bloomsbury Publishing.
Stankiewicz, J., & de Wit, M. J. (2006). A proposed drainage evolution
model for Central Africa—Did the Congo flow east? Journal of
African Earth Sciences , 44 , 75–84.
Stein, A., Gerstner, K., & Kreft, H. (2014). Environmental
heterogeneity as a universal driver of species richness across taxa,
biomes and spatial scales. Ecology Letters , 17 , 866–880.
Stevens, G. C. (1989). The latitudinal gradient in geographical range:
How so many species coexist in the tropics. American Naturalist ,133 , 240–256.
Stevens, R. D. (2011). Relative effects of time for speciation and
tropical niche conservatism on the latitudinal diversity gradient of
phyllostomid bats. Proceedings of the Royal Society of London B:
Biological Sciences , 278 , 2528–2536.
Stewart, J. R., Lister, A. M., Barnes, I., & Dalén, L. (2010). Refugia
revisited: Individualistic responses of species in space and
time. Proceedings of the Royal Society B: Biological
Sciences , 277 , 661–671.
Sukumaran, J., & Holder, M. T. (2010). DendroPy: A Python library for
phylogenetic computing. Bioinformatics , 26 , 1569–1571.
Swofford, D. L. (2003). PAUP*. Phylogenetic Analysis Using Parsimony
(*and Other Methods). Version 4. Sunderland, MA: Sinauer Associates.
Telfer, P. T., Souquiere, S., Clifford, S. L., Abernethy, K. A.,
Bruford, M. W., Disotell, T. R., … Wickings, E. J. (2003). Molecular
evidence for deep phylogenetic divergence in Mandrillus sphinx .Molecular Ecology , 12 , 2019–2024.
Templeton, A. R. (2001). Using phylogeographic analyses of gene trees to
test species status and processes. Molecular Ecology, 10,779–791.
Terborgh, J. (1973). On the notion of favorableness in plant
ecology. The American Naturalist , 107 , 481– 501.
Terhorst, J., & Song, Y. S. (2015). Fundamental limits on the accuracy
of demographic inference based on the sample frequency
spectrum. Proceedings of the National Academy of Sciences,
USA , 112 , 7677– 7682.
Tolley, K. A., Alexander, G. J., Branch, W. R., Bowles, P., & Maritz,
B. (2016). Conservation status and threats for African
reptiles. Biological Conservation , 204 , 63–71.
Tosi, A. J. (2008). Forest monkeys and Pleistocene refugia: A
phylogeographic window onto the disjunct distribution of theChlorocebus lhoesti species group. Zoological Journal of
the Linnean Society , 154 , 408–418.
Vanzolini, P.E. & Williams, E.E. (1970). South American anoles:
geographic differentiation and evolution of the Anolis
chrysolepis species group (Sauria, Iguanidae). Arquivos de
Zoologia, São Paulo , 19 , 291–298.
Vanzolini, P.E. (1973). Paleoclimates, relief, and species
multiplication in equatorial forests. In Meggers, B. J., Ayensu, E. S.,
& Duckworth, W. D. (Eds.) Tropical Forest Ecosystems in Africa
and South America: A Comparative Review . (pp. 255–258). Washington D.
C.: Smithsonian Press.
Vitorino, L. C., Lima-Ribeiro, M. S., Terribile, L. C., & Collevatti,
R. G. (2016). Demographical history and palaeodistribution modelling
show range shift towards Amazon Basin for a Neotropical tree species in
the LGM. BMC Evolutionary Biology , 16 , 213–228.
Wallace, A. R. (1853). A Narrative of Travels on the Amazon and
Rio Negro . London, UK: Reeve.
Wallace, A. R. (1878). Tropical Nature, and Other Essays . London,
UK: Macmillan and Company.
Warren, D. L., & Seifert, S. N. (2011). Ecological niche modeling in
Maxent: The importance of model complexity and the performance of model
selection criteria. Ecological Applications , 21 , 335–342.
Weir, J. T. (2006). Divergent timing and patterns of species
accumulation in lowland and highland neotropical
birds. Evolution , 60 , 842–855.
Weir, J. T., & Schluter, D. (2007). The latitudinal gradient in recent
speciation and extinction rates of birds and
mammals. Science , 315 , 1574–1576.
White, F. (1981). The history of the Afromontane archipelago and the
scientific need for its conservation. African Journal of Ecology ,19 , 33–54.
Whittaker, R. J., Nogués‐Bravo, D., & Araújo, M. B. (2007).
Geographical gradients of species richness: A test of the water‐energy
conjecture of Hawkins et al. (2003) using European data for five
taxa. Global Ecology and Biogeography , 16 , 76–89.
Wiens, J. J. & Donoghue, M. J. (2004). Historical biogeography, ecology
and species richness. Trends in Ecology and
Evolution , 19 , 639–644.
Wiens, J. J., Sukumaran, J. S., Pyron, R. A. & Brown, R. M. (2009).
Evolutionary and biogeographic origins of high tropical diversity in old
world frogs (Ranidae). Evolution, 64 , 1217–1231.
Wieczorek, A. M., Drewes, R. C., & Channing, A. (2000). Biogeography
and evolutionary history of Hyperolius species: application of
molecular phylogeny. Journal of Biogeography , 27 ,
1231–1243.
Wüster, W., Chirio, L., Trape, J. F., Ineich, I., Jackson, K.,
Greenbaum, E., … Hall, C. (2018). Integration of nuclear and
mitochondrial gene sequences and morphology reveals unexpected diversity
in the forest cobra (Naja melanoleuca ) species complex in Central
and West Africa (Serpentes: Elapidae). Zootaxa , 4455 ,
68–98.
Yannic, G., Pellissier, L., Ortego, J., Lecomte, N., Couturier, S.,
Cuyler, C., … Cote, S. D. (2014). Genetic diversity in caribou
linked to past and future climate change. Nature Climate Change ,4 , 132–137.
Zimkus, B. M., Lawson, L. P., Barej, M. F., Barratt, C. D., Channing,
A., Dash, K. M., … & Gvoždík, V. (2017). Leapfrogging into new
territory: How Mascarene ridged frogs diversified across Africa and
Madagascar to maintain their ecological niche. Molecular
Phylogenetics and Evolution , 106 , 254–269.
Zimkus, B. M., Rödel, M. O., & Hillers, A. (2010). Complex patterns of
continental speciation: molecular phylogenetics and biogeography of
sub-Saharan puddle frogs (Phrynobatrachus ). Molecular
Phylogenetics and Evolution , 55 , 883–900.