Demenou Et Al.2016 Journal-of-Biogeography

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Origin and history of the Dahomey Gap separating West and Central African
rain forests: Insights from the phylogeography of the legume tree
Distemonanthus benthamianus
Article in Journal of Biogeography · January 2016

DOI: 10.1111/jbi.12688
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1 Original article
2
3 Origin and history of the Dahomey Gap separating West and Central
4 African rain forests: insights from the phylogeography of the legume tree
5 Distemonanthus benthamianus.
6
7 Boris B. DEMENOU1*, Rosalía PIÑEIRO2 & Olivier J. HARDY1
8 1 Evolution Biologique et Ecologie, Université Libre de Bruxelles, Faculté des Sciences, CP160/12, Av.
9 F. D. Roosevelt 50, BE-1050 Brussels, Belgium,

2 Evolutionary Genomics, Centre for Geogenetics -
10 Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
11
12 * Correspondence : Boris Demenou, Evolution Biologique et Ecologie, Université
13 Libre de Bruxelles, Faculté des Sciences, CP160/12, Av. F. D. Roosevelt 50, BE-1050
14 Bruxelles, Belgique;
15 E-mail : bdemenou@ulb.ac.be
16
17 SRH: African forest tree phylogeography in Dahomey Gap
18
19 Word count: 7000
20 Number of journal page: 12
21
1
Journal of Biogeography

22 ABSTRACT
23 Aim: Understand the origin of the forest flora currently found in the Dahomey Gap
24 (DG), a 200 km wide forest-savanna mosaic separating the West African and Central
25 African rain forest blocks. More specifically, using a widespread rain forest tree
26 species, Distemonanthus benthamianus (Fabaceae), we will test the hypothesis that
27 the DG populations are remnants of a population dating back from the African
28 Humid Period of the Holocene, when West African and Central African rain forests
29 were supposedly connected.
30 Location: Tropical forests of Upper Guinea (West Africa) and Lower Guinea
31 (Atlantic Central Africa) and the forest-savanna mosaic of the DG extending from
32 eastern Ghana to Benin.
33 Methods: 429 D. benthamianus samples from West to Central Africa were
34 genotyped with 11 nuclear microsatellite markers. After detecting geographically
35 coherent gene pools, their genetic diversity and differentiation were estimated and
36 their demographic histories were inferred using coalescent simulations and
37 Approximate Bayesian Computation (ABC) tests.
38 Results: Five parapatric gene pools were identified: three in Lower Guinea, one in
39 Upper Guinea and one in the DG. ABC tests indicate that the DG gene pool probably
40 originates from the admixture of adjacent Upper and Lower Guinean gene pools, with
41 a higher contribution from Upper Guinea, at a timeframe consistent with the early
42 Holocene (around 13-7 ka). The lower genetic diversity documented in the DG could
43 result from a founder effect and/or from a demographic decline consistent with the
44 Holocene climatic pejoration documented around 3 ka.
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45 Main conclusions: This phylogeographical study inferring the history of the DG
46 populations of D. benthamianus is globally consistent with palaeovegetation data
47 that suggest that the forest flora of the DG might be essentially relicts of the early
48 Holocene period when the Guineo-Congolian forest reached its maximum
49 geographical distribution.
50
51 Kew words: African Humid Period, Dahomey Gap, demographic tests, Holocene,
52 nuclear microsatellites, phylogeography, Quaternary climate changes, rain forest
53
3

54 Introduction
55 The African Guineo-Congolian phytochoria constitutes the second largest block of
56 rain forest on earth. White (1979) defined it as a phytogeographic centre of species
57 endemism (comprising ca. 8,000 plant species of which ca. 80% are endemic), and
58 subdivided it into three sub-centres (Fig. 1): Upper Guinea (hereafter UG), Lower
59 Guinea (hereafter LG), and Congolia. UG corresponds to the West African rain forest
60 extending from Sierra Leone to Ghana. LG corresponds to the western part of the
61 Central African rain forest, from southern Nigeria to the western part of the Republic
62 of Congo and of the Democratic Republic of Congo.
63 UG and LG are separated by the so-called Dahomey Gap (hereafter DG), a ca. 200 km
64 wide corridor dominated by open vegetation in Benin, Togo and eastern Ghana. The
65 DG is characterized by a decline in annual precipitation from more than 2000 mm in
66 the adjacent rain forest areas to about 1000-1200 mm in the DG. The DG vegetation
67 is constituted mainly of savanna, but also of gallery forests and fragments of swamp
68 forest and dense semi-deciduous forest. We hypothesize that these forest fragments
69 would be legacies of past climatic conditions that maintained a rain forest over the
70 DG in the early Holocene.
71 The important climatic oscillations of the Pleistocene, especially from 1.05 Ma, have
72 largely influenced the history of the Africa rain forest (Dupont et al., 2001; Miller &
73 Gossling, 2014). Palynological records and oxygen isotope stratigraphy show that
74 equatorial Africa became dryer and cooler during glacial periods, exhibiting a sharp
75 reduction in rain forest species in favour of grass species characteristic of open
76 vegetation (Maley, 1996; Dupont et al., 2000; Miller & Gossling, 2014). Hence,
77 during the glacial periods, savannas expanded and rain forests withdrew and became
4

78 fragmented, so that the DG was dominated by open vegetation. During the
79 interglacial periods the rain forest extended up, possibly to a distribution slightly
80 greater than today, as was the case during the Holocene Humid Period, c. 9,000-
81 5,500 yr BP, where the Guineo-Congolian rain forest presumably formed a single
82 block because the DG became forested (Salzmann & Hoelzmann, 2005).
83 Nevertheless, in West Africa the Holocene Humid Period might have been more
84 humid than previous interglacial periods (Miller & Gossling 2014), so that it is not
85 guaranteed that the DG became forested during previous interglacials. During the
86 late Holocene, a climatic pejoration characterized by less rainfall and more
87 seasonality affected most of the African rain forest area c. 4-2.5 ka (Marchant &
88 Hooghiemstra, 2004). The opening of the DG, well documented since 4.5-3.4 ka
89 (Salzmann & Hoelzmann, 2005), correlates with this dry period. In addition, human
90 activities may have accelerated the deforestation process (Assi-Kaudjhis et al., 2010).
91 The origin of the forest-dwelling flora of the DG is uncertain as it may correspond to
92 recent migrations from the main forest blocks or to remnants of the last period where
93 the DG was forested. In the latter case, if we look further in time, floristic elements
94 may originate from one of the main forest blocks that expanded to cover the DG or
95 from forest remnants during one of the previous periods where the DG was opened.
96 New insights into these questions could be provided by phylogeographical and
97 population genetics studies, which can detect past events of population
98 fragmentation, colonization, or demographic changes and date them using coalescent
99 simulations (Piñeiro et al., in prep.). A few recent genetic studies performed on
100 tropical rain forest tree species (e.g. Budde et al., 2013; Daïnou et al., 2014; Duminil
101 et al., 2013) revealed phylogeographical breaks separating differentiated gene pools
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102 in most species, suggesting past forest fragmentation (reviewed in Hardy et al., 2013).
103 Piñeiro et al. (in prep.) and Duminil et al. (2015) furthermore reported signatures of
104 past demographic changes occurring during the late Pleistocene. These studies
105 focussed on forests from LG and sometimes UG but none inferred the origin of forest
106 species in the DG.
107 To fill this gap, this paper focuses on a tree species, Distemonanthus benthamianus,
108 which is characteristic of UG and LG rain forests but also occurs in the DG, in isolated
109 forest fragments and gallery forests. Using nuclear microsatellite markers, Debout et
110 al. (2011) already documented three gene pools in LG. Here, using additional samples
111 from UG and the DG and new microsatellite loci, we address the following questions:
112 (i) Do UG and DG samples form additional gene pools? (ii) How do gene pools
113 compare in terms of genetic diversity and differentiation? (iii) Are there distinct
114 signatures of past demographic changes (decline, expansion or bottleneck) in each
115 gene pool and, if so, when did they take place? (iv) Does the DG population originate
116 from UG and/or LG and when did it separate from its ancestral population(s)? Under
117 the hypothesis that the forest fragments currently found in the DG originate from the
118 forest extension that occurred during the Humid Holocene period 9-4,5 ka, and are
119 relics of the recent Holocene climate pejoration (starting c. 4 ka), we can expect that
120 current DG populations of D. benthamianus (i) may come exclusively from UG or
121 from LG, or may result from a population admixture of UG and LG populations after
122 their the expansion during the Humid Holocene period, and (ii) may have suffered
123 from a decline in population size with a loss of diversity due to genetic drift.
124
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125 MATERIAL AND METHODS
126 Study taxon and sampling
127 Distemonanthus benthamianus Baillon (Caesalpinioideae) is a tropical tree widely
128 and sparsely distributed throughout the rain forests of LG and UG. It is also found in
129 the DG, mainly in the dense semi-deciduous forest fragments but also in mosaics of
130 fields and plantations, when it is spared during deforestation. It is a big tree up to 40
131 m height and a trunk diameter up to 1.2 m. Being a light-demanding species, its
132 natural regeneration in mature forest is very limited with few saplings observed in
133 closed-canopy forests (J-L Doucet, pers. comm.), while it regenerates well in canopy
134 openings. Trees grow on average between 3 and 4 mm in diameter annually. Flowers
135 are hermaphroditic but self-fertilization is rare and c. 60% of the pollen disperse
136 >1000 meters in closed canopy forest (B. Delaide & O.J. Hardy, unpublished). The
137 pollinators are not documented but the size and structure of flowers suggest that the
138 African bee (Apis mellifera scutellata) could be an important pollinator, known to be
139 able to carry pollen over a few kilometers in open landscapes (Dick, 2001). Fruiting
140 begins at a diameter at breast height of 20 cm, but only trees with a diameter >40 cm
141 fruit regularly. The fruit is a flat indehiscent pod measuring 10 cm by 3.5 cm which is
142 wind-dispersed up to 50-100 m, though dispersal over at least 500 m can sometimes
143 occur (B. Delaide & O.J. Hardy, unpublished). Mature pods are predated by parrots
144 (Psittacus erithacus; White & Abernethy, 1996).
145 We used samples (leaves or bits of cambium dried in silica gel) from 429
146 georeferenced (GPS) individuals of D. benthamianus in 12 different countries from
147 Guinea to Congo, specifically, 336 samples from LG (including 80 samples used by
148 Debout et al., 2011), 60 from UG and 33 from DG (Fig. 1). Our sampling covers well
7

149 the whole known distribution of the species but only a few individuals were available
150 from Guinea-Conakry, Liberia and Sierra Leone.
151
152 DNA extraction and nuclear microsatellites genotyping
153 Total DNA was extracted using the NucleoSpin plant kit (Macherey-Nagel) following
154 the manufacturer’s instructions. Eleven polymorphic nuclear microsatellite (nSSR)
155 loci isolated for D. benthamianus and named dis054, dis069s, dis092, dis103, dis112,
156 dis116, dis125, dis127, dis130, dis138 and dis140 were used. They include 8 loci
157 characterized by Debout et al. (2011) and three additional loci described in this study
158 (Table S1, Appendix S1). Amplification was performed following the protocol
159 described in Appendix S1. When there was no trace of PCR amplification product for
160 a given locus while alleles were clearly visible at the other loci amplified in the same
161 PCR mix, an individual was considered to be homozygote for a null allele and coded
162 as such. Six nSSR loci, Dis054, Dis112, Dis130, Dis140, Dis103 and Dis116, were
163 coded as missing data or null alleles in 5, 4, 24, 8, 8 and 39 individuals, respectively.
164
165 Identification of genetic discontinuities
166 Gene pools were inferred using the individual-based Bayesian genetic assignment
167 method implemented in STRUCTURE 2.3.4 (Falush et al., 2003) using the admixture
168 and independent allele frequencies models, with no a priori partitioning of
169 individuals into groups. K=1 to 10 gene pools were tested with runs of 106 generations
170 (burnin period of 105 generations) and 10 runs at each K. In order to compute and
171 plot the mean and variance of the log-likelihood of the data, Ln P(D), against the
172 range of K values, we used the online tool STRUCTURE HARVESTER (Earl &
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173 vonHoldt, 2012). We determined the best number of gene pools K as the one where
174 Ln P(D) starts reaching a plateau as K increases. Individuals were considered as
175 admixed when their probability of assignment to the most likely gene pool was below
176 0.7.
177
178 Diversity and differentiation parameters: detecting phylogeographical
179 signal
180 Diversity and differentiation parameters for nSSRs (Table 1) were computed for each
181 Bayesian gene pool using unadmixed individuals only (243 in LG, 58 in UG, and 33 in
182 DG). Deviation from Hardy–Weinberg equilibrium (HWE) was tested for each locus
183 in each gene pool with SPAGeDi 1.5 (Hardy & Vekemans, 2002). Null allele
184 frequencies were estimated with INEst 1.0 (Chybicki & Burczyk, 2009), which also
185 provided corrected estimates of the inbreeding coefficient (Fi).
186 For each gene pool, the following multilocus genetic diversity parameters were
187 computed with SPAGeDi 1.5: total number of alleles (A0), allelic richness (RS),
188 expected heterozygosity (He). The private allelic richness (Rpriv) was computed with
189 the rarefaction procedure implemented in HP-RARE 1.1 (Kalinowski, 2005),
190 considering random resampling of 60 gene copies per gene pool and locus to
191 compute a mean number of private alleles per gene pool (Table 1). Differentiation
192 between pairs of gene pools was computed using FST and phylogeographic signal was
193 checked by computing RST, which is based on allele sizes and expected to be larger
194 than FST if mutations (under stepwise mutation model) have contributed to
195 differentiation (Hardy et al., 2003).
196
9

197 Demographic history of each gene pool
198 In order to infer processes such as population fragmentation, gene flow and
199 expansion/bottleneck, phylogeographical data can be treated using model-based
200 analyses (Pelletier & Carstens, 2014). The demographic history of each gene pool was
201 investigated in two steps using coalescent simulations and Approximate Bayesian
202 Computation (ABC) tests implemented with DIYABC 2.0.4 (Cornuet et al., 2014).
203 ABC is a bayesian approach in which the posterior distributions of the model
204 parameters are determined by replacing the computation of the likelihood
205 (probability of observed data given the values of the model parameters) by a measure
206 of similarity between observed and simulated data through the use of summary
207 statistics. We first tested demographic evolution scenarios for each of the five gene
208 pools detected (see results) to identify the most likely demographic event that had
209 shaped its genetic structure, considering four models with broad time priors (A.
210 DEMOGRAPHIC EVENT MODELS, Fig. 2): (a1) constant population size, (a2)
211 population decline, (a3) population expansion, (a4) population bottleneck followed
212 by expansion (hereafter “population bottleneck” for short). To have a global
213 assessment of possible demographic changes without a priori hypotheses on the
214 timing of these changes, we choose broad priors from 1 Ma to the present, hence
215 including several glacial cycles of the Pleistocene. In doing so, we implicitly assumed
216 that genetic signatures within gene pools reflect demographic changes occurring after
217 that gene pools diverged in in isolation. Subsequently, once the most likely
218 demographic scenario was identified, temporal priors were narrowed down in order
219 to test specific time scales (B. NARROW TIME MODELS, Fig. 2). Here, the choice of
220 time priors for demographic expansion, bottleneck or decline events were guided by
10

221 current palynological and palaeoclimatic knowledge of tropical African rain forests
222 (e.g., Dupont et al., 2001), assuming that population sizes could increase during
223 interglacial periods and decrease during glacial periods or the Holocene climatic
224 pejoration. More specifically, for the DG gene pool where a population decline was
225 detected (see results), we tested: (b1) null model of constant population size, (b2)
226 decline before the Penultimate Glacial Period [Pre-PGP, 1Ma - 190 ka], (b3) decline
227 during the Penultimate Glacial Period [PGP, 190-140 ka], (b4) decline during the Last
228 Glacial Period [LGP, 70-20 ka], (b5) decline during the climatic pejoration of the
229 recent Holocene [HCP, 4- 2ka]. For the three LG gene pools and the UG gene pool
230 where demographic expansion or bottleneck were detected (see results), we tested:
231 (b1) null model of constant population size, (b2) bottleneck and/or expansion before
232 the Penultimate Glacial Period [Pre-PGP, 1Ma - 190 ka], (b3) bottleneck during the
233 Penultimate Glacial Period [PGP, 190-140 ka] and/or expansion during the
234 Penultimate Deglaciation [PD, 130-120 ka]; (b4) bottleneck during the Last Glacial
235 Period [LGP, 70-20 ka] and/or expansion during the Last Deglaciation [LD, 12-10
236 ka]; and (b5) bottleneck during the climatic pejoration of the recent Holocene [HCP,
237 4- 2ka] and/or subsequent expansion [3-1 ka].
238
239 Origin of the Dahomey Gap gene pool
240 DIYABC was also used to infer the origin of the DG gene pool, considering its
241 relationship with the geographically adjacent gene pools in UG and LG (“UG” and
242 “wLG” gene pools, see results). Six possible scenarios were built (C: ORIGIN
243 MODELS; Fig. 3): (c1) DG gene pool originates from UG; (c2) DG gene pool
244 originates from LG; (c3) all the three gene pools diverged simultaneously from an
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245 ancestral population; (c4) all the three gene pools diverged simultaneously from an
246 ancestral population followed by a decline of the DG population size; (c5) DG gene
247 pool diverged first with an ancestral population leading to the UG and LG gene pools,
248 and (c6) DG gene pool results from the admixture of the two other gene pools. Here
249 we used broad priors for all events of populations split, admixture or demographic
250 changes between 1 Ma to present.
251 After choosing the most likely scenario (c6: admixture, see results) and integrating
252 the results of models A and B (bottleneck in PGP in the western LG gene pool and the
253 UG gene pool, recent decline in DG gene pool, see results) we tested again six
254 scenarios with narrow time intervals to infer when the admixture occurred and
255 whether the population decline was concomitant with admixture due to founder
256 effects or occurred after admixture in a period of forest decline (D: ADMIXTURE
257 MODELS): (d1) formation of DG by admixture before the PGP [Pre-PGP, 1Ma - 190
258 ka] with decline of the population size later in the PGP [PGP, 190-140 ka]; (d2)
259 formation of DG by admixture with small effective population size in the interglacial
260 period before PGP [Pre-PGP, 1Ma - 190 ka]; (d3) formation of DG by admixture
261 before the LGP with decline of the population size later in the LGP [LGP, 70-20 ka];
262 (d4) formation of DG by admixture with small effective population size (actual size)
263 in the last interglacial [LIG, 130-115 ka]; (d5) formation of DG by admixture during
264 the Holocene humid period with decline of the population size later in the Holocene
265 climatic pejoration [HCP, 4-2 ka] and (d6) formation of DG by admixture with small
266 effective population size (actual size) during the African Holocene humid period
267 [AHP, 10-4 ka].
268
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269 Summary statistics, setting of priors, and robustness tests in ABC
270 analyses
271 Summary statistics provided by DIYABC 2.0.4 were used (Appendix S2). A million
272 simulations were performed for each scenario. We assumed a mean generation time
273 of 100 yr for this species. Given that the mean generation time of most tropical tree
274 species seems to range from 100 yr to 200 yr (Baker et al., 2014), we also performed
275 tests assuming a mean generation time of 200 yr, but as results regarding scenario
276 testing proved to be robust, they are not shown hereafter.
277 To perform the DIYABC analysis, setting priors is essential for credible results. As
278 part of this work, outside the range of well-fixed time priors based on models and
279 scenarios to be tested, the choice of values of the priors for the effective population
280 sizes remain problematic. In line with recent studies on African rain forest tree
281 species (Budde et al., 2013; Piñeiro et al., in prep.) the A-B-C-D models described
282 above were based on Ne values distributed uniformly between 1,000 and 50,000 for
283 phases of large population size, and N1 ranging uniformly between 10 and 500 for
284 phases of small population size in case of bottleneck or decline scenarios.
285 To assess the robustness of our results, we tested population size priors reflecting less
286 intense bottlenecks in models A and B with Ne ranging uniformly between 10 and
287 10,000, and N1 between 10 and 2,000 (Ne>N1).
288
289 RESULTS
290 Inferred gene pools
291 The Bayesian clustering algorithm showed that the log-likelihood of the data
292 increased with the number of gene pools, K, until a plateau was reached at K= 5. The
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293 hierarchical Evanno’s delta K method (Evanno et al., 2005) indicated that the most
294 likely numbers of gene pools were K= 2 and K=5.
295 At K=2, the first gene pool gathers all the populations from UG (from Sierra Leone to
296 Ghana) and DG (Eastern Ghana to the east of Benin), and the second gene pool, all
297 the populations of LG from the Congo to central Nigeria (Fig. 4). At K=5 we observe
298 three closely related gene pools in LG (“Western LG” (wLG) gene pool; “Northern LG”
299 (nLG) gene pool; and “Southern LG” (sLG) gene pool), one gene pool in UG (“Upper
300 Guinean” (UG) gene pool), and one grouping populations from the DG (“Dahomey
301 Gap” (DG) gene pool, Fig. 1). Given the clear geographic pattern obtained we will
302 hereafter keep the clustering solution for K =5. However, it is worth noting that at
303 K=3, we observed that UG and DG form distinct gene pools, while all LG samples
304 remain in a single gene pool.
305 Pairwise FST differentiation among the five gene pools revealed that the three LG gene
306 pools were closely related (FST between 0.039 and 0.094) and well differentiated
307 from the DG and UG gene pools (FST ranging from 0.173 to 0.291). The DG gene pool
308 was the most differentiated (FST =0.204 and 0.173 with UG and wLG, respectively).
309 RST values, which account of microsatellite allele sizes, showed a similar trend as FST
310 but with larger values indicating phylogeographical signals that were significant
311 (p<0.01) between the nLG gene pool and the DG and UG gene pools (allele size
312 permutation tests; Hardy et al., 2003).
313
314 Variation of genetic diversity among regions
315 Gene pools from forested areas, in general, displayed higher genetic diversity (Rs
316 ranging from 5.41 to 8.06, He from 0.52 to 0.69) and private alleles richness (Rpriv
14

317 ranging from 0.47 to 1.19 private alleles) than the DG gene pool (Rs =3.90, He =0.55,
318 Rpriv=0.20; Table 1). However, DG, despite low allelic richness, exhibits a similar He
319 than some forest gene pools (sLG: 0.54 and UG: 0.52). We note a low inbreeding
320 coefficient for all gene pools (Fi<0.1) after correcting for null alleles. In general, most
321 of the loci were in HWE in all forest gene pools (except for dis130 in wLG, nLG and
322 sLG gene pools; dis130, dis069, dis116 and dis140 in UG gene pool). In the DG, six
323 loci, dis054, dis92, dis130, dis069, dis116 and dis140 exhibited strong deficits in
324 heterozygotes which might be related to the presence of null alleles (frequency
325 between 0.097 and 0.252, Table S2 in Appendix S1) but also to a higher
326 substructuring of the genetic diversity in the DG where local populations are often
327 distant from each other.
328
329 Inference of demographic events within each gene pool
330 The tests of DEMOGRAPHIC EVENT MODELS with broad time priors revealed high
331 support for the population bottleneck scenario for the wLG (posterior probability of
332 79%) and sLG (87%) gene pools (Table 2A). The nLG gene pool showed a similar
333 support for bottleneck (42%) and population size constancy (41%). In contrast, high
334 support was found for a population decline in the DG gene pool (87%). In the UG
335 gene pool, the test also supported a bottleneck (59%) or an expansion scenario
336 without bottleneck (41%). Population decline scenarios were rejected for all gene
337 pools from forested areas, and scenarios of expansion showed low but not negligible
338 posterior probabilities for the LG gene pools (7%, 17% and 10% respectively for wLG,
339 nLG and sLG).
15

340 The power to select the correct scenario was high (99% and 89% respectively) for
341 gene pools DG and nLG and moderate (60-66%) for the other ones. The mean bias
342 was below 0.5 for several parameters and around 0.8 for the other ones, while factor
343 2 was below 1 for all parameters and gene pools (Table S3, Appendix S3), indicating
344 good confidence in parameters estimates.
345
346 The NARROW TIME MODELS tests clearly rejected scenarios for demographic
347 events occurring before the penultimate glacial period (PGP) for all gene pools except
348 UG (posterior probability of 37%). These tests showed stronger support for
349 demographic events occurring from the PGP in forested areas (90%, 53%, 91% and
350 63% respectively in wLG, nLG, sLG and UG gene pools; Table 2B). However, in the
351 DG gene pool, a decline during the last glacial period (LGP, 55%) or the Holocene
352 (40%) received highest support. Confidence in scenario choice was high for all gene
353 pools (> 91%) (Table 2B). The relative mean bias was low (0 for several parameters
354 and <0.4 for all the rest) and factor 2 ranged from 0.8 to 1 for all parameters and
355 gene pools, revealing a good accuracy of parameter estimates (Table S3, Appendix
356 S3).
357
358 Influence of the priors on population effective sizes
359 The use of the second set of priors on effective sizes influenced significantly the
360 posterior probabilities of scenarios, times, mutation rates and, obviously, effective
361 sizes (Table S4, Appendix S3). However, it did not affect the choice of the most likely
362 scenarios, which appears robust (Table 2A). Nevertheless, we observe non negligible
16

363 changes in the posterior probabilities of each scenario, particularly when inferring the
364 time scale of demographic events (Table 2B).
365
366 Origin of the Dahomey Gap population
367 The ORIGIN MODELS tests regarding the origin of the DG gene pool showed a
368 relatively high support for the admixture scenario (scenario c6: posterior probability
369 of 60%) and low probabilities for the other scenarios, especially the one assuming a
370 LG origin (scenario c2: 1%), or a basal origin (scenarios c5: 0%, c3: 1% ; Table 2C).
371 The posterior distribution of scenario c6 for population mixture indicates r =29 %
372 (i.e. DG population would result from 29% of gene pool wLG and 71 % of gene pool
373 UG). This is consistent with the higher support for the scenario c1 (UG origin, 27%)
374 compared to c2 (wLG origin, 1%). Posterior parameters estimation under the most
375 likely scenario (c6) revealed that admixture time estimates is 142 [21.1-492]
376 generations (mean and 2.5–97.5% quantiles of the posterior distribution respectively,
377 Appendix S3). The confidence of scenario choice is 72%.
378
379 Furthermore, when we compare the ADMIXTURE MODELS with specific time scales
380 for a population decline occurring after admixture (scenarios d1, d3, d5) or
381 simultaneously with the admixture event (scenarios d2, d4, d6), we observed high
382 support for scenarios d5 and d6 involving a decline during the Holocene climatic
383 pejoration, with somewhat higher support for the scenario d6 (51%) than d5 (39%;
384 Table 2D), which suggests the formation of the DG population by admixture with
385 small populations size (actual size). Note that our results rejected all other
386 hypotheses of formation of the DG population involving a decline in size before the
17

387 Holocene (PGP and LGP: scenarios d1, d2, d3 and d4 close to zero). The confidence of
388 scenario choice (d6) is 73%.
389
390 DISCUSSION
391 The Dahomey Gap is a band of open vegetation bordered by two Guineo-Congolian
392 forest blocks, a pattern explained by current rainfall gradients. Nevertheless, rain
393 forest plant species still survive in scattered microhabitats throughout the DG,
394 questioning when and how these species appeared there. Palaeovegetation data
395 indicate that the DG was forested during the Humid Holocene Period while it was
396 probably covered by an open vegetation during glacial periods of the Pleistocene, as it
397 is now since c. 4000 years (Salzmann & Hoelzmann, 2005). The forest flora of the DG
398 may thus be relict of the time the DG was forested, in which case the forest may result
399 from the postglacial expansion of Lower Guinean and/or Upper Guinean forests, but
400 it may also have arisen through more recent dispersal.
401 To address these biogeographical questions, the present study is the first to
402 investigate the history of the DG vegetation using genetic data and state-of-the-art
403 methodology for quantitative demographic history inference. It reveals contrasted
404 signals of demographic history of the Guineo-Congolian legume tree, D.
405 benthamianus, within forested and non-forested areas.
406
407 Genetic discontinuities among D. benthamianus populations
408 Our phylogeographical study of the tropical rain forest tree D. benthamianus
409 detected five gene pools with a clear geographical pattern (Fig. 1). One potential
410 explanation for the existence of several gene pools in the range of one species
18

411 displaying a rather continuous distribution is the presence of (past) barriers to gene
412 flow, as suggested by Debout et al. (2011).
413 In west African forests, only one gene pool was observed, suggesting a genetic
414 homogeneity. A similar result was obtained on other African forest species, like
415 Pentadesma butyracea (Ewedje, 2012) and Milicia excelsa (Dainou et al., 2014),
416 suggesting that the West African forest has not been deeply fragmented following
417 past climate changes. However, the absence of detected discontinuity may be due to
418 an insufficient sampling in the western end of the Upper Guinean forest and also to
419 the limited number of forest species studied so far.
420 In central Africa, we obtained three gene pools with limited differentiation (FST<0.1),
421 as observed by Debout et al. (2011). Within inland regions a genetic discontinuity
422 separated northern LG (Cameroon) and southern LG (Gabon) gene pools, and a
423 clearly defined western LG gene pool contained mostly individuals from coastal
424 regions of Gabon, Cameroon and Nigeria, but also encompassed a few individuals
425 with further inland location. Contrary to our results, Debout et al. (2011) reported a
426 Cameroon gene pool ranging westwards to the coast and a western gene pool limited
427 to Gabon. This difference probably results from the limited sampling in western
428 Cameroon (and none from Nigeria) in the study of Debout et al.(2011). This shows
429 the importance of a sufficient sampling for a good resolution of phylogeographical
430 pattern.
431
432 High distinctiveness of the relict populations of the Dahomey Gap
433 The DG gene pool, which regroups individuals from south east Ghana, Togo and
434 Benin, shows a high genetic differentiation from both western (RST = 0.208) and
19

435 central forest gene pools (RST between 0.212 and 0.345), despite the absence of a real
436 physical barrier. Contrary to the situation in UG or LG, D. benthamianus in the DG
437 forms scattered and probably isolated populations because open vegetation types
438 dominate the landscape. Despite the large dispersal potential of pollen of this species
439 in dense forests (B. Delaide and O.J. Hardy, unpublished), gene flow seems to be
440 limited among the scattered populations of the DG because the FST between these
441 populations increases faster with geographic distance than the FST between
442 populations from forested areas (results not shown). However, the recognition of a
443 single gene pool encompassing individuals from the DG indicates that the DG
444 populations were more connected in the past.
445 Our results also suggest that either there is no gene flow between the DG and
446 adjacent populations or that gene flow, if it exists, is too rare or recent to be traced by
447 our data. Indeed, if the DG populations were connected to the adjacent forest gene
448 pools through continuous gene flow, or if they resulted from the contemporaneous
449 admixture of these gene pools, the clustering algorithm would have detected within
450 the DG a rather continuous gradient of genetic admixture between the UG and LG
451 gene pools rather than a distinct gene pool. As current physical barriers to gene flow
452 cannot explain the origin of the genetic differentiation between the DG gene pool and
453 those of forest areas, nor the genetic homogeneity between isolated populations of the
454 DG, these patterns should be related to past climate changes.
455 We observed a low genetic diversity in the DG gene pool comparatively to the UG and
456 LG gene pools, a result consistent with those obtained in Pentadesma butyracea in
457 DG (Ewedje, 2012). Interestingly, the decay of diversity in DG is much more
458 pronounced for allelic richness than for He, a situation expected after a recent
20

459 increase in genetic drift which affects more rapidly the allelic richness than He. In
460 addition, the number of private alleles is also lower in the DG. This low diversity may
461 be due to the small size of the populations as seen currently in the DG, and/or to
462 founder effects that may have occurred at the formation of the DG population.
463 Human action in the recent past, reducing furthermore the DG populations, might
464 also contribute to the limited genetic diversity. In fact, human impact might explain
465 the absence of D. benthamianus in southwestern Benin and southeastern Togo.
466
467 Admixture origin and decline of DG population during the Holocene
468 The ABC tests on the origin of the DG populations of D. benthamianus show great
469 support for the scenario of admixture between UG and western LG populations, with
470 a higher contribution from UG (71%). The latter is also supported by the results of the
471 Bayesian clustering analysis for K = 2, which places all DG samples with the West
472 African forest samples (Fig. 4). An admixture origin of the DG would also explain its
473 low number of private alleles. Ancient admixture is the best explanation for the origin
474 of the DG gene pool since no recent gene flow was detected between DG and forested
475 areas. The case of D. benthamianus differs from the pattern obtained on the tree
476 Pentadesma butyracea where DG populations would originate only from UG
477 (Ewedje, 2012).
478 If admixture occurred relatively recently, it implies that the assumption that each
479 gene pool was isolated when performing the first demographic tests is violated.
480 Hence, the timing of the population decline (Table 2B) inferred in the DG (i.e. LGP or
481 Holocene) must be interpreted with caution. Nevertheless, the tests of the different
482 admixture models integrating simultaneously gene pools divergence, admixture and
21

483 demographic changes (Table 2C), definitively support the formation of the current
484 DG population during the humid Holocene period, around 9-5 ka. The colonization of
485 the DG could have occurred with small population sizes (51% support) or with large
486 populations that declined afterwards towards 4-2 ka during the Holocene climatic
487 pejoration (39% support). Both hypotheses would explain the low diversity of the DG
488 gene pool, respectively through initial founder events or through subsequent high
489 genetic drift, but our data cannot disentangle them.
490
491 Consistency between genetic and paleoenvironmental reconstructions
492 The formation of the D. benthamianus population in the DG during the early
493 Holocene followed by a population size decline is consistent with palaeovegetation
494 data acquired in the DG (Sélé Lake, Nokoué lake and others core: Tossou, 2002;
495 Salzmann & Hoelzmann, 2005) and around in lake Bosumtwi in Ghana (Talbot et al.
496 1984; Miller & Gossling, 2014), lake Barombi Mbo in Cameroon (Maley & Brenac,
497 1998), and the Gulf of Guinea (Dupont et al., 2000).
498 By contrast, in forested areas, ABC demographic tests indicate a bottleneck followed
499 by expansion (except possibly for the northern LG gene pool which might have
500 remained stable) during the penultimate glacial period, suggesting that the more
501 recent glacial period (LGP) and the Holocene climatic pejoration have had no or little
502 effect on the populations of D. benthamianus, or at least have not left strong genetic
503 signatures. A more important impact of the PGP compared to the LGP is not usually
504 expected but is similar to recent findings in LG for two shade-tolerant African tree
505 species (Piñeiro et al., in prep.). Hence, it might be important to consider not only the
22

506 LGP but also previous glacial periods when attempting to interpret phylogeographic
507 patterns in terms of forest refugia in tropical Africa.
508 In the light of the ABC tests, we can argue that the dense semi deciduous forest
509 fragments found nowadays in the DG would be relics of a forest which was installed
510 by the expansion and admixture of the LG and UG forest blocks during the wet
511 Holocene and have declined in size (as shown by low allelic richness compared to
512 expected heterozygosity) during the Holocene climatic pejoration c. 4 ka.
513
514 Importance of adequate priors for ABC analysis
515 ABC inferences are sensitive to the priors imposed. Defining adequate priors for the
516 effective population sizes (Ne) remains tricky because there is little biological
517 evidence to assess an asymptotic Ne integrating the impact of genetic drift over
518 evolutionary time. As shown in the different simulations, posterior parameter
519 estimations of models A and B were largely influenced by the maximum values of Ne
520 priors. Although, the choice of the best scenario in models A and B remained robust
521 to the Ne priors, which is reassuring, it is important in ABC inferences to explore
522 different priors and check the robustness of the results obtained.
523
524 CONCLUSION
525 Overall, our study illustrates the relevance of genetic data to better understand and
526 complete the history of African tropical vegetation. The Guineo-Congolian forest has
527 undergone profound changes following the Quaternary climate changes. The DG has
528 probably been dominated by open vegetation during most of the time in the late
529 Pleistocene but it was forested during the early and middle Holocene. Genetic data
23

530 indicate that, for D. benthamianus at least, the DG was colonized from both UG and
531 LG populations at the beginning of the Holocene, suggesting that local forests
532 resulted from the expansion of the UG and LG forest blocks at the onset of the African
533 Humid period. The climatic pejoration that occurred in the DG c. 4 ka dramatically
534 reduced the DG forest cover and, probably, also the genetic diversity of the forest
535 species due to increased genetic drift. This scenario can leave a genetic signature
536 whereby DG populations form a distinct gene pool with less diversity in terms of
537 allelic richness and private alleles than in the UG and LG forest blocks, as observed in
538 D. benthamianus.
539
540 ACKNOWLEDGEMENTS
541 This research was supported by the Fonds de la Recherche Scientifique (F.R.S.-
542 FNRS) through a PhD fellowship (FRIA) awarded to Boris DEMENOU and through
543 project T.0163.13, and by the Belgian Science Policy (project AFRIFORD). For their
544 help with sampling, we thank Nils Bourland, Kasso Dainou, Gilles Dauby, Eben-Ezer
545 Ewédjè, Myriam Heuertz, Guillaume Koffi and Franck Monthe Kameni. For help in
546 the laboratory, we also thank Esra Kaymak. We are especially grateful to Gilles Dauby
547 and two anonymous reviewers for their comments that improved the manuscript.
548
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633 Gulliksen, S. (1984) Preliminary results from sediment cores from Lake Bosumtwi,
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643 SUPPORTING INFORMATION
644 Additional Supporting Information may be found in the online version of this article:
645 Appendix S1. Microsatellite amplification protocol and primers details.
28

646 Appendix S2. Summary statistics of ABC tests; Posterior Probability and Posterior
647 value computation.
648 Appendix S3. Demographic analyses of nSSR data of Distemonanthus
649 benthamianus, Posterior probability, Posterior distributions of demographic
650 parameters, Bias and Confidence in parameter estimates obtained with first priors
651 and second priors on effective population sizes.
652
653 DATA ACCESSIBILITY
654 Three new microsatellites sequences have been submitted to GenBank and accession
655 numbers are indicated in Appendix S1. For the eight microsatellites developed by
656 Debout et. al. (2011), the accession numbers are also indicated in Appendix S1.
657
658
659 Biosketch
660 BD is a PhD student, RP a postdoc and OJH a senior research associate, who are
661 interested in plant ecology and evolution, using (phylo)genetic approaches to infer
662 the history of plant populations, with a special focus on African forest species.
663
664 Editor: Stephen cavers
29

665 Figure legends
666 Figure 1. Spatial genetic structure of D. benthamianus according to Bayesian
667 clustering (STRUCTURE) of 429 individuals genotyped at 11 nuclear microsatellites.
668 The inset delimits the part of Africa covered.
669
670
671 Figure 2: Design of demographic ABC tests applied on each gene pool using
672 DIYABC. (a) DEMOGRAPHIC EVENT MODELS: compare four scenarios to identify
673 the nature of population size changes using broad time priors t0 and t1 (0-1 Ma). (b)
674 NARROW TIME MODELS: compare five scenarios guided by paleoenvironmental
675 data to identify the time scale of demographic changes. For (a) and (b), first priors on
676 effective population sizes were Ne: 1000-50000, N1: 10-500; second priors were Ne:
677 10-10000, N1: 10-2000 with Ne>N1. (c) Time priors: illustration of the time priors (t0
678 to t9) used to test the impact of particular climatic periods: PGP (Penultimate Glacial
679 Period), PD (Penultimate Deglaciation), LGP (Last Glacial Period), LD (Last
680 Deglaciation), HCP (Holocene Climatic Pejoration), with t2 and t3 : 190-1000 ka
681 (t2>t3), t4: 140-190 ka, t5: 120-130 ka, t6: 20-70 ka, t7: 10-12 ka, t8: 2-4 ka , t9: 1-3 ka.
682 Left graph: variations of deuterium (δD) in Antartic ice core as a proxy for global
683 temperature between 600-0 ka (IPCC 2007,
684 http://www.ipcc.ch/publications_and_data/ar4/wg1/en/figure-6-3.html). Right graph:
685 temperature change between 18-0 ka
686 (http://www.lakepowell.net/sciencecenter/paleoclimate.htm).
687
30

688 Figure 3: Design of ABC tests models to assess the origin and timing of the DG gene
689 pool. (a) ORIGIN MODELS: compare six scenarios of relationships between the DG
690 and its adjacent UG and wLG gene pools (effective size priors on Ne, Ne1, N1 and N3:
691 1000 – 50000, and N2 : 10 – 500, and time priors on T0 and T1 : 0-1 Ma with T1>T0).
692 (b) ADMIXTURE MODELS: compare six admixture scenarios involving pre-
693 admixture founder effects (d2, d4, d6) or post-admixture population size decline (d1,
694 d3, d5) and ancestral demographic changes (effective size priors as above,
695 Ts>Td>Te>Ta>Td). (c) Time priors used to test the impact of particular climatic
696 periods in (b): LIG (Last interglacial), AHP (African Humid Period), and see Fig. 2
697 legend.
698
699 Fig.4: Gene pools detected in D. benthamianus samples from Upper Guinea (UG),
700 Lower Guinea (LG) and the Dahomey Gap (DG) using the Bayesian clustering
701 algorithm implemented in STRUCTURE. The histograms show the individual
702 assignment to clusters for K=2 (above) and K=5 (below).
703
704
705
31

706 Table 1. Genetic diversity and differentiation parameters of the five gene pools
707 inferred in D. benthamianus using 11 nuclear SSR loci (only samples assigned to a
708 gene pool with a probability ≥ 0.7 were included).
709
Differentiation parameters : FST \ RST Diversity parameters
Gene pool
wLG nLG sLG DG UG N A0 RS He Fi Rpriv
wLG 0.064 NS 0.107 NS 0.212 NS 0.303 NS 70 106 8.06 0.688 0.001 1.19
nLG 0.039 0.068 NS 0.286 * 0.352 * 96 89 6.53 0.665 0.012 0.55
sLG 0.082 0.094 0.345 NS 0.362 NS 77 85 6.13 0.545 0.020 0.48
DG 0.173 0.177 0.291 0.208 NS 33 43 3.90 0.553 0.047 0.20
UG 0.173 0.177 0.281 0.204 58 69 5.41 0.522 0.059 0.47
All samples FST = 0.116 RST = 0.164 334 138 8.02 0.689
710
Differentiation: FST below and RST above the diagonal; test of phylogeographic signal (i.e. RST>FST) are indicated by NS (P>0.05) and
711 *P<0.05. Diversity: N: sample size, AO: Number of alleles, Rs: rarefied allele richness (among k=60 gene copies per locus), He: expected
712 heterozygosity corrected for sample size, Fi: inbreeding coefficient estimated by INest, Rpriv: private alleles richness (k=60).
713
714
32

715 Table 2. Demographic analyses of nSSR data of Distemonanthus benthamianus
716 implemented with DIYABC (see details in Figs 2 & 3): posterior probabilities of
717 demographic scenarios and confidence in scenario choice under the most likely
718 scenario. (A) DEMOGRAPHIC EVENT MODELS, (B) NARROW TIME MODELS, (C)
719 ORIGIN MODELS and (D) ADMIXTURE MODELS. Values are given for the first set
720 of priors on effective population sizes (Ne: 1000 – 50000, N2 : 10 – 500), except
721 those under parentheses corresponding to the second set of priors for models A and B
722 (Ne: 10 – 10000, N2 : 10 – 2000).
723
724 A. DEMOGRAPHIC EVENT MODELS (nature of demographic changes; Fig. 2)
a1: a2: a3: a4: Confidence Scenario
Gene pool Constant Decline Expansion Bottleneck Choice
wLG 0.14 (0.29) 0.00 (0.00) 0.07 (0.14) 0.79 (0.57) 0.60
nLG 0.41 (0.32) 0.00 (0.13) 0.17 (0.17) 0.42 (0.38) 0.89
sLG 0.03 (0.07) 0.00 (0.02) 0.10 (0.22) 0.87 (0.69) 0.62
DG 0.01 (0.05) 0.97 (0.82) 0.01 (0.06) 0.01 (0.07) 0.99
UG 0.00 (0.01) 0.00 (0.01) 0.40 (0.42) 0.60 (0.56) 0.66
725 Bottleneck: population decline followed by an expansion
726
727 B. NARROW TIME MODELS (timing of demographic changes; Fig. 2)
b1: b2: b3: b4: b5: Confidence
Gene pool Constant Pre PGP PGP LGP Holocene Scenario Choice
wLG (Bottleneck) 0.01 (0.11) 0.09 (0.18) 0.90 (060) 0.00 (0.06) 0.00 (0.05) 0.94
nLG (Bottleneck) 0.12 (0.14) 0.12 (0.14) 0.53 (0.34) 0.18 (0.27) 0.05 (0.11) 0.91
sLG (Bottleneck) 0.00 (0.03) 0.06 (0.11) 0.91 (0.71) 0.03 (0.13) 0.00 (0.02) 0.93
DG (Decline) 0.00 (0.01) 0.01 (0.10) 0.04 (0.25) 0.55 (0.47) 0.40 (0.17) 0.91
UG (Bottleneck) 0.00 (0.01) 0.37 (0.29) 0.63 (0.68) 0.01 (0.01) 0.00 (0.01) 0.94
728 PGP: penultimate glacial period; LGP: last glacial period
729
730 C. ORIGIN MODELS (relationships between the DG and its adjacent gene pools; Fig. 3)
Confidence Scenario
c1 c2 c3 c4 c5 c6 Choice

wLG, DG, UG 0.27 0.01 0.01 0.11 0 0.60 0.72
731
732 D. ADMIXTURE MODELS (timing of the admixture origin of the DG gene pool; Fig. 3)
Confidence Scenario
d1 d2 d3 d4 d5 d6 Choice
derived from
DG
0 0 0.10 0 0.39 0.51 0.73
admixture
733
33

734
735
736
737 Dahomey Gap (DG)
738
739
740
Upper Guinea (UG)
741
742 Lower Guinea (LG)
743
744
745
746
747
748
749
750
751
752
753
754
755 Fig.1: Spatial genetic structure of D. benthamianus according to Bayesian clustering
756 (STRUCTURE) of 429 individuals genotyped at 11 nuclear microsatellites. The inset delimits
757 the part of Africa covered.
758
34

(a) DEMOGRAPHIC EVENT MODELS
a1: CONSTANT a2: DECLINE a3: EXPANSION a4: BOTTLENECK
Ne N1 Ne
t1 t1 t1
Ne N1 Ne N1
t0
Ne
(b) NARROW TIME MODELS

b1: CONSTANT b2: Pre PGP b3: PGP b4: LGP b5: HOLOCENE
t2 t4
t6
t3 t5
t7 t8
t9
759 (c) Time priors (in ka)
Change in Temperature (°C)

PD
Pre PGP PGP LGP LD HCP

t7 t8
t9
t4 t5 t6
760
761 Fig.2: Design of demographic ABC tests applied on each gene pool using DIYABC. (a)
762 DEMOGRAPHIC EVENT MODELS: compare four scenarios to identify the nature of
763 population size changes using broad time priors t0 and t1 (0-1 Ma). (b) NARROW TIME
764 MODELS: compare five scenarios to identify the time scale of demographic changes. For (a)
765 and (b), first priors on effective population sizes were Ne: 1000-50000, N1: 10-500; second
766 priors were Ne: 10-10000, N1: 10-2000 with Ne>N1. (c) Time priors: illustration of the time
767 priors (t0 to t9) used to test the impact of particular climatic periods: PGP (Penultimate Glacial
768 Period), PD (Penultimate Deglaciation), LGP (Last Glacial Period), LD (Last Deglaciation),
769 HCP (Holocene Climatic Pejoration), with t2 and t3 : 190-1000 ka (t2>t3), t4: 140-190 ka, t5:
770 120-130 ka, t6: 20-70 ka, t7: 10-12 ka, t8: 2-4 ka , t9: 1-3 ka. The graph on the left: variations of
771 deuterium (δD) in Antartic ice core as a proxy for global temperature between 600-0 ka (IPCC
772 2007, http://www.ipcc.ch/publications_and_data/ar4/wg1/en/figure-6-3.html). The graph on the right:
773 temperature change between 18-0 ka (http://www.lakepowell.net/sciencecenter/paleoclimate.htm).
774
35

775 (a) ORIGIN MODELS
776 c1 c2 c3
T1 T1 T1

T0 T0

0 0 0
UG DG wLG DG wLG UG wLG DG UG
777
778 c4 c5 c6
T1 T1 T1

T0 T0 r 1 -r
T0

0 0 0
779 DG wLG UG wLG UG DG wLG DG UG
780
781 (b) ADMIXTURE MODELS
782 d1, d3, d5 d2, d4, d6
Ts Ts
Tb Tb
Te
Te
Ta
1 -r r Ta
Td 1 -r r
0 0
UG DG wLG UG DG wLG
783
784
785 (c) Time priors (in ka)
Change in Temperature (°C)
HCP
LIG
Pre PGP PGP LGP AHP

1,000 I-‐-‐-‐-‐-‐-‐-‐-‐-‐
786
787 T0, T1, Ts (d1-‐d6), Tb (d1,d2), Te (d1,d2),Ta(d1, d3, d5) Ta (d6) Td (d5)
788 Ta (d2)
789 Te (d3-‐d6), Ta (d4)
790 Tb (d3-‐d6),Td (d1)

Td (d3)
Fig.3: Design of ABC tests models to assess the origin and timing of the DG gene pool. (a) ORIGIN36 MODELS:
compare six scenarios of relationships between the DG and its adjacent UG and wLG gene pools (effective size
priors on Ne, Ne1, N1 and N3: 1000 – 50000, andof
Journal N2Biogeography
: 10 – 500, and time priors on T0 and T1 : 0-1 Ma with
T1>T0). (b) ADMIXTURE MODELS: compare six admixture scenarios involving pre-admixture founder effects
(d2, d4, d6) or post-admixture population size decline (d1, d3, d5) and ancestral demographic changes
(effective size priors as above, Ts>Td>Te>Ta>Td). (c) Time priors used to test the impact of particular climatic
periods in (b): LIG (Last interglacial), AHP (African Humid Period), and see Fig. 2 legend.
791
UG + DG wLG + nLG + sLG
792
793
UG DG wLG sLG nLG
794
795
796
797
798 Fig.4: Gene pools detected in D. benthamianus samples from Upper Guinea (UG), Lower
799 Guinea (LG) and the Dahomey Gap (DG) using the Bayesian clustering algorithm
800 implemented in STRUCTURE. The histograms show the individual assignment to clusters for
801 K=2 (above) and K=5 (below).
802
37
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Article in Journal of Biogeography · January 2016

Boris Demenou Rosalía Piñeiro

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Ancient Genomics of Rainforests (AGORA, Marie-Curie IEF program) View project

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7 Boris B. DEMENOU1*, Rosalía PIÑEIRO2 & Olivier J. HARDY1

9 F. D. Roosevelt 50, BE-1050 Brussels, Belgium,

12 * Correspondence : Boris Demenou, Evolution Biologique et Ecologie, Université

17 SRH: African forest tree phylogeography in Dahomey Gap

19 Word count: 7000

20 Number of journal page: 12

26 species, Distemonanthus benthamianus (Fabaceae), we will test the hypothesis that

29 were supposedly connected.

32 eastern Ghana to Benin.

33 Methods: 429 D. benthamianus samples from West to Central Africa were

34 genotyped with 11 nuclear microsatellite markers. After detecting geographically

36 their demographic histories were inferred using coalescent simulations and

37 Approximate Bayesian Computation (ABC) tests.

44 Holocene climatic pejoration documented around 3 ka.

46 populations of D. benthamianus is globally consistent with palaeovegetation data

48 Holocene period when the Guineo-Congolian forest reached its maximum

52 nuclear microsatellites, phylogeography, Quaternary climate changes, rain forest

55 The African Guineo-Congolian phytochoria constitutes the second largest block of

56 rain forest on earth. White (1979) defined it as a phytogeographic centre of species

62 of Congo and of the Democratic Republic of Congo.

65 DG is characterized by a decline in annual precipitation from more than 2000 mm in

70 DG in the early Holocene.

75 reduction in rain forest species in favour of grass species characteristic of open

82 block because the DG became forested (Salzmann & Hoelzmann, 2005).

86 late Holocene, a climatic pejoration characterized by less rainfall and more

91 The origin of the forest-dwelling flora of the DG is uncertain as it may correspond to

96 New insights into these questions could be provided by phylogeographical and

97 population genetics studies, which can detect past events of population

98 fragmentation, colonization, or demographic changes and date them using coalescent

99 simulations (Piñeiro et al., in prep.). A few recent genetic studies performed on

106 species in the DG.

114 signatures of past demographic changes (decline, expansion or bottleneck) in each

120 current DG populations of D. benthamianus (i) may come exclusively from UG or

126 Study taxon and sampling

127 Distemonanthus benthamianus Baillon (Caesalpinioideae) is a tropical tree widely

144 (Psittacus erithacus; White & Abernethy, 1996).

146 georeferenced (GPS) individuals of D. benthamianus in 12 different countries from

150 from Guinea-Conakry, Liberia and Sierra Leone.

152 DNA extraction and nuclear microsatellites genotyping

154 the manufacturer’s instructions. Eleven polymorphic nuclear microsatellite (nSSR)

165 Identification of genetic discontinuities

168 and independent allele frequencies models, with no a priori partitioning of

174 Ln P(D) starts reaching a plateau as K increases. Individuals were considered as

178 Diversity and differentiation parameters: detecting phylogeographical

185 provided corrected estimates of the inbreeding coefficient (Fi).

189 the rarefaction procedure implemented in HP-RARE 1.1 (Kalinowski, 2005),

195 differentiation (Hardy et al., 2003).

199 expansion/bottleneck, phylogeographical data can be treated using model-based

204 parameters are determined by replacing the computation of the likelihood

212 by expansion (hereafter “population bottleneck” for short). To have a global

213 assessment of possible demographic changes without a priori hypotheses on the

237 4- 2ka] and/or subsequent expansion [3-1 ka].

239 Origin of the Dahomey Gap gene pool

250 changes between 1 Ma to present.

267 [AHP, 10-4 ka].

276 testing proved to be robust, they are not shown hereafter.

284 phases of small population size in case of bottleneck or decline scenarios.