BACKGROUND
the contribution of reticulate evolution, in particular natural and introgressive hybridization to the origin and development of humans and primates in general has recently gained much attention  <cit> .
one primate species complex that turned out to be of particular interest in this respect are baboons .
they diverged on a time scale analogous to that of homo in similar, if not the same habitats in southern and eastern africa, and it has been proposed to use them as an analogous model, when exploring the evolution of the hominin lineages  <cit> .
it was estimated that they have radiated across africa approximately  <dig>  million years ago   <cit> .
baboons are now distributed all over sub-saharan africa, excluding most parts of the west and central african rainforest, and have even colonized parts of the arabian peninsula  <cit>  .
they form morphologically and geographically distinct populations but demonstrate no pre- or postzygotic reproductive isolation  <cit> .
additionally, baboons are known to produce fertile hybrid offspring with geladas   <cit> .
the divergence between these sister genera is estimated at  <dig> – <dig> mya .
the five generally acknowledged baboon types are the guinea baboon  papio) from west africa, the olive baboon  anubis) from the northern savannah belt, the hamadryas baboon  hamadryas) from north-east africa and the south-western arabian peninsula, the yellow baboon  cynocephalus) from the east african coastal lowlands, zambia and angola and the chacma baboon  ursinus) from southern africa .
the taxonomic status of the five baboon types has been debated for more than  <dig> years without reaching a consensus .
they are either classified as  subspecies of the superspecies papio hamadryas  <cit>  or as distinct species  <cit> .
in addition to the five traditional types several other geographic variants have been described  <cit> , of which at least some deserve the same taxonomic level as the five basic types  <cit> .
here we follow groves  <cit> , grubb et al.
<cit>  and jolly  <cit>  and recognize baboon allotaxa as phylogenetic species.
since the question regarding the appropriate taxonomic level is more a matter of philosophy, depending largely on the underlying species concept  <cit> , an accurate and well-supported phylogeny is crucial for understanding the evolution of the genus.
this is of particular relevance for all studies where phylogenies have to be correlated such as in co-evolution studies, for example, the evolution of primates and their pathogens  <cit> .
similarly, in studies concerning the evolution of certain traits, such as particular heritable social behaviours, it is important to distinguish between ancestral  and derived  states.
if, for example, hamadryas baboons are the most basal baboons, as in the phylogeny proposed by purvis  <cit> , their peculiar social organization with its one-male units  <cit>  could be regarded as the ancestral social organization of the baboon clade and not the multi-male organization of other baboon taxa  <cit> .
hence, incorrect phylogenies will inevitably lead to incorrect inferences about the evolution of species.
the origin of papio is suggested to be in southern africa  and the oldest mitochondrial haplotypes so far were found in chacma baboons which live in southern africa  <cit> .
apart from its origin, the evolutionary course of different baboon taxa is a subject of great debate and speculation.
based on morphological and behavioural characters several contradictory intra-generic phylogenetic hypotheses have been proposed .
in molecular studies discordance between mitochondrial dna  phylogenies and morphology-based taxonomy became obvious, suggesting that reticulation events affected the evolutionary history of baboons  <cit> .
in this study, we determined the phylogenetic relationships within the genus papio and estimated the dates of divergence events between lineages.
our analyses are based on complete mitochondrial cytochrome b gene  and 'brown region'  <cit>  sequences.
we expanded geographic and taxon sampling to make our phylogenetic analysis more robust  <cit> , because taxon sampling is particularly important in paraphyletic species  <cit> .
thus, our sampling covered most of the range of papio and included previously unsampled regions and taxa, and does not include samples from captive animals with the exception of one sample from a confiscated animal in cameroon.
therefore only samples of clear provenance are present in the analysed data set.
this enabled us to extend previous analyses substantially and to refine the phylogenetic resolution among mtdna haplotypes.
comparisons of the biogeographic distribution of mtdna haplotypes and morphotypes allowed us to detect indications for introgressive hybridization and reticulate evolution.
RESULTS
phylogenetic relationships
we successfully amplified and sequenced the mitochondrial 'brown region' and the complete cytb gene from  <dig> individuals from  <dig> localities .
concatenated 'brown region' and cytb sequences  resulted in  <dig> haplotypes , which were defined by  <dig> variable sites, of which  <dig> were parsimony-informative.
identical haplotypes were found mainly in animals, that came from the same locality , but were also found from sites located more than  <dig>  km apart .
when examining each locus separately,  <dig> haplotypes were detected in the 'brown region' , defined by  <dig> variable sites, of which  <dig> were parsimony-informative.
in baboons from the southern part of the republic of south africa , southern and western namibia and western angola, a triplet deletion in the nd <dig> gene of the 'brown region' was detected.
the complete cytb sequence  contained  <dig> variable sites, of which  <dig> were parsimony-informative defining  <dig> haplotypes.
according to the akaike information criterion , the 'brown region' was found to best fit the tamura-nei model , while for both the cytb gene alone and the concatenated data set a transition model  was selected.
for all data sets a model with both gamma distributed rate heterogeneity  and a proportion of invariant sites  was proposed.
simple neighbor-joining reconstructions based on uncorrected distances for both data sets  revealed identical tree topologies and similar branch lengths , indicating that both data sets contain solely mitochondrial fragments and no nuclear pseudogenes.
moreover, no inconsistent nucleotides were detected in overlapping regions of both studied loci.
detailed phylogenetic relationships were estimated with bayesian and maximum-likelihood  approaches, which both led to identical topologies and similar support values .
several well-supported clades were detected which however, do not concur with the five baboon species.
the only exception are guinea baboons, which form a monophyletic group.
all other species were mitochondrially paraphyletic.
in contrast, we found a strong geographical signal with local populations forming monophyletic groups irrespective of their species affiliations, which clearly showed the discordance between mtdna phylogeny and morphology .
in total, seven larger haplogroups were detected , which are distributed in two major clades, a southern and a northern one.
however, respective monophylies of the southern and northern clades are only weakly supported, suggesting that the divergence of the two clades most likely happened within a short time period.
the major southern clade further divides into three clades, the southern chacma clade , representing haplotypes from the drakensberg, the cape, western rsa, southern and western namibia and south-western angola, the northern mixed chacma and yellow baboon clade , which includes chacma haplotypes from mozambique, northern rsa, zimbabwe, botswana, south-central zambia and north-eastern namibia, and yellow baboon haplotypes from malawi, eastern zambia and south-eastern tanzania, and finally,  a clade of baboons that originated from central zambia, which morphologically represent kinda baboons.
the triplet deletion in the nd <dig> region is an autapomorphy of clade  since it was not found in any other papionin.
the major northern clade divides into a western and an eastern clade.
the western clade consists of one clade of olive baboon haplotypes found in ivory coast and western nigeria , a second clade of olive baboon haplotypes mainly from central and eastern nigeria and northern cameroon , and a well-defined clade of guinea baboon haplotypes covering the area from guinea to senegal .
the eastern clade is comprised of a mixture of different species.
the first separation concerns yellow baboons from the kenyan coast, whereas the second includes olive baboons  from western uganda and eastern democratic republic of congo .
furthermore, we found two more clades, one comprised of yellow and olive baboon haplotypes from northern tanzania, kenya and somalia while the other represents a mixture of olive and hamadryas baboon haplotypes from ethiopia, eritrea and the arabian peninsula.
in total, ten well-supported terminal clades/lineages became apparent in our study, which represent geographic populations or demes.
the only exceptions are southern yellow baboons, which are paraphyletic.
the approximate geographical distribution of the respective haplogroups is shown in figure  <dig>
estimation of divergence times
the data set used to estimate divergence times contains  <dig>  bp of sequence information from  <dig> primate individuals.
over half of the characters  were variable and  <dig> were parsimony-informative.
the coding regions were found to best fit a trn model with both gamma distributed rate heterogeneity  and a proportion of invariant sites , and non-coding regions were found to best fit a tvm + Γ + i model.
using three divergence dates as calibrations , the papio-theropithecus divergence  was dated at  <dig>  million years ago  , which is in the same range as both, the estimate given by newman et al.
<cit>  and the divergence date suggested by fossil evidence  .
the subsequent divergences within papio are considerably younger  and started in the late pliocene.
the divergence of the ancestral papio stem into a southern and a northern lineage  was inferred to have occurred at  <dig>   mya.
shortly afterwards, the respective northern lineage diverged further into a western and an eastern clade  and the respective southern lineage into a southern and a northern proto-chacma baboon clade .
within the lineage leading to northern chacma baboons, kinda baboons diverged  <dig>   mya , followed by the separation of southern yellow baboons  <dig>   mya .
the age of the most recent common ancestor  of the north-western lineage leading to guinea and western olive baboons was estimated at  <dig>   mya .
in this lineage, the earliest divergence was between olive baboons of clade w <dig> and a common clade of guinea/olive w <dig>  the separation between the latter was estimated at  <dig>   mya .
* not shown in figure 4
nodes used as calibrations are labelled with a "c", all others with an "n".
in the north-eastern clade, coastal yellow baboons diverged first  <dig>   mya , followed by central olive baboons  <dig>   mya .
eastern olive and northern yellow were mitochondrially separated from north-eastern olive and hamadryas baboons  <dig>   mya .
the divergence ages for the north-eastern clade fall in the same range as found in earlier studies.
newman et al.
<cit>  estimated separations within the north-eastern clade of less than  <dig>   mya.
shotake et al.
<cit>  reported that ethiopian olive and hamadryas baboons have been separate lineages since approximately  <dig>  mya.
discussion
our phylogenetic reconstruction suggests that baboon populations can be diagnosed through mtdna and are sorted into several coherent and reasonably well-supported haplogroups that do not match with recognized baboon species.
the discordance between mitochondrial phylogeny and baboon morphology, which is most likely equivalent to a discordance between mitochondrial and nuclear phylogeny, results in mitochondrial paraphyly, which is common among animal taxa including primates  <cit> .
the observed discordance might be explained by introgressive hybridization or incomplete lineage sorting since both can result in similar phylogenetic patterns and hence, complicate interpretation of phylogenetic reconstructions  <cit> .
although we can not rule out completely that incomplete lineage sorting may have had an effect, the strict geographical pattern of the baboon haplogroups provides some evidence against incomplete lineage sorting, because lineage sorting is a random process and the paraphyletic relationships that result from the failure of haplotypes to sort during speciation events should be random with respect to geography  <cit> .
in contrast, in our mitochondrial phylogeny geographic close populations cluster together, which is often a strong indication of reticulation  <cit> .
thus, we conclude that introgressive hybridization rather than incomplete lineage sorting has resulted in the discordance between mitochondrial and morphological phylogeny present in baboons.
the introgression hypothesis becomes even more likely by the fact that baboons and other papionins show a strong tendency for intra- and intergeneric hybridization.
generic hybridization was observed between papio and theropithecus and between papio and rungwecebus  <cit> .
for baboons, intrageneric hybrid zones are known for olive and northern yellow baboons  <cit> , olive and hamadryas baboons  <cit>  and kinda and southern yellow baboons  <cit> .
male dispersal and female philopatry are the norm in baboons and other papionins  <cit>  and one can assume that this is the ancestral state.
therefore male introgression would be the most likely introgression scenario, where males from one taxon invade groups of a neighbouring taxon and reproduce successfully.
extensive backcrossing of the hybrid offspring over generations with more invading males of the first taxon would result in nuclear swamping.
this process can lead to the extinction of the introgressed taxon and only their mitochondrial genomes would remain as vestiges of their former existence in a population which morphologically would be the same as the introgressing taxon.
together with a recurrent isolation and reconnection of local baboon populations in many parts of their range due to climate changes the male introgression and nuclear swamping hypothesis can explain the striking discordance between mitochondrial phylogeny and baboon morphology.
phylogeography
the paraphyletic pattern suggests a complicated biogeographic history of baboon species.
multiple phases of isolation, hybridization and introgression are highly probable, most likely triggered by the multiple cycles of expansion and retreat of savannah biomes during pleistocene glacial and inter-glacial periods  <cit> .
during the last  <dig>  million years there have been about  <dig> glacial cycles of major forest expansions and retreats in africa  <cit> .
environments during glacial periods were characterized by dry, tropical scrub and grassland with limited gallery forest along drainages, and thus, with the retreat of dense forest into high altitude and large river refugia, savannah corridors opened and provided pioneering and recurrent dispersal possibilities for savannah adapted mammal populations, such as baboons.
evidence for the multiple savannah and forest cycles come from pollen core data and the current distribution patterns of forest organisms  <cit> .
the divergence of the papio lineage accompanied by the dispersal from southern africa to the north  and the further division into several distinct southern  and northern lineages  appears to be temporally in accordance with the expansion of savannah habitats and a major radiation of antelopes  and the diversification of hominins  <cit> , all as a result of the onset and recurrence of the northern hemisphere glaciations since ~ <dig>  mya.
a similar phylogeographic pattern of an early north-south division and the subsequent division of the northern clade into an eastern and western clade have also been shown for other large african savannah mammals, such as hartebeest alcelaphus buselaphus  <cit> , topi damaliscus lunatus and wildebeest connochaetes taurinus <cit> , roan antelope hippotragus equinus  <cit> , warthog phacochoerus africanus  <cit> , giraffe giraffa camelopardalis  <cit>  and lion panthera leo  <cit> .
within several of these taxa paraphyletic relationships were detected, similar to the pattern found in baboons  <cit> .
these biogeographic patterns have been interpreted as results of plio-pleistocene climate cycles when the expansion of savannah habitats supported the dispersal of these taxa, although not for all taxa on the same time scale.
however, a detailed analysis of these processes and a comparison with detailed data on climate and habitat change in africa during the last  <dig>  mya is far beyond the scope of our paper.
our findings are almost consistent with the scenario for the mitochondrial population structure of papio laid out by c.j.
jolly in his "north-south split" and "philopatry at the frontier" hypotheses .
from our data the following scenario can be developed.
baboons dispersed to the south and north from a southern african origin at times when climate and habitat conditions were suitable , that is if during dry conditions dense forests were replaced by savannah and savannah woodland.
there is evidence from various sources that two savannah corridors existed during arid periods in the plio-pleistocene, which baboons could have followed on their way north  <cit> .
one migration route lead through a savannah corridor in eastern africa and a second through a savannah corridor in eastern drc west of the pleistocene forest refuge in the rift mountains.
baboons migrating to the north subsequently dispersed over the complete northern savannah belt, from eritrea to senegal.
changes of the climate to more humid condition with expanding forests probably led to the isolation of local baboon populations, because for most baboons dense forests constitute biogeographical barriers.
these allopatric populations evolved for certain periods of time independently.
subsequent climate changes to more arid conditions again opened savannah corridors so that isolated populations were able to reconnect, with the chance of gene flow.
as an extreme outcome, some of the historical baboon populations might have been "swallowed" by invading populations and became extinct.
male olive baboons, for example, reproduced with females from neighbouring populations, with subsequent nuclear swamping.
olive baboons, thus, most likely absorbed these local baboon forms, such as w <dig> and w <dig>  from which we can still find the mitochondrial genome  in western olive baboons.
a similar process occurred in east and north-east africa where olive baboons from kenya and northern tanzania carry mitochondria derived from a neighbouring yellow or proto-yellow baboon stock or in ethiopia and eritrea, where they carry hamadryas or proto-hamadryas mitochondria.
in the latter cases, parts of the original populations still exist, as northern yellow and hamadryas baboons.
however, hybridization between olive and yellow baboons and olive and hamadryas baboons  is still going on.
it is also likely that hybridization occurs at the western end of the olive baboon range, where olive and guinea baboons meet.
similarly, introgression and nuclear swamping can explain why yellow baboons of zambia carry mitochondria only distantly related to those of northern tanzanian and kenyan yellow baboons, and chacma baboons from botswana and zambia are mitochondrially very distant from those living in south africa.
in case of southern and northern yellow baboons a possible scenario could be that yellow baboons introgressed from the south into a neighbouring northern population  after the retreat of an east african forest barrier.
complete nuclear swamping would lead to a replacement of the local northern population with yellow baboons, which, however, would carry the mitochondria of the northern population.
in case of chacma baboons we assume that they introgressed into parts of the southern yellow baboon population, thus replaced the yellow baboon nuclear genome, but retained the yellow baboon mitochondria.
these events most likely took place early in the speciation process so that there was time for resulting chacma baboon population to evolve further into grey-footed chacmas.
interestingly, zinner et al.
<cit>  found that the recently described genus rungwecebus  <cit>  also carries mitochondria of the northern chacma – southern yellow baboon haplogroup, suggesting that also on this intergeneric level introgression events occurred.
our introgression hypothesis is partly built on similar sexually-differentiated introgression scenarios envisioned by wildman et al.
<cit> .
taxonomic implications
our study shows that mtdna does not constitute a useful marker for the identification of the five traditionally recognized papio species.
if terminal clades in our phylogeny would be regarded as phylogenetic species, one would have to split haplogroups of the same morphotype into different species  or one would have to lump members of different morphotypes as one species, e.g.
hamadryas and eastern olive baboons which are different not only in their morphology but even more in their social system  <cit> .
guinea baboons, which morphologically and genetically constitute a monophyletic clade seem to be the only exception.
however, there are indications for introgression also from western olive baboons into guinea baboons  <cit> .
despite these limitations, our data, in combination with morphological  <cit> , behavioural  <cit>  and additional genetic data  <cit>  support the recognition of kinda baboons as a distinct species .
in our sample, we did not find any overlap between kinda and either southern yellow or northern chacma baboons.
in contrast, in a more detailed study of the kinda baboons and neighbouring baboon populations, burrell  <cit>  found some evidence for gene flow between kinda and yellow baboons in a narrow contact zone in eastern zambia.
similarly, clifford jolly  found some intermediate morphotypes between grey-footed and kinda baboons where they meet.
baboons of the southern chacma haplogroup possibly represent cape chacmas  ursinus) and those of the northern chacma haplogroup grey-footed chacmas .
griseipes), as was proposed by jolly  <cit> .
however, it remains to be explored, whether various haplogroups of yellow and olive baboons from eastern and western africa may represent formerly described, but now synonymised taxa  <cit> .
CONCLUSIONS
the present study shows paraphyly in the genus papio and discordance between baboon morphology and mitochondrial phylogeny.
accordingly, a classification of baboons based on mitochondrial sequence data is inappropriate.
however, the geographic distribution of haplogroups provides insights into the evolutionary history of baboons and emphasizes the possible role of introgressive hybridization.
periodical isolation of populations and subsequent range overlap, most likely triggered by climatic changes, might have led to a gradual hybridization influencing baboon diversification and speciation  <cit> .
the extent of introgression reaches from ongoing introgression of male olive baboon into yellow baboon population in amboseli to the complete extinction of historical populations or taxa in west or south-east africa by introgression where only the former mitochondrial genome remained as a trace in the current olive or grey-footed chacma baboon populations.
since the evolutionary history of baboons shows some similarities with that of the human lineage, it seems plausible that the introgression scenario depicted herein might also be an extended model for reconstructing the evolution of homo.
defining the extent of the reticulate  events will require further molecular studies that incorporate additional samples and in particular nuclear loci.
our study showed that collecting samples from all over the baboon range with known provenances is indispensable, but samples from further locations as indicated in figure  <dig>  should be included in ongoing studies.
the analysis of nuclear loci, however, might be hampered by the fact that nuclear sequence variation is expected to be relatively low in baboons as shown for parts of the y-chromosome  <cit> .

 the contribution of reticulate evolution, in particular natural and introgressive hybridization to the origin and development of humans and primates in general has recently gained much attention. one primate species complex that turned out to be of particular interest in this respect are baboons. they diverged on a time scale analogous to that of homo in similar, if not the same habitats in southern and eastern africa, and it has been proposed to use them as an analogous model, when exploring the evolution of the hominin lineages. it was estimated that they have radiated across africa approximately million years ago. baboons are now distributed all over sub-saharan africa, excluding most parts of the west and central african rainforest, and have even colonized parts of the arabian peninsula. they form morphologically and geographically distinct populations but demonstrate no pre- or postzygotic reproductive isolation. additionally, baboons are known to produce fertile hybrid offspring with geladas. the divergence between these sister genera is estimated at – mya. the five generally acknowledged baboon types are the guinea baboon papio) from west africa, the olive baboon anubis) from the northern savannah belt, the hamadryas baboon hamadryas) from north-east africa and the south-western arabian peninsula, the yellow baboon cynocephalus) from the east african coastal lowlands, zambia and angola and the chacma baboon ursinus) from southern africa. the taxonomic status of the five baboon types has been debated for more than years without reaching a consensus. they are either classified as subspecies of the superspecies papio hamadryas or as distinct species. in addition to the five traditional types several other geographic variants have been described, of which at least some deserve the same taxonomic level as the five basic types. here we follow groves, grubb et al. and jolly and recognize baboon allotaxa as phylogenetic species. since the question regarding the appropriate taxonomic level is more a matter of philosophy, depending largely on the underlying species concept, an accurate and well-supported phylogeny is crucial for understanding the evolution of the genus. this is of particular relevance for all studies where phylogenies have to be correlated such as in co-evolution studies, for example, the evolution of primates and their pathogens. similarly, in studies concerning the evolution of certain traits, such as particular heritable social behaviours, it is important to distinguish between ancestral and derived states. if, for example, hamadryas baboons are the most basal baboons, as in the phylogeny proposed by purvis, their peculiar social organization with its one-male units could be regarded as the ancestral social organization of the baboon clade and not the multi-male organization of other baboon taxa. hence, incorrect phylogenies will inevitably lead to incorrect inferences about the evolution of species. the origin of papio is suggested to be in southern africa and the oldest mitochondrial haplotypes so far were found in chacma baboons which live in southern africa. apart from its origin, the evolutionary course of different baboon taxa is a subject of great debate and speculation. based on morphological and behavioural characters several contradictory intra-generic phylogenetic hypotheses have been proposed. in molecular studies discordance between mitochondrial dna phylogenies and morphology-based taxonomy became obvious, suggesting that reticulation events affected the evolutionary history of baboons. in this study, we determined the phylogenetic relationships within the genus papio and estimated the dates of divergence events between lineages. our analyses are based on complete mitochondrial cytochrome b gene and'brown region' sequences. we expanded geographic and taxon sampling to make our phylogenetic analysis more robust, because taxon sampling is particularly important in paraphyletic species. thus, our sampling covered most of the range of papio and included previously unsampled regions and taxa, and does not include samples from captive animals with the exception of one sample from a confiscated animal in cameroon. therefore only samples of clear provenance are present in the analysed data set. this enabled us to extend previous analyses substantially and to refine the phylogenetic resolution among mtdna haplotypes. comparisons of the biogeographic distribution of mtdna haplotypes and morphotypes allowed us to detect indications for introgressive hybridization and reticulate evolution.  phylogenetic relationships we successfully amplified and sequenced the mitochondrial'brown region' and the complete cytb gene from individuals from localities. concatenated'brown region' and cytb sequences resulted in haplotypes, which were defined by variable sites, of which were parsimony-informative. identical haplotypes were found mainly in animals, that came from the same locality, but were also found from sites located more than km apart. when examining each locus separately, haplotypes were detected in the'brown region', defined by variable sites, of which were parsimony-informative. in baboons from the southern part of the republic of south africa, southern and western namibia and western angola, a triplet deletion in the nd gene of the'brown region' was detected. the complete cytb sequence contained variable sites, of which were parsimony-informative defining haplotypes. according to the akaike information criterion, the'brown region' was found to best fit the tamura-nei model, while for both the cytb gene alone and the concatenated data set a transition model was selected. for all data sets a model with both gamma distributed rate heterogeneity and a proportion of invariant sites was proposed. simple neighbor-joining reconstructions based on uncorrected distances for both data sets revealed identical tree topologies and similar branch lengths, indicating that both data sets contain solely mitochondrial fragments and no nuclear pseudogenes. moreover, no inconsistent nucleotides were detected in overlapping regions of both studied loci. detailed phylogenetic relationships were estimated with bayesian and maximum-likelihood approaches, which both led to identical topologies and similar support values. several well-supported clades were detected which however, do not concur with the five baboon species. the only exception are guinea baboons, which form a monophyletic group. all other species were mitochondrially paraphyletic. in contrast, we found a strong geographical signal with local populations forming monophyletic groups irrespective of their species affiliations, which clearly showed the discordance between mtdna phylogeny and morphology. in total, seven larger haplogroups were detected, which are distributed in two major clades, a southern and a northern one. however, respective monophylies of the southern and northern clades are only weakly supported, suggesting that the divergence of the two clades most likely happened within a short time period. the major southern clade further divides into three clades, the southern chacma clade, representing haplotypes from the drakensberg, the cape, western rsa, southern and western namibia and south-western angola, the northern mixed chacma and yellow baboon clade, which includes chacma haplotypes from mozambique, northern rsa, zimbabwe, botswana, south-central zambia and north-eastern namibia, and yellow baboon haplotypes from malawi, eastern zambia and south-eastern tanzania, and finally, a clade of baboons that originated from central zambia, which morphologically represent kinda baboons. the triplet deletion in the nd region is an autapomorphy of clade since it was not found in any other papionin. the major northern clade divides into a western and an eastern clade. the western clade consists of one clade of olive baboon haplotypes found in ivory coast and western nigeria, a second clade of olive baboon haplotypes mainly from central and eastern nigeria and northern cameroon, and a well-defined clade of guinea baboon haplotypes covering the area from guinea to senegal. the eastern clade is comprised of a mixture of different species. the first separation concerns yellow baboons from the kenyan coast, whereas the second includes olive baboons from western uganda and eastern democratic republic of congo. furthermore, we found two more clades, one comprised of yellow and olive baboon haplotypes from northern tanzania, kenya and somalia while the other represents a mixture of olive and hamadryas baboon haplotypes from ethiopia, eritrea and the arabian peninsula. in total, ten well-supported terminal clades/lineages became apparent in our study, which represent geographic populations or demes. the only exceptions are southern yellow baboons, which are paraphyletic. the approximate geographical distribution of the respective haplogroups is shown in figure estimation of divergence times the data set used to estimate divergence times contains bp of sequence information from primate individuals. over half of the characters were variable and were parsimony-informative. the coding regions were found to best fit a trn model with both gamma distributed rate heterogeneity and a proportion of invariant sites, and non-coding regions were found to best fit a tvm + Γ + i model. using three divergence dates as calibrations, the papio-theropithecus divergence was dated at million years ago, which is in the same range as both, the estimate given by newman et al. and the divergence date suggested by fossil evidence. the subsequent divergences within papio are considerably younger and started in the late pliocene. the divergence of the ancestral papio stem into a southern and a northern lineage was inferred to have occurred at mya. shortly afterwards, the respective northern lineage diverged further into a western and an eastern clade and the respective southern lineage into a southern and a northern proto-chacma baboon clade. within the lineage leading to northern chacma baboons, kinda baboons diverged mya, followed by the separation of southern yellow baboons mya. the age of the most recent common ancestor of the north-western lineage leading to guinea and western olive baboons was estimated at mya. in this lineage, the earliest divergence was between olive baboons of clade w and a common clade of guinea/olive w the separation between the latter was estimated at mya. * not shown in figure 4 nodes used as calibrations are labelled with a "c", all others with an "n". in the north-eastern clade, coastal yellow baboons diverged first mya, followed by central olive baboons mya. eastern olive and northern yellow were mitochondrially separated from north-eastern olive and hamadryas baboons mya. the divergence ages for the north-eastern clade fall in the same range as found in earlier studies. newman et al. estimated separations within the north-eastern clade of less than mya. shotake et al. reported that ethiopian olive and hamadryas baboons have been separate lineages since approximately mya. discussion our phylogenetic reconstruction suggests that baboon populations can be diagnosed through mtdna and are sorted into several coherent and reasonably well-supported haplogroups that do not match with recognized baboon species. the discordance between mitochondrial phylogeny and baboon morphology, which is most likely equivalent to a discordance between mitochondrial and nuclear phylogeny, results in mitochondrial paraphyly, which is common among animal taxa including primates. the observed discordance might be explained by introgressive hybridization or incomplete lineage sorting since both can result in similar phylogenetic patterns and hence, complicate interpretation of phylogenetic reconstructions. although we can not rule out completely that incomplete lineage sorting may have had an effect, the strict geographical pattern of the baboon haplogroups provides some evidence against incomplete lineage sorting, because lineage sorting is a random process and the paraphyletic relationships that result from the failure of haplotypes to sort during speciation events should be random with respect to geography. in contrast, in our mitochondrial phylogeny geographic close populations cluster together, which is often a strong indication of reticulation. thus, we conclude that introgressive hybridization rather than incomplete lineage sorting has resulted in the discordance between mitochondrial and morphological phylogeny present in baboons. the introgression hypothesis becomes even more likely by the fact that baboons and other papionins show a strong tendency for intra- and intergeneric hybridization. generic hybridization was observed between papio and theropithecus and between papio and rungwecebus. for baboons, intrageneric hybrid zones are known for olive and northern yellow baboons, olive and hamadryas baboons and kinda and southern yellow baboons. male dispersal and female philopatry are the norm in baboons and other papionins and one can assume that this is the ancestral state. therefore male introgression would be the most likely introgression scenario, where males from one taxon invade groups of a neighbouring taxon and reproduce successfully. extensive backcrossing of the hybrid offspring over generations with more invading males of the first taxon would result in nuclear swamping. this process can lead to the extinction of the introgressed taxon and only their mitochondrial genomes would remain as vestiges of their former existence in a population which morphologically would be the same as the introgressing taxon. together with a recurrent isolation and reconnection of local baboon populations in many parts of their range due to climate changes the male introgression and nuclear swamping hypothesis can explain the striking discordance between mitochondrial phylogeny and baboon morphology. phylogeography the paraphyletic pattern suggests a complicated biogeographic history of baboon species. multiple phases of isolation, hybridization and introgression are highly probable, most likely triggered by the multiple cycles of expansion and retreat of savannah biomes during pleistocene glacial and inter-glacial periods. during the last million years there have been about glacial cycles of major forest expansions and retreats in africa. environments during glacial periods were characterized by dry, tropical scrub and grassland with limited gallery forest along drainages, and thus, with the retreat of dense forest into high altitude and large river refugia, savannah corridors opened and provided pioneering and recurrent dispersal possibilities for savannah adapted mammal populations, such as baboons. evidence for the multiple savannah and forest cycles come from pollen core data and the current distribution patterns of forest organisms. the divergence of the papio lineage accompanied by the dispersal from southern africa to the north and the further division into several distinct southern and northern lineages appears to be temporally in accordance with the expansion of savannah habitats and a major radiation of antelopes and the diversification of hominins, all as a result of the onset and recurrence of the northern hemisphere glaciations since ~ mya. a similar phylogeographic pattern of an early north-south division and the subsequent division of the northern clade into an eastern and western clade have also been shown for other large african savannah mammals, such as hartebeest alcelaphus buselaphus, topi damaliscus lunatus and wildebeest connochaetes taurinus, roan antelope hippotragus equinus, warthog phacochoerus africanus, giraffe giraffa camelopardalis and lion panthera leo. within several of these taxa paraphyletic relationships were detected, similar to the pattern found in baboons. these biogeographic patterns have been interpreted as results of plio-pleistocene climate cycles when the expansion of savannah habitats supported the dispersal of these taxa, although not for all taxa on the same time scale. however, a detailed analysis of these processes and a comparison with detailed data on climate and habitat change in africa during the last mya is far beyond the scope of our paper. our findings are almost consistent with the scenario for the mitochondrial population structure of papio laid out by c.j. jolly in his "north-south split" and "philopatry at the frontier" hypotheses. from our data the following scenario can be developed. baboons dispersed to the south and north from a southern african origin at times when climate and habitat conditions were suitable, that is if during dry conditions dense forests were replaced by savannah and savannah woodland. there is evidence from various sources that two savannah corridors existed during arid periods in the plio-pleistocene, which baboons could have followed on their way north. one migration route lead through a savannah corridor in eastern africa and a second through a savannah corridor in eastern drc west of the pleistocene forest refuge in the rift mountains. baboons migrating to the north subsequently dispersed over the complete northern savannah belt, from eritrea to senegal. changes of the climate to more humid condition with expanding forests probably led to the isolation of local baboon populations, because for most baboons dense forests constitute biogeographical barriers. these allopatric populations evolved for certain periods of time independently. subsequent climate changes to more arid conditions again opened savannah corridors so that isolated populations were able to reconnect, with the chance of gene flow. as an extreme outcome, some of the historical baboon populations might have been "swallowed" by invading populations and became extinct. male olive baboons, for example, reproduced with females from neighbouring populations, with subsequent nuclear swamping. olive baboons, thus, most likely absorbed these local baboon forms, such as w and w from which we can still find the mitochondrial genome in western olive baboons. a similar process occurred in east and north-east africa where olive baboons from kenya and northern tanzania carry mitochondria derived from a neighbouring yellow or proto-yellow baboon stock or in ethiopia and eritrea, where they carry hamadryas or proto-hamadryas mitochondria. in the latter cases, parts of the original populations still exist, as northern yellow and hamadryas baboons. however, hybridization between olive and yellow baboons and olive and hamadryas baboons is still going on. it is also likely that hybridization occurs at the western end of the olive baboon range, where olive and guinea baboons meet. similarly, introgression and nuclear swamping can explain why yellow baboons of zambia carry mitochondria only distantly related to those of northern tanzanian and kenyan yellow baboons, and chacma baboons from botswana and zambia are mitochondrially very distant from those living in south africa. in case of southern and northern yellow baboons a possible scenario could be that yellow baboons introgressed from the south into a neighbouring northern population after the retreat of an east african forest barrier. complete nuclear swamping would lead to a replacement of the local northern population with yellow baboons, which, however, would carry the mitochondria of the northern population. in case of chacma baboons we assume that they introgressed into parts of the southern yellow baboon population, thus replaced the yellow baboon nuclear genome, but retained the yellow baboon mitochondria. these events most likely took place early in the speciation process so that there was time for resulting chacma baboon population to evolve further into grey-footed chacmas. interestingly, zinner et al. found that the recently described genus rungwecebus also carries mitochondria of the northern chacma – southern yellow baboon haplogroup, suggesting that also on this intergeneric level introgression events occurred. our introgression hypothesis is partly built on similar sexually-differentiated introgression scenarios envisioned by wildman et al.. taxonomic implications our study shows that mtdna does not constitute a useful marker for the identification of the five traditionally recognized papio species. if terminal clades in our phylogeny would be regarded as phylogenetic species, one would have to split haplogroups of the same morphotype into different species or one would have to lump members of different morphotypes as one species, e.g. hamadryas and eastern olive baboons which are different not only in their morphology but even more in their social system. guinea baboons, which morphologically and genetically constitute a monophyletic clade seem to be the only exception. however, there are indications for introgression also from western olive baboons into guinea baboons. despite these limitations, our data, in combination with morphological, behavioural and additional genetic data support the recognition of kinda baboons as a distinct species. in our sample, we did not find any overlap between kinda and either southern yellow or northern chacma baboons. in contrast, in a more detailed study of the kinda baboons and neighbouring baboon populations, burrell found some evidence for gene flow between kinda and yellow baboons in a narrow contact zone in eastern zambia. similarly, clifford jolly found some intermediate morphotypes between grey-footed and kinda baboons where they meet. baboons of the southern chacma haplogroup possibly represent cape chacmas ursinus) and those of the northern chacma haplogroup grey-footed chacmas. griseipes), as was proposed by jolly. however, it remains to be explored, whether various haplogroups of yellow and olive baboons from eastern and western africa may represent formerly described, but now synonymised taxa.  the present study shows paraphyly in the genus papio and discordance between baboon morphology and mitochondrial phylogeny. accordingly, a classification of baboons based on mitochondrial sequence data is inappropriate. however, the geographic distribution of haplogroups provides insights into the evolutionary history of baboons and emphasizes the possible role of introgressive hybridization. periodical isolation of populations and subsequent range overlap, most likely triggered by climatic changes, might have led to a gradual hybridization influencing baboon diversification and speciation. the extent of introgression reaches from ongoing introgression of male olive baboon into yellow baboon population in amboseli to the complete extinction of historical populations or taxa in west or south-east africa by introgression where only the former mitochondrial genome remained as a trace in the current olive or grey-footed chacma baboon populations. since the evolutionary history of baboons shows some similarities with that of the human lineage, it seems plausible that the introgression scenario depicted herein might also be an extended model for reconstructing the evolution of homo. defining the extent of the reticulate events will require further molecular studies that incorporate additional samples and in particular nuclear loci. our study showed that collecting samples from all over the baboon range with known provenances is indispensable, but samples from further locations as indicated in figure should be included in ongoing studies. the analysis of nuclear loci, however, might be hampered by the fact that nuclear sequence variation is expected to be relatively low in baboons as shown for parts of the y-chromosome. 
to further elucidate the phylogenetic relationships among baboons, we extended earlier studies by analysing the complete mitochondrial cytochrome b gene and the'brown region' from specimens collected at sites, which represent all species and which cover most of the baboons' range. most likely all these biogeographic events were triggered by multiple cycles of expansion and retreat of savannah biomes during pleistocene glacial and inter-glacial periods. moreover, these studies revealed para- and polyphyletic mitochondrial clades for baboons from eastern africa, and it was hypothesized that introgressive hybridization might have contributed substantially to their evolutionary history. our study confirms earlier findings for eastern africa, but shows that baboon species from other parts of the continent are also mitochondrially paraphyletic. the phylogenetic patterns suggest a complex evolutionary history with multiple phases of isolation and reconnection of populations. traditionally, five phenotypically distinct species are recognized, but recent molecular studies were not able to resolve their phylogenetic relationships. based on phylogenetic tree reconstructions seven well supported major haplogroups were detected, which reflect geographic populations and discordance between mitochondrial phylogeny and baboon morphology. baboons of the genus papio are distributed over wide ranges of africa and even colonized parts of the arabian peninsula. defining the extent of the introgressive hybridization will require further molecular studies that incorporate additional sampling sites and nuclear loci.
 baboons of the genus papio are distributed over wide ranges of africa and even colonized parts of the arabian peninsula. traditionally, five phenotypically distinct species are recognized, but recent molecular studies were not able to resolve their phylogenetic relationships. moreover, these studies revealed para- and polyphyletic mitochondrial clades for baboons from eastern africa, and it was hypothesized that introgressive hybridization might have contributed substantially to their evolutionary history. to further elucidate the phylogenetic relationships among baboons, we extended earlier studies by analysing the complete mitochondrial cytochrome b gene and the'brown region' from specimens collected at sites, which represent all species and which cover most of the baboons' range.  based on phylogenetic tree reconstructions seven well supported major haplogroups were detected, which reflect geographic populations and discordance between mitochondrial phylogeny and baboon morphology. our divergence age estimates indicate an initial separation into southern and northern baboon clades million years ago. we found deep divergences between haplogroups within several species, but also recent divergence ages among species.  our study confirms earlier findings for eastern africa, but shows that baboon species from other parts of the continent are also mitochondrially paraphyletic. the phylogenetic patterns suggest a complex evolutionary history with multiple phases of isolation and reconnection of populations. most likely all these biogeographic events were triggered by multiple cycles of expansion and retreat of savannah biomes during pleistocene glacial and inter-glacial periods. during contact phases of populations reticulate events were highly likely, similar to ongoing hybridization, which is observed between east african baboon populations. defining the extent of the introgressive hybridization will require further molecular studies that incorporate additional sampling sites and nuclear loci. 