Palaeoclimatic events, dispersal and migratory losses along the Afro-European axis as drivers of biogeographic distribution in Sylvia warblers
© Voelker and Light; licensee BioMed Central Ltd. 2011
Received: 21 December 2010
Accepted: 14 June 2011
Published: 14 June 2011
The Old World warbler genus Sylvia has been used extensively as a model system in a variety of ecological, genetic, and morphological studies. The genus is comprised of about 25 species, and 70% of these species have distributions at or near the Mediterranean Sea. This distribution pattern suggests a possible role for the Messinian Salinity Crisis (from 5.96-5.33 Ma) as a driving force in lineage diversification. Other species distributions suggest that Late Miocene to Pliocene Afro-tropical forest dynamics have also been important in the evolution of Sylvia lineages. Using a molecular phylogenetic hypothesis and other methods, we seek to develop a biogeographic hypothesis for Sylvia and to explicitly assess the roles of these climate-driven events.
We present the first strongly supported molecular phylogeny for Sylvia. With one exception, species fall into one of three strongly supported clades: one small clade of species distributed mainly in Africa and Europe, one large clade of species distributed mainly in Africa and Asia, and another large clade with primarily a circum-Mediterranean distribution. Asia is reconstructed as the ancestral area for Sylvia. Long-distance migration is reconstructed as the ancestral character state for the genus, and sedentary behavior subsequently evolved seven times.
Molecular clock calibration suggests that Sylvia arose in the early Miocene and diverged into three main clades by 12.6 Ma. Divergence estimates indicate that the Messinian Salinity Crisis had a minor impact on Sylvia. Instead, over-water dispersals, repeated loss of long-distance migration, and palaeo-climatic events in Africa played primary roles in Sylvia divergence and distribution.
The avian genus Sylvia is an Old World warbler lineage comprising roughly 25 species, to include species which were until recently placed in other genera [[1–3]; Parisoma, Pseudalcippe, and Horizhorinus, respectively]. The genus as a whole is distributed from central Eurasia to the tip of South Africa, and about 70% of Sylvia species have ranges that abut, or very nearly abut, the Mediterranean Sea. Individual species' ranges vary from widespread inter-continental migrants such as the Greater Whitethroat (Sylvia communis) to highly restricted island endemics in the Mediterranean Sea and Gulf of Guinea to include the Balearic Warbler (Sylvia balearica) and Dohrn's Thrush-babbler [Sylvia dohrni; [3, 4]].
Because Sylvia species are highly variable in distribution, range sizes and migratory behavior, they have been used extensively as a model system in a variety of studies including morphological evolution, the genetics of migration, the effects of climate change on migration, and the evolution of range size [e.g., [2, 5–10]]. Some of these studies have relied on molecular phylogenies as the basis for understanding evolutionary patterns in the genus [e.g., [2, 9]]. The phylogenies used, however, have generally been based on neighbor-joining algorithms and the resulting phylogenetic hypotheses have lacked support for most relationships. The only study to use molecular tools to investigate the historical biogeography of the genus relied on DNA-DNA hybridization of 20 Sylvia species; results were such that only a few broad-brush biogeographic questions could be addressed .
Although lasting for a rather short period of evolutionary time [from 5.96-5.33 Ma; ], the desiccation of the Mediterranean would have allowed land-based colonization routes for population expansion to islands (e.g., Sardinia) and between Europe and Africa. Subsequent re-filling of the Mediterranean at the end of the MSC would have created a vicariant barrier to further land-based colonization, thus driving lineage diversification between (now isolated) populations. This same mechanism could explain the trans-Mediterranean distribution of a number of Sylvia species . Alternatively, lineages could have diverged while the Mediterranean was filled, before or after the MSC, suggesting that over-water dispersal might have been important in the evolution of Sylvia, as has been shown in other avian lineages [e.g., [14, 15]]. Molecular clock dates are key to being able to discriminate between vicariance and dispersal hypotheses [e.g., ]. Similar questions relating to the possible vicariant impact of the MSC on lineage divergence, or the Mediterranean as a dispersal barrier to island or intercontinental colonization have been addressed for a variety of animal taxa to include butterflies [e.g., ], fish [e.g., [18, 19]], mammals [e.g., [20, 21]], and reptiles and amphibians [e.g., [22–24]].
Away from the Mediterranean, distributions of other Sylvia species suggest that both Asian-African and Northeastern (e.g., Ethiopia)-Southern African interchanges were important in the evolution of the genus (Figure 1). There are good palaeo-climatic and palaeo-ecological records of African habitats extending back to the late Miocene, and major shifts in climate had a significant impact on Afrotropical forest expansion and contraction. These forest shifts have been shown to have been important in the evolution of a variety of vertebrate lineages, serving as vicariance barriers for species breeding in arid or montane regions, and as dispersal corridors from Asia for forest adapted species [e.g., [16, 25–31]].
Our aims in this paper were to develop a well-resolved molecular phylogenetic hypothesis of Sylvia warblers, and to use this phylogeny in conjunction with molecular clock calibrations to reconstruct the historical biogeography of the genus. Based on Sylvia distributions, we hypothesize that the Messinian Salinity Crisis will have played a major role in lineage diversification around the Mediterranean Sea. Because most African breeding Sylvia species do not breed in tropical forests, we further hypothesize that expansion and contraction of Afrotropical forests will have played a role in lineage diversification between northern and southern African species. In assessing these hypotheses, we also assess the possible role that changes in migratory habit might have played in the evolution of Sylvia distributions.
Molecular methods and phylogenetic analysis
Species, museum voucher specimen or tissue number, and country of collection for specimens examined
Country of collection
Russia: Avtonomna Respublika Krym
Russia: Krasnodarskiy Kray
Russia: Vologodskaya Oblast
Russia: Krasnodarskiy Kray
Russia: Chitinskaya Oblast
Russia: Chitinskaya Oblast
Russia: Avto. Respublika Krym
Russia: Vologodskaya Oblast
Mallorca: Cabrera Island
We obtained extracted DNA for a number of species (those preceded by a "B" in Table 1), which have been previously used in assessments of Sylvia relationships [e.g., [2, 9]]. For new samples, whole genomic DNA was extracted from tissue using the DNeasy tissue extraction kit (Qiagen). For all samples, we used the polymerase chain reaction (PCR) to amplify the mitochondrial NADH dehydrogenase subunit 2 (ND2) and cytochrome-b (cyt-b) genes using published primers and protocols . Automated sequencing was performed using BigDye (Applied Biosystems) and products were run out on an ABI 377 sequencer.
We used SEQUENCHER, version 4.5 (Gene Codes) to align ND2 and cyt-b sequences for each sample. To ensure the accuracy of amplification of the ND2 and cyt-b genes, we sequenced both heavy and light strands, and verified that sequence data were protein-coding. Sequences have been deposited on GenBank under accession numbers JF502273-JF502352 and alignments are available on TreeBase (submission S11495).
Combined sequence data were analyzed under three different weighting schemes using Bayesian methods. In our first weighting scheme (two partitions) the ND2 and cyt-b genes were unlinked and allowed to estimate gene appropriate GTR + I + Γ parameters. In the second (four partitions), first and second codons were linked for ND2, linked for cyt-b gene, and third codon positions for each gene were treated as independent partitions. In the third scheme (six partitions), each codon position was unlinked. We used MrModelTest  to determine appropriate models of nucleotide substitution and to choose best-fit model of sequence evolution for each partition.
For each weighting scheme, we used MRBAYES  to initiate four runs of four Markov-chain Monte Carlo (MCMC) chains of 2 million generations each from a random starting tree, sampling every 100 generations. Each run resulted in 20,000 trees and converged on the same topology. The first 50,000 generations (5000 trees) from each analysis were removed as our "burn-in", and the remaining 60,000 trees were used to create a majority rule consensus tree. A longer run of 4 million generations did not affect tree topology or posterior probability values. Bayes factors were computed using the harmonic means of the likelihoods calculated from the sump command within MRBAYES. A difference of 2 ln Bayes factor >10 was used as the minimum value to discriminate between analysis schemes [38, 39], and the six partition weighting scheme was identified as the best fit to the data.
In addition to assessing nodal support via posterior probabilities derived from MRBAYES, we also assessed nodal support via 1000 bootstrap pseudo-replicates in Randomized Axelerated Maximum Likelihood Computing [RAxML-VI-Abe; ], using GTR + I + Γ parameters for each codon position.
We used the program BEAST v1.6.1 to estimate divergence times within Sylvia [41, 42]. Prior to these analyses, the data set was pruned to include only one representative of each species in most cases; two representatives per species were included when high levels of genetic differentiation were present within a species (e.g., curruca). Because of the absence of an acceptable fossil calibration point within Sylvia, we employed a lineage substitution rate of 0.0105 per site/million years. This mean substitution rate translates to 2.1% per million years, and is generally accepted as applicable to the cyt-b gene in songbirds [e.g., ]. We employed a normal distribution for this prior and assigned a standard deviation of 0.0013, which encompasses a slower (1.6%) and faster (2.53%) estimate calculated for songbird cyt-b substitution rates in other studies [44, 45]. Before estimating divergence times, likelihood ratio tests were performed using PAUP* 4.0b10s  to determine if the cyt-b sequence data departed significantly from clocklike behavior. These analyses revealed the Sylvia cyt-b data are not clocklike, therefore our substitution rate was enforced using a relaxed, uncorrelated lognormal clock. In BEAST, a Yule process speciation prior and an uncorrelated lognormal model of rate variation were implemented in each analysis. The best-fit model of nucleotide substitution for the entire cyt-b gene was selected as described above (GTR+I+G). Two separate MCMC analyses were run for 10,000,000 generations with parameters sampled every 1000 steps, and a 10% burn-in. Independent runs were combined using LogCombiner v.1.6.1 . Tracer v.1.5  was used to measure the effective sample size of each parameter (all resulting effective sample sizes exceeded 200) and calculate the mean and upper and lower bounds of the 95% highest posterior density interval (95% HPD) for divergence times. Tree topologies were assessed using TreeAnnotator v.1.6.1  and FigTree v.1.3.1 . Analyses performed separating codon positions into individual partitions resulted in failure of the BEAST run to converge after 100,000,000 generations in the MCMC analyses.
For biogeographic analysis, we used both Dispersal-Vicariance Analysis [DIVA; ] and likelihood analysis of geographic range evolution (dispersal-extinction cladogenesis) implemented in LaGrange v. 2.0.1 . In DIVA we used the "maxareas" option to limit the range of ancestral distributions to no more than two areas. In LaGrange we used the default number of ancestral distributions which is based on the overall number of area distributions. In both analyses, we used range maps  to code each species as present or absent in each of five areas: Africa south of the Sahara, North Africa, Mediterranean Islands, Europe, and Asia (which was broadly defined to include the Saudi Peninsula and the Middle East; Figure 1). The dividing point between Europe and Asia was Turkey (Figure 1). In LaGrange, ancestral areas were reconstructed by performing likelihood optimizations on the BEAST maximum clade credibility tree.
We ran two sets of analyses based on the above distributions. In the first, we included island distributions for those species that also had broad continental distributions; this led to a result of Mediterranean Islands being the ancestral area at most nodes in one major clade (see below). In the second analyses, we only scored a species as having an island distribution if it was an island endemic (balearica, sarda, melanothorax) or nearly endemic (rueppelli).
We classified each species as having migratory or sedentary behavior, following the designations used by Böhning-Gaese et al. . We used MacClade  to trace and reconstruct ancestral character states across the phylogeny.
Maximum likelihood (ML) and Bayesian analyses identified a monophyletic Sylvia relative to the outgroup taxa (Figure 2). Both Bayesian posterior probabilities (PP) and ML bootstrap support (BS) values indicated very strong support for most relationships in Sylvia. Just four nodes were supported at less than 0.95 PP, and only two nodes were supported at less than 75% BS (Figure 2).
Three major clades are evident in the phylogeny (Figure 2). Clade 1 comprises a group of four species, two of which are endemic to Africa (dohrni and abysinnicus) and two that breed largely in Europe or Eurasia and winter largely in Africa (borin and atricapilla). Voelker et al.  previously suggested that dohrni belonged in this clade as sister to abysinnicus, rather than in the monotypic genus Horizorhinus, and our results here confirm this.
The next divergence places Sylvia nana basal to the two remaining major clades (Clades 2 and 3), although the sister relationship between these major clades is not well supported by either PP or BS measures (Figure 2). Clade 2 comprises a group of 11 species with breeding distributions around the Mediterranean (including southwestern Asia), and includes three Mediterranean island endemics (balearica, sarda, and melanothorax). Nodal support values for most relationships in this clade are high under one or both measures of support.
Clade 3 is comprised of species that breed around the Mediterranean (including southwestern Asia), as well as four African endemics (boehmi, subcaeruleum, layardi, and lugens). Ten, and perhaps 11 species are included in this clade, depending on how curruca 1 is defined (Figure 2). The relatively deep divergence between our curruca samples (8% uncorrected cyt-b data) suggests that two species could be included here. Based on phenotypic and molecular data two species, minula and althaea, have been recognized as species distinct from curruca. However the systematics and species status of minula and althaea remains controversial . Our curruca 1 is from the defined range of "minula" but we did not have a sample from the range of althaea (2 and 3 are from the defined range of curruca). Regardless, as minula is a Eurasian breeding migrant its recognition here would not influence our additional analyses, and we keep this sample identified as curruca. As with the other major clades, relationships in this third clade are strongly supported.
Biogeographic history and divergence dating
Sylvia nana diverged from the remaining Sylvia 14.5 Ma, and Clades 2 and 3 diverged from one another 12.6 Ma (Figure 4). Asia is reconstructed as the ancestral area for these clades (Figure 3). Within Clade 3, four Asian to African movements are evident. One movement accounts for the North African component of the range of hortensis, while the remaining movements account for sub-Saharan distributions of lugens, leucomelaena and the boehmi clade (Figure 3). Most divergences in Clade 3 occur in the Miocene and Pliocene; just one divergence is dated in the Pleistocene (Figure 4).
Lineage divergence within Clade 2 began 6.8 Ma, prior to the beginning of the MSC at 5.96 Ma (Figure 4). Six subsequent divergences occur in the late Miocene and four occur in the Pliocene (Figure 4). In Clade 2, Island endemics are not each other's closest relatives, indicating multiple vicariance or dispersal events. In this clade, ancestral area reconstructions conflicted depending on how species distributions were coded. If Island distribution was restricted to island endemics (balearica, sarda, melanothorax) and rueppelli (a species with a combined island and very small continental distribution), then continental areas are reconstructed as ancestral for the clade (Figure 3). However, if broadly distributed continental species that also have island distributions are coded as such, then Island is reconstructed as the sole ancestral area for every node in Clade 2 by LaGrange, and for all but two nodes by DIVA (Island + another area; Figure 3). This conflict results in competing interpretations of the biogeographic history of this clade (see below).
Evolution of migration
Migration is reconstructed as the ancestral state for Sylvia, and as the ancestral state for each of the three major clades (Figure 3). Seven changes in migratory habit are evident but several branches are reconstructed as equivocal under the most parsimonious reconstruction of character state (Figure 3). Using ACCTRAN (change forced to base of tree) to resolve character states at these equivocal nodes suggests that sedentary behavior independently evolved four times, with migratory behavior subsequently evolving three times in two otherwise sedentary clades. Using DELTRAN (change delayed toward tree tips) to resolve character states suggests that migration was lost seven times (no gains; Figure 4). Deciding when to use ACCTRAN or DELTRAN can be problematic [e.g., ], but we suggest that assuming more recent evolutionary changes (DELTRAN) in migratory behaviors are consistent with similar studies (both inter- and intraspecific) of other avian lineages which suggest that birds can and do respond rapidly to environmental changes by changing migratory behaviors [e.g., ].
Even with long-standing interest in Sylvia systematic relationships, and the use of Sylvia as a model system to explore the evolution of patterns in morphology and range sizes [e.g., [1, 2, 6, 8, 9]], the ML phylogeny presented here is the first strongly supported hypothesis of relationships for the genus. Despite this, however, there is topological concordance between our phylogeny and a recent neighbor-joining (NJ) phylogeny used to assess range size in Sylvia [9; BGEA hereafter]. Although the BGEA phylogeny had just 10 of 24 nodes supported at >74% BS, it recovered the three major clades that we recovered in our more exhaustive searches; Sylvia nana was similarly positioned as well.
Intra-clade differences do exist between the BGEA NJ and our ML topologies. Our Clade 1 places S. atricapilla basally and places S. borin as sister to other clade members (abyssinica + dohrni), whereas abyssinica occupies the basal position with atricapilla and borin as sisters in BGEA. Our Clade 2 places the deserticola, melanothorax, and mystacea clade as sister to all other clade members, while BGEA places communis as the basal taxon. Our placement of communis renders a "Mediterranean species group" [2, 8] polyphyletic. Differences in Clade 2 also include the placement of rueppelli, deserticola, conspicillata, and consequently sister relationship differences are evident as well. Our Clade 3 is topologically congruent with that of BGEA, with the exception of hortensis which BGEA placed basally to crassirostris and leucomelaena. Thus, while there are topological similarities between our phylogeny and that of BGEA (which is itself similar to previous phylogenies based on NJ or DNA-DNA hybridization [1, 2, 8]), sufficient differences exist to warrant reassessment of results based on those topologies, all of which were less well supported than our ML phylogeny.
It is possible that nuclear sequence data could provide support for the few nodes that have low support in our phylogeny (Figure 2), or narrow the confidence intervals on our divergence estimates (Figure 4). However, in most avian systematic studies which combine nuclear with mtDNA data or that use nuclear data to test mtDNA results, the nuclear data have not been overly successful at supporting relationships except when species are highly divergent or species-level sampling within a genus is low [e.g. [54, 55]]. With respect to divergence dating, studies that examine ways to narrow credibility intervals find that the most important factors affecting divergence time estimation using molecular data are the number and distribution of calibration points on the tree [56–59]. These calibrations are primarily fossils, which are generally lacking in number and temporal distribution for most songbird lineages.
Biogeography and lineage diversification: the MSC versus over-water dispersal
Did the MSC impact speciation in Sylvia, as it has other animal lineages [e.g., [17–24]]? Our divergence dating results suggest that the MSC probably did have an impact, albeit very limited. This is particularly relevant with respect to Clade 2 where most species are distributed around the Mediterranean Sea or on Mediterranean Islands (Figures 3, 4). The initial divergences within Clade 2 occur before the beginning of the MSC, with confidence intervals indicating a possibility that diversification could have begun during the MSC. However, these pre-MSC diversifications are not divergences between terminal taxa or between Island versus mainland (or Africa versus Europe) groups. Therefore, we cannot make a convincing argument for population expansion during MSC followed by population fragmentation and isolation as the Mediterranean refilled (i.e., vicariance) as a main driver of speciation in Sylvia.
Consequently, we must instead argue that there has been substantial overwater (trans-Mediterranean) dispersal in Clade 2 since the MSC to explain why many species have Europe + North African distributions (Figure 3). A dispersal argument is supported by the high number of dispersal events inferred by DIVA, and the high number of dispersals can probably be linked to most species with Europe + North African (or broader) distributions being migratory (Figure 3).
Further, several Island restricted species (balearica and sarda) clearly achieved their distributions well after the MSC, which suggests over-water dispersals (Figure 4). However, divergence estimates for melanothorax (island endemic) and rueppelli (near island endemic) suggest the possibility that these species achieved their island distributions during the MSC, and became isolated as the Mediterranean refilled at 5.33 Ma (Figure 4). As mentioned above, ancestral area reconstructions and thus biogeographic reconstructions conflict depending on how Island is coded. As such, Islands are either the ancestral distribution for this clade, or they are derived distributions from an Asian ancestral area (Figure 3). While island distributions are typically derived from continental areas [e.g., [16, 28, 55]], it is clear that islands may also be the source area(s) from which continental distributions are established [e.g., [14, 15, 28, 56]]; migratory behavior is often invoked in the establishment of these distributions.
Post-Miocene divergence dates suggest that Plio-Pleistocene Mediterranean Sea level changes and glacial cycles can also be implicated as factors in driving speciation in Clade 2, where many species have distributions that include Europe (Figure 3). If these factors can be implicated this would suggest that lineage divergence occurred in and between refugial areas [e.g., [34, 57–59]]. However, given the extensive range overlap of many closely related species (e.g., rueppelli, melanocephala, cantillans) in Clade 2, we are unable to address this possibility with our data. Phylogeographic studies of European species would be necessary to identify ancestral populations, and to determine whether currently overlapping species were in fact isolated in different refugial areas.
Biogeography and lineage diversification: the role of migration
It does seem likely that migration played a role in the diversification and distribution of Sylvia, as migratory changes in Clade 2 are consistent with the establishment of all three Island endemic distributions (Figure 3). If Island is the ancestral area for Clade 2, then migratory + Island are the states reconstructed at most basal nodes; subsequently some Island endemics became non-migratory residents, and continental distribution evolves six times (Figure 3). However, given that migration is the ancestral state for the clade and because no extant Island breeding endemic species has retained long-distance migratory behavior, we feel it more parsimonious to assume that Island endemic distributions in Clade 2 were derived from continental distributions as function of the loss of migration (Figure 3). This then suggests that broadly distributed migratory ancestors' established Island distributions, lost their migratory habit, and were then isolated to become sedentary residents. An exception to this pattern could be melanothorax, which may have lost migration after isolation during the MSC (see above; Figure 3). A loss of long-distance migration is also related to the distribution of deserticola in North Africa, and the Island + mainland (coastal Mediterranean) distribution of undata (Figure 3).
It is less clear how the loss of migration might have played a role in lineage divergence and distribution elsewhere on the phylogeny. In Clade 1, a migratory loss is inferred for the African species dohrni and abysinnicus and is related to their divergence from borin (Figure 3), a Eurasian-breeding species which winters in Africa. This migratory drop-off in Africa suggests a response to ecological change or opportunity, which can clearly play a role in whether migration is gained or lost [e.g., [54, 60]]. However, the dohrni-abysinnicus divergence from borin at 12.7 Ma cannot be directly linked to Afro-tropical forest expansion which has been widely implicated in vertebrate speciation in Africa (see below) at ca. 5 Ma [Figure 4; [61–63]]. Neither forest dynamics nor change in migratory behavior can explain the divergence between abysinnicus (widespread in Africa) and dohrni [endemic to Príncipe in the Gulf of Guinea; ]. This divergence is necessarily explained by an over-water dispersal event by our data here, and the fact that Príncipe is part of the oceanic sector of the volcanic Cameroon Line, and as such has never been connected to mainland Africa . Given the recent discovery that dohrni belongs within Sylvia  it is possible that other Sylvia taxa are currently recognized under other genera. One possible example is Lioptilus nigricapillus, which was shown to fall between atricapilla and abysinnicus [but no other Sylvia included; ]. Inclusion of Lioptilus in a Bayesian analysis (unpublished data from S. Reddy) indicates a sister relationship with dohrni and abysinnicus (not shown) thereby supporting just a single loss of migration in this clade. Additional "unrecognized" African Sylvia could change both the sister relationship we report for dohrni-abysinnicus, as well as our inference regarding when migration was lost in Clade 1.
In Clade 3, migration was lost three times (Figure 3) and these losses are primarily associated with African taxa. Given that Asia is reconstructed as the ancestral area for this clade, and that migratory behavior is also ancestral, this suggests that these sedentary African lineages are the result of migratory drop-offs (see also below).
Biogeographic and lineage diversification: other factors driving speciation in Sylvia
It is clear that for species with breeding distributions across Eurasia or that are endemic to Asia or Africa south of the Sahara, factors other than the MSC must be considered to explain lineage divergences. These divergences can include deep intra-specific differences. For example, the divergence between our samples of curruca (dated to 4.9 Ma; Figure 4), could be related to Central Asian aridification peaks which fragmented multiple Eurasian avian lineages through time . This explanation is less likely to explain the deep divergences in either atricapilla or borin, as neither breeds in Eastern Asia . However, divergences in both species are dated near the Plio-Pleistocene boundary (ca. 1.8 Ma; Figure 4), suggesting that European glacial events may have been involved in their divergences. European Pleistocene refugia have been suggested to explain divergences within cantillans , although that study did not attempt to date lineage divergences; our results suggest that very late Pliocene events might also have been important for atricapilla and borin. An alternative for the divergence of atricapilla is that disjunct wintering ranges translate to genetically isolated breeding populations. Although wintering range is not fragmented for borin, there is clear evidence that migratory route is under strong genetic control in this species [5, 7], and ringing recoveries indicate that breeding populations winter, to some extent, in different areas  and are therefore potentially isolated from one another year-round.
At ca. 9.8 Ma Clade 3 diverged in to two sub-clades (Figure 4), one of which is endemic to Africa and is the result of a dispersal event (with migratory loss) from Asia according to ancestral area reconstructions (Figure 3). This clade comprises three arid-adapted species: boehmi is distributed from Ethiopia to Tanzania, while both layardi and subcaeruleum are distributed in southern-most Africa . The timing of movement of this clade from Asia into Africa (Figure 4) was likely facilitated by climate and habitat changes that resulted in an increase in grasses (i.e., more open habitats) in east Africa from 9-5 Ma [see [25, 26]], and an inferred movement during this period is consistent with Eurasian to African dispersals by other arid-adapted birds [e.g., [16, 35]]. Isolation from an Asian ancestor (and a migratory loss) could be explained by tropical forest expansion at 5 Ma, which would have served as a vicariance event isolating this clade in southern Africa [e.g., [16, 35]].
A second dispersal in this sub-clade, from southern to northeastern Africa, is necessary to explain the distribution of boehmi which diverged from a common ancestor with subcaeruleum 7 Ma (Figure 4). This date seems inconsistent with the general pattern of speciation in arid-adapted species, in that the current range of boehmi spans, both to the north and to the south, the region of eastern Africa where the Afrotropical forest expanded to coastal Kenya. We suggest that prior to establishing its current range, boehmi was either isolated in the north (Ethiopia) from subcaeruleum prior to forest expansion with an extended period for divergence, or that boehmi was isolated in the south (Tanzania). The latter seems more likely given the divergence and palaeo-climatic dates (a phylogeographic study could discriminate between scenarios). A Tanzanian isolation scenario suggests that subcaeruleum and boehmi may have diverged across different arid zone habitats; a similar explanation is necessary to explain their divergence from layardi, whose distribution extensively overlaps that of subcaeruleum .
Distributions of the remaining species in Clade 3 involve one dispersal to North Africa + Europe + Islands (hortensis) and two dispersals to Africa (lugens and leucomelaena; Figure 3). The Red Sea is involved in both the distribution of leucomelaena (western and southern Saudi Peninsula + Egypt to Eritrea) and the lugens (Ethiopia to Tanzania) divergence from its common ancestor with buryi (Saudi Peninsula). The Red Sea expanded ca. 7 Ma and seawater had penetrated the northern region of the sea by at least 5 Ma [67, 68], suggesting that the sea has been a barrier to biotic dispersion since the Miocene-Pliocene boundary. The exception to this is evidence of land-bridges thought to have formed five times during the last 500,000 years, as a result of sea-level lowering during glacial maxima [69, 70]. The lugens-buryi divergence is dated at 2.9 Ma (Figure 4), suggesting a dispersal event across the Red Sea. This date is consistent with Pliocene tropical forest retraction ca. 3-2.5 Ma ago [61–63], and the concomitant expansion of grassland and desert environments in northeastern Africa . Thus, the lugens-buryi divergence occurred when suitable habitat became available; similar 'suitable habitat' arguments have, when temporally associated with lineage divergences, been used to explain African-Asian interchange in lizards , birds [16, 27, 28] and mammals [25, 26, 30]. Although our single sample does not allow us to discuss the evolution of distribution in S. leucomelaena, additional sampling could reveal whether its trans-Red Sea distribution is the result of over-water dispersal, movement between the Saudi Peninsula and Egypt, or movement across land-bridges during the last 500,000 years.
Our analyses provide the first well-resolved phylogeny for Sylvia warblers, a focal genus for a variety of morphological, behavioral, systematic, and evolutionary studies [e.g., [1, 2, 5, 7–9]]. Molecular clock calibration suggests that Sylvia arose in the early Miocene (19.4 Ma), and that few lineage divergences in the genus were directly driven by palaeo-climatic changes associated with the Messinian Salinity Crisis. Losses of long-distance migratory behavior are correlated with several lineage divergences and distributions, particularly African lineages or Island endemic species. Elsewhere in the phylogeny, divergences can be linked to broad-scale palaeo-climatic events that have been shown to have affected a multitude of vertebrate lineages in both Eurasia [e.g., ] and Africa [e.g., [16, 26, 29, 31, 35]]. There is evidence that palaeo-climatic changes near the Plio-Pleistocene boundary may have impacted lineage divergences in Sylvia [34, this study], and additional study is needed to determine if these divergences warrant the recognition of additional Sylvia species.
We thank the following researchers and museums for the loan of samples used in the study: Katrin Böhning-Gaese, Barrick Museum of Natural History, Moscow State University Zoological Museum, San Diego State University, United States National Museum, University of Washington Burke Museum, Yale Peabody Museum of Natural History, and Zoological Museum University of Copenhagen, and especially Martin Haase for samples from the collection of Andreas Helbig. Laboratory work was supported by NSF DEB-0613668 to GV and R.C.K. Bowie. We thank K. Arnold for her efforts in the lab and two anonymous reviewers for helpful comments for improving the manuscript. This is publication number 1371 of the Texas Cooperative Wildlife Collection and number 191 of the Center for Biosystematics and Biodiversity, both at Texas A&M University.
- Blondel J, Catzeflis F, Perret P: Molecular phylogeny and the historical biogeography of the warblers of the genus Sylvia (Aves). J Evol Biol. 1996, 9: 871-891. 10.1046/j.1420-9101.1996.9060871.x.View ArticleGoogle Scholar
- Böhning-Gaese K, Schuda MD, Helbig AJ: Weak phylogenetic effects on ecological niches of Sylvia warblers. J Evol Biol. 2003, 16: 956-965. 10.1046/j.1420-9101.2003.00605.x.View ArticlePubMedGoogle Scholar
- Voelker G, Melo M, Bowie RCK: A Gulf of Guinea island endemic is a member of a Mediterranean-centered bird genus. Ibis. 2009, 151: 580-583. 10.1111/j.1474-919X.2009.00934.x.View ArticleGoogle Scholar
- del Hoyo J, Elliott A, Christie DA: Handbook of the Birds of the World. Vol. 11, Old World Flycatchers to Old World Warblers. 2006, Barcelona: Lynx EdicionsGoogle Scholar
- Gwinner E, Wiltschko W: Endogenously controlled changes in migratory direction of the Garden Warbler, Sylvia borin. J Comp Physiol. 1978, 125: 267-273. 10.1007/BF00656605.View ArticleGoogle Scholar
- Leisler B, Winkler H: Ecomorphology. Curr Ornithol. 1985, 2: 155-186.View ArticleGoogle Scholar
- Gwinner E: Circannual rhythms in bird migration: control of temporal patterns and interactions with photoperiod. Bird Migration--Physiology and Ecophysiology. Edited by: Gwinner E. 1990, New York: Springer-Verlag, 257-268.View ArticleGoogle Scholar
- Shirihai H, Gargallo G, Helbig AJ: Sylvia Warblers. Identification, Taxonomy and Phylogeny of the Genus Sylvia. 2001, London: A & C BlackGoogle Scholar
- Böhning-Gaese K, Caprano T, van Ewijk K, Veith M: Range Size: Disentangling current traits and phylogenetic and biogeographic factors. American Naturalist. 2006, 167: 555-567. 10.1086/501078.View ArticlePubMedGoogle Scholar
- Doswald N, Willis SG, Collingham YC, Pain DJ, Green RE, Huntley B: Potential impacts of climatic change on the breeding and non-breeding ranges and migration distance of European Sylvia warblers. J Biogeogr. 2009, 36: 1194-1208. 10.1111/j.1365-2699.2009.02086.x.View ArticleGoogle Scholar
- Hsü KJ, Montadert L, Bernouilli D, Cita MB, Erikson A, Garrison RE, Kidd RB, Melieres F, Muller C, Wright R: History of the Mediterranean salinity crisis. Nature. 1978, 267: 399-403.View ArticleGoogle Scholar
- Hsü KJ, Ryan WBF, Cita MB: Late Miocene desiccation of the Mediterranean. Nature. 1973, 242: 240-244. 10.1038/242240a0.View ArticleGoogle Scholar
- Krijgsman W, Hilgen FJ, Raffi I, Sierro FJ, Wilson DS: Chronology, causes and progression of the Messinian salinity crisis. Nature. 1999, 400: 652-655. 10.1038/23231.View ArticleGoogle Scholar
- Filardi CE, Moyle RG: Single origin of a pan-Pacific bird group and upstream colonization of Australasia. Nature. 2005, 438: 216-219. 10.1038/nature04057.View ArticlePubMedGoogle Scholar
- Voelker G, Rohwer S, Outlaw DC, Bowie RCK: Repeated trans-Atlantic dispersal catalyzed a global songbird radiation. Global Ecology and Biogeography. 2009, 18: 41-49. 10.1111/j.1466-8238.2008.00423.x.View ArticleGoogle Scholar
- Voelker G: Dispersal, vicariance and clocks: Historical biogeography and speciation in a cosmopolitan passerine genus (Anthus: Motacillidae). Evolution. 1999, 53: 1536-1552. 10.2307/2640899.View ArticleGoogle Scholar
- Kodandaramaiah U, Wahlberg N: Phylogeny and biogeography of Coenonympha butterflies (Nymphalidae: Satyrinae) - patterns of colonization in the Holarctic. Syst Entomol. 2009, 34: 315-323. 10.1111/j.1365-3113.2008.00453.x.View ArticleGoogle Scholar
- Reichenbacher B, Kowalke T: Neogene and present-day zoogeography of killifishes (Aphanius and Aphanolebias) in the Mediterranean and Paratethys areas. Palaeogeography, Palaeoclimatology, Palaeoecology. 2009, 281: 43-56. 10.1016/j.palaeo.2009.07.008.View ArticleGoogle Scholar
- Perea S, Bohme M, Zupancic P, Freyhof J, Sanda R, Ozulug M, Abdoli A, Doadrio I: Phylogenetic relationships and biogeographical patterns in Circum-Mediterranean Subfamily Leuciscinae (Teleostei, Cyprinidae) inferred from both mitochondrial and nuclear data. BMC Evol Biol. 2010, 10: 265-10.1186/1471-2148-10-265.View ArticlePubMedPubMed CentralGoogle Scholar
- Agustí J, Garcés M, Krijgsman W: Evidence for African-Iberian exchanges during the Messinian in the Spanish mammalian record. Palaeogeography, Palaeoclimatology, Palaeoecology. 2006, 238: 5-14. 10.1016/j.palaeo.2006.03.013.View ArticleGoogle Scholar
- Dubey S, Koyasu K, Parapanov R, Ribi M, Hutterer R, Vogel P: Molecular phylogenetics reveals Messinian, Pliocene, and Pleistocene colonizations of islands by North African shrews. Mol Phylogenet Evol. 2008, 47: 877-882. 10.1016/j.ympev.2007.12.014.View ArticlePubMedGoogle Scholar
- Fromhage L, Vences M, Veith M: Testing alternative vicariance scenarios in Western Mediterranean discoglossid frogs. Mol Phylogenet Evol. 2004, 31: 301-322.View ArticleGoogle Scholar
- Veith M, Mayer C, Samraoui B, Barroso D, Bogaerts S: From Europe to Africa and vice versa: evidence for multiple intercontinental dispersal in ribbed salamanders (Genus Pleurodeles). J Biogeogr. 2004, 31: 159-171. 10.1111/j.1365-2699.2004.00957.x.View ArticleGoogle Scholar
- Kornilios P, Kyriazi P, Poulakakis N, Kumlutaş Y, Ilgaz Ҫ, Mylonas M, Lymberakis P: Phylogeography of the ocellated skink Chalcides ocellatus (Squamata, Scincidae), with the use of mtDNA sequences: A hitch-hiker's guide to the Mediterranean. Mol Phylogenet Evol. 2010, 54: 445-456. 10.1016/j.ympev.2009.09.015.View ArticlePubMedGoogle Scholar
- Vrba ES: African Bovidae: Evolutionary events since the Miocene. S Afr J Sci. 1985, 81: 263-266.Google Scholar
- Vrba ES: Mammal evolution in the African Neogene and a new look at the Great American Interchange. Biological Relationships between Africa and South America. Edited by: Goldblatt P. 1993, New Haven: Yale University Press, 393-434.Google Scholar
- Voelker G: Systematics and historical biogeography of wagtails (Aves: Motacilla): Dispersal versus vicariance revisited. Condor. 2002, 104: 725-739. 10.1650/0010-5422(2002)104[0725:SAHBOW]2.0.CO;2.View ArticleGoogle Scholar
- Voelker G, Outlaw RK: Establishing a perimeter position: thrush speciation around the Indian Ocean Basin. J Evol Biol. 2008, 21: 1779-1788. 10.1111/j.1420-9101.2008.01588.x.View ArticlePubMedGoogle Scholar
- Voelker G, Outlaw RK, Bowie RCK: Pliocene forest dynamics as a primary driver of African bird speciation. Global Ecology and Biogeography. 2010, 19: 111-121. 10.1111/j.1466-8238.2009.00500.x.View ArticleGoogle Scholar
- Montgelard C, Matthee CA, Robinson TJ: Molecular systematics of dormice (Rodentia: Gliridae) and the radiation of Graphiurus in Africa. P Roy Soc B-Biol Sci. 2003, 270: 1947-1955. 10.1098/rspb.2003.2458.View ArticleGoogle Scholar
- Amer SAM, Kumazawa Y: Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements. Biol J Linnean Soc. 2005, 85: 247-260. 10.1111/j.1095-8312.2005.00485.x.View ArticleGoogle Scholar
- Sibley CG, Monroe BL: Distribution and Taxonomy of Birds of the World. 1990, New Haven: Yale University PressGoogle Scholar
- Gelang M, Cibois A, Pasquet E, Olsson U, Alström P, Ericson PGP: Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification. Zool Scr. 2009, 38: 225-236. 10.1111/j.1463-6409.2008.00374.x.View ArticleGoogle Scholar
- Brambilla M, Vitulano S, Spina F, Baccetti N, Gargallo G, Fabbri E, Guidali F, Randi E: A molecular phylogeny of the Sylvia cantillans complex: Cryptic species within the Mediterranean basin. Mol Phylogenet Evol. 2008, 48: 461-472. 10.1016/j.ympev.2008.05.013.View ArticlePubMedGoogle Scholar
- Outlaw RK, Voelker G, Outlaw DC: Molecular systematics and historical biogeography of the Rock-Thrushes (Muscicapidae: Monticola). Auk. 2007, 124: 561-577. 10.1642/0004-8038(2007)124[561:MSAHBO]2.0.CO;2.View ArticleGoogle Scholar
- Nylander JAA: MrModeltest v2. Program distributed by the author. 2004, Evolutionary Biology Centre, Uppsala University, 2Google Scholar
- Huelsenbeck JP, Ronquist F: MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001, 17 (8): 754-755. 10.1093/bioinformatics/17.8.754.View ArticlePubMedGoogle Scholar
- Brandley MC, Schmitz A, Reeder TW: Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst Biol. 2005, 54 (3): 373-390. 10.1080/10635150590946808.View ArticlePubMedGoogle Scholar
- Brown JM, Lemmon AR: The importance of data partitioning and the utility of bayes factors in Bayesian phylogenetics. Syst Biol. 2007, 56 (4): 643-655. 10.1080/10635150701546249.View ArticlePubMedGoogle Scholar
- Stamatakis AT: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006, 22: 2688-2690. 10.1093/bioinformatics/btl446.View ArticlePubMedGoogle Scholar
- Drummond AJ, Ho SYW, Phillips MJ, Rambaut A: Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4 (5): 699-710.View ArticleGoogle Scholar
- Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007, 7: 214-10.1186/1471-2148-7-214.View ArticlePubMedPubMed CentralGoogle Scholar
- Weir JT, Schluter D: Calibrating the avian molecular clock. Mol Ecol. 2008, 17: 2321-2328. 10.1111/j.1365-294X.2008.03742.x.View ArticlePubMedGoogle Scholar
- Nabholz B, Glémin S, Galtier N: The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals. BMC Evol Biol. 2009, 9: 54-10.1186/1471-2148-9-54.View ArticlePubMedPubMed CentralGoogle Scholar
- Fleisher RC, McIntosh CE, Tarr CL: Evolution on a volcanic conveyer belt: using phylogeographic reconstructions and K-Ar-based ages on the Hawaiian Islands to estimate molecular evolutionary rates. Mol Ecol. 1998, 7: 533-545. 10.1046/j.1365-294x.1998.00364.x.View ArticleGoogle Scholar
- Swofford DL: PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). 2002, Sunderland, Massachusetts: Sinauer Associates, 4Google Scholar
- Rambaut A, Drummond AJ: TRACER. 2004, Oxford: University of OxfordGoogle Scholar
- Rambaut A: FigTree. 2008, [http://tree.bio.ed.ac.uk/software/figtree/]Google Scholar
- Ronquist F: Dispersal-vicariance analysis: A new approach to the quantification of historical biogeography. Syst Biol. 1997, 46: 195-203. 10.1093/sysbio/46.1.195.View ArticleGoogle Scholar
- Ree RH, Smith SA: Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst Biol. 2008, 57: 4-14.View ArticlePubMedGoogle Scholar
- Maddison DR, Maddison WP: MacClade. 2003, Sunderland, MA, USA: Sinauer Associates, 4.06.OSXGoogle Scholar
- Johansson US, Fjeldså J, Bowie RCK: Phylogenetic relationships within Passerida (Aves: Passeriformes): A review and a new molecular phylogeny based on three nuclear intron markers. Mol Phylogenet Evol. 2008, 48: 858-876. 10.1016/j.ympev.2008.05.029.View ArticlePubMedGoogle Scholar
- Agnarsson I, Miller JA: Is ACCTRAN better than DELTRAN?. Cladistics. 2008, 24: 1032-1038. 10.1111/j.1096-0031.2008.00229.x.View ArticleGoogle Scholar
- Outlaw DC, Voelker G: Phylogenetic tests of hypotheses for the evolution of avian migration: a case study using the Motacillidae. Auk. 2006, 123: 455-466. 10.1642/0004-8038(2006)123[455:PTOHFT]2.0.CO;2.View ArticleGoogle Scholar
- Warren BH, Bermingham E, Prys-Jones RP, Thebaud C: Tracking island colonization history and phenotypic shifts in Indian Ocean bulbuls (Hypsipetes: Pycnonotidae). Biol J Linnean Soc. 2005, 85: 271-287. 10.1111/j.1095-8312.2005.00492.x.View ArticleGoogle Scholar
- Raxworthy CR, Forstner MRJ, Nussbaum RA: Chameleon radiation by oceanic dispersal. Nature. 2002, 415: 784-787.View ArticlePubMedGoogle Scholar
- Kasapidis P, Magoulas A, Mylonas M, Zouros E: The phylogeography of the gecko Cyrtopodion kotschyi (Reptilia: Gekkonidae) in the Aegean archipelago. Mol Phylogenet Evol. 2005, 35: 612-623. 10.1016/j.ympev.2005.02.005.View ArticlePubMedGoogle Scholar
- Summer RS, Zachos FE: Fossil evidence and phylogeography of temperate species: 'glacial refugia' and post-glacial recolonizatio. J Biogeogr. 2009, 36: 2013-2020. 10.1111/j.1365-2699.2009.02187.x.View ArticleGoogle Scholar
- Vega R, Amori G, Aloise G, Cellini S, Loy A, Searle JB: Genetic and morphological variation in a Mediterranean glacial refugium: evidence from Italian pygmy shrews, Sorex minutus (Mammalia: Soricomorpha). Biol J Linnean Soc. 2010, 100: 774-787. 10.1111/j.1095-8312.2010.01454.x.View ArticleGoogle Scholar
- Cox G: The evolution of avian migration systems between temperate and tropical regions of the New World. American Naturalist. 1985, 126: 451-474. 10.1086/284432.View ArticleGoogle Scholar
- Hamilton AC, Taylor D: History of climate and forests in tropical Africa during the last 8 million years. Climatic Change. 1991, 19: 65-78. 10.1007/BF00142215.View ArticleGoogle Scholar
- Feakins SJ, de Menocal PB, Eglinton TI: Biomarker records of late Neogene changes in northeast African vegetation. Geology. 2005, 33: 977-980. 10.1130/G21814.1.View ArticleGoogle Scholar
- Sepulchre P, Ramstein G, Fluteau F, Schuster M, Tiercelin J-J, Brunet M: Tectonic uplift and eastern African aridification. Science. 2006, 313: 1419-1423. 10.1126/science.1129158.View ArticlePubMedGoogle Scholar
- Sinclair I, Ryan P: Birds of Africa, south of the Sahara. 2003, Cape Town: Struik PublishersGoogle Scholar
- Lee D-C, Halliday AN, Fitton JG, Poli G: Isotopic variations with distance and time in the volcanic islands of the Cameroon line: evidence for a mantle plume origin. Earth Plaent Sc Lett. 1994, 123: 119-138. 10.1016/0012-821X(94)90262-3.View ArticleGoogle Scholar
- Voelker G: Repeated vicariance of Eurasian songbird lineages since the late Miocene. J Biogeogr. 2010, 37: 1251-1261. 10.1111/j.1365-2699.2010.02313.x.View ArticleGoogle Scholar
- Girdler RW: The Afro-Arabian rift system. An overview. Tectonophysics. 1991, 197: 139-153. 10.1016/0040-1951(91)90038-T.View ArticleGoogle Scholar
- Ross DA, Schlee J: Shallow structure and geologic development of the southern Red Sea. Geol Soc Am Bull. 1973, 84: 3827-3843. 10.1130/0016-7606(1973)84<3827:SSAGDO>2.0.CO;2.View ArticleGoogle Scholar
- Rohling EJ, Fenton M, J JF, Bertrand B, Ganssen G, Caulet JP: Magnitudes of sealevel lowstands of the past 500,000 years. Nature. 1998, 394: 162-164. 10.1038/28134.View ArticleGoogle Scholar
- Siddall M, J RE, Almogi-Labin A, Hemleben C, Meischner D, Schmelzer I, Smeed DA: Sea-level fluctuations during the last glacial cycle. Nature. 2003, 423: 853-858. 10.1038/nature01690.View ArticlePubMedGoogle Scholar
- McClanahan TR, Young TP: East African ecosystems and their conservation. 1996, Oxford: Oxford University PressGoogle Scholar