Population history,gene flow,and bottlenecks in island populations of a secondary seed disperser,the southern grey shrike (Lanius meridionalis koenigi)

Studying the population history and demography of organisms with important ecological roles can aid understanding of evolutionary processes at the community level and inform conservation. We screened genetic variation (mtDNA and microsatellite) across the populations of the southern grey shrike (Lanius meridionalis koenigi) in the Canary Islands, where it is an endemic subspecies and an important secondary seed disperser. We show that the Canarian subspecies is polyphyletic with L. meridionalis elegans from North Africa and that shrikes have colonized the Canary Islands from North Africa multiple times. Substantial differences in genetic diversity exist across islands, which are most likely the product of a combination of historical colonization events and recent bottlenecks. The Eastern Canary Islands had the highest overall levels of genetic diversity and have probably been most recently and/or frequently colonized from Africa. Recent or ongoing bottlenecks were detected in three of the islands and are consistent with anecdotal evidence of population declines due to human disturbance. These findings are troubling given the shrike's key ecological role in the Canary Islands, and further research is needed to understand the community‐level consequences of declines in shrike populations. Finally, we found moderate genetic differentiation among populations, which largely reflected the shrike's bottleneck history; however, a significant pattern of isolation‐by‐distance indicated that some gene flow occurs between islands. This study is a useful first step toward understanding how secondary seed dispersal operates over broad spatial scales.     

Phylogeography of the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico

We quantify the population divergence processes that shaped population genetic structure in the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico. Multilocus genetic data from nine nuclear loci and mitochondrial (mt)DNA were used to estimate the population divergence history for 47 samples of S. bicanthalis. Bayesian clustering methods partitioned S. bicanthalis into three populations: (1) a southern population in Oaxaca and southern Puebla; (2) a population in western Puebla; and (3) a northern population with a broad distribution across Hidalgo, Puebla, and Veracruz. The multilocus nuclear data and mtDNA both supported a Late Pleistocene increase in effective population size, and the nuclear data revealed low levels of unidirectional gene flow from the widespread northern population into the southern and western populations. Populations of S. bicanthalis experienced different demographic histories during the Pleistocene, and phylogeographical patterns were similar to those observed in many co‐distributed highland taxa. Although we recommend continuing to recognize S. bicanthalis as a single species, future research on the evolution of viviparity could gain novel insights by contrasting physiological and genomic patterns among the different populations located across the highlands of south‐eastern Mexico. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 852–865.     

Genetic isolation in an endemic African habitat specialist

The Chestnut‐banded Plover Charadrius pallidus is a Near‐Threatened shorebird species endemic to mainland Africa. We examined levels of genetic differentiation between its two morphologically and geographically distinct subspecies, C. p. pallidus in southern Africa (population size 11 000–16 000) and C. p. venustus in eastern Africa (population size 6500). In contrast to other plover species that maintain genetic connectivity over thousands of kilometres across continental Africa, we found profound genetic differences between remote sampling sites. Phylogenetic network analysis based on four nuclear and two mitochondrial gene regions, and population genetic structure analyses based on 11 microsatellite loci, indicated strong genetic divergence, with 2.36% mitochondrial sequence divergence between individuals sampled in Namibia (southern Africa) and those of Kenya and Tanzania (eastern Africa). This distinction between southern and eastern African populations was also supported by highly distinct genetic clusters based on microsatellite markers (global F_ST = 0.309,  = 0.510, D = 0.182). Behavioural factors that may promote genetic differentiation in this species include habitat specialization, monogamous mating behaviour and sedentariness. Reliance on an extremely small number of saline lakes for breeding and limited dispersal between populations are likely to promote reproductive and genetic isolation between eastern and southern Africa. We suggest that the two Chestnut‐banded Plover subspecies may warrant elevation to full species status. To assess this distinction fully, additional sample collection will be needed, with analysis of genetic and phenotypic traits from across the species’ entire breeding range.     

Species limits within the Praomys delectorum group (Rodentia: Muridae: Murinae) of East Africa: a morphometric reassessment and biogeographical implications

We examined approximately 600 specimens that represent the Praomys delectorum species group (Muridae: Murinae: Praomyini), a rodent complex restricted to Afromontane landscapes in East Africa and currently viewed as a single species. Morphometric analyses of 21 population samples consistently disclosed cohesive patterns of craniodental differentiation that support the recognition of three species: Praomys delectorum Thomas, confined to extreme southern Malawi; P. melanotus Allen & Loveridge, found in highlands of south‐western Tanzania and contiguous northern Malawi; and P. taitae Heller (including octomastis Hatt), distributed in mountains and foothills of southern Kenya and northern and central Tanzania. Populations of the P. delectorum group are patchily distributed in moist montane forest, most collecting localities falling within 1000–2400 m, and their range collectively coincides with the Tanganyika–Nyasa Montane Forest Group sensu Moreau. Patterns of faunal similarity derived from distributions of 65 species of terrestrial small mammals recorded from Tanzania's highlands, including the Eastern Arc Mountains, demonstrated pronounced geographical discontinuities in montane associations but failed to uncover a prominent vicariant role for the Makambako Gap. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 420–469.     

Leopard tortoises in southern Africa have greater genetic diversity in the north than in the south (Testudinidae)

In contrast to mammals, little is known about the phylogeographic structuring of widely distributed African reptile species. With the present study, we contribute data for the leopard tortoise (Stigmochelys pardalis). It ranges from the Horn of Africa southward to South Africa and westwards to southern Angola. However, its natural occurrence is disputed for some southern regions. To clarify the situation, we used mtDNA sequences and 14 microsatellite loci from 204 individuals mainly from southern Africa. Our results retrieved five mitochondrial clades; one in the south and two in the north‐west and north‐east of southern Africa, respectively, plus two distributed further north. Using microsatellites, the southern clade matched with a well‐defined southern nuclear cluster, whilst the two northern clades from southern Africa corresponded to another nuclear cluster with three subclusters. One subcluster had a western and central distribution, another occurred mostly in the north‐east, and the third in a small eastern region (Maputaland), which forms part of a biodiversity hotspot. Genetic diversity was low in the south and high in the north of our study region, particularly in the north‐east. Our results refuted that translocations influenced the genetic structure of leopard tortoises substantially. We propose that Pleistocene climatic fluctuations caused leopard tortoises to retract to distinct refugia in southern and northern regions and ascribe the high genetic diversity in the north of southern Africa to genetic structuring caused by the survival in three refuges and subsequent admixture, whereas tortoises in the south seem to have survived in only one continuous coastal refuge.     

GENERAL NOTES

Macdonald, M. A. 1980. The ecology of the Fiscal Shrike in Ghana, and a comparison with studies from southern Africa. Ostrich 51:65-74.

The Fiscal Shrike Lanius collaris was studied in southern Ghana in order to compare its ecology there with that in southern Africa. The bird was found mainly in the damper coastal areas and usually in habitats created by man. Feeding behaviour is described. Food consisted mainly of a wide variety of insects. Territories were small at around 0,6 ha. Most nests were built 1,8-2,4 m from the ground, and eggs were laid from December to October. Moult appeared to take place in September to November when breeding activity was low. The normal and maximum clutch was three eggs. At most, 10–17% of clutches produced fledged young. Most losses were probably caused by predators. Two successful broods per pair were reared annually. Post-fledging survival of the young was high, and they remained on the parental territory for 5–7 months. Contrasts between the breeding biology in Ghana and southern Africa may be related to differences in environmental seasonality and perhaps also in the severity of nest losses.     

Effects of historical forest contraction on the phylogeographic structure of Australo‐Papuan populations of the red‐legged pademelon (Macropodidae: Thylogale stigmatica)

Geographic patterns of genetic variation are strongly influenced by historical changes in species habitats. Whether such patterns are common to co‐distributed taxa may depend on the extent to which species vary in ecology and vagility. We investigated whether broad‐scale phylogeographic patterns common to a number of small‐bodied vertebrate and invertebrate species in eastern Australian forests were reflected in the population genetic structure of an Australo‐Papuan forest marsupial, the red‐legged pademelon (Macropodidae: Thylogale stigmatica). Strong genetic structuring of mtDNA haplotypes indicated the persistence of T. stigmatica populations across eastern Australia and southern New Guinea in Pleistocene refugial areas consistent with those inferred from studies of smaller, poorly dispersing species. However, there was limited divergence of haplotypes across two known historical barriers in the northeastern Wet Tropics (Black Mountain Barrier) and coastal mideastern Queensland (Burdekin Gap) regions. Lack of divergence across these barriers may reflect post‐glacial recolonization of forests from a large, central refugium in the Wet Tropics. Additionally, genetic structure is not consistent with the present delimitation of subspecies T. s. wilcoxi and T. s. stigmatica across the Burdekin Gap. Instead, the genetic division occurs further to the south in mideastern Queensland. Thus, while larger‐bodied marsupials such as T. stigmatica did persist in Pleistocene refugia common to a number of other forest‐restricted species, species‐specific local extinction and recolonization events have resulted in cryptic patterns of genetic variation. Our study demonstrates the importance of understanding individualistic responses to historical climate change in order to adequately conserve genetic diversity and the evolutionary potential of species.     

Genetic analysis of the endemic island loggerhead shrike, <Emphasis Type="Italic">Lanius ludovicianus anthonyi</Emphasis>

Based on limited research, the island loggerhead shrike, Lanius ludovicianus anthonyi has been considered a distinct subspecies endemic to the northern California Channel Islands. We used mtDNA control region sequences and microsatellite genotyping to compare loggerhead shrikes from the southern California mainland (L. l. gambeli), San Clemente Island (L. l. mearnsi), and the northern islands (L. l. anthonyi). Habitats on the islands are recovering due to the removal of non-native ungulates on the islands, but may be transitioning to habitats less supportive of loggerhead shrikes, so this evaluation comes at a critical time. We utilized 96 museum specimens that were collected over a century to evaluate both spatial and temporal genetic patterns. Analysis of multilocus microsatellite genotypes indicated that historical specimens of loggerhead shrikes (collected between 1897 and 1986) from the two northern islands of Santa Rosa and Santa Cruz are genetically distinct from adjacent mainland and island shrikes. Birds from Santa Catalina Island showed mixed ancestry and did not cluster with the northern island birds. Historical specimens of L. l. mearnsi from San Clemente Island also showed mixed ancestry. Our study provides evidence that a genetically distinct form of loggerhead shrikes, L. l. anthonyi, occurred on the islands of Santa Rosa and Santa Cruz.     

Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone

Aim We used inferences of phylogeographical structure and estimates of divergence times for three species of gophersnakes (Colubridae: Pituophis) distributed across the Mexican Transition Zone (MTZ) to evaluate the postulated association of three Neogene geological events (marine seaway inundation of the Isthmus of Tehuantepec, formation of the Transvolcanic Belt across central Mexico, and secondary uplifting of the Sierra Madre Occidental) and of Pleistocene climate change with inter‐ and intraspecific diversification. Location Mexico, Guatemala, and the western United States. Methods We combined range‐wide sampling (67 individuals representing three putative species distributed across northern Middle America and western North America) and phylogenetic analyses of 1637 base pairs of mitochondrial DNA to estimate genealogical relationships and divergence times. The hypothesized concordance of inferred gene trees with geological histories was assessed using topology tests. Results We identified three major lineages of Middle American gophersnakes, and strong phylogeographical structure within each lineage. Gene trees were statistically congruent with hypothesized geological histories for two of the three postulated geological events. Estimated divergence dates and the geographical distribution of genetic variation further support mixed responses to these geological events. Considerable phylogeographical structure appears to have been generated during the Pleistocene. Main conclusions Phylogenetic and phylogeographical structure in gophersnakes distributed across northern Middle America and western North America highlights the influence of both Neogene vicariance events and Pleistocene climate change in shaping genetic diversity in this region. Despite the presence of two major geographical barriers in southern Mexico, extreme geological and environmental heterogeneity in this area may have differentially structured genetic diversity in highland taxa. To the north, co‐distributed taxa may display a more predictable pattern of diversification across the warm desert regions. Future studies should incorporate nuclear data to disentangle inferred lineage boundaries and further elucidate patterns of mitochondrial introgression.     

Bridging the gap: western rock skinks (Trachylepis sulcata) have a short history in South Africa

Phylogeographic patterns in wide-ranging species in southern Africa remain largely unexplored, especially in areas north of South Africa. Here, we investigate population structuring, demographic history, and the colonization pattern of the western rock skink (Trachylepis sulcata), a rock-dwelling species with a range extending from southwestern South Africa into Angola. Using 1056 bp from the mitochondrial marker ND2 and > 2.5 kb from three nuclear genes (EXPH5, KIF24, RAG-1), we constructed allele networks, generated extended Bayesian skyline plots and performed population clustering analyses. Analyses of historical demographic patterns show an overall southward range expansion from Northern Namibia into Southern Namibia and South Africa, although we find contrasting genetic breaks across these geographic regions using nuclear and mitochondrial data. We suggest that mtDNA has introgressed across a nuclear break corresponding to the Knersvlakte region of South Africa, a previously proposed biogeographic barrier for rupicolous species. This pattern of mitochondrial variation contrasts sharply to that of other South African taxa previously investigated, which all show significant mtDNA differentiation across the Knersvlakte region. Additionally, while other taxa show divergences dating to the Pliocene, T. sulcata appears to be a recent arrival in southern Africa, having crossed this barrier and colonized South Africa in the mid-Pleistocene. The complex phylogeographic history of T. sulcata corroborates the intricate patterns of genetic variation found in South African taxa and provides novel insight into historical processes affecting species distributed across Namibia.     

Identifying Biologically Meaningful Hot-Weather Events Using Threshold Temperatures That Affect Life-History

Increases in the frequency, duration and intensity of heat waves are frequently evoked in climate change predictions. However, there is no universal definition of a heat wave. Recent, intense hot weather events have caused mass mortalities of birds, bats and even humans, making the definition and prediction of heat wave events that have the potential to impact populations of different species an urgent priority. One possible technique for defining biologically meaningful heat waves is to use threshold temperatures (T_thresh) above which known fitness costs are incurred by species of interest. We set out to test the utility of this technique using T_thresh values that, when exceeded, affect aspects of the fitness of two focal southern African bird species: the southern pied babbler Turdiodes bicolor (T_thresh = 35.5°C) and the common fiscal Lanius collaris (T_thresh = 33°C). We used these T_thresh values to analyse trends in the frequency, duration and intensity of heat waves of magnitude relevant to the focal species, as well as the annual number of hot days (maximum air temperature > T_thresh), in north-western South Africa between 1961 and 2010. Using this technique, we were able to show that, while all heat wave indices increased during the study period, most rapid increases for both species were in the annual number of hot days and in the maximum intensity (and therefore intensity variance) of biologically meaningful heat waves. Importantly, we also showed that warming trends were not uniform across the study area and that geographical patterns in warming allowed both areas of high risk and potential climate refugia to be identified. We discuss the implications of the trends we found for our focal species, and the utility of the T_thresh technique as a conservation tool.     

Quarantine host range of Bikasha collaris,a potential biological control agent of Chinese tallowtree (Triadica sebifera) in North America

Chinese tallowtree, Triadica sebifera (L.) Small (Euphorbiaceae), is one of the worst invasive weeds of the southeastern USA impacting coastal wetlands, forests, and natural areas. Traditional mechanical and chemical controls have been unable to limit the spread, and this invasive species continues to expand its range. A proposed biological control candidate, the flea beetle Bikasha collaris (Baly) (Coleoptera: Chrysomelidae), shows high specificity for the target weed Chinese tallowtree. Results from a series of no‐choice and choice feeding tests of B. collaris adults and larvae indicated that this flea beetle was highly specific to Chinese tallowtree. The larvae of B. collaris feed by tunneling in the roots, whereas the adults feed on the leaves of Chinese tallowtree. A total of 77 plant taxa, primarily from members of the tallow plant family Euphorbiaceae, were tested in numerous test designs. Larval no‐choice tests indicated that larvae completed development only on two of the non‐target taxa. Of 80 B. collaris larvae fed roots of Hippomane mancinella L. and 50 larvae fed roots of Ricinus communis L., two and three larvae completed development, respectively. The emerging adults of these five larvae died within 3 days without reproducing. Larval choice tests also indicated little use of these non‐target taxa. Adult no‐choice tests indicated little leaf damage by B. collaris on the non‐targets except for Ditrysinia fruticosa (Bartram) Govaerts & Frodin and Gymnanthes lucida Sw. When given a choice, however, B. collaris adults consumed much less of the non‐targets D. fruticosa (7.4%) and G. lucida (6.1%) compared with the control leaves. Finally, no‐choice oviposition tests indicated that no eggs were produced when adults were fed all non‐target taxa, except those fed G. lucida. These B. collaris adults fed G. lucida leaves produced an average of 4.6 eggs compared with 115.0 eggs per female when fed Chinese tallowtree. The eggs produced from adults fed G. lucida were either inviable or the emerging larvae died within 1 day. These results indicate that the flea beetle B. collaris was unable to complete its life cycle on any of the non‐target taxa tested. If approved for field release, B. collaris will be the first biological control agent deployed against Chinese tallowtree in the USA. This flea beetle may play an important role in suppressing Chinese tallowtree and contribute to the integrated control of this invasive weed.     

Tracing the origins of widespread highland species: a case of Neogene diversification across the Mexican sierras in an endemic lizard

The evolutionary history of the Mexican sierras has been shaped by various geological and climatic events over the past several million years. The relative impacts of these historical events on diversification in highland taxa, however, remain largely uncertain owing to a paucity of studies on broadly‐distributed montane species. We investigated the origins of genetic diversification in widely‐distributed endemic alligator lizards in the genus Barisia to help develop a better understanding of the complex processes structuring biological diversity in the Mexican highlands. We estimated lineage divergence dates and the diversification rate from mitochondrial DNA sequences, and combined divergence dates with reconstructions of ancestral geographical ranges to track lineage diversification across geography through time. Based on our results, we inferred ten geographically structured, well supported mitochondrial lineages within Barisia. Diversification of a widely‐distributed ancestor appears tied to the formation of the Trans‐Mexican Volcanic Belt across central Mexico during the Miocene and Pliocene. The formation of filter barriers such as major river drainages may have later subdivided lineages. The results of the present study provide additional support for the increasing number of studies that suggest Neogene events heavily impacted genetic diversification in widespread montane taxa. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 382–394.     

Comparative phylogeography of reef fishes from the Gulf of Aden to the Arabian Sea reveals two cryptic lineages

The Arabian Sea is a heterogeneous region with high coral cover and warm stable conditions at the western end (Djibouti), in contrast to sparse coral cover, cooler temperatures, and upwelling at the eastern end (southern Oman). We tested for barriers to dispersal across this region (including the Gulf of Aden and Gulf of Oman), using mitochondrial DNA surveys of 11 reef fishes. Study species included seven taxa from six families with broad distributions across the Indo-Pacific and four species restricted to the Arabian Sea (and adjacent areas). Nine species showed no significant genetic partitions, indicating connectivity among contrasting environments spread across 2000 km. One butterflyfish (Chaetodon melannotus) and a snapper (Lutjanus kasmira) showed phylogenetic divergences of d = 0.008 and 0.048, respectively, possibly indicating cryptic species within these broadly distributed taxa. These genetic partitions at the western periphery of the Indo-Pacific reflect similar partitions recently discovered at the eastern periphery of the Indo-Pacific (the Hawaiian and the Marquesan Archipelagos), indicating that these disjunctive habitats at the ends of the range may serve as evolutionary incubators for coral reef organisms.

     

Survival in northern microrefugia in an endemic Carpathian gammarid (Crustacea: Amphipoda)

Gammarus leopoliensis (Crustacea: Amphipoda) is considered a north‐eastern Carpathian endemic species and therefore can be regarded as an appropriate model for testing the hypothesis of Quaternary glacial survival in northern microrefugia. However, 250 km south, the south‐western Carpathians harbour populations that resemble phenotypically both G. leopoliensis and Gammarus kischineffensis, a similar species distributed east of the Carpathians. We used maximum‐likelihood and Bayesian methods to evaluate the phylogenetic relationships of these three taxa based on mitochondrial and nuclear markers, and quantitatively compared diversity patterns, phylogeography and divergence times among north‐eastern and south‐western Carpathian taxa. Results indicate that G. leopoliensis and the south‐western populations form together a strongly supported group (G. leopoliensis s.l.) which, along with G. kischineffensis, belongs to the Gammarus balcanicus clade. This group contains 12 lineages mainly of Pliocene age. G. leopoliensis consists of two widely distributed and recently expanded allopatric sister lineages that diverged from the southern ones ca. 4 Ma, indicating long‐term survival in northern microrefugia. The southern lineages are micro‐endemic and display a scattered distribution, suggesting a more ancient, relict pattern. We conclude that the contrasting diversity patterns between the disjunct distributional areas of G. leopoliensis s.l. reflect differential survival of lineages across the latitudinal gradient, offering a promising system for comparing the evolutionary ecology of lineages persisting in latitudinally disconnected microrefugia. These results fill an important gap in the knowledge of European gammarid biogeography and reveal that all Carpathian Gammarus taxa are ancient and diverse species complexes.     

Genetic diversity and geographic distribution of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) genotypes associated with cassava in East Africa

The genetic variability of whitefly (Bemisia tabaci) species, the vectors of cassava mosaic begomoviruses (CMBs) in cassava growing areas of Kenya, Tanzania, and Uganda, was investigated through comparison of partial sequences of the mitochondria cytochrome oxidase I (mtCOI) DNA in 2010/11. Two distinct species were obtained including sub‐Saharan Africa 1 (SSA1), comprising of two sub‐clades (I and II), and a South West Indian Ocean Islands (SWIO) species. Among the SSA1, sub‐clade I sequences shared a similarity of 97.8–99.7% with the published Uganda 1 genotypes, and diverged by 0.3–2.2%. A pairwise comparison of SSA1 sub‐clade II sequences revealed a similarity of 97.2–99.5% with reference southern Africa genotypes, and diverged by 0.5–2.8%. The SSA1 sub‐clade I whiteflies were widely distributed in East Africa (EA). In comparison, the SSA1 sub‐clade II whiteflies were detected for the first time in the EA region, and occurred predominantly in the coast regions of Kenya, southern and coast Tanzania. They occurred in low abundance in the Lake Victoria Basin of Tanzania and were widespread in all four regions in Uganda. The SWIO species had a sequence similarity of 97.2–97.7% with the published Reunion sequence and diverged by 2.3–2.8%. The SWIO whiteflies occurred in coast Kenya only. The sub‐Saharan Africa 2 whitefly species (Ug2) that was associated with the severe CMD pandemic in Uganda was not detected in our study.     

Using satellite imagery to assess breeding habitat availability of the endangered loggerhead shrike in Québec

The loggerhead shrike (Lanius ludovicianus) is a grassland bird species whose preferred nesting habitat in eastern Canada is pastureland. This species has been extirpated from much of its historical range in this region, and breeding habitat loss is suspected to be an important cause of this decline. We evaluated the availability of suitable breeding habitats in Québec using satellite imagery. Because this species no longer breeds in Québec, we established habitat selection criteria from known nesting sites in the adjacent province of Ontario, from analysis of a Landsat-TM satellite image, and applied these criteria to Landsat-TM images covering southern Québec. We developed regional landscape criteria in 100 km² plots and patch indices criteria at the pasture level. Spatial analyses were conducted to characterize plots and pastures on the basis of pasture availability and spatial distribution. Pastures suitable for nesting loggerhead shrikes were those fulfilling patch criteria at the pasture level and located in plots fulfilling regional landscape criteria. Overall, 310 out of 1700 plots located in the historical breeding range of the loggerhead shrike in Québec fulfilled landscape criteria, supporting 3988 pastures that fulfilled patch criteria. More than 500 of these pastures were visited to validate their current status. The Outaouais region would be the most suitable region for nesting loggerhead shrikes in southern Québec, where suitable breeding habitat still remains because more than two-thirds of visited sites were still pastureland, hawthorns were well-distributed in the region, and pastureland fragmentation was lowest. We conclude that the availability of breeding habitat does not limit the establishment of a breeding population of loggerhead shrike in southern Québec, as we estimated that thousands of hectares of suitable habitat still remain in that province.     

Phylogeography and genetic differentiation along the distributional range of the orchid Epidendrum fulgens: a Neotropical coastal species not restricted to glacial refugia

Aim Phylogeographical studies in the Brazilian Atlantic Forest (BAF) have mostly included species associated with forest habitats, whereas taxa associated with grassland and sand‐dune plant communities have so far been largely overlooked. This study examines the phylogeography of the orchid Epidendrum fulgens, which occurs on coastal sand dunes and granitic outcrops, in order to identify major genetic divergences or disjunctions across the range of the species and to investigate the genetic signatures of past range contractions and expansions. Location Southern and south‐eastern seashore vegetation along the BAF biome, and granitic and arenitic outcrops that occur in the subtropical grassland plant communities located south of the BAF. Methods Nine nuclear and four plastid microsatellite loci were used to genotype 424 individuals from 16 populations across the distributional range of E. fulgens. For both sets of markers, we estimated genetic diversity and population differentiation, testing for a north–south gradient of genetic diversity. The plastid haplotype network and a Bayesian assignment analysis of nuclear markers were used to infer population structure. Past demographic changes were investigated using a coalescence approach. Results A deep disjunction was found between northern populations within the BAF and southern populations outside the BAF that occur on granitic and arenitic outcrops. Recent demographic reductions were detected in northern populations on coastal sands. Such demographic changes were not expected for those populations, as previous studies with forest species had found evidence of population expansion in the same areas. Higher genetic diversity was found in southern populations on granite, in contrast to patterns observed in previous studies of forest species. Main conclusions The results are consistent with the long‐term persistence of E. fulgens. Bottlenecks were detected in populations from areas where population expansion events have been detected in other plant (and animal) species, suggesting that forest expansion after the Last Glacial Maximum played a role in the population fragmentation and decrease in genetic diversity in E. fulgens. A substantial genetic division in E. fulgens corresponds to the ‘Portal de Torres’, a region that demarcates the northern limits of subtropical grassland plant communities and the southern limits of the BAF.