Initial diversification,glacial survival,and continuous range expansion of Gentiana straminea (Gentianaceae) in the Qinghai–Tibet Plateau

The Qinghai–Tibet Plateau (QTP) has been considered as one of the most sensitive regions to climate change on Earth, and the growth and distribution of alpine species on this plateau have been suggested to depend greatly on their ability to survive within a small range of temperatures. However, the responses of most species in the QTP to the Quaternary climatic oscillation remain largely unknown. We sequenced two cpDNA fragments and nrITS to examine genetic variations in 22 natural populations across the range of distribution in this region to investigate the phylogeographical distributional pattern of Gentiana straminea (Gentianaceae) in the QTP. The high haplotype diversity from populations on the platform suggested the existence of intraspecific diversification. Molecular dating estimated that all haplotypes have differentiated before the Last Glacial Maximum (LGM). Moreover, the haplotype distribution map based on both cpDNA and nrDNA data suggested expansions from QTP to its outer edges. Finally, ecological niche modeling further demonstrated the glacial survival of this species on the platform and continuous expansion to the platform edge. These findings imply that G. straminea should have experienced initial diversification, glacial survival on the platform, and continuous expansion to the QTP edge during the glacial period.     

Phylogeography of Eriotheca species complex: insights into the origin and range expansion of apomictic and polyploid trees in Neotropical Savannas

• Polyploidy and whole genome duplication are major evolutionary drivers in plants. Climate variations during the Pleistocene have influenced distribution and range expansion worldwide. Similar trends have been reported for Cerrado plants, but no attempt has been made to link phylogeography with ploidy and breeding changes. Thus, we aimed to (i) assess ploidy and genome size of Eriotheca estevesiae Carv.-Sobr., and compare it with E. pubescens (Mart.) Schott & Endl. (Both included into the Eriotheca Stellate Trichome Species Complex – ESTSC). (ii) Subsequently, we investigated their phylogeography to see whether genetic structure and range expansion trends were similar to those previously described for the Cerrado biome. Finally (iii), we discuss whether ESTSC phylogeographic patterns could be associated with geographic parthenogenesis processes.
• Common cytogenetic techniques and flow cytometry were used to confirm chromosome number and genome size of E. estevesiae. We used three cpDNA regions to analyse 14 ESTSC Cerrado populations, for which we also obtained ploidy level and breeding information. We investigated haplotype diversity, population structure and tested neutrality, aiming to reconstruct phylogeographic scenarios.
• We found three ploidy levels and eight cpDNA haplotypes in ESTSC, one shared by most populations. Haplotype and ploidy distribution corroborated that E. pubescens, the widely distributed polyploid and apomictic species, may have originated from northern diploid and probably sexual E. estevesiae.
• Matrilinear cpDNA links support the idea that apomixis and polyploidy in ESTSC may have allowed range expansion during the Pleistocene, in a process analogous to the geographic parthenogenesis described elsewhere.

     

青藏高原东南部山丹nrDNA ITS和cpDNA petB/petD 序列的分子进化特点

采用改良CTAB法提取青藏高原东南部山丹25个居群所有个体的基因组DNA,选取核基因ITS和叶绿体petB/petD区域进行PCR扩增、纯化和测序。对所有序列对位排列,其中ITS序列总长696bp,变异位点有4处,共产生7种单倍型,变异位点百分率为0.72%,（G+C）含量60.4%;petB/petD序列总长616bp,仅1处变异位点和2种单倍型,变异位点百分率为0.16%,（G+C）含量34.6%。表明山丹中,petB/petD区域较ITS序列保守,变异速率较慢。对ITS序列单倍型进行失配分布和中性检验分析发现,山丹现有分布范围可能经历了近期居群小范围扩张,AMOVA分析发现山丹居群的遗传变异主要存在于居群内,N_ST >G_ST（P>0.01）,表明山丹的遗传变异有着不显著的谱系地理结构。因此,山丹ITS序列适合该种的谱系地理学研究。     

Phylogeography of Plathymenia reticulata (Leguminosae) reveals patterns of recent range expansion towards northeastern Brazil and southern Cerrados in Eastern Tropical South America

Little is known about past vegetation dynamics in Eastern Tropical South America (ETSA). Here we describe patterns of chloroplast (cp) DNA variation in Plathymenia reticulata, a widespread tree in the ETSA Atlantic Forest and Cerrado biomes, but not found in the xeromorphic Caatinga. Forty one populations, comprising 220 individuals, were analysed by sequencing the trnS‐trnG and trnL‐trnL‐trnF cpDNA regions. Combined, they resulted in 18 geographically structured haplotypes. The central region of the sampling area, comprising Minas Gerais and Goiás Brazilian states, is a centre of genetic diversity and probably the most longstanding area of the distribution range of the species. In contrast, populations from northeastern Brazil and the southern Cerrados showed very low diversity levels, almost exclusively with common haplotypes which are also found in the central region. Coupled with a long‐branched star‐like network, these patterns suggest a recent range expansion of P. reticulata to those regions from central region sources. The recent origin of the species (in the early Pleistocene) or the extinction of some populations due to drier and cooler climate during the last glacial maximum could have been responsible for that phylogeographic pattern. The populations from northeastern Brazil originated from two colonization routes, one eastern (Atlantic) and one western (inland). Due to its high diversity and complex landscape, the central region, especially central‐north Minas Gerais (between 15°–18° S and 42°–46° W), should be given the highest priority for conservation.     

Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae)

In this study, we examined spatial patterns of chloroplast DNA (cpDNA) variation in a total of 30 populations of Castanopsis carlesii Hayata (Fagaceae), a subtropical and temperate tree species, including 201 individuals sampled throughout Taiwan. By sequencing two cpDNA fragments using universal primers (the trnL intron and the trnV-trnM intergenic spacer), we found a total of 1663 bp and 21 polymorphic sites. These gave rise to a total of 28 cpDNA haplotypes. The level of differentiation among the populations studied was relatively high (GST = 0.723). Two ancestral haplotypes are widely distributed. The Central Mountain Ridge (CMR) of Taiwan represents an insurmountable barrier to the east-west gene flow of C. carlesii. Among the populations studied, three separated populations, at Lienhuachih, Fushan and Lichia, have high nucleotide diversity. Estimates of NST-GST for populations on both sides of the CMR indicate that no phylogeographical structure exists. According to the genealogical tree, number of rare haplotype and population genetic divergence, this study suggests that two potential refugia existed during the last glaciation: the first refugium was located in a region to the north of Hsuehshan Range (HR) and west of the CMR; the second refugium was located in south, especially southeastern Taiwan. In fact, the second refugium happens to be the same as that reported for Quercus glauca. A 'star-like' genealogy is characteristic when all haplotypes rapidly coalesce and is a general outcome of population expansion. The neutrality test and mismatch distribution also suggest demographic expansion recovering from a bottleneck.     

High genetic differentiation in the alpine plant Campanula alpina Jacq. (Campanulaceae): evidence for glacial survival in several Carpathian regions and long-term isolation between the Carpathians and the Alps

A survey of amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) variation was conducted to elucidate the phylogeography of Campanula alpina , a key species of silicicolous alpine grasslands in the Carpathians with a disjunct distribution in the Eastern European Alps. The Carpathians experienced a different glacial history from the Alps: local glaciers were present only in the highest massifs, while alpine habitats extended over larger areas related to their present distribution in this region. We asked: (i) whether in the Carpathians a high-mountain plant exhibits a complex phylogeographical structure or rather signatures of recent migrations, and (ii) whether the disjunct part of the species' distribution in the Alps resulted from a recent colonization from the Carpathians or from a restricted expansion from separate Eastern Alpine refugia. Our study revealed a clear phylogeographical pattern in AFLPs supported by congruent groups of distinct cpDNA haplotypes. Highest genetic differentiation was observed between the Alps and the Carpathians, indicating a long-term isolation between populations from these two mountain ranges. Further genetic division within the Carpathians suggests that current species' distribution is composed of several groups which have been isolated from each other for a long period. One genetic break separates Western from Southeastern Carpathian material, which is in line with a classical biogeographical boundary. A further, strongly supported genetic group was identified at the southwestern edge of the Carpathian arch. In the Eastern Alps, genetic traces of glacial survival in separate refugial areas in the calcareous northern part and the siliceous central part were found.     

Glacial history of the alpine herb Rumex Nivalis (Polygonaceae): a comparison of common phylogeographic methods with nested clade analysis

The glacial history of the alpine herb Rumex nivalis was investigated using amplified fragment length polymorphisms (AFLPs) and restriction fragment length polymorphisms with polymerase chain reaction (PCR-RFLPs) of cpDNA. Both traditional statistical methods widely applied in phylogeographic research and nested clade analysis were used. The AFLPs indicated little geographic structure probably due to the wind-pollinated reproductive system of the dioecious R. nivalis. Because cpDNA haplotypes exhibited distinct distributional patterns, correlation between AFLPs and PCR-RFLPs was low. The results of common statistical methods and of nested clade analysis were largely congruent. Both supported in situ survival of one group of common haplotypes in the Central Alps. For another group of common haplotypes, classical phylogeographic analyses gave strong evidence for survival in peripheral refugia at the northern alpine border, whereas this conclusion was not as clearly supported in the nested clade analysis. Nested clade analysis provided several detailed insights on past and ongoing populational demographic processes. Thus, it is a valuable tool in the phylogeographical analysis of haplotype data, but it should preferably be combined with other statistical analyses. In situations with low genetic variation in cpDNA, classical phylogeographic analytical tools on nuclear DNA will still be the methods of choice.     

As old as the hills: Pliocene palaeogeographical processes influence patterns of genetic structure in the widespread,common shrub Banksia sessilis

The impact of Quaternary glaciation on the development of phylogeographic structure in plant species is well documented. In unglaciated landscapes, phylogeographic patterns tend to reflect processes relating to persistence and stochasticity, yet other factors, associated with the palaeogeographical history of the landscape, including geomorphological events, can also have a significant influence. The unglaciated landscape of south‐western Western Australia is an ideal location to observe these ancient drivers of lineage diversification, with tectonic activity associated with the Darling Fault in the late Pliocene attributed to patterns of deep phylogeographic divergence in a widespread tree from this region. Interestingly, other species within this region have not shown this pattern and this palaeogeographical boundary therefore presents an opportunity to examine age and historical distribution of plant species endemic to this region. In this study, we assess patterns of genetic diversity and structure across 28 populations of the widespread shrub Banksia sessilis using three cpDNA markers and nine nuclear microsatellite markers. Sixteen cpDNA haplotypes were identified, comprising two major chloroplast DNA lineages that are estimated to have diverged in the Pliocene, approximately 3.3 million years ago. This timing coincides with major geomorphological processes in the landscape, including the separation of the Darling Plateau from the adjacent Swan Coastal Plain, as well as eustatic changes on the Swan Coastal Plain that are likely to have resulted in the physical isolation of historical plant lineages. Chloroplast lineages were broadly aligned with populations associated with older lateritic soils of the Darling Plateau and Geraldton sandplains or the younger sandy soils associated with the Swan Coastal Plain and Southern Coastline. This structural pattern of lateritic versus non‐lateritic division was not observed in the nuclear microsatellite data that identified three genetic clades that roughly corresponded to populations in the North, South, and Central portions of the distributions.     

Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum

Aim We examine several hypotheses emerging from biogeographical and fossil records regarding glacial refugia of a southern thermophilic plant species. Specifically, we investigated the glacial history and post‐glacial colonization of a forest understorey species, Trillium cuneatum. We focused on the following questions: (1) Did T. cuneatum survive the Last Glacial Maximum (LGM) in multiple refugia, and (if so) where were they located, and is the modern genetic structure congruent with the fossil record‐based reconstruction of refugia for mesic deciduous forests? (2) What are the post‐glacial colonization patterns in the present geographical range? Location South‐eastern North America. Methods We sampled 45 populations of T. cuneatum throughout its current range. We conducted phylogeographical analyses based on maternally inherited chloroplast DNA (cpDNA haplotypes) and used TCS software to reconstruct intraspecific phylogeny. Results We detected six cpDNA haplotypes, geographically highly structured into non‐overlapping areas. With one exception, none of the populations had mixed haplotype composition. TCS analysis resulted in two intraspecific cpDNA lineages, with one clade subdivided further by shallower diversification. Main conclusions Our investigation revealed that T. cuneatum survived the LGM in multiple refugia, belonging to two (western, eastern) genealogical lineages geographically structured across south‐eastern North America. The western clade is confined to the south‐western corner of T. cuneatum’s modern range along the Lower Mississippi Valley, where fossil records document a major refugium of mesic deciduous forest. For the eastern clade, modern patterns of cpDNA haplotype distribution suggest cryptic vicariance, in the form of forest contractions and subsequent expansions associated with Pleistocene glacial cycles, rather than simple southern survival and subsequent northward colonization. The north–south partitioning of cpDNA haplotypes was unexpected, suggesting that populations of this rather southern thermophilic species may have survived in more northern locations than initially expected based on LGM climate reconstruction, and that the Appalachian Mountains functioned as a barrier to the dispersal of propagules originating in more southern refugia. Furthermore, our results reveal south‐west to north‐east directionality in historical migration through the Valley and Ridge region of north‐west Georgia.     

Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N _ST =0.751> G _ST =0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s F_S indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.     

Patterns of intraspecific diversification in the Piriqueta caroliniana complex in southeastern North America and the Bahamas

Abstract.— We use chloroplast DNA (cpDNA) variation and nested clade phylogeographic analyses to infer the historical processes that have contributed to the high level of morphological and ecological diversification present in a group of herbaceous perennials (the Piriqueta caroliniana complex) in North America and the Bahamas. The presence of morphologically distinct and intercompatible varieties (morphotypes) that can be distinguished based on suites of taxonomic characters (e.g., leaf shape, pubescence type, stature) and contrasting habitat affinities (from marshes to dry pinelands and sand scrub) makes this group particularly appropriate for studies of intraspecific diversification. To examine the distribution of haplotypes among populations, we sampled 467 individuals from 55 locations in Florida, Georgia, and the northern Bahamas (Grand Bahama and Abaco) and screened each individual for cpDNA variation using restriction fragment length polymorphism (RFLP) and heteroduplex analyses. We develop a one-step haplotype phylogeny for this group and use the geographic distributions of haplotypes and clades to test specific phylogeographic hypotheses using the methods developed by Templeton and his colleagues (Templeton 1998). In general, the distribution of haplotypes was strongly influenced by limited dispersal distances, with the more recently derived haplotypes having much lower levels of dispersion and lower frequencies in populations than the ancestral haplotypes. The patterns of clade and haplotype dispersion and displacement and the distribution of morphotypes imply at least three cases of long-distance dispersal and one case of historical fragmentation. The historical patterns inferred for populations of Piriqueta are consistent with known biogeographical events, historical vegetation change, and the concordant patterns of multiple Pleistocene refugia that have been observed for a number of other taxa in southeastern North America.     

Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas

Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi‐taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional‐scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low‐structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long‐distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene–Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in‐depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.     

Phylogeography of a species complex of lowland Neotropical rain forest trees (Carapa,Meliaceae)

Aim Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species. Location Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America. Methods Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH–psbA and trnC–ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times. Results Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation‐by‐distance process or exhibit a phylogeographical signal. Main conclusions The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.     

The lizard assemblage from Seasonally Dry Tropical Forest enclaves in the Cerrado biome, Brazil, and its association with the Pleistocenic Arc

Aim  To determine if the distributions of lizard species from Seasonally Dry Tropical Forest (SDTF) enclaves within the Cerrado biome in central Brazil are associated with the Tropical Seasonal Forests Region, a recently proposed phytogeographic unit of South America, corroborating the existence of a Pleistocenic Arc of SDTFs.
Location  SDTF remnants in the Paranã River valley, municipality of São Domingos, Goiás, Brazil.
Methods  Lizards were extensively sampled using haphazard sampling, funnel traps, and pitfall traps with drift fences during four expeditions. The composition of the SDTF lizard assemblage was compared with those from other South American phytogeographic regions (Caatinga, Cerrado, Chaco, Llanos, and the dry forests of Colombia and Bolivia), based on the literature and our own unpublished data.
Results  The SDTF lizard assemblage contained 20 species, including 11 species with extensive distributions among the regions considered, seven species shared exclusively with Cerrado localities, a single species shared exclusively with other SDTFs, and one endemic species. The presence of Lygodactylus klugei (Smith, Martin & Swain, 1977), presumably endemic to the Pleistocenic Arc formed by the Tropical Seasonal Forests Region, considerably extends the known distribution of this species, suggesting historical connections between Caatinga and Cerrado SDTF enclaves.
Main conclusions  The composition of the lizard assemblage in Cerrado SDTF enclaves seems to corroborate the recent proposal that the SDTF should be recognized as a phytogeographic unit (or dominium). The presence of disjunct populations and endemic species highlights the urgency of considering the uniqueness of the Paranã River valley SDTFs and the importance of its conservation.     

Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

ABSTRACT: BACKGROUND: As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. RESULTS: Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; pi = 0.00314) were almost as high as at PAL (h = 0.836; pi = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P < 0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel's test of nrDNA haplotypes (r = 0.234, P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species. CONCLUSIONS: We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.     

MOLECULAR PHYLOGEOGRAPHY, RETICULATION, AND LINEAGE SORTING IN MEDITERRANEAN SENECIO SECT. SENECIO (ASTERACEAE)

Abstract The Mediterranean species complex of Senecio serves to illustrate evolutionary processes that are likely to confound phylogenetic inference, including rapid diversification, gene tree‐species tree discordance, reticulation, interlocus concerted evolution, and lack of complete lineage sorting. Phylogeographic patterns of chloroplast DNA (cpDNA) haplotype variation were studied by sampling 156 populations (502 individuals) across 18 species of the complex, and a species phylogeny was reconstructed based on sequences from the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. For a subset of species, randomly amplified polymorphic DNAs (RAPDs) provided reference points for comparison with the cpDNA and ITS datasets. Two classes of cpDNA haplotypes were identified, with each predominating in certain parts of the Mediterranean region. However, with the exception of S. gallicus, intraspecific phylogeographic structure is limited, and only a few haplotypes detected were species‐specific. Nuclear sequence divergence is low, and several unresolved phylogenetic groupings are suggestive of near simultaneous diversification. Two well‐supported ITS clades contain the majority of species, amongst which there is a pronounced sharing of cpDNA haplotypes. Our data are not capable of diagnosing the relative impact of reticulation versus insufficient lineage sorting for the entire complex. However, there is firm evidence that S. flavus subsp. breviflorus and S. rupestris have acquired cpDNA haplotypes and ITS sequences from co‐occurring species by reticulation. In contrast, insufficient lineage sorting is a viable hypothesis for cpDNA haplotypes shared between S. gallicus and its close relatives. We estimated the minimum coalescent times for these haplotypes by utilizing the inferred species phylogeny and associated divergence times. Our data suggest that ancestral cpDNA polymorphisms may have survived for ca. 0.4–1.0 million years, depending on molecular clock calibrations.     

The major diversity centre for Neotropical Turneraceae

The Neotropical country where the Turneraceae are best represented is Brazil; 82% of the American species are native, and 73% of them are endemic to this country. The most diverse states are Bahia, Minas Gerais and Goiás. Within this area the diversity – in terms of number of species – was analysed at a level of one degree square, taking into account the phytogeographic domains (biomes) recognized in Brazil. The distribution of endemic and rare species was also explored. The major centre of diversity is located in the Chapada Diamantina, Bahia, inside the biome ‘Caatinga’, but there are hotspots in Minas Gerais and Goiás, within the biome ‘Cerrado’. The biome with highest number of endemic species is the ‘Cerrado’, followed by the ‘Caatinga’.     

East-west divergence in central Brazilian Cerrado revealed by cpDNA sequences of a bird-dispersed tree species

Population genetic studies of plant species can contribute to understanding the evolutionary history of the Brazilian Cerrado, a highly threatened hotspot and the richest tropical savanna in the world. Therefore, this study aimed at investigating the diversity and genetic structure of Byrsonima coccolobifolia (Malpighiaceae), one of the most common tree species in the Brazilian Cerrado, focusing mainly on the central area of the biome. This is a bird-dispersed species, and studies targeting species with this seed dispersal syndrome are scarce. First, we performed a careful screening of cpDNA markers to identify regions suitable for intraspecific genetic studies, and then we investigated the diversity and genetic structure in ten populations of B. coccolobifolia. The cpDNA regions selected (trnS-trnG and trnH-trnK) revealed considerable divergence among populations and a striking geographical structure, separating populations in two groups, east and west. Although seed dispersal by birds is expected to reach long distances, our results strongly corroborate studies targeting trees with limited seed dispersal. This suggests that historical fragmentation of Cerrado (possibly during cold and dry periods of the Quaternary) might have limited long distance dispersal events after climate amelioration even in bird-dispersed species, especially while Cerrado was expanding but still fragmented.     

秦巴山区漆树nrDNAITS和cpDNA序列分子进化特点的分析

应用PCR产物直接测序法分析漆树种群nrDNA （核糖体DNA） ITS序列和cpDNA序列（matK、rbcL、psbA-trnH）的碱基差异,初步研究两套植物基因组的变异速率。结果表明：nrDNA ITS序列共有518 bp,有变异位点15处,变异位点百分率为2.9%,（G+C）含量为61.8%。cpDNA序列合并后长度1 907 bp,有变异位点20处,变异位点百分率为1.05%,（G+C）含量为36.1%。通过对ITS序列核糖型（Ribotype）和叶绿体序列单倍型（Haploype）进行分析发现,秦巴山区漆树区域性分布明显,不同区域拥有自己独特的单倍型,漆树居群历史近期没有扩张。nrDNA ITS序列较叶绿体序列进化较快,变异速率较快。nrDNA ITS序列及叶绿体matK、psbA-trnH适合漆树的亲缘地理学研究。     

Phylogeographical studies in disjunct populations of <Emphasis Type="Italic">Symplocos laurina</Emphasis> Wall. using cytoplasmic PCR-RFLP approach

Genetic variation, haplotype relationships, and potential regions of diversity in Symplocos laurina Wall. (Symplocaceae), a montane tree species from India, have been tested using molecular and biogeographical data to infer phylogeographic patterns. The polymerase chain reaction-restriction fragment length polymorphism technique was used to determine the chloroplast (cp) and mitochondrial (mt) DNA haplotypes of 218 individuals from 12 populations, collected from Northeast India (NEI), which is a part of Indo-Burma biodiversity hotspot, and South India, which includes the Western Ghats (WG), another biodiversity hotspot from India and Eastern Ghats (EG). Nine cpDNA (chlorotypes) and 24 mtDNA haplotypes (mitotypes) were identified; the WG region was identified as the most diverse for chlorotypes and the NEI region for mitotypes. Although a strong population differentiation was observed, phylogeographic structure was found to be absent for both the genomes. The haplotype network revealed the presence of two main lineages: NEI-WG lineage and EG lineage, largely without overlapping distributions. The study tests two hypotheses, namely vicariance and dispersal, to understand the distribution of plants in India. The population structure of S. laurina strongly suggests the persistence of the species in putative refugial areas preglaciation and further establishment of other populations of S. laurina from these refugial populations.