Genetic examination of the type specimen of Ulva australis suggests that it was introduced to Australia

‘Ana‐aosa’, one of the most common marine green algae in Japan, was described as Ulva pertusa Kjellman in 1897 from Hakodate in northern Japan. Ulva pertusa was considered to be a temperate species, with its native distributional range restricted to northeastern Asia. Although this species has been reported from various regions outside northeastern Asia, these records have been explained as non‐indigenous populations. Recently, on the basis of genetic data and nomenclatural priority, U. pertusa was synonymized with U. australis Areschoug, a species described in 1851 from specimens collected in South Australia. Based on genetic studies, Australian populations identified as U. pertusa had been considered to have originated from Japan. However, the published genetic data on U. australis in Australia have been based only on recent collections and no historical specimens have been examined. We tested the hypothesis that native (true) U. australis is an independent species of very similar morphology to U. pertusa, but that its natural domination of shoreline habitats has been suppressed by introduced populations of U. pertusa from Asia. In the present study, we extracted DNA from the type specimen of U. australis housed in the Swedish Museum of Natural History (S) and obtained DNA sequences of the chloroplast rbcL gene and the nuclear rDNA ITS2 region. Our results show that U. australis and U. pertusa are genetically virtually identical, confirming that U. pertusa is a synonym of U. australis. This suggests that the introduction of U. australis to Australia occurred by the middle of the 19th century, when the type was collected and before there was a direct shipping route between Japan and Australia. We speculate that the introduction of U. australis to Australia occurred as a secondary introduction from non‐indigenous populations in northeastern Asia, but not directly from Japan.     

Phylogeography of the Coastal Mosquito Aedes togoi across Climatic Zones: Testing an Anthropogenic Dispersal Hypothesis

The coastal mosquito Aedes togoi occurs more or less continuously from subarctic to subtropic zones along the coasts of the Japanese islands and the East Asian mainland. It occurs also in tropical Southeast Asia and the North American Pacific coast, and the populations there are thought to have been introduced from Japan by ship. To test this hypothesis, the genetic divergence among geographic populations of A. togoi was studied using one mitochondrial and three nuclear gene sequences. We detected 71 mitochondrial haplotypes forming four lineages, with high nucleotide diversity around temperate Japan and declining towards peripheral ranges. The major lineage (L1) comprised 57 haplotypes from temperate and subarctic zones in Japan and Southeast Asia including southern China and Taiwan. Two other lineages were found from subtropical islands (L3) and a subarctic area (L4) of Japan. The Canadian population showed one unique haplotype (L2) diverged from the other lineages. In the combined nuclear gene tree, individuals with mitochondrial L4 haplotypes diverged from those with the other mitochondrial haplotypes L1—L3; although individuals with L1—L3 haplotypes showed shallow divergences in the nuclear gene sequences, individuals from Southeast Asia and Canada each formed a monophyletic group. Overall, the genetic composition of the Southeast Asian populations was closely related to that of temperate Japanese populations, suggesting recent gene flow between these regions. The Canadian population might have originated from anthropogenic introduction from somewhere in Asia, but the possibility that it could have spread across the Beringian land bridge cannot be ruled out.     

Genetic variation and biogeography of the disjunct Vitis subg. Vitis (Vitaceae)

Aim Vitis subg. Vitis provides an example of a plant disjunction occurring in the Northern Hemisphere. It shows broad morphological variation but is assumed to be a species complex with limited genetic differentiation. Based on a comprehensive sampling of taxa and polymorphism in both chloroplast and nuclear DNA, we assessed genetic variation within this subgenus. Our aims were to clarify the relationships among species and to examine their historical biogeography. Location Asia, Europe, North America. Methods We analysed a total of 30 species and putative hybrids from subgenus Vitis and examined the infra‐specific variation in some species. Polymorphism in chloroplast DNA was assessed in trnL and trnH–psbA–trnK sequences (c. 2170 bp) and in 15 microsatellite loci. We also obtained nuclear data for size variation at 24 microsatellite loci. Phylogenetic inference was performed with Bayesian analyses. A maximum parsimony network was constructed to depict the evolutionary relationships among haplotypes, and microsatellite data were also subjected to hierarchical clustering analysis using the Ward distance. In addition, we assessed size homoplasy by sequencing both chloroplast and nuclear microsatellite loci. Results Chloroplast polymorphisms resolved subgenus Vitis as a monophyletic group with limited genetic variation. The ancestral haplotypes were found in Eurasia. American taxa all harboured derived haplotypes. Most of them formed a monophyletic group that did not include Vitis californica. The four main haplotypes in Vitis vinifera corresponded to two different origins. Nuclear microsatellites indicated that genetic variation was especially large in North America. Asian species exhibited a lower level of nuclear divergence and the European V. vinifera corresponded to a differentiated nuclear lineage. Main conclusions We obtained some evidence that subgenus Vitis has an Asian origin and then dispersed to Europe and North America. Geographic separation was followed by diversification, presumably during the Pleistocene, resulting in phylogeographic patterns similar to other biota. In contrast to chloroplast DNA, nuclear DNA shows a larger than expected genetic variation. Our molecular data also highlight the need to re‐examine certain aspects of the current subgeneric classification.     

Phylogeographic analysis of the brown alga Cutleria multifida (Tilopteridales,Phaeophyceae) suggests a complicated introduction history

In depth genetic comparisons of populations of Cutleria multifida (Tilopteridales, Phaeophyceae) collected from Europe, the northwestern Pacific Ocean, Australia and New Zealand using the DNA sequences of four gene regions (the mitochondrial cox2 and cox3 genes, the intergeneric spacer region adjacent to cox3, and the open reading frame) suggested that the northwestern European and Japanese populations were considerably greater in terms of their genetic divergence than Mediterranean, Australian or New Zealand populations. The haplotypes of the populations in northwestern European (distribution range including the type locality, seven haplotypes) and Japanese populations (seven haplotypes) were unique except for one shared haplotype. There were weak but positive correlations between the geographical distance and the genetic divergence among northwestern European and Japanese populations. Moreover, both female and male gametophytes occurred in eight of the nine Japanese localities, suggesting Japanese populations showed normal sexual heteromorphic life history of the species. In light of these results, it appears that Japanese populations were native to the area despite earlier hypothesis. In contrast, Australian and New Zealand populations were composed of only one haplotype that is very close to those found in northwestern Europe and Japan, suggesting a recent introduction history from Europe (or from northeastern Asia via Europe) by ship transport to Australia and New Zealand. The Mediterranean populations included two haplotypes identical to those found in northwestern Europe and Japan, and it is suggestive of transoceanic introductions of some populations between Mediterranean and Japanese coasts.     

Contrasting genetic patterns between two coexisting Eleutherococcus species in northern China

Climate oscillations are the key factors to understand the patterns in modern biodiversity. East Asia harbors the most diverse temperate flora, largely because an extensive terrestrial ice cap was absent during repeated Pleistocene glaciation–interglacial cycles. Comparing the demographic histories of species that are codistributed and are close relatives may provide insight into how the process of climate change influences species ranges. In this study, we compared the spatial genetic structure and demographic histories of two coexisting Eleutherococcus species, Eleutherococcus senticosus and E. sessiliflorus. Both species are distributed in northern China, regions that are generally considered to be sensitive to climatic fluctuations. These regions once hosted temperate forest, but this temperate forest was replaced by tundra and taiga forest during the Last Glacial Maximum (LGM), according to pollen records. Using three chloroplast DNA fragments, we assessed the genetic structure of 20 and 9 natural populations of E. senticosus and E. sessiliflorus, respectively. Extremely contrasting genetic patterns were found between the two species; E. sessiliflorus had little genetic variation, whereas E. senticosus had considerably higher levels of genetic variation (15 haplotypes). We speculated that a recent severe bottleneck may have resulted in the extremely low genetic diversity in E. sessiliflorus. In E. senticosus, populations in Northeast China (NEC) harbored all of the haplotypes found in this species and included private haplotypes. The populations in NEC had higher levels of genetic diversity than did those from North China (NC). Therefore, we suggest that both the NC and NEC regions can sustain LGM refugia and that lineage admixture from multiple refugia took place after the LGM elevated the local genetic diversity in NEC. In NEC, multiple genetic hot spots were found in the Changbai Mountains and the Xiaoxing'an Range, which implied that multiple locations in NEC may sustain LGM refugia, even in the Xiaoxing'an Range.     

MOLECULAR SYSTEMATICS OF THE GRACILARIACEAE (GRACILARIALES,RHODOPHYTA) WITH EMPHASIS ON SOUTHERN AFRICA1

Southern Africa has economically exploited populations of terete gracilarioids on the cool temperate west coast and numerous species of endemic and Indo‐Pacific tropical Gracilariaceae on the south and east coasts. Gross morphological characters have been the main means of identification, and incorrect applications have led to a number of misidentifications. In this study, small subunit rDNA and RUBISCO spacer sequences were used to determine phylogenetic relationships. Whereas rDNA sequences successfully differentiate major groups within the family as well as species belonging to the Gracilariopsis and the Curdiea/Melanthalia clade, RUBISCO spacer sequencing was required to distinguish between species of Gracilaria. The southern African gracilarioid complex (stringy, terete, elongate members of the Gracilariaceae) was resolved into three species: Gracilaria gracilis, Gracilariopsis longissima, and Gracilariopsis funicularis. South African Gracilaria protea was shown to be conspecific with tropical Indian Ocean G. corticata. Apart from G. gracilis and G. corticata, South African Gracilaria species were differentiated into a temperate‐tropical terete grouping and a temperate‐tropical flattened grouping.     

Chloroplast phylogeography of Iris dichotoma (Iridaceae), a widespread herbaceous species in East Asia

Both a complex topography and climate change have huge impacts on the distribution and genetic structure of extant species. Due to the lack of relevant molecular research, little is definitively known about the phylogeography of herbaceous plants in East Asia. Here we investigate the genetic diversity, population structure and historical population dynamics of Iris dichotoma Pallas, a widespread perennial herbaceous species in northeastern and northern China. Twenty-nine populations, totalling 297 individuals, were sampled throughout the Chinese distributional range of I. dichotoma. The combined sequences of six chloroplast DNA fragments (petA-psbE, rps18-clpp, psbJ-petA, trnD-trnT, rps16 and ndhA) were used to identify 13 haplotypes, of which six were private ones restricted in a single population. Genetic differentiation among I. dichotoma populations, enabled us to infer potential refugia during the glacial period in the Yinshan Mountains–Yanshan Mountains, where high levels of haplotype and nucleotide diversity were detected. The results of a neutral test and mismatch distribution analysis both indicated that I. dichotoma underwent a recent population expansion. In East Asia, postglacial environmental and climatic changes appear to have promoted genetic diversification not only in better-studied woody species, but also in herbaceous ones like I. dichotoma. Future studies of more herbaceous plant species are needed to obtain better insight into how modern temperate biodiversity has developed in East Asia.     

Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil‐calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron region of nitrate reductase (NIA‐i3) to examine genetic diversity within species, rates of gene flow among species and ancestral population size of disjunct sister species. Transitions in functional and morphological traits associated with ecological and climatic niche axes were examined across the phylogeny. We found the Virentes to be monophyletic with three subclades, including a southwest clade, a southeastern US clade and a Central American/Cuban clade. Despite high leaf morphological variation within species and transpecific chloroplast haplotypes, RADseq and nuclear SSR data showed genetic coherence of species. We estimated a crown date for Virentes of 11 Ma and implicated the formation of the Sea of Cortés in a speciation event ~5 Ma. Tree height at maturity, associated with fire tolerance, differs among the sympatric species, while freezing tolerance appears to have diverged repeatedly across the tropical–temperate divide. Sympatric species thus show evidence of ecological niche differentiation but share climatic niches, while allopatric and parapatric species conserve ecological niches, but diverge in climatic niches. The mode of speciation and/or degree of co‐occurrence may thus influence which niche axis plants diverge along.     

Geographic structure, genetic diversity and source tracking of Spartina alterniflora

Aim To examine the distribution and structure of genetic variation among native Spartina alterniflora and to characterize the evolutionary mechanisms underlying the success of non‐native S. alterniflora. Location Intertidal marshes along the Atlantic, Gulf and Pacific coasts of North America. Methods amova , parsimony analysis, haplotype networks of chloroplast DNA (cpDNA) sequences, neighbour‐joining analysis, Bayesian analysis of population structure, and individual assignment testing were used. Results Low levels of gene flow and geographic patterns of genetic variation were found among native S. alterniflora from the Atlantic and Gulf coasts of North America. The distribution of cpDNA haplotypes indicates that Atlantic coast S. alterniflora are subdivided into ‘northern’ and ‘southern’ groups. Variation observed at microsatellite loci further suggests that mid‐Atlantic S. alterniflora are differentiated from S. alterniflora found in southern Atlantic and New England coastal marshes. Comparisons between native populations on the Atlantic and Gulf coasts and non‐native Pacific coast populations substantiate prior studies demonstrating reciprocal interspecific hybridization in San Francisco Bay. Our results corroborate historical evidence that S. alterniflora was introduced into Willapa Bay from multiple source populations. However, we found that some Willapa Bay S. alterniflora are genetically divergent from putative sources, probably as a result of admixture following secondary contact among previously allopatric native populations. We further recovered evidence in support of models suggesting that S. alterniflora has secondarily spread within Washington State, from Willapa Bay to Grays Harbor. Main conclusions Underlying genetic structure has often been cited as a factor contributing to ecological variation of native S. alterniflora. Patterns of genetic structure within native S. alterniflora may be the result of environmental differences among biogeographical provinces, of migration barriers, or of responses to historical conditions. Interactions among these factors, rather than one single factor, may best explain the distribution of genetic variation among native S. alterniflora. Comprehensive genetic comparisons of native and introduced populations can illustrate how biological invasions may result from dramatically different underlying factors – some of which might otherwise go unrecognized. Demonstrating that invasions can result from several independent or interacting mechanisms is important for improving risk assessment and future forecasting. Further research on S. alterniflora not only may clarify what forces structure native populations, but also may improve the management of non‐native populations by enabling post‐introduction genetic changes and the rapid evolution of life‐history traits to be more successfully exploited.     

Disrupted phylogeographical microsatellite and chloroplast DNA patterns indicate a vicariance rather than long‐distance dispersal origin for the disjunct distribution of the Chilean endemic Dioscorea biloba (Dioscoreaceae) around the Atacama Desert

Aim The Chilean endemic Dioscorea biloba (Dioscoreaceae) is a dioecious geophyte that shows a remarkable 600 km north–south disjunction in the peripheral arid area of the Atacama Desert. Its restricted present‐day distribution and probable Neogene origin indicate that its populations have a history linked to that of the Atacama Desert, making this an ideal model species with which to investigate the biogeography of the region. Location Chile, Atacama Desert and peripheral arid area. Methods Two hundred and seventy‐five individuals from nine populations were genotyped for seven nuclear microsatellite loci, and plastid trnL–F and trnT–L sequences were obtained for a representative subset of these. Analyses included the estimation of genetic diversity and population structure through clustering, Bayesian and analysis of molecular variance analyses, and statistical parsimony networks of chloroplast haplotypes. Isolation by distance was tested against alternative dispersal hypotheses. Results Microsatellite markers revealed moderate to high levels of genetic diversity within populations, with those from the southern Limarí Valley showing the highest values and northern populations showing less exclusive alleles. Bayesian analysis of microsatellite data identified three genetic groups that corresponded to geographical ranges. Chloroplast phylogeography revealed no haplotypes shared between northern and southern ranges, and little haplotype sharing between the two neighbouring southern valleys. Dispersal models suggested the presence of extinct hypothetical populations between the southern and northern ranges. Main conclusions Our results are consistent with prolonged isolation of the northern and southern groups, mediated by the life‐history traits of the species. Significant isolation was revealed at both large and moderate distances as gene flow was not evident even between neighbouring valleys. Bayesian analyses of microsatellite and chloroplast haplotype diversity identified the southern area of Limarí as the probable area of origin of the species. Our data do not support recent dispersal of D. biloba from the southern range into Antofagasta, but indicate the fragmentation of an earlier wider range, concomitant with the Pliocene–Pleistocene climatic oscillations, with subsequent extinctions of the Atacama Desert populations and the divergence of the peripheral ones as a consequence of genetic drift.     

Taxonomic study of Scytosiphon (Phaeophyceae) from temperate coasts of Argentina

Scytosiphon is a common intertidal genus widely distributed on temperate coasts worldwide. Recently, eight species have been delimited with molecular tools. Although S. lomentaria is the only species that predominates in the macroalgal literature of the Southwestern Atlantic Ocean (SwAO), unpublished molecular data obtained for a population study of S. lomentaria revealed hidden species diversity of Scytosiphon among the individuals collected from four localities at the SwAO. The aim of this study was to revise the identity and phylogenetic relationships of Scytosiphon from temperate coasts of the SwAO using DNA data. Thalli were collected from the Argentinean coast between 39° S and 43° S, from which cox1 and rbcL gene sequences were obtained. Phylogenies and haplotype networks were inferred and morphology of gametophytes was studied. Four species were recognized, S. lomentaria, S. promiscuus, S. shibazakiorum, and one species that belongs to a complex of species known as “Scytosiphon Atlantic complex.” This complex was known to occur only in the North Atlantic, however, the results found in this study revealed that it has an extended distribution range that includes the southern hemisphere, where its populations have high genetic diversity and unique haplotypes. The morphological differences among the four species were subtle; denoting that previous Scytosiphon records from the SwAO attributed to the renowned S. lomentaria could represent different species. In addition, sex ratio and genome-wide single nucleotide polymorphisms (SNPs) analyses were done for populations of S. promiscuus presumably introduced to the SwAO, and the results indicated that they included female-dominant parthenogenetic populations, which were probably introduced from Japan.     

Multiple glacial refugia for cool‐temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

In East Asia, temperate forests are predicted to have retracted southward to c. 30° N during the last glacial maximum (LGM) based on fossil pollen data, whereas phylogeographic studies have often suggested glacial in situ survival of cool‐temperate deciduous trees in their modern northern ranges. Here we report a study of the genetic diversity and structure of 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear simple sequence repeat (nSSR) loci and four chloroplast DNA fragments. Bayesian clustering analysis with nSSRs revealed five groups, which were inferred by approximate Bayesian computation (ABC) to have diverged in multiple refugia through multiple glacial–interglacial cycles. Analysis of chloroplast DNA variation revealed four lineages that were largely but incompletely geographically disjunct. Ecological niche modelling (ENMs) indicated a southward range shift of the oak's distribution at the LGM, although high suitability scores were also evident in the Changbai Mts. (Northeast China), the Korean Peninsula, areas surrounding the Bohai Sea, and along the coast of the Russian Far East. In addition, endemic chloroplast DNA haplotypes and nuclear lineages occurred in high‐latitude northern areas where the ENM predicted no suitable habitat. The combined evidence from nuclear and chloroplast DNA, and the results of the ENM clearly demonstrate that multiple northern refugia, including cryptic ones, were maintained across the current distributional range of the Mongolian oak during the LGM or earlier glacial periods. Though spatially limited, postglacial expansions from these refugia have led to a pattern of decreased genetic diversity with increasing latitude.     

Understanding invasion history: genetic structure and diversity of two globally invasive plants and implications for their management

Aim Resolving the origin of invasive plant species is important for understanding the introduction histories of successful invaders and aiding strategies aimed at their management. This study aimed to infer the number and origin(s) of introduction for the globally invasive species, Macfadyena unguis‐cati and Jatropha gossypiifolia using molecular data. Location Native range: Neotropics; Invaded range: North America, Africa, Europe, Asia, Pacific Islands and Australia. Methods We used chloroplast microsatellites (cpSSRs) to elucidate the origin(s) of introduced populations and calculated the genetic diversity in native and introduced regions. Results Strong genetic structure was found within the native range of M. unguis‐cati, but no genetic structuring was evident in the native range of J. gossypiifolia. Overall, 27 haplotypes were found in the native range of M. unguis‐cati. Only four haplotypes were found in the introduced range, with more than 96% of introduced specimens matching a haplotype from Paraguay. In contrast, 15 haplotypes were found in the introduced range of J. gossypiifolia, with all invasive populations, except New Caledonia, comprising multiple haplotypes. Main conclusions These data show that two invasive plant species from the same native range have had vastly different introduction histories in their non‐native ranges. Invasive populations of M. unguis‐cati probably came from a single or few independent introductions, whereas most invasive J. gossypiifolia populations arose from multiple introductions or alternatively from a representative sample of genetic diversity from a panmictic native range. As introduced M. unguis‐cati populations are dominated by a single haplotype, locally adapted natural enemies should make the best control agents. However, invasive populations of J. gossypiifolia are genetically diverse and the selection of bio‐control agents will be considerably more complex.     

Chloroplast microsatellites and mitochondrial nad1 intron 2 sequences indicate congruent phylogenetic relationships among Swiss stone pine (Pinus cembra), Siberian stone pine (Pinus sibirica), and Siberian dwarf pine (Pinus pumila)

We studied the phylogenetic relationships among the three stone pine species, Pinus cembra, P. sibirica, and P. pumila, using chloroplast microsatellites and mitochondrial nad1 intron 2 sequences. The three chloroplast microsatellite loci combined into a total of 18 haplotypes. Fourteen haplotypes were detected in 15 populations of P. cembra and one population of P. sibirica, five of which were shared between the two species, and the two populations of P. pumila comprised four species-specific haplotypes. Mitochondrial intron sequences confirmed this grouping of species. Sequences of P. cembra and P. sibirica were identical, but P. pumila differed by several nucleotide substitutions and insertions/deletions. A repeat region found in the former two species showed no intraspecific variation. These results indicate a relatively recent evolutionary separation of P. cembra and P. sibirica, despite their currently disjunct distributions. The species-specific chloroplast and mitochondrial markers of P. sibirica and P. pumila should help to trace the hybridization in their overlapping distribution area and to identify fossil remains with respect to the still unresolved postglacial re-colonization history of these two species.     

Multiple introductions promote range expansion of the mollusc Cyclope neritea (Nassariidae) in France: evidence from mitochondrial sequence data

Since the 1970s, the nassariid gastropod Cyclope neritea has been extending its range north along the French Atlantic coasts from the Iberian Peninsula. This may be due to natural spread because of the recent warming of the northeastern Atlantic. However, human-mediated introductions related to shellfish culture may also be a probable explanation for this sudden range expansion. To examine these two hypotheses, we carried out a comprehensive study based on mitochondrial gene sequences (cytochrome oxidase I) of the five recently colonized French bays as well as 14 populations located in the recognized native range of the species. From a total of 594 individuals, we observed 29 haplotypes to split into three divergent clades. In the native range, we observed a low molecular diversity, strong genetic structure and agreement between geography and gene genealogies. Along the French coasts, we observed the opposite: high genetic diversity and low genetic structure. Our results show that recurrent human-mediated introductions from several geographical areas in the native range may be a source for the French Atlantic populations. However, despite the low dispersal ability of C. neritea, the isolation-by-distance pattern in France suggested that this gastropod may have been present (although unnoticed) on the French Atlantic coasts before the 1970s. As C. neritea shows characteristics of a cryptogenic species, the classification of Atlantic populations as either native or introduced is not straightforward. Cryptogenic species should be studied further to determine the status of new populations close to their recognized native range.     

Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum

Aim Palaeontologial data suggest that all temperate forest species in northern China migrated southwards during the Last Glacial Maximum (LGM) and recolonized post‐glacially within the Holocene. We tested this assumption using phylogeographical studies of a temperate deciduous shrub species (Ostryopsis davidiana Decne., Betulaceae), which has a wide distribution in northern China. Location Northern China. Methods We sequenced two chloroplast DNA (cpDNA) fragments (trnL–trnF and psbA–trnH, together about 1300 bp in length) of 294 plants from 21 populations across the total distribution range of this species. We used maximum parsimony and haplotype network methods to construct phylogenetic relationships among haplotypes. Results The analysis of cpDNA variation identified eight haplotypes. A single haplotype was fixed in all populations except for one population that was polymorphic, having two haplotypes. The population subdivisions were extremely high (G_ST = 0.972 and N_ST = 0.974), suggesting very low gene flow between populations. Haplotypes clustered into two tentative clades, both of which occur in the southern region of the species’ range but only one of which occurs in the northern region. Across the sampled populations, the haplotype distributions were differentiated geographically. Main conclusions Our analyses suggest that multiple refugia were maintained across the range of O. davidiana in both northern (north of the Qing Mountains) and southern (south of the Qing Mountains) regions during the LGM rather than that the species survived only in the south and subsequently colonized northwards. The extremely low within‐population diversity of this species suggests strong bottleneck or founder effects within each fragmented region during the Quaternary climatic oscillations. These findings provide important clues for understanding range shifts and changes in within‐ and/or between‐population genetic diversity of temperate forests in response to past climatic oscillations in northern China.     

Phylogeography and population genetics of Acanthophyllum squarrosum complex (Caryophyllaceae) in the Irano-Turanian region

Acanthophyllum squarrosum and two closely related species, A. heratense and A. laxiusculum (Caryophyllaceae), form a complex that covers parts of subalpine steppes of the Irano-Turanian (IT) region. In this study, we explored the genetic structure and phylogeography of this complex based on partial sequences of two chloroplasts (psbA–trnH and rpl32–trnL (UAG)) and two nuclear (EST24 and nrITS) DNA regions. We analysed 80 individuals from eight populations and detected 12 chloroplast haplotypes, 16 and eight nuclear alleles in EST24 and nrITS sequences, respectively. Phylogenetic trees and haplotype networks did not show distinct genetic groups in the complex and this could be explained by incomplete lineage sorting or introgression between species. Divergence time analysis revealed a Quaternary origin for A. squarrosum complex at approximately 1.8 million years ago (Mya) and the neutrality test results indicated that this complex experienced a recent population expansion. AMOVA analysis of the chloroplast regions showed a significant genetic differentiation among populations and low genetic differentiation within populations, but opposite results were found with nuclear markers, implying introgression between A. squarrosum complex populations.     

Phylogeography of <Emphasis Type="Italic">Ceriops tagal</Emphasis> (Rhizophoraceae) in Southeast Asia: the land barrier of the Malay Peninsula has caused population differentiation between the Indian Ocean and South China Sea

The genetic structure of mangrove species is greatly affected by their geographic history. Nine natural populations of Ceriops tagal were collected from Borneo, the Malay Peninsula, and India for this phylogeographic study. Completely different haplotype compositions on the east versus west coasts of the Malay Peninsula were revealed using the atpB-rbcL and trnL-trnF spacers of chloroplast DNA. The average haplotype diversity (Hd) of the total population was 0.549, nucleotide diversity (θ) was 0.030, and nucleotide difference (π) was 0.0074. The cladogram constructed by the index of population differentiation (G _ST) clearly separated the South China Sea populations from the Indian Ocean populations. In the analysis of the minimum spanning network, the Indian Ocean haplotypes were all derived from South China Sea haplotypes, suggesting a dispersal route of C. tagal from Southeast Asia to South Asia. The Sunda Land river system and surface currents might be accountable for the gene flow directions in the South China Sea and Bay of Bengal, respectively. The historical geography not only affected the present genotype distribution but also the evolution of C. tagal. These processes result in the genetic differentiation and the differentiated populations that should be considered as Management Units (MUs) for conservation measurements instead of random forestation, which might lead to gene mixing and reduction of genetic variability of mangrove species. According to this phylogeographic study, populations in Borneo, and east and west Malay Peninsula that have unique genotypes should be considered as distinct MUs, and any activities resulting in gene mixing with each other ought to be prevented.     

Development of microsatellite markers for Diaphanosoma dubium (Crustacea,Cladocera) and application to seasonal population dynamics

Diaphanosoma, the “tropical Daphnia”, is common and ubiquitous in South China. Like other ctenopods, Diaphanosoma has a reproductive mode similar to Daphnia’s, but its resting eggs are rarely observed and lack an ephippium. With limited dispersal and reduced buffer effect from resting egg banks, Diaphanosoma is expected to have a population genetic structure different from that of temperate Daphnia. To facilitate genetic comparison, we developed microsatellite markers using next-generation sequencing for the most common species in tropical and subtropical East Asia, Diaphanosoma dubium. Thirty-one polymorphic microsatellite markers were obtained, and 29 of them were efficient for the congeneric species D. excisum, D. orghidani, D. mongolianum and D. chankensis. The markers allowed intra- and interspecific genetic analysis, including population structure, hybridization and introgression. We used 11 selected microsatellite markers to analyze spatial and temporal heterogeneity of genetic diversity in four (sub)tropical D. dubium populations from two large reservoirs and two temporary ponds. In contrast to temperate Cladocera, higher genetic diversity in summer rather than in spring suggested weak contribution from resting eggs in spring. Clustering of DAPC and STRUCTURE analyses indicated a clear-cut genetic structure in the four populations. Variation partitioning revealed that water storage and depth were key factors in genetic differentiation. Within large reservoirs, we detected backward (reversing time) gene flow from resting egg banks. We conclude that resting eggs have an effective contribution to the genetic diversity in large water bodies during growing seasons and that large water bodies can host higher genetic diversity in summer due to environmental heterogeneity and high carrying capacity. Spatial and temporal heterogeneity of genetic diversity detected by our microsatellite markers showed the newly developed markers can be applied for further study of populations of D. dubium and other species of Diaphanosoma at a contemporary scale.

     

Population genetic structure of Bryde’s whales (<Emphasis Type="Italic">Balaenoptera brydei</Emphasis>) at the inter-oceanic and trans-equatorial levels

Bryde’s whales (Balaenoptera brydei) differ from other typical baleen whale species because they are restricted to tropical and warm temperate waters in major oceans, and frequent trans-equatorial movement has been suggested for the species. We tested this hypothesis by analyzing genetic variation at 17 microsatellite loci (N = 508) and 299 bp of mitochondrial DNA (mtDNA) control region sequences (N = 472) in individuals obtained from the western North Pacific, South Pacific, and eastern Indian Ocean. Combined use of microsatellite and mtDNA markers allowed us to distinguish between contemporary gene flow and ancestral polymorphism and to describe sex-specific philopatry. A high level of genetic diversity was found within the samples. Both nuclear and mtDNA markers displayed similar population structure, indicating a lack of sex-specific philopatry. Spatial structuring was detected using both frequency-based population parameters and individual-based Bayesian approaches. Whales in the samples from different oceanic regions came from genetically distinct populations with evidence of limited gene flow. We observed low mtDNA sequence divergence among populations and a lack of concordance between geographic and phylogenetic position of mtDNA haplotypes, suggesting recent separation of populations rather than frequent trans-equatorial and inter-oceanic movement. We conclude that current gene flow between Bryde’s whale populations is low and that effective management actions should treat them as separate entities to ensure continued existence of the species.