Liverworts of Magadan: Life on the Edge of Beringia.

Magadan Province, located on the southwestern edge of Greater Beringia, combines various floristic elements in its flora, including Beringian and circum-boreal species. The geographic position and habitat diversity of Magadan Province predicts its liverwort flora is one of the richest hemiarctic floras in Asia. The distribution of species throughout the region is uneven, and while its southern part shows close connections with the suboceanic floras of Kamchatka, the middle and central parts are clearly related to the floras of Chukotka, where the Beringian land bridge directly lies in the past. The wide distribution of basic rocks here leads to the existence of a significant complex of basiphylous taxa. A total of 214 taxa (including 205 species and nine varieties) are reported in the present paper. The study of liverworts of Magadan Province should be continued and several new additions to the floral list are highly likely.

Formation of the Holarctic Fauna: Dated molecular phylogenetic and biogeographic insights from the Quedius-lineage of Ground-Dwelling Rove Beetles (Coleoptera, Staphylinidae).

Although the Holarctic fauna has been explored for centuries, many questions on its formation are still unanswered. For example, i) what was the impact of the uplift of the Himalaya and Tibetan Plateau?, ii) what were the timings and climate of the faunal bridges connecting the Nearctic and Palearctic regions?, and iii) how did insect lineages respond to the late Paleogene global cooling and regional aridification? To answer these, we developed a phylogenetic dataset of 1229 nuclear loci for a total of 222 species of rove beetles (Staphylinidae) with emphasis in the tribe Quediini, especially Quedius-lineage and its subclade Quedius sensu stricto. Using eight fossils for calibrating molecular clock, we estimated divergence times and then analysed in BioGeoBEARS paleodistributions of the most recent common ancestor for each target lineage. For each species we generated climatic envelopes of the temperature and precipitation and mapped them across the phylogeny to explore evolutionary shifts. Our results suggest that the warm and humid Himalaya and Tibetan Plateau acted as an evolutionary cradle for the Quedius-lineage originating during the Oligocene from where, in the Early Miocene, the ancestor of the Quedius s. str. dispersed into the West Palearctic. With the climate cooling from the Mid Miocene onwards, new lineages within Quedius s. str. emerged and gradually expanded distributions across the Palearctic. In Late Miocene, a member of the group dispersed to the Nearctic region via Beringia before the closure of this land bridge 5.3 Ma. Paleogene global cooling and regional aridification largely shaped the current biogeographic pattern for Quedius s. str. species, many of them originating during the Pliocene and shifting or contracting their ranges during Pleistocene.

Cenozoic migration of a desert plant lineage across the North Atlantic.

Previous paleobotanical work concluded that Paleogene elements of the sclerophyllous subhumid vegetation of western Eurasia and western North America were endemic to these disjunct regions, suggesting that the southern areas of the Holarctic flora were isolated at that time. Consequently, molecular studies invoked either parallel adaptation to dry climates from related ancestors, or long-distance dispersal in explaining disjunctions between the two regions, dismissing the contemporaneous migration of dry-adapted lineages via land bridges as unlikely. We report Vauquelinia (Rosaceae), currently endemic to western North America, in Cenozoic strata of western Eurasia. Revision of North American fossils previously assigned to Vauquelinia confirmed a single fossil-species of Vauquelinia and one of its close relative Kageneckia. We established taxonomic relationships of fossil-taxa using diagnostic character combinations shared with modern species and constructed a time-calibrated phylogeny. The fossil record suggests that Vauquelinia, currently endemic to arid and subdesert environments, originated under seasonally arid climates in the Eocene of western North America and subsequently crossed the Paleogene North Atlantic land bridge (NALB) to Europe. This pattern is replicated by other sclerophyllous, dry-adapted and warmth-loving plants, suggesting that several of these taxa potentially crossed the North Atlantic via the NALB during Eocene times.

Phylogeography of the Fiddler Crab Tubuca arcuata (Crustacea: Brachyura: Ocypodidae) in East Asia and Northern Vietnam.

The fiddler crab Tubuca arcuata (Crustacea: Ocypodidae: Gelasiminae) is widely distributed across East Asia and northern Vietnam. Particularly, this species inhabits estuarine mangroves and mudflats of the East Asian continent, as well as the main islands of Japan and the Ryukyus. By comparing sequences of the mitochondrial 16S, cytochrome oxidase subunit I (COI), and control region genes, two main clades of this species were elucidated. The northern (N) clade was mostly restricted to the region north of the Taiwan Strait, whereas the wide (W) clade could be found throughout the entire range inhabited by this species. Based on the distribution of the ancestral haplotypes of COI and the divergence time of the two clades, our findings suggest that the land bridge barrier present in the Taiwan Strait during glaciations might have played an important role in their cladogenesis, approximately 0.93 million years ago. Here, we propose that the distribution of the ancestral haplotype of the W clade in the Ryukyus and the main islands of Japan was determined by the Paleo-Kuroshio Current, whereas the modern distribution pattern is shaped by the modern Kuroshio Current and other warm currents during the crab reproduction season in the summer.

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It is of great significance to understand the pattern of soil respiration rate in fragmented forests for further revealing terrestrial ecosystem carbon cycling. With different habitats (island vs. mainland, island edge vs. island interior) of the artificial land-bridge island system in Thousand Island Lake (TIL) region as the objects, we analyzed the seasonal dynamics of soil respiration rate and its relationships with soil physicochemical factors. The results showed that: 1) Soil respiration rates varied significantly across different seasons, with an order of summer (3.74 µmol·m-2·s-1) > autumn (2.30 µmol·m-2·s-1) > spring (1.82 µmol·m-2·s-1) > winter (1.40 µmol·m-2·s-1). 2) Forest fragmentation had significant effects on soil respiration rate, with soil respiration rate of island (2.37 µmol·m-2·s-1) being significantly higher than that of mainland (2.08 µmol·m-2·s-1) and the soil respiration rate of island edge (2.46 µmol·m-2·s-1) being significantly higher than that of island interior (2.03 µmol·m-2·s-1). 3) Soil temperature significantly promoted soil respiration rate, explaining 56.1% of the total variation. 4) There was a significant positive correlation between soil respiration rate and soil total carbon, ammo-nium nitrogen content, and vegetation coverage. The soil total carbon and ammonium nitrogen content of island edge were significantly higher than those of island interior. In all, forest fragmentation promoted soil respiration rate, with soil physicochemical factors as the drivers for its variation.

Phylogenetic relationship, biogeography, and conservation genetics of endangered Fraxinus chiisanensis (Oleaceae), endemic to South Korea.

Endemic plants are important for understanding phylogenetic relationships, biogeographical history, and genetic variation because of their restricted distribution and their role in conserving biodiversity. Here, we investigated the phylogenetic relationships of the Korean endemic Fraxinus chiisanensis by reconstructing the molecular phylogeny of Fraxinus based on two nuclear DNA (nrITS and phantastica) and two chloroplast DNA (psbA-trnH and rpl32-trnL) regions. Within our fossil-calibrated phylogenetic framework, we also inferred the biogeographical history of F. chiisanensis. To provide a scientific basis for the conservation of F. chiisanensis, we determined the levels of genetic diversity and genetic differentiation in this species. Combining information from nuclear and chloroplast DNA sequence data, our molecular phylogenetic analyses identified F. chiisanensis as a genetically distinct unit from its sister group, Fraxinus platypoda from Japan. Our molecular dating analyses using nuclear and chloroplast DNA data sets show F. chiisanensis diverged from its sister F. platypoda in the Early or Middle Miocene and differentiated in the Late Miocene on the Korean Peninsula. Our results suggest that the divergence of F. chiisanensis was associated with the submergence of the East China Sea land bridge and enhanced monsoons in East Asia. When compared to F. platypoda, F. chiisanensis exhibits low genetic diversity within populations and high genetic differentiation among populations. These results help us to understand the evolutionary history of F. chiisanensis and to develop a conservation strategy for this species.

Molecular Phylogeny and Historical Biogeography of Goodyera R. Br. (Orchidaceae): A Case of the Vicariance Between East Asia and North America.

Understanding of intercontinental distribution in the Northern Hemisphere has attracted a lot of attention from botanists. However, although Orchidaceae is the largest group of angiosperms, biogeographical studies on the disjunctive pattern have not been sufficient for this family. Goodyera R. Br. (tribe Cranichideae, subfamily Orchidoideae, family Orchidaceae) is widely distributed in temperate and tropical regions. Although the phylogenetic relationship of Goodyera inferred from both morphological and molecular data has been conducted, the sampled taxa were mainly distributed in Asia regions that resulted in non-monophyly of this genus. In this study, the complete plastid genomes of Goodyera, generated by next-generation sequencing (NGS) technique and sampled in East Asia and North America, were used to reconstruct phylogeny and explore the historical biogeography. A total of 18 Goodyera species including seven newly sequenced species were analyzed. Based on 79 protein-coding genes, the phylogenetic analysis revealed that Goodyera could be subdivided into four subclades with high support values. The polyphyletic relationships among Goodyera taxa were confirmed, and the unclear position of G. foliosa was also resolved. The datasets that are composed of the 14 coding sequences (CDS) (matK, atpF, ndhK, accD, cemA, clpP, rpoA, rpl22, ndhF, ccsA, ndhD, ndhI, ndhA, and ycf 1) showed the same topology derived from 79 protein-coding genes. Molecular dating analyses revealed the origin of Goodyera in the mid-Miocene (15.75 Mya). Nearctic clade of Goodyera was diverged at 10.88 Mya from their most recent common ancestor (MRCA). The biogeographical reconstruction suggests that subtropical or tropical Asia is the origin of Goodyera and it has subsequently spread to temperate Asia during the Miocene. In addition, Nearctic clade is derived from East Asian species through Bering Land Bridge (BLB) during the Miocene. The speciation of Goodyera is most likely to have occurred during Miocene, and climatic and geological changes are thought to have had a part in this diversification. Our findings propose both origin and vicariance events of Goodyera for the first time and add an example for the biogeographical history of the Northern Hemisphere.

Out of Asia: Intercontinental dispersals after the Eocene-Oligocene transition shaped the zoogeography of Limenitidinae butterflies (Lepidoptera: Nymphalidae).

Most members of the nymphalid subfamily Limenitidinae are distributed in tropical regions of Africa, Asia, and the Americas. Previous studies have inferred their higher-level phylogeny and found that Southeast Asia seems to be the center of origin, with numerous dispersal events to other continents. However, the complete biogeographic history of Limenitidinae butterflies is still largely unknown. We sampled 181 taxa from 164 species and used a metagenomic method to obtain 40 genes (mitogenomes and three nuclear ribosomal loci) for inferring the historical biogeography of the group. We find that Limenitidinae originated in eastern Asia during the early Eocene (ca. 52 Ma) and started to diversify and disperse into Africa before the end of Eocene. Intercontinental exchanges between Africa and eastern Asia continued in the early Miocene: Asian Adoliadini and Asian endemic taxa Bhagadatta had African origins in the Oligocene, whereas African Neptini dispersed in the opposite direction from Asia in the early Miocene. In addition, ancestors of the tribes Limenitidini and Adoliadini dispersed into the Neotropics and Australasia multiple times during the early-to-middle Miocene. Eastern Asia is the center of origin of the tribe Limenitidini, with several taxa disjunctly distributed in eastern Asia and the Americas. Our work provides a robust phylogenetic hypothesis of relationships in the tribe Limenitidini and suggests that the alala-species group of Adelpha should be placed in the genus Limenitis. Renamed taxa comb. nov. based on our findings are listed in the text.

Origin and evolutionary history of Populus (Salicaceae): Further insights based on time divergence and biogeographic analysis.

Introduction: Populus (Salicaceae) species harbour rich biodiversity and are widely distributed throughout the Northern Hemisphere. However, the origin and biogeography of Populus remain poorly understood. Methods: We infer the divergence times and the historical biogeography of the genus Populus through phylogenetic analysis of 34 chloroplast fragments based on a large sample. Results and Discussion: Eurasia is the likely location of the early divergences of Salicaceae after the Cretaceous-Paleogene (K-Pg) mass extinction, followed by recurrent spread to the remainder of the Old World and the New World beginning in the Eocene; the extant Populus species began to diversity during the early Oligocene (approximately 27.24 Ma), climate changes during the Oligocene may have facilitated the diversification of modern poplar species; three separate lineages of Populus from Eurasia colonized North America in the Cenozoic via the Bering Land Bridges (BLB); We hypothesize that the present day disjunction in Populus can be explained by two scenarios: (i) Populus likely originated in Eurasia and subsequently colonized other regions, including North America; and (ii) the fact that the ancestor of the genus Populus that was once widely distributed in the Northern Hemisphere and eventually wiped out due to the higher extinction rates in North America, similar to the African Rand flora. We hypothesize that disparities in extinction across the evolutionary history of Populus in different regions shape the modern biogeography of Populus. Further studies with dense sampling and more evidence are required to test these hypotheses. Our research underscores the significance of combining phylogenetic analyses with biogeographic interpretations to enhance our knowledge of the origin, divergence, and distribution of biodiversity in temperate plant floras.

Phylogeography of Artemisia frigida (Anthemideae, Asteraceae) based on genotyping-by-sequencing and plastid DNA data: Migration through Beringia.

Artemisia frigida is a temperate grassland species that has the largest natural range among its genus, with occurrences across the temperate grassland biomes of Eurasia and North America. Despite its wide geographic range, we know little about the species' distribution history. Hence, we conducted a phylogeographical study to test the hypothesis that the species' distribution pattern is related to a potential historical migration over the 'Bering land bridge'. We applied two molecular approaches: genotyping-by-sequencing (GBS) and Sanger sequencing of the plastid intergenic spacer region (rpl32 - trnL) to investigate genetic differentiation and relatedness among 21 populations from North America, Middle Asia, Central Asia and the Russian Far East. Furthermore, we identified the ploidy level of individuals based on GBS data. Our results indicate that A. frigida originated in Asia, spread northwards to the Far East and then to North America across the Bering Strait. We found a pronounced genetic structuring between Middle and Central Asian populations with mixed ploidy levels, tetraploids in the Far East, and nearly exclusively diploids in North America except for one individual. According to phylogenetic analysis, two populations of Kazakhstan (KZ2 and KZ3) represent the most likely ancestral diploids that constitute the basally branching lineages, and subsequent polyploidization has occurred on several occasions independently. Mantel tests revealed weak correlations between genetic distance and geographical distance and climatic conditions, which indicates that paleoclimatic fluctuations may have more profoundly influenced A. frigida's spatial genetic structure and distribution than the current environment.

Giant Tree Frog diversification in West and Central Africa: Isolation by physical barriers, climate, and reproductive traits.

Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter- and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome-wide single-nucleotide polymorphism data, we demonstrated that species-level divergence coincides temporally and geographically with a period of large-scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.

La sympatrie secondaire parmi les espèces sœurs est fortement associée à la divergence génétique et écologique. Ce modèle suggère que pour que des espèces étroitement liées coexistent en sympatrie secondaire, elles doivent accumuler des différences dans les traits qui contribuent à l'isolement écologique ou reproductif. Ici, nous avons caractérisé la divergence inter- et intra-spécifique chez trois espèces de grenouilles arboricoles géantes dont les distributions s'étendent à travers l'Afrique de l'Ouest et Centrale. Avec des données génétiques, nous avons démontré que la divergence au niveau des espèces coïncide temporellement et géographiquement avec une période de fragmentation forestière à la fin du Pliocène. Nos modèles de niches environnementales ont soutenu une histoire dynamique de stabilité climatique, et ont indiqué que les trois espèces occupent des niches environnementales distinctes. Nous avons trouvé une différenciation morphologique modeste parmi les trois espèces mais une divergence significative dans le diamètre du tympan et les cris des mâles. De plus, nous avons confirmé que deux espèces sont présentes en sympatrie secondaire en Afrique Centrale mais n'avons trouvé aucune preuve d'hybridation. Ces résultats soutiennent l'hypothèse que les cycles d'échange génétique et d'isolement à travers l'Afrique de l'Ouest et Centrale ont contribué à une profonde concentration de biodiversité dans la région. De plus, la divergence des traits écologiques et reproducteurs semble avoir joué un rôle important dans le maintien de lignées distinctes. Au niveau intra-spécifique, nous avons constaté que les refuges climatiques, les gradients de précipitation, les incursions marines et potentiellement les barrières fluviales ont généré une structure phylogéographique pendant le Pléistocène et jusqu'à l'Holocène. Des études examinant la divergence phénotypique et le contact secondaire entre ces populations géographiquement structurées pourraient démontrer comment des barrières biogéographiques à échelle plus petite et plus récentes contribuent à la diversification régionale.

Phylogenomic framework of the IRLC legumes (Leguminosae subfamily Papilionoideae) and intercontinental biogeography of tribe Wisterieae.

The inverted repeat-lacking clade (IRLC) is one of the most derived clades within the subfamily Papilionoideae of the legume family, and includes various economically important plants, e.g., chickpeas, peas, liquorice, and the largest genus of angiosperms, Astragalus. Tribe Wisterieae is one of the earliest diverged groups of the IRLC, and its generic delimitation and spatiotemporal diversification needs further clarifications. Based on genome skimming data, we herein reconstruct the phylogenomic framework of the IRLC, and infer the inter-generic relationships and historical biogeography of Wisterieae. We redefine tribe Caraganeae to contain Caragana only, and tribe Astragaleae is reduced to the Erophaca-Astragalean clade. The chloroplast capture scenario was hypothesized as the most plausible explanation of the topological incongruences between the chloroplast CDSs and nuclear ribosomal DNA trees in both the Glycyrrhizinae-Adinobotrys-Wisterieae clade and the Chesneyeae-Caraganeae-Hedysareae clade. A new name, Caragana lidou L. Duan & Z.Y. Chang, is proposed within Caraganeae. Thirteen genera are herein supported within Wisterieae, including a new genus, Villosocallerya L. Duan, J. Compton & Schrire, segregated from Callerya. Our biogeographic analyses suggest that Wisterieae originated in the late Eocene and its most recent common ancestor (MRCA) was distributed in continental southeastern Asia. Lineages of Wisterieae remained in the ancestral area from the early Oligocene to the early Miocene. By the middle Miocene, Whitfordiodendron and the MRCA of Callerya-Kanburia-Villosocallerya Clade became disjunct between the Sunda area and continental southeastern Asia, respectively; the MRCA of Wisteria migrated to North America via the Bering land bridge. The ancestor of Austrocallerya and Padbruggea migrated to the Wallacea-Oceania area, which split in the early Pliocene. In the Pleistocene, Wisteria brachybotrys, W. floribunda and Wisteriopsis japonica reached Japan, and Callerya cinerea dispersed to South Asia. This study provides a solid phylogenomic for further evolutionary/biogeographic/systematic investigations on the ecologically diverse and economically important IRLC legumes.

Past connections with the mainland structure patterns of insular species richness in a continental-shelf archipelago (Aegean Sea, Greece).

Recent research in island biogeography has highlighted the important role of late Quaternary sea-level fluctuations in shaping biogeographic patterns in insular systems but focused on oceanic systems. Through this study, we aim investigate how late Quaternary sea-level fluctuations shaped species richness patterns in continental-shelf island systems. Focusing on the Aegean archipelago, we first compiled maps of the area's geography using published data, under three sea-level stands: (a) current; (b) median sea-level over the last nine glacial-interglacial cycles (MSL); and (c) Last Glacial Maximum (LGM). We gathered taxon-island occurrences for multiple chorotypes of angiosperms, butterflies, centipedes, and reptiles. We investigated the impact of present-day and past geographic settings on chorological groups by analyzing island species-area relationships (ISARs) and using generalized linear mixed models (GLMMs) selection based on multiple metrics of goodness of fit. Our results confirm that the Aegean's geography has changed dramatically since the LGM, whereas the MSL only modestly differs from the present configuration. Apart for centipedes, paleogeographic changes affected both native and endemic species diversity through altering connections between land-bridge islands and the mainland. On land-bridge islands, we detected over-representation of native species and under-representation of endemics. Unlike oceanic islands, sea-level-driven increase of isolation and area contraction did not strongly shape patterns of species richness. Furthermore, the LGM configurations rather than the MSL configuration shaped patterns of endemic species richness. This suggests that even short episodes of increased connectivity with continental populations are sufficient to counteract the genetic differentiation of insular populations. On the other hand, the over-representation of native nonendemic species on land-bridge islands reflected MSL rather than LGM mainland connections. Our study shows that in terms of processes affecting species richness patterns, continental archipelagos differ fundamentally from oceanic systems because episodic connections with the mainland have profound effects on the biota of land-bridge islands.

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge.

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.

Phylotranscriptomics reveals the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution.

The disjunct distribution between East Asia and North America is one of the best established biogeographic patterns. A robust phylogeny is fundamental for understanding the biogeographic histories of taxa with this distribution pattern. Tsuga (hemlock) is a genus of Pinaceae with a typical intercontinental disjunct distribution in East Asia and eastern and western North America, and its phylogeny has not been completely reconstructed in previous studies. In this study, we reconstructed a highly resolved phylogeny of Tsuga using 881 nuclear genes, 60 chloroplast genes and 23 mitochondrial genes and explored its biogeographic and reticulate evolutionary history. The results of phylogenetic analysis, molecular dating and ancestral area reconstruction indicate that Tsuga very likely originated from North America in the late Oligocene and dispersed from America to East Asia via the Bering Land Bridge during the middle Miocene. In particular, we found complex reticulate evolutionary pattern among the East Asian hemlock species. T. sieboldii possibly originated from hybridization with the ancestor of T. chinensis from mainland China and T. forrestii as the paternal donor and the ancestor of T. diversifolia and T. ulleungensis as the maternal donor. T. chinensis (Taiwan) could have originated by hybridization together with T. sieboldii and then evolved independently after dispersal to the Taiwan Island, subsequently experiencing mitochondrial DNA introgression with T. chinensis from mainland China. Moreover, our study found that T. chinensis from western China is more closely related to T. forrestii than to T. chinensis from eastern China. The nonmonophyletic T. chinensis needs taxonomic reconsideration.

Phylogeography of the Japanese greater horseshoe bat Rhinolophus nippon (Mammalia: Chiroptera) in Northeast Asia: New insight into the monophyly of the Japanese populations.

The Japanese greater horseshoe bat (Rhinolophus nippon) is distributed widely in East Asia. Within the species, R. nippon in Northeast Asia is regarded as the lineage that diverged most recently. However, the monophyly of the Japanese populations is unclear due to insufficient data about phylogenetic relationship of the western Japanese populations. To test the monophyly of the Japanese populations of R. nippon, we sampled R. nippon from western Japan and performed a phylogeographic analysis based on mitochondrial DNA cytochrome b and the D-loop. The Northeast Asian lineage consisted of three main clades in eastern Japan (clade I), western Japan (clade II), and the continent as well as the Kumamoto population in westernmost Japan (clade III). The results of this study do not support the monophyly of the Japanese population. The findings suggest the "reverse colonization" of R. nippon from the Japanese Archipelago to the Eurasian continent, and provide important insight into the role of the island system in creation and supply of diversity to the continent.

Fossil fruits of Firmiana and Tilia from the middle Miocene of South Korea and the efficacy of the Bering land bridge for the migration of mesothermal plants.

Determining whether the high-latitude Bering land bridge (BLB) was ecologically suitable for the migration of mesothermal plants is significant for Holarctic phytogeographic inferences. Paleobotanical studies provide a critical source of data on the latitudinal positions of different plant lineages at different times, permitting assessment of the efficacy of the BLB for migration. Here we report exceptionally preserved fossils of Firmiana and Tilia endochrysea from the middle Miocene of South Korea. This represents a new reliable record of Firmiana and the first discovery of the T. endochrysea lineage in the fossil record of Asia. The occurrence of these fossils in South Korea indicates that the two lineages had a distribution that extended much farther north during the middle Miocene, but they were still geographically remote from the BLB. In light of the broader fossil record of Asia, our study shows that, in the middle Miocene, some mesothermal plants apparently inhabited the territory adjacent to the BLB and thus they were possibly capable of utilizing the BLB as a migratory corridor. Some other mesothermal plants, such as Firmiana and the T. endochrysea lineages, however, are restricted to more southern regions relative to the BLB based on current fossil evidence. These lineages may have been ecologically unable to traverse the BLB, which raises questions about the efficacy of the BLB as a universal exchange route for mesothermal plants between Asia and North America during the middle Miocene.

Study of the independent gametophytes found on Jeju Island in South Korea and the first record of the obligate independent gametophyte of Antrophyum obovatum Baker.

Fern gametophytes have often been neglected in research; however, studies on gametophytes are crucial for a better understanding of the evolution of ferns. During their life cycle, some gametophytes produce large and long-lived populations without producing sporophytes and reproduce independently through asexual means, such as through the formation of gemmae. In this study, we investigated independent gametophytes on the Jeju Island of Korea, which was located on the land bridge between East China and Japan during the glacial periods. Fourteen gametophyte populations were collected from seven sites, of which 13 populations were clearly identified as belonging to four fern species known to occur in Jeju Island with BLAST searches using rbcL and trnL-F sequences. Surprisingly, the last remaining population constituted undescribed taxa in Korea. We presented the first report of the independent gametophytes of Antrophyum obovatum Baker which has not been previously recorded in Korea. It has been supposed that many ferns sought suitable habitat throughout the land bridge between China and Japan. However, Jeju Island might be unsuitable for vittarioid ferns that prefer a tropical or subtropical environment. Consequently, only two species of vittariod ferns (A. obovatum and Haplopteris flexuosa (Fée) E.H. Crane) in the form of a gametophyte and sporophyte, respectively, exist on Jeju Island. Therefore, this gametophyte population must be protected and managed from a conservation perspective. In the case of the independent gametophyte of Hymenophyllum wrightii Bosch, haplotype analysis was conducted based on the rbcL sequences and the result supported that the North American populations were migrated from Japan through land bridge during the glacial periods and Jeju populations were recently established by long-distance dispersal of the Japanese populations.

Habitat fragmentation changes top-down and bottom-up controls of food webs.

Top-down and bottom-up controls regulate the structure and stability of ecosystems, but their relative roles in terrestrial systems have been debated. Here we studied a hydro-inundated land-bridge system in subtropical China and tested the relative importance of these two controls in determining the rodent-mediated regeneration of a locally dominant tree species. Our results showed that both controls operated in terrestrial habitats and that their relative importance switched as habitat size changed. Habitat loss initially removed predators of rodents that released rodent populations and triggered massive seed predation (top-down control), leading to reduced seedling establishment. A further reduction in habitat size led to decrease in rodent population that was supposed to increase seedling survival of the tree species, but the decline in habitat size deteriorated the abiotic environments (bottom-up control) that severely prevented seedling recruitment. As the ongoing global land use change is creating increasing number of small-sized forest fragments, our findings provide novel insights into the restoration of seriously fragmented forests.

A fossil-calibrated phylogeny reveals the biogeographic history of the Cladrastis clade, an amphi-Pacific early-branching group in papilionoid legumes.

The early-branching Cladrastis clade of papilionoid legumes (Leguminosae, Papilionoideae) has an intriguing amphi-Pacific disjunct distribution in eastern Asia and temperate-tropical Americas. Here we used nuclear and three plastid regions to reconstruct the phylogenetic relationships and divergence times in the Cladrastis clade, as well as the evolution of morphological characters that might have been key in its biogeographic history. The ancestral character state estimation revealed that the most recent common ancestor of the Cladrastis clade was deciduous trees possessing compressed, winged fruits. The Cladrastis clade was inferred to have originated in the mid-latitude thermophilic forests of North America in the early Eocene, followed by the split between ancestors of wing-fruited Platyosprion and the non-wing-fruited group, and later the divergence of Cladrastis s.s. from the non-wing-fruited group in middle Eocene. Platyosprion and Cladrastis s.s. display an "out-of-North-America" biogeographic pattern and might have migrated to Asia via the Bering land bridge (BLB) or the North Atlantic land bridges (NALB) during middle to late Eocene. Our results, coupled with the relatively well documented fossil record for the clade, suggest that Platyosprion experienced an extinction event in North America caused by climatic cooling around the Eocene-Oligocene transition, which drove a major vegetation shift in western North America, in turn serving as a barrier for the vicariance of Pickeringia and Styphnolobium. The evolution of shrubby habit and sclerophyllous leaves in the former might be adaption to the chaparral vegetation in southwestern North America; the latter gained the trait of moniliform, succulent fruit. Styphnolobium further dispersed southward to tropical North America in the Oligocene, and eastward to Asia through BLB during middle Miocene. Subsequent sundering of BLB facilitated the vicariance of St. affine and St. japonicum.