Evidence of extreme habitat stability in a Southeast Asian biodiversity hotspot based on the evolutionary analysis of neotenic net-winged beetles

The diversification of neotenic beetle lineages has not been studied, despite the potential for defining biodiversity hotspots and elucidating the history of regional faunas. Additionally, neotenics may provide insight into the process of speciation in small populations with extremely low dispersal ability and a limited range. Here, we used two rDNA and three mtDNA markers to investigate the phylogeny of Scarelus, a neotenic lineage endemic to Southeast Asian rainforests. Most genetic differentiation was associated with Palaeogene geographical divisions, which remain distinct despite temporary connections. Dispersal events were rare, with only two inferred for Scarelus: from Borneo to the Philippines 28.3 million years ago (Ma) and from Sumatra to Java 13.9 Ma. We suggest that speciation resulted from allopatric range fragmentation, and Scarelus diversified readily when conditions were favourable; in this case, at different times in the eastern (19.3-39.1 Ma) and western (3.5-13.9 Ma) parts of Sundaland. The observed strong phenotypic similarity was preserved under speciation through complete allopatry. Neotenic Lycidae have survived for a long time in very stable habitats, and extremely low dispersal activity has not limited their persistence; however, the long-term diversification rate of neotenics is low and diversification is nonexistent under stable conditions. The modern ranges of neotenic lineages are indicative of ancient rainforest refugia and may be used in biodiversity conservation management. Most neotenics are at risk of extinction because of their small ranges and a low dispersal potential.     

Genetic structure of Gymnures (genus Hylomys; Erinaceidae) on continental islands of Southeast Asia: historical effects of fragmentation

Eustatic sea level changes during Pleistocene climatic fluctuations produced several cycles of connection-isolation among continental islands of the Sunda shelf. To explore the potential effects of these fluctuations, we reconstructed a model of the vicariant events that separated these islands, based on bathymetric information. Among many possible scenarios, two opposite phylogenetic patterns of evolution were predicted for terrestrial organisms living in this region: one is based on the classical allopatric speciation mode of evolution, while the other is the outcome of a sequential dispersal colonization of the archipelago. We tested the applicability of these predictions with an analysis of sequence variation of the cytochrome b gene from several taxa of Hylomys. They were sampled throughout SE-Asia and the Sunda islands. High levels of haplotype differentiation characterize the different island taxa. Such levels of differentiation support the existence of several allopatric species, as was suggested by previous allozyme and morphological data. Also in accordance with previous results, the occurrence of two sympatric species from Sumatra is suggested by their strongly divergent haplotypes. One species, Hylomys suillus maxi, is found both on Sumatra and in Peninsular Malaysia, while the other, H. parvus, is endemic to Sumatra. Its closest relative is H. suillus dorsalis from Borneo. Phylogenetic reconstructions also demonstrate the existence of a Sundaic clade composed of all island taxa, as opposed to those from the continent. Although there is no statistical support for either proposed biogeographic model of evolution, we argue that the sequential dispersal scenario is more appropriate to describe the genetic variation found among the Hylomys taxa. However, despite strong differentiation among island haplotypes, the cladistic relationships between some island taxa could not be resolved. We argue that this is evidence of a rapid radiation, suggesting that the separation of the islands may have been perceived as a simultaneous event rather than as a succession of vicariant events. Furthermore, the estimates of divergence times between the haplotypes of these taxa suggest that this radiation may actually have predated the climatic fluctuations of the Pleistocene. Further refinement of the initial palaeogeographic models of evolution are therefore needed to account for these results.     

Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

The use of genome-wide genetic markers is an emerging approach for informing evidence-based management decisions for highly threatened species. Pangolins are the most heavily trafficked mammals across illegal wildlife trade globally, but critically endangered Sunda pangolins (Manis javanica) have not been widely studied in insular Southeast Asia. We used?>?12,000 single nucleotide polymorphic markers (SNPs) to assign pangolin seizures from illegal trade of unknown origin to possible geographic sources via genetic clustering with pangolins of known origin. Our SNPs reveal three previously unrecognized genetic lineages of Sunda pangolins, possibly from Borneo, Java and Singapore/Sumatra. The seizure assignments suggest the majority of pangolins were traded from Borneo to Java. Using mitochondrial markers did not provide the same resolution of pangolin lineages, and to explore if admixture might explain these differences, we applied sophisticated tests of introgression using?>?2000 SNPs to investigate secondary gene flow between each of the three Sunda pangolin lineages. It is possible the admixture which we discovered is due to human-mediated movements of pangolins. Our findings impact a range of conservation actions, including tracing patterns of trade, repatriation of rescue animals, and conservation breeding. In order to conserve genetic diversity, we suggest that, pending further research, each pangolin lineage should as a precaution be protected and managed as an evolutionarily distinct conservation unit.     

Coalescent species delimitation of a Sumatran parachuting frog

We conduct species delimitation of the widespread parachuting frog species Rhacophorus catamitus using samples from across the island of Sumatra, Indonesia. We use mitochondrial, genomic and morphological data, and find that R. catamitus is composed of three lineages corresponding to northern, central and southern lineages. Mitochondrial and genomic data show admixture or incomplete lineage sorting between the central and southern lineages, but deep divergence from the northern lineage. Coalescent species delimitation supports a three species model for this complex, and we recommend that the northern lineage be described as a new species. Our study highlights the power of coalescent species delimitation in an integrative framework for identifying unrecognised diversity in understudied tropical species complexes. We also emphasise the evolutionary importance of northern Sumatra, a region that harboured montane refugia during Pliocene–Pleistocene climate change, but has also been heavily affected by volcanic activity.     

Into the Himalayan Exile: The Phylogeography of the Ground Beetle Ethira clade Supports the Tibetan Origin of Forest-Dwelling Himalayan Species Groups

The Himalayan mountain arc is one of the hotspots of biodiversity on earth, and species diversity is expected to be especially high among insects in this region. Little is known about the origin of the Himalayan insect fauna. With respect to the fauna of high altitude cloud forests, it has generally been accepted that Himalayan lineages are derived from ancestors that immigrated from Western Asia and from adjacent mountainous regions of East and Southeast Asia (immigration hypothesis). In this study, we sought to test a Tibetan Origin as an alternative hypothesis for groups with a poor dispersal ability through a phylogeographic analysis of the Ethira clade of the genus Pterostichus. We sequenced COI mtDNA and the 18S and 28S rDNA genes in 168 Pterostichini specimens, including 46 species and subspecies of the Ethira clade. In our analysis, we were able to show that the Ethira clade is monophyletic and, thus, represents a Himalayan endemic clade, supporting endemism of two of the basal lineages to the Central Himalaya and documenting large distributional gaps within the phylogeographic structure of the Ethira clade. Furthermore, the molecular data strongly indicate very limited dispersal abilities of species and subspecies of these primary wingless ground beetles. These results are consistent with the hypothesis of a Tibetan Origin, which explains the evolution, diversity and distribution of the Himalayan ground beetle Ethira clade much more parsimoniously than the original immigration hypothesis.     

The distribution of the Malay civet Viverra tangalunga (Carnivora: Viverridae) across Southeast Asia: natural or human‐mediated dispersal?

The Malay civet Viverra tangalunga Gray, 1832 is a fairly large viverrid that has a wide distribution in both the Sundaic and Wallacea regions of Southeast Asia. We investigated the genetic diversity of V. tangalunga by analysing the mitochondrial DNA of 81 individuals throughout its range in order to elucidate the evolutionary history of this species and to test the hypotheses of natural dispersal and/or potential human introductions to some islands and regions. Our phylogenetic analyses revealed that V. tangalunga has a low matrilinear genetic diversity and is poorly structured geographically. Borneo is likely to have served as the ancestral population source from which animals dispersed during the Pleistocene. Viverra tangalunga could have naturally dispersed to Peninsular Malaysia, Sumatra, and Belitung, and also to several other Sunda Islands (Bangka, Lingga, and Bintang in the Rhio Archipelago), and to Palawan, although there is possible evidence that humans introduced V. tangalunga to the latter islands. Our results strongly suggested that V. tangalunga was transported by humans across Wallace's Line to Sulawesi and the Moluccas, but also to the Philippines and the Natuna Islands. Our study has shown that human‐mediated dispersal can be an important factor in understanding the distribution of some species in this region. © 2014 The Linnean Society of London     

The taxonomy and diversity of Platerodrilus (Coleoptera,Lycidae) inferred from molecular data and morphology of adults and larvae

The Oriental neotenic net-winged beetles attracted attention of biologists due to conspicuous large-bodied females; nevertheless phylogenetic relationships remain contentious and only a few species are known in both the fully metamorphosed males and neotenic females. The phylogenetic analyses and morphology of larvae and adults provide data for investigation of relationships and species delineation. Platrilus Kazantsev, 2009, Platerodriloplesius Wittmer, 1944, and Falsocalochromus Pic, 1942 are synonymized to Platerodrilus Pic, 1921. Platrilus hirtus (Wittmer, 1938) and Pl. crassicornis (Pic, 1923) are transferred to Platerodrilus Pic, 1921. Platerodrilus hoiseni Wong, 1996 is proposed as a junior subjective synonym of Falsocalochromus ruficollis Pic, 1942. Platerodrilus is divided in three species-groups: P. paradoxus, P. major, and P. sinuatus groups defined based on the shape of genitalia and molecular phylogeny. The following species are described: Platerodrilus foliaceus sp. n., P. wongi sp. n. (P. paradoxus group); P. ngi sp. n., P. wittmeri (P. major group), P. ijenensis sp. n., P. luteus sp. n., P. maninjauensis sp. n., P. montanus sp. n., P. palawanensis sp. n., P. ranauensis sp. n., P. sibayakensis sp. n., P. sinabungensis sp. n., P. talamauensis sp. n., and P. tujuhensis sp. n. (P. sinuatus group). P. korinchiana robinsoni Blair, 1928 is elevated to the species rank as P. robinsoni Blair, 1928, stat. n. The conspecific semaphoronts are identified using molecular phylogeny for P. foliaceus sp. n., P. tujuhensis sp. n., P. montanus sp. n., P. maninjauensis sp. n.; additional female larvae are assigned to the species-groups. Diagnostic characters are illustrated and keys are provided for P. paradoxus and P. major groups.     

Congruent patterns of lineage diversity in two species complexes of planktonic crustaceans,Daphnia longispina (Cladocera) and Eucyclops serrulatus (Copepoda), in East European mountain lakes

Cladocerans and copepods are globally important freshwater zooplankton groups, differing in reproductive modes and dispersal abilities. We compared genetic variation of two common taxa of these crustaceans, the Daphnia longispina species complex (known to harbour multiple cryptic lineages) and Eucyclops serrulatus (morphologically and ecologically variable morphospecies), in lakes of ten Eastern European mountain ranges. We expected to discover cryptic lineages in both groups, and to observe different geographical patterns of diversity because of differences in life cycles. Within E. serrulatus, limited sampling through lowland habitats indeed showed the presence of eight highly divergent clades, probably cryptic species, but most of these were not found in the studied mountain lakes. Such a pattern was congruent with the diversity of the D. longispina complex. Regional coexistence of multiple clades within respective species complexes (two in Eucyclops and three in Daphnia) was observed only in the Tatra Mountains (on the Polish?Slovak border). In all other studied mountain ranges (in the Balkans), only single lineages of Daphnia and Eucyclops, respectively, were present, showing similar intraspecific patterns and no evidence for stronger dispersal limitation in Eucyclops than in Daphnia. Our results indicate that substantial cryptic variation may be expected in seemingly widespread copepod taxa. However, detection of cryptic lineages is not a general pattern in mountain lakes, although these habitats harbour substantial genetic diversity in crustacean zooplankton. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 754–767.     

The ‘paradigm of extremes’: extremely low genetic diversity in an extremely narrow endemic species, Coristospermum huteri (Umbelliferae)

Low levels of genetic diversity in endemic species are generally attributable to the small size of their populations. This lack of genetic variability will, predictably, be more evident in those species that occur in only one or a very few localities with a total population consisting of a few dozen individuals, or sometimes fewer (i.e. ‘extremely narrow endemics’, ENEs). We used allozyme electrophoresis to survey the genetic variability of Coristospermum huteri, an endemic species from the island of Majorca (Balearic Islands, W. Mediterranean Basin) with a single natural population of about 100 individuals. As expected, allozyme variability was virtually nil for this species (P = 8.3 %, A = 1.08, H _e = 0.022), which seems to be a general rule for ENEs (mean H _e = 0.057). A founder effect associated with a dispersal event from the continent is probably behind the lack of genetic diversity in this highly threatened species. Preservation of the mountain summit where the plant is found (Puig Major) is essential for the survival of C. huteri, and would also guarantee the conservation of other ENEs and rare and threatened species.     

The geography of diversification in mutualistic ants: a gene's-eye view into the Neogene history of Sundaland rain forests

We investigate the geographical and historical context of diversification in a complex of mutualistic Crematogaster ants living in Macaranga trees in the equatorial rain forests of Southeast Asia. Using mitochondrial DNA from 433 ant colonies collected from 32 locations spanning Borneo, Malaya and Sumatra, we infer branching relationships, patterns of genetic diversity and population history. We reconstruct a time frame for the ants' diversification and demographic expansions, and identify areas that might have been refugia or centres of diversification. Seventeen operational lineages are identified, most of which can be distinguished by host preference and geographical range. The ants first diversified 16-20 Ma, not long after the onset of the everwet forests in Sundaland, and achieved most of their taxonomic diversity during the Pliocene. Pleistocene demographic expansions are inferred for several of the younger lineages. Phylogenetic relationships suggest a Bornean cradle and major axis of diversification. Taxonomic diversity tends to be associated with mountain ranges; in Borneo, it is greatest in the Crocker Range of Sabah and concentrated also in other parts of the northern northwest coast. Within-lineage genetic diversity in Malaya and Sumatra tends to also coincide with mountain ranges. A series of disjunct and restricted distributions spanning northern northwest Borneo and the major mountain ranges of Malaya and Sumatra, seen in three pairs of sister lineages, further suggests that these regions were rain-forest refuges during drier climatic phases of the Pleistocene. Results are discussed in the context of the history of Sundaland's rain forests.     

Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea

Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD ) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu Postaire et al ., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive F _IS values (from ?0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (<10 km distance) and among islands (100 to >11,000 km distance), with significant pairwise F _ST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo‐Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.     

Genetically depauperate in the continent but rich in oceanic islands: Cistus monspeliensis (Cistaceae) in the Canary Islands

Background

Population genetic theory holds that oceanic island populations are expected to have lower levels of genetic variation than their mainland counterparts, due to founder effect after island colonization from the continent. Cistus monspeliensis (Cistaceae) is distributed in both the Canary Islands and the Mediterranean region. Numerous phylogenetic results obtained in the last years allow performing further phylogeographic analyses in Cistus.

Methodology/Principal Findings

We analyzed sequences from multiple plastid DNA regions in 47 populations of Cistus monspeliensis from the Canary Islands (21 populations) and the Mediterranean basin (26 populations). The time-calibrated phylogeny and phylogeographic analyses yielded the following results: (1) a single, ancestral haplotype is distributed across the Mediterranean, whereas 10 haplotypes in the Canary Islands; (2) four haplotype lineages are present in the Canarian Islands; (3) multiple colonization events across the archipelago are inferred; (4) the earliest split of intraspecific lineages occurred in the Early to Middle Pleistocene (<930,000 years BP).

Conclusions/Significance

The contrasting pattern of cpDNA variation is best explained by genetic bottlenecks in the Mediterranean during Quaternary glaciations, while the Canarian archipelago acted as a refugium of high levels of genetic diversity. Active colonization across the Canarian islands is supported not only by the distribution of C. monspeliensis in five of the seven islands, but also by our phylogeographic reconstruction in which unrelated haplotypes are present on the same island. Widespread distribution of thermophilous habitats on every island, as those found throughout the Mediterranean, has likely been responsible for the successful colonization of C. monspeliensis, despite the absence of a long-distance dispersal mechanism. This is the first example of a plant species with higher genetic variation among oceanic island populations than among those of the continent.     

The species of Thalerosphyrus Eaton, 1881 (Insecta,Ephemeroptera, Heptageniidae,Ecdyonurinae) in Java and Sumatra,with some comments on the diversity of the genus in the Oriental Realm

Three species belonging to the genus Thalerosphyrus Eaton, 1881 are reported from Java and Sumatra. The nymphs of Th. determinatus (Walker, 1853) from Java, Th. sinuosus (Navás, 1933) from Java and Sumatra and Th. lamuriensis Sartori, 2014 from Sumatra are redescribed. The egg morphology of the three species is also presented for the first time. A key to the nymphs is proposed. General considerations on the composition of the genus Thalerosphyrus in the Oriental Realm are given. The distribution of the genus is greatly expended, and currently ranges over the Himalaya and Sumbawa in the Sunda Islands.     

Integrating phylogenetic and taxonomic evidence illuminates complex biogeographic patterns along Huxley’s modification of Wallace’s Line

Aim Nearly 150 years ago, T. H. Huxley modified Wallace’s Line, including the island of Palawan as a component of the Asian biogeographic realm and separating it from the oceanic Philippines. Although Huxley recognized some characteristics of a transition between the regions, Palawan has since been regarded primarily as a peripheral component of the Sunda Shelf. However, several recent phylogenetic studies of Southeast Asian lineages document populations on Palawan to be closely related to taxa from the oceanic Philippines, apparently contradicting the biogeographic association of Palawan with the Sunda Shelf. In the light of recent evidence, we evaluate taxonomic and phylogenetic data in an attempt to identify the origin(s) of Palawan’s terrestrial vertebrate fauna. Location The Sunda Shelf and the Philippines. Methods We review distributional and phylogenetic data for populations of terrestrial vertebrates from Palawan. Using taxonomic data, we compare the number of Palawan taxa (species and genera) shared with the Sunda Shelf and oceanic Philippines. Among widespread lineages, we use phylogenetic data to identify the number of Palawan taxa with sister relationships to populations or species from the Sunda Shelf or oceanic Philippines. Results Although many terrestrial vertebrate taxa are shared between Palawan and the Sunda Shelf, an increasing number of species and populations are now recognized as close relatives of lineages from the oceanic Philippines. Among the 39 putative lineages included in molecular phylogenetic studies with sampling from the Sunda Shelf, Palawan and the oceanic Philippines, 17 of them reveal sister relationships between lineages from Palawan and the oceanic Philippines. Main conclusions Rather than a simple nested subset of Sunda Shelf populations, Palawan is best viewed as having played multiple biogeographic roles, including a young and old extension of the Sunda Shelf, a springboard to diversification in the oceanic Philippines, and a biogeographic component of the Philippine archipelago. Palawan has a long, complex geological history, which may explain this variation in pattern. Huxley originally noted transitional elements in Palawan’s fauna; we therefore suggest that his modification of Wallace’s Line should be recognized as a filter zone, reflecting both his original intent and available taxonomic and molecular evidence.     

Population Genetic Structure and Reproductive Strategy of the Introduced Grass Centotheca lappacea in Tropical Land-Use Systems in Sumatra

Intensive transformation of lowland rainforest into oil palm and rubber monocultures is the most common land-use practice in Sumatra (Indonesia), accompanied by invasion of weeds. In the Jambi province, Centotheca lappacea is one of the most abundant alien grass species in plantations and in jungle rubber (an extensively used agroforest), but largely missing in natural rainforests. Here, we investigated putative genetic differentiation and signatures for adaptation in the introduced area. We studied reproductive mode and ploidy level as putative factors for invasiveness of the species. We sampled 19 populations in oil palm and rubber monocultures and in jungle rubber in two regions (Bukit Duabelas and Harapan). Amplified fragment length polymorphisms (AFLP) revealed a high diversity of individual genotypes and only a weak differentiation among populations (F_ST = 0.173) and between the two regions (F_ST = 0.065). There was no significant genetic differentiation between the three land-use systems. The metapopulation of C. lappacea consists of five genetic partitions with high levels of admixture; all partitions appeared in both regions, but with different proportions. Within the Bukit Duabelas region we observed significant isolation-by-distance. Nine AFLP loci (5.3% of all loci) were under natural diversifying selection. All studied populations of C. lappacea were diploid, outcrossing and self-incompatible, without any hints of apomixis. The estimated residence time of c. 100 years coincides with the onset of rubber and oil palm planting in Sumatra. In the colonization process, the species is already in a phase of establishment, which may be enhanced by efficient selection acting on a highly diverse gene pool. In the land-use systems, seed dispersal might be enhanced by adhesive spikelets. At present, the abundance of established populations in intensively managed land-use systems might provide opportunities for rapid dispersal of C. lappacea across rural landscapes in Sumatra, while the invasion potential in rainforest ecosystems appears to be moderate as long as they remain undisturbed.     

Phylogeography of the Coccus scale insects inhabiting myrmecophytic Macaranga plants in Southeast Asia

Comparative historical biogeography of multiple symbionts occurring on a common host taxa can shed light on the processes of symbiont diversification. Myrmecophytic Macaranga plants are associated with the obligate mutualistic symbionts: Crematogaster (subgenus Decacrema) ants and Coccus scale insects. We conduct phylogeographic analyses based on mitochondrial cytochrome oxidase I (COI) from 253 scale insects collected from 15 locations in Borneo, Malaya and Sumatra, to investigate the historical biogeography of the scales, and then to draw comparisons with that of the symbiotic, but independently dispersing, Decacrema ants which are not specific to different Coccus lineages. Despite the different mode of ancient diversification, reconstruction of ancestral area and age estimation on the Coccus phylogeny showed that the scales repeatedly migrated between Borneo and Malaya from Pliocene to Pleistocene, which is consistent with the Decacrema ants. Just as with the ants, the highest number of lineages in the scale insects was found in northern northwest Borneo, suggesting that these regions were rainforest refugia during cool dry phases of the Pleistocene. Overall, general congruence between the Plio–Pleistocene diversification histories of the symbiotic scales and ants suggests that they experienced a common history of extinction/migration despite their independent mode of dispersal and host-colonization.     

Homogeneous Population of the Brown Alga Sargassum polycystum in Southeast Asia: Possible Role of Recent Expansion and Asexual Propagation

Southeast Asia has been known as one of the biodiversity hotspots in the world. Repeated glacial cycles during Pleistocene were believed to cause isolation of marine taxa in refugia, resulting in diversification among lineages. Recently, ocean current was also found to be another factor affecting gene flow by restricting larval dispersal in animals. Macroalgae are unique in having mode of reproduction that differs from that of animals. Our study on the phylogeographical pattern of the brown macroalga Sargassum polycystum using nuclear Internal Transcribed Spacer 2 (ITS2), plastidal RuBisCO spacer (Rub spacer) and mitochondrial cytochrome oxidase subunit-III (Cox3) as molecular markers revealed genetic homogeneity across 27 sites in Southeast Asia and western Pacific, in sharp contrast to that revealed from most animal studies. Our data suggested that S. polycystum persisted in single refugium during Pleistocene in a panmixia pattern. Expansion occurred more recently after the Last Glacial Maximum and recolonization of the newly flooded Sunda Shelf could have involved asexual propagation of the species. High dispersal ability through floating fronds carrying developing germlings may also contribute to the low genetic diversity of the species.     

Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South‐East Asia

Tropical rainforests in South‐East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag‐based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south‐western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28–0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.     

Phylogeography of related diadromous species in continental and island settings,and a comparison of their potential and realized dispersal patterns

Aim To compare patterns of potential and realized dispersal in ecologically similar and phylogenetically related amphidromous shrimps (Atyidae) in continental and island‐dominated landscapes. Location Eastern Australia and the Caribbean region. Methods Population genetic and phylogeographic analyses of mitochondrial DNA data for Australatya striolata from eastern Australia (a continental landscape) and Atya scabra from the Caribbean (an island‐dominated landscape). Results Australatya striolata contained two highly divergent genetic lineages in eastern Australia, corresponding to the disjunct northern and southern populations, respectively. These lineages probably represent allopatric cryptic species, both of which were found to have genetically homogeneous population structures within their regions of occurrence. Atya scabra was genetically homogeneous throughout the Caribbean. Recent population expansions were detected for Atya scabra in the Caribbean, but not for northern or southern Australatya striolata. Main conclusions The findings of this study are consistent with previously reported patterns of genetic population structure in amphidromous species in both continental and island‐dominated landscapes, suggesting that potential for widespread dispersal is typically matched by realized patterns of panmixia. We therefore raise the hypothesis that landscape setting (i.e. continent or island‐dominated) does not influence dispersal patterns in amphidromous species. Further studies, especially of population genetic patterns of amphidromous species on continents, are needed to test this idea. Interestingly, results of the genetic neutrality tests led us to hypothesize that demographic and drift‐mutation equilibrium is attainable although not always evident for amphidromous species on continents, but is not attainable for those species distributed across island settings.     

Narrow endemics to Mediterranean islands: Moderate genetic diversity but narrow climatic niche of the ancient,critically endangered Naufraga (Apiaceae)

Narrow endemics constitute the cornerstone of Mediterranean plant diversity. Naufraga balearica (Apiaceae) is a critically endangered, extremely narrow endemic plant from the western Mediterranean island of Majorca. Because the species belongs to a monotypic genus, N. balearica was hypothesized to be a palaeoendemism. Here we conducted phylogenetic dating, population genetic and climatic niche analyses in order to understand the evolutionary history and conservation perspectives of this flagship species. Phylogenetic dating analysis of nuclear and plastid DNA sequences revealed a late Miocene to early Pliocene divergence between Naufraga and its sister genus Apium, supporting the palaeoendemic status of the former. Amplified fragment length polymorphism (AFLP) markers and plastid DNA sequences of the five Naufraga populations revealed moderate genetic diversity. This diversity is in line with that of other palaeoendemisms from western Mediterranean islands, as revealed by a comparison with 22 other narrow endemic species from this region. Despite the fact that all Naufraga populations are located at a maximum distance of 10 km in a straight line, a strikingly strong population differentiation was found for AFLP markers, which is explained by long-term isolation likely related to short-range pollination and dispersal strategies of the species. While the species is not genetically impoverished, species distribution modelling and microclimatic monitoring revealed that narrow ecological requirements underlie the current extreme rarity of Naufraga and may jeopardize its long-term survival. Our results indicate that a multidisciplinary approach provides powerful tools to develop conservation strategies for evolutionarily singular lineages.