Cryptic species,taxonomic inflation,or a bit of both? New species phenomenon in Sri Lanka as suggested by a phylogeny of dwarf geckos (Reptilia,Squamata, Gekkonidae,Cnemaspis)

We evaluated the status of 16 of 22 recognized Sri Lankan Cnemaspis Strauch species, and flagged overlooked diversity with two mitochondrial (cyt b & ND2) and two nuclear markers (RAG1 & PDC) totalling 2829 base pairs. A fossil-calibrated timetree and sampling of other South Asian Cnemaspis provide insights into the diversification of the genus in peninsular India and Sri Lanka. Phylogenetic analyses consistently inferred two broad clades within South Asian Cnemaspis, with Sri Lankan species in two clades, which we call the podihuna and kandiana clades. Each Sri Lankan clade as a whole is sister to Indian taxa and nested within Indian lineages. Cnemaspis modigliani Das from Indonesia is a member of the kandiana clade. This suggests a minimum of two dispersal events between India and Sri Lanka and one between Sri Lanka/India and South-east Asia. South Asian Cnemaspis date back to at least the Eocene, in Sri Lanka to the early Miocene, with late Miocene diversification in the kandiana clade. All but one of the named species we sampled is likely to be valid, and 10 divergent unnamed lineages may warrant specific recognition. A resolution of Sri Lankan Cnemaspis taxonomy will require thorough sampling and the use of both morphological and molecular data.     

Pliocene climatic change in insular Southeast Asia as an engine of diversification in Ficedula flycatchers

Aims Insular Southeast Asia and adjacent regions are geographically complex, and were dramatically affected by both Pliocene and Pleistocene changes in climate, sea level and geology. These circumstances allow the testing of several biogeographical hypotheses regarding species distribution patterns and phylogeny. Avian species in this area present a challenge to biogeographers, as many are less hindered by barriers that may block the movements of other species. Widely distributed Southeast Asian avian lineages, of which there are many, have been generally neglected. Ficedula flycatchers are distributed across Eurasia, but are most diverse within southern Asia and Southeast Asian and Indo‐Australian islands. We tested the roles of vicariance, dispersal and the evolution of migratory behaviours as mechanisms of speciation within the Ficedula flycatchers, with a focus on species distributed in insular Southeast Asia. Methods Using a published molecular phylogeny of Ficedula flycatchers, we reconstructed ancestral geographical areas using dispersal vicariance analysis, weighted ancestral area analysis, and a maximum likelihood method. We evaluated the evolution of migratory behaviours using maximum likelihood ancestral character state reconstruction. Speciation timing estimates were calculated via local molecular clock methods. Results Ficedula originated in southern mainland Asia, c. 6.5 Ma. Our analyses indicate that two lineages within Ficedula independently and contemporaneously colonized insular Southeast Asia and Indo‐Australia, c. 5 Ma. The potential impact of vicariance due to rising sea levels is difficult to assess in these early colonization events because the ancestral areas to these clades are reconstructed as oceanic islands. Within each of these clades, inter‐island dispersal was critical to species’ diversification across oceanic and continental islands. Furthermore, Pliocene and Pleistocene climatic change may have caused the disjunct island distributions between several pairs of sister taxa. Both vicariance and dispersal shaped the distributions of continental species. Main conclusions This study presents the first evaluation, for Ficedula, of the importance of vicariance and dispersal in shaping distributions, particularly across insular Southeast Asia and Indo‐Australia. Although vicariant speciation may have initially separated the island clades from mainland ancestors, speciation within these clades was driven primarily by dispersal. Our results contribute to the emerging body of literature concluding that dynamic geological processes and climatic change throughout the Pliocene and Pleistocene have been important factors in faunal diversification across continental and oceanic islands.     

Population genetic evidence for the east–west division of the narrow-barred Spanish mackerel (<Emphasis Type="Italic">Scomberomorus commerson,</Emphasis> Perciformes: Teleostei) along Wallace’s Line

Mitochondrial DNA D-loop (control) region (426-bp) was used to infer the genetic structure of Spanish mackerel (Scomberomorus commerson) from populations in Southeast Asia (Brunei, East and West Malaysia, Philippines, Thailand, Singapore, and China) and northern Australia (including western Timor). An east–west division along Wallace’s Line was strongly supported by a significant AMOVA, with 43% of the total sequence variation partitioned among groups of populations. Phylogenetic and network analyses supported two clades: clade A and clade B. Members of clade A were found in Southeast Asia and northern Australia, but not in locations to the west (Gulf of Thailand) or north (China). Clade B was found exclusively in Southeast Asia. Genetic division along Wallace’s Line suggests that co-management of S. commerson populations for future sustainability may not be necessary between Southeast Asian nations and Australia, however all countries should share the task of management of the species in Southeast Asia equally. More detailed genetic studies of S. commerson populations in the region are warranted.     

亚洲地区人类群体亲缘关系：活体测量数据统计分析

本文采用多元统计方法分析了亚洲地区２５个人群的活体测量资料以探讨亚洲地区各人类群体之间的相互关系,数据分析结果显示这一地区的人类按活体特征的差异可以划分为两大类型。包括中国、朝鲜、日本等东北亚的人类构成一个组群;东南亚的人类形成另一个组群。南亚地区的人类在分类上与东南亚的人类接近但仍呈现一些特殊性。日本列岛的人类具有两种体质特征类型。本岛居民与东北亚人类接近;而包括阿伊努、硫球群岛岛民及台湾土著在     

Shaped by uneven Pleistocene climate: mitochondrial phylogeographic pattern and population history of white wagtail Motacilla alba (Aves: Passeriformes)

We studied the phylogeography and population history of the white wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of white wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in central and south Europe; and clade SE was distributed in central and east Asia. The deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of east Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. The recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.     

High genetic diversity in southwest Asian populations of Philaenus spumarius (Hemiptera: Auchenorrhyncha)

The genus Philaenus is one of the best investigated among Auchenorrhyncha, and several morphological, ecological, karyological, and molecular data have led to a designation of up to 10 species, distributed mainly in the Mediterranean and south-western Asia. The only widespread Palaearctic species, P. spumarius, is known to be structured phylogeographically as it consists of two highly divergent mitochondrial clades (northeast, NE and southwest, SW), with several subclades. This study contributes to the species phylogeography through the study of the genetic diversity and affinity of P. spumarius populations from southwestern Asia. Mitochondrial DNA (cytochrome B) show a high level of genetic diversity within Turkish and Iranian populations, the majority of which belong to the SW clade, and only single populations from northeastern Turkey are found to be substantially highly divergent lineages within the NE clade. One of the NE populations also showed significant differences in the distribution and amount of heterochromatin compared to other populations. According to the results of this study and previous phylogenetic and phylogeographic works on this species, we conclude that Southwestern Asia is probably the place of origin of the Philaenus spumarius.     

Diversification and subspecies patterning of the goitered gazelle (Gazella subgutturosa) in Iran

Goitered gazelles, Gazella subgutturosa, exist in arid and semiarid regions of Asia from the Middle to the Far East. Although large populations were present over a vast area until recently, a decline of the population as a result of hunting, poaching, and habitat loss led to the IUCN classification of G. subgutturosa as “vulnerable." We examined genetic diversity, structure, and phylogeny of G. subgutturosa using mitochondrial cytochrome b sequences from 18 geographically distant populations in Iran. The median‐joining network of cyt b haplotypes indicated that three clades of goitered gazelles can be distinguished: a Middle Eastern clade west of the Zagros Mountains (and connected to populations in Turkey and Iraq), a Central Iranian clade (with connection to Azerbaijan), and an Asiatic clade in northeastern Iran (with connection to Turkmenistan, Uzbekistan, and other Asian countries as far as northeastern China and Mongolia). Based on our results, we argue that Iran is the center of diversification of goitered gazelles, due to the presence of large mountain ranges and deserts that lead to the separation of populations. In accordance with previous morphological studies, we identified the Asiatic clade as the subspecies G. s. yarkandensis, and the other two clades as the nominate form G. s. subgutturosa. The new genetic information for goitered gazelles in Iran provides the basis for future national conservation programs of this species.     

Phylogeny of Cerberus (Serpentes: Homalopsinae) and phylogeography of Cerberus rynchops: diversification of a coastal marine snake in Southeast Asia

Aim The biogeography of Southeast Asia has been greatly affected by plate tectonic events over the last 10 Myr and changing sea levels during the Quaternary. We investigated how these events may have influenced the evolution of Cerberus Cuvier, a marine coastal snake belonging to the Homalopsinae (Oriental‐Australian Rear‐fanged Water Snakes). This study is an expansion of a previous study on the biogeography and systematics of Cerberus. Location We obtained species from localities across the range of the widely distributed Cerberus: India, Sri Lanka, the Andaman islands, Myanmar, the Philippines, Borneo, Suluwesi, Sumatra, Vietnam, Thailand, Singapore and Australia. Methods We analysed mtDNA sequences (12S, ND3, ATPase, 2338 nucleotide characters) from 21 localities. The sample consisted of 65 Cerberus rynchops (Schneider), three Cerberus australis (Gray) and four Cerberus microlepis Boulenger. One Homalopsis buccata (Linnaeus), one Bitia hydroides Gray, one Enhydris enhydris (Schneider), and two Enhydris plumbea (Boie) were used as outgroups. Results We produced phylogenetic trees based on parsimony, maximum likelihood and Bayesian analysis. We did not find unambiguous support for the monophly of Cerberus. Cerberus austalis, H. buccata and all other Cerberus populations formed a three‐way basal polytomy under parsimony and C. australis formed the sister group to a clade consisting of H. buccata and all other Cerberus in likelihood and Bayesian analysis. The non‐Australian Cerberus were monophyletic and consisted of four primary biogeographical clades: Indian and Mayanmar, Philippines, Greater Sunda Islands and Suluwesi, and the Thai‐Malay peninsula and Gulf of Thailand. The range of genetic divergence between these clades and Australian Cerberus was 0.06–0.12. Genetic divergence among clades to the west of Australia was less pronounced (Thai‐Malay peninsula and Gulf of Thailand = 0.02–0.05; Sunda Islands and Suluwesi = 0.02–0.05; Philippines = 0.02–0.06; India and Myanmar = 0.04–0.06, Philippines = 0.02–0.5). Main conclusions Gyi [University of Kansas Publications, Museum of Natural History 20 (1970), 47] recognized three species of Cerberus: C. australis (from Australia), C. microlepis (known only from Lake Buhi in the Philippines), and the widely distributed C. rynchops (India to Wallacea). We did not find strong support for the monophyly of the genus. Cerberus australis is highly divergent from all other Cerberus lineages sampled from this region. The geographically widespread C. rynchops is resolved into four biogeographical clades (Indian and Myanmar, Philippines, Greater Sunda Islands and Suluwesi, and the Thai‐Malay Peninsula and Gulf of Thailand). We discuss how the dispersal biology of a salt‐water tolerant, coastal marine taxon and the complex geological history of the region (Tertiary plate tectonic movements and Quaternary sea‐level changes) could produce the observed patterns of diversification.     

Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus

Utilization of multiple putatively neutral DNA markers for inferring evolutionary history of species population is considered to be the most robust approach. Molecular population genetic studies have been conducted in many species of Anopheles genus, but studies based on single nucleotide polymorphism (SNP) data are still very scarce. Anopheles minimus is one of the principal malaria vectors of Southeast (SE) Asia including the Northeastern (NE) India. Although population genetic studies with mitochondrial genetic variation data have been utilized to infer phylogeography of the SE Asian populations of this species, limited information on the population structure and demography of Indian An. minimus is available. We herewith have developed multilocus nuclear genetic approach with SNP markers located in X chromosome of An. minimus in eight Indian and two SE Asian population samples (121 individual mosquitoes in total) to infer population history and test several hypotheses on the phylogeography of this species. While the Thai population sample of An. minimus presented the highest nucleotide diversity, majority of the Indian samples were also fairly diverse. In general, An. minimus populations were moderately substructured in the distribution range covering SE Asia and NE India, largely falling under three distinct genetic clusters. Moreover, demographic expansion events could be detected in the majority of the presently studied populations of An. minimus. Additional DNA sequencing of the mitochondrial COII region in a subset of the samples (40 individual mosquitoes) corroborated the existing hypothesis of Indian An. minimus falling under the earlier reported mitochondrial lineage B.     

Phylogeny and biogeography of Rhododendron subsection Pontica, a group with a tertiary relict distribution

Rhododendron subgenus Hymenanthes subsection Pontica is exceptional among Tertiary relict groups in having a high proportion of species (4 of 11) native to SW Eurasia. A phylogeny based on cpDNA matK and trnL-F indicated that multiple Pontica lineages colonised each of SW Eurasia, SE North America, and NE Asia, with little or no speciation within regions thereafter. Therefore, multiple (3-4) Pontica lineages survived the Quaternary in SW Eurasia, in contrast to other Tertiary relict genera. Pontica comprises two major clades, one of which is wholly Eurasian, and paraphyletic with respect to at least some of the remaining 200 species of subgenus Hymenanthes, which are all distributed in SE Asia. The other clade has species from W and SE North America, SW Eurasia, and NE Asia. According to synonymous matK substitution data, the two clades diverged 9-6 million years ago (mya), whereas most divergence within them happened 5-3 mya. Although the phylogeny indicates probable trans-Atlantic migration for one of two America-Eurasia disjunctions in Pontica, the timing supports migration via Beringia for both.     

Homogeneity of common cosmopolitan inversion frequencies in Southeast AsianDrosophila melanogaster

East AsianDrosophila melanogaster are known for great variation in morphological and physiological characters among populations, variation that is believed to be maintained by genetic drift. To understand the genetic properties of AsianD. melanogaster populations, we initiated a population genetic study of chromosome inversion polymorphisms in hitherto unanalysed population samples from Southeast (SE) Asia. We generally found a high frequency of each of the four common cosmopolitan inversions in comparison to populations from Africa, Asia, and Australia. In contrast to the great phenotypic variation among Asian populations, however, we could not detect differences in inversion frequencies among populations. Furthermore, we observed neither correlations of inversion frequencies with population latitude and longitude, nor evidence for linkage disequilibrium between different inversion loci. We propose two explanations for the observed genetic homogeneity among these SE AsianD. melanogaster populations: (i) the observed pattern simply reflects the retention of ancestral polymorphisms originating from a panmictic population that was once present on a large single landmass (Sundaland), and/or is a consequence of high recent gene flow between populations; and (ii) it is caused by selective forces (e.g. balancing selection).     

Extensive intraspecific genetic diversity of a freshwater crayfish in a biodiversity hotspot

1. The freshwater crayfish Cherax dispar (Decapoda: Parastacidae) inhabits coastal regions and islands of South East Queensland, Australia. We hypothesised that populations of C. dispar on different islands would be more genetically divergent from each other than populations from different drainages within the same island or on the mainland. 2. Phylogenetic and phylogeographic analyses were conducted on two mitochondrial genes (cytochrome oxidase subunit I & 16S ribosomal DNA) and one nuclear gene (Internal Transcribed Spacer region 2). Phylogeographic patterns were compared with those for other freshwater organisms in the area. 3. Deep genetic divergences were found within C. dispar, including four highly divergent (up to 20%) clades. The geographic distribution of each of the clades revealed strong latitudinal structuring along the coast rather than structuring among the islands. The high genetic divergence observed among the C. dispar clades was estimated to have pre‐dated island formation and may represent ancient river drainage patterns. 4. A restricted distribution was observed for the most divergent clade, which was discovered only on two of the sand islands (North Stradbroke Island and Moreton Island). Furthermore, strong phylogeographic structuring was observed within this clade on North Stradbroke Island, where no haplotypes were shared between samples from opposite sides of the island. This low connectivity within the island supports the idea that C. dispar rarely disperse terrestrially (i.e. across watersheds).     

THE EVOLUTIONARY HISTORY OF DARWIN'S FINCHES: SPECIATION,GENE FLOW,AND INTROGRESSION IN A FRAGMENTED LANDSCAPE

Many classic examples of adaptive radiations take place within fragmented systems such as islands or mountains, but the roles of mosaic landscapes and variable gene flow in facilitating species diversification is poorly understood. Here we combine phylogenetic and landscape genetic approaches to understand diversification in Darwin's finches, a model adaptive radiation. We combined sequence data from 14 nuclear introns, mitochondrial markers, and microsatellite variation from 51 populations of all 15 recognized species. Phylogenetic species‐trees recovered seven major finch clades: ground, tree, vegetarian, Cocos Island, grey and green warbler finches, and a distinct clade of sharp‐beaked ground finches (Geospiza cf. difficilis) basal to all ground and tree finches. The ground and tree finch clades lack species‐level phylogenetic structure. Interisland gene flow and interspecies introgression vary geographically in predictable ways. First, several species exhibit concordant patterns of population divergence across the channel separating the Galápagos platform islands from the separate volcanic province of northern islands. Second, peripheral islands have more admixed populations while central islands maintain more distinct species boundaries. This landscape perspective highlights a likely role for isolation of peripheral populations in initial divergence, and demonstrates that peripheral populations may maintain genetic diversity through outbreeding during the initial stages of speciation.     

Historical biogeography of Rhododendron section Vireya and the Malesian Archipelago

Aim Vireya rhododendrons are distinctive and easily recognizable by their general form; however, they are virtually circumscribed geographically, predominantly distributed throughout the biogeographically intriguing Malesian Archipelago. Hypotheses of the evolutionary relationships of the group have been proposed but the biogeography of vireyas has not been analysed based on molecular phylogeny. Recently, the first detailed molecular phylogenetic investigation of section Vireya was completed based on cp‐ and nrDNA sequence data, therefore making this cladistic biogeographic study of vireya rhododendrons possible. Location Malesia, Australia, Solomon Islands, Taiwan, Himalayas, north Vietnam and south China. Methods Based on distribution maps, areas of endemism were determined for the biogeographic region of Malesia. Area relationships were analysed based on a recent molecular phylogeny of species in section Vireya. The method of paralogy‐free subtree analysis was applied. Results Individual distribution maps were produced for 74 species of Rhododendron section Vireya. Species clades with bootstrap support proved to be biogeographically informative. Major clades correspond to three regions: eastern Malesia, western/middle Malesia and Taiwan/north Vietnam/south China. Within eastern Malesia, Australia, New Guinea, the Bismarck Archipelago and Solomon Islands are related. In western Malesia, northern Philippines, Borneo, southern Moluccas and north and west Sulawesi are related. These areas are more distantly related to Sumatra, the Malay peninsula, Java, Bali, Palawan, Lesser Sunda islands and the southern Philippines. The position of the Himalayas is equivocal and part of a basal polytomy in the summary area cladogram. Main conclusions Two alternative hypotheses are proposed for the evolution of vireya rhododendrons based on the pattern of area relationships. The first hypothesis is that the vireyas are an old group, with ancestors present on Gondwana, rifting north in the Cretaceous. The second alternative hypothesis is that vireyas are a young group that has dispersed eastwards from India to Australia and the Solomon Islands since the current Malesian islands formed.     

The genetic differentiation of a cricket (Velarifictorus micado) with two modes of life cycle in East Asia after the middle Pleistocene and the invasion origin of the United States of America

The cricket Velarifictorus micado is widely distributed in East Asia and colonized the United States of America (the USA) in 1959. It has two life cycles: egg and nymph diapause. We aimed to investigate the biogeographic boundary between them and determine when and why V. micado diverged. Mitochondrial fragments including COI and CytB were used for haplotype network, demographic analysis, and divergence time estimation in individuals of East Asia. We selected several samples from the USA to find out the colonization origin. The haplotype network indicated there were three lineages based on COI, NE lineage (the egg diapause and mainly distributed in the northern regions), SE lineage (the egg diapause and mainly distributed in the southern regions), and SN lineage (the nymph diapause and mainly distributed in the southern regions). The molecular chronograms indicated that the first divergence of V. micado into two main lineages, NE and southern lineages (SE and SN), was essentially bounded by the Yangtze River. It occurred around ~0.79 Ma (95% HPD: 1.13–0.46 Ma) in the Middle Pleistocene Transition. This was followed by the divergence of the southern lineage into two sublineages, SE and SN lineage, occurred around ~0.50 Ma (95% HPD: 0.71–0.25 Ma), corresponding to the time of development of glaciers in various parts of the Qinghai–Tibet Plateau (QTP) (0.73–0.46 Ma). SE lineage might originate from southwestern China based on the comparison between the haplotype network based on COI and CytB. Our study suggested that divergences of lineages have twice co‐occurred with tendency of cooling climatic in Asia after the Mid‐Pleistocene, and the life‐history strategy may play an important role in lineage diversification. Additionally, our results indicated that the USA populations were revealed at least twice separate Asian invasions. These both belonged to the egg diapause, which might provide a new perspective for invasion control.     

Biogeography and speciation patterns of the golden orb spider genus Nephila (Araneae: Nephilidae) in Asia

The molecular phylogeny of the globally distributed golden orb spider genus Nephila (Nephilidae) was reconstructed to infer its speciation history, with a focus on SE Asian/W Pacific species. Five Asian, two Australian, four African, and one American species were included in the phylogenetic analyses. Other species in Nephilidae, Araneidae, and Tetragnathidae were included to assess their relationships with the genus Nephila, and one species from Uloboridae was used as the outgroup. Phylogenetic trees were reconstructed from one nuclear (18S) and two mitochondrial (COI and 16S) markers. Our molecular phylogeny shows that the widely distributed Asian/Australian species, N. pilipes, and an African species, N. constricta, form a clade that is sister to all other Nephila species. Nested in this Nephila clade are one clade with tropical and subtropical/temperate Asian/Australian species, and the other containing African and American species. The estimated divergence times suggest that diversification events within Nephila occurred during mid-Miocene to Pliocene (16 Mya-2 Mya), and these time periods were characterized by cyclic global warming/cooling events. According to Dispersal and Vicariance Analysis (DIVA), the ancestral range of the Asian/Australian clade was tropical Asia, and the ancestral range of the genus Nephila was either tropical Asia or Africa. We conclude that the speciation of the Asian/Australian Nephila species was driven by Neogene global cyclic climate changes. However, further population level studies comparing diversification patterns of sister species are needed to determine the mode of speciation of these species.     

西南地区6种魔芋属植物基于cpDNA序列的遗传多样性研究

研究野生作物资源的遗传变异及分化机制对种质资源的收集与改良具有重要意义。魔芋是我国西南地区的特色经济作物,但由于受到人为活动干扰,野生种群不断衰退。为评估西南地区魔芋属(Amorphophallus)野生群体的遗传多样性,探究代表性物种的系统发育地位,该研究利用3个叶绿体DNA(cpDNA)片段,分析了魔芋6个物种的遗传多样性,重建了种间系统发育关系。结果表明:(1)西南地区野生魔芋群体的遗传多样性普遍较低,虽然单倍型多样性(H_d)均值为0.428,但近一半群体只有1个单倍型,6个物种整体水平上的单倍型多样性在0.704到0.983之间。(2)在6个物种间检测到高水平的遗传分化,遗传分化系数(F_ST)值在0.481到0.967之间。(3)系统发育分析表明,选取的27个魔芋种主要聚成3个分支:非洲分支、东南亚分支和东亚大陆分支。疣柄魔芋(A. paeoniifolius)隶属于东南亚分支,而东亚大陆分支A包含花魔芋(A. konjac)和西盟魔芋(A. krausei),东亚大陆分支B由东亚魔芋(A. kiusianus)、滇魔芋(A. yunnanensis)和东京魔芋(A. tonkinensis)构成。生境隔离与人为干扰造成了西南地区野生魔芋群体较低的遗传多样性,魔芋属东亚大陆分支的分化可能与早期的快速扩张和生态适应有关。该研究为西南地区魔芋资源的合理保护、可持续利用和杂交育种提供了参考资料。     

Comparative developmental and reproductive biology of geographical populations from two cryptic species in Brontispa longissima (Coleoptera: Chrysomelidae)

Brontispa longissima is a serious pest of the coconut palm Cocos nucifera, presumed to have originated in Papua New Guinea and Indonesia. It recently invaded Southeast and East Asia, where outbreaks have been reported. Mitochondrial DNA analysis reveals two cryptic species in B. longissima: one is distributed over a wide area including Asia and the Pacific region (the Asian clade) and the other in a limited area in the Pacific region (the Pacific clade). Recent invasions and outbreaks have been reported only from the area where the Asian clade has been found, suggesting that this clade has become a pest in Asia. To infer if the Asian clade has the ability to establish, spread and outbreak in novel habitats more effectively than the Pacific clade, we compared life‐history traits between the two populations of different clades. The net reproduction rate (R₀) was 130.0 and 94.0, the mean length of a generation (T) was 57.7 and 54.7 days, and the intrinsic rate of natural increase (r) was 0.084 and 0.083 per day for the population from Ishigaki Island, Japan (ISH) (the Asian clade) and for the population from Papua New Guinea (PNG) (the Pacific clade), respectively. Although the difference in r was little, the simulated population growth showed that the ISH population can be 1.6 times larger than that of the PNG after ten generations. The rapid population growth of the Asian clade would be partly responsible for its establishment, spread and frequent outbreaks in Asia.     

PHYLOGEOGRAPHY OF THE ASIAN ELEPHANT (ELEPHAS MAXIMUS) BASED ON MITOCHONDRIAL DNA

Abstract Populations of the Asian elephant (Elephas maximus) have been reduced in size and become highly fragmented during the past 3000 to 4000 years. Historical records reveal elephant dispersal by humans via trade and war. How have these anthropogenic impacts affected genetic variation and structure of Asian elephant populations? We sequenced mitochondrial DNA (mtDNA) to assay genetic variation and phylogeography across much of the Asian elephant's range. Initially we compare cytochrome b sequences (cyt b) between nine Asian and five African elephants and use the fossil‐based age of their separation (～5 million years ago) to obtain a rate of about 0.013 (95% CI = 0.011–0.018) corrected sequence divergence per million years. We also assess variation in part of the mtDNA control region (CR) and adjacent tRNA genes in 57 Asian elephants from seven countries (Sri Lanka, India, Nepal, Myanmar, Thailand, Malaysia, and Indonesia). Asian elephants have typical levels of mtDNA variation, and coalescence analyses suggest their populations were growing in the late Pleistocene. Reconstructed phylogenies reveal two major clades (A and B) differing on average by HKY85/Γ‐corrected distances of 0.020 for cyt b and 0.050 for the CR segment (corresponding to a coalescence time based on our cyt b rate of ～1.2 million years). Individuals of both major clades exist in all locations but Indonesia and Malaysia. Most elephants from Malaysia and all from Indonesia are in well‐supported, basal clades within clade A, thus supporting their status as evolutionarily significant units (ESUs). The proportion of clade A individuals decreases to the north, which could result from retention and subsequent loss of ancient lineages in long‐term stable populations or, perhaps more likely, via recent mixing of two expanding populations that were isolated in the mid‐Pleistocene. The distribution of clade A individuals appears to have been impacted by human trade in elephants among Myanmar, Sri Lanka, and India, and the subspecies and ESU statuses of Sri Lankan elephants are not supported by molecular data.     

Did geckos ride the Palawan raft to the Philippines?

Aim We examine the genetic diversity within the lizard genus Gekko in the Philippine islands to understand the role of geography and geological history in shaping species diversity in this group. We test multiple biogeographical hypotheses of species relationships, including the recently proposed Palawan Ark Hypothesis. Location Southeast Asia and the Philippines. Methods Samples of all island endemic and widespread Philippine Gekko species were collected and sequenced for one mitochondrial gene (NADH dehydrogenase subunit 2) and one nuclear gene (phosducin). We used maximum likelihood and Bayesian phylogenetic methods to derive the phylogeny. Divergence time analyses were used to estimate the time tree of Philippine Gekko in order to test biogeographical predictions of species relationships. The phylogenetic trees from the posterior distribution of the Bayesian analyses were used for testing biogeographical hypotheses. Haplotype networks were created for the widespread species Gekko mindorensis to explore genetic variation within recently divergent clades. Results Both maximum likelihood and Bayesian phylogenetic analyses indicated that Philippine Gekko species are a diverse clade with a long history in the archipelago. Ancestral range reconstruction and divergence time analyses suggest a Palawan microcontinental origin for this clade, coinciding with Palawan’s separation from Asia beginning 30 Ma, with subsequent diversification in the oceanic Philippine islands. The widespread species G. mindorensis and G. monarchus diversified in the late Miocene/early Pliocene and are potentially complexes of numerous undescribed species. Main conclusions The view of the Philippine islands as a ‘fringing archipelago’ does not explain the pattern of species diversity in the genus Gekko. Philippine Gekko species have diversified within the archipelago over millions of years of isolation, forming a large diverse group of endemic species. Furthermore, the Philippine radiation of gekkonid lizards demonstrates biogeographical patterns most consistent with stochastic colonization followed by in situ diversification. Our results reveal the need to consider deeper time geological processes and their potential role in the evolution of some Philippine terrestrial organisms.