Systematics of the extinct reed warblers Acrocephalus of the Society Islands of eastern Polynesia

In the Society archipelago (French Polynesia), Acrocephalus reed warblers are known only from four islands: Tahiti, Mo'orea, Huahine and Raiatea. All populations are now extinct except on Tahiti. Our knowledge of these birds is based on a small number of specimens preserved in museums, collected mostly during the 19th century. We present here a review of the past and present distribution, habitat and threats to the Society Islands reed warblers, including details on the specimens in museum collections. We compare the external morphology of the different populations, and use samples from museum specimens to propose a molecular phylogeny of all taxa based on partial cytochrome b gene sequences. The genetic data do not support the monophyly of the Society Islands reed warblers, which probably derived from three different lineages, found in Tahiti, Mo'orea and in the cluster Raiatea–Huahine. We outline the taxonomic consequences of this phylogeny. Our results support the hypothesis that evolutionary pattern, not distance between islands, shaped the long-distance colonization of oceanic islands by reed warblers.     

Molecular phylogeny and systematics of Blue and Grey Noddies (Procelsterna)

We used a mitochondrial and nuclear DNA phylogeny to evaluate the relationships among all noddies (Anous and Procelsterna, Laridae) and to clarify their classification. The Lesser Noddy Anous tenuirostris and Black Noddy Anous minutus form a pair of closely related sister‐species, as do the Blue Noddy Procelsterna albivitta and Grey Noddy Procelsterna cerulea. Blue and Grey Noddies are embedded within the dark noddies and are the sister‐clade to the Lesser and Black Noddies, indicating that the genus Anous in its current definition is not monophyletic. Thus, we propose to merge all noddies into the genus Anous Stephens 1826 , and to consider Procelsterna Lafresnaye 1842 as a junior synonym.     

The historic biogeography and community ecology of Polynesian pigeons and doves

The species richness, taxonomic diversity, and geographic distribution of pigeons and doves (Columbidae) have been altered irreversibly in Polynesia by 3500 years of human activity. Natural (without human influence) columbid faunas are estimated primarily by studying prehistoric bones. In all Polynesian island groups studied (except outlying Easter Island, Hawaiian Islands, or New Zealand), the prehistoric columbid faunas had more species, more genera, and more species per genus than modern faunas from the same island. Congeneric species pairs or triplets occurred on many islands for Ducula , Ptilinopus , and Gallicolumba. The losses of Polynesian columbids include the extinction of at least 9 species in the genera Ducula , Ptilinopus , Macropygia , Caloenas , Gallicolumba , and Didunculus as well as the extirpation of numerous island populations of extant species. If not for human impact, a typical East Polynesian island would support at least 5–6 species of columbids in 3–4 genera (compared to 0–3 species in 0–3 genera today). A typical West Polynesian island would support at least 6–7 species in 4–5 genera (compared to 1–6 species in 1–5 genera today). Since all Polynesian pigeons and doves are frugivorous and/or granivorous, their decline in recent millennia probably has affected the composition of Polynesian forests by limiting inter- and intra-island dispersal of plant propagules.     

‘After Africa’: the evolutionary history and systematics of the genus Charaxes Ochsenheimer (Lepidoptera: Nymphalidae) in the Indo‐Pacific region

The predominantly Afrotropical genus Charaxes is represented by 31 known species outside of Africa (excluding subgenus Polyura Billberg). We explored the biogeographic history of the genus using every known non‐African species, with several African species as outgroup taxa. A phylogenetic hypothesis is proposed, based on molecular characters of the mitochondrial genes cytochrome oxidase subunit I (COI) and NADH dehydrogenase 5 (ND5), and the nuclear wingless gene. Phylogenetic analyses based on maximum parsimony and Bayesian inference of the combined dataset implies that the Indo‐Pacific Charaxes form a monophyletic assemblage, with the exception of Charaxes solon Fabricius. Eight major lineages are recognized in the Indo‐Pacific, here designated the solon (+African), elwesi, harmodius, amycus, mars, eurialus, latona, nitebis, and bernardus clades. Species group relationships are concordant with morphology and, based on the phylogeny, we present the first systematic appraisal and classification of all non‐African species. A biogeographical analysis reveals that, after the genus originated in Africa, the evolutionary history of Charaxes in the Indo‐Pacific, in particular Wallacea, may be correlated with the inferred geological and climatic history of the region. We propose that Wallacea was the area of origin of all Charaxes (excluding C. solon) occurring to the east of Wallace's [1863] Line. The earliest Indo‐Pacific lineages appear to have diverged subsequent to the initial fragmentation of a palaeo‐continent approximately 13 million years ago. Further diversification in Indo‐Pacific Charaxes appears primarily related to climatic changes during the Pliocene and possibly as recently as the Pleistocene. Although both dispersal and vicariance have played important roles in the evolution of the genus within the region, the latter has been particularly responsible for diversification of Charaxes in Wallacea. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 457–481.     

New insights into the species problem

Historical opinions of the “species problem” are briefly reviewed, and four salient stages are recognized according to origin of species concepts. We propose that species is the unit preserving superior gene assembly and is maintained by specific mechanisms. Based on characteristics of plant evolution, we assume that understanding plant species may include three stages, i.e. morphological recognition stage, multidisciplinary verification stage, and illuminating mechanisms preserving superior gene assembly.     

Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds

Comparative study of character evolution in the shorebirds is presently limited because the phylogenetic placement of some enigmatic genera remains unclear. We therefore used Bayesian methods to obtain a well-supported phylogeny of 90 recognized genera using 5 kb of mitochondrial and nuclear sequences. The tree comprised three major clades: Lari (gulls, auks and allies plus buttonquails) as sister to Scolopaci (sandpipers, jacanas and allies), and in turn sister to Charadrii (plovers, oystercatchers and allies), as in previous molecular studies. Plovers and noddies were not recovered as monophyletic assemblages, and the Egyptian plover Pluvianus is apparently not a plover. Molecular dating using multiple fossil constraints suggests that the three suborders originated in the late Cretaceous between 79 and 102 Mya, and at least 14 lineages of modern shorebirds survived the mass extinction at the K/T boundary. Previous difficulties in determining the phylogenetic relationships of enigmatic taxa reflect the fact that they are well-differentiated relicts of old, genus-poor lineages. We refrain from suggesting systematic revisions for shorebirds at this time because gene trees may fail to recover the species tree when long branches are connected to deep, shorter branches, as is the case for some of the enigmatic taxa.     

New insights on molecular systematics of opsariichthines based on cytochrome b sequencing

Species or sub-species including Parazacco spilurus fasciatus , Candidia barbatus , Zacco temminckii , Zacco sieboldii , Zacco platypus , Zacco macrolepis , Zacco pachycephalus , some undetermined Zacco taxa formerly misidentified as Chinese Z. platypus and Opsariichthys uncirostris were sampled, and their mitochondrial cytochrome b genes were sequenced. In the phylogenetic analysis, the genus Parazacco forms the basal taxon for the remaining members of the opsariichthine fishes, which can be divided into two major groups. The first group includes species with one longitudinal stripe on the flanks and contains Z. temminckii , Z. sieboldii and C. barbatus with sequence divergences of 12·7–16·5%. The second group has species with 10 cross bars on the body and includes O. uncirostris , Z. macrolepis , Z. platypus , Z. pachycephalus and five undetermined Zacco spp. (A–E) lineages. The estimated divergence times of mtDNA lineages within the nominal species of Z. pachycephalus and C. barbatus are >2 million years ago. According to geological evidence, this predates the earliest possible time for their arrival in Taiwan Island and indicates that the population differentiations might have been taken place in mainland China before their subsequent dispersal to Taiwan.     

Freshwater paths across the ocean: molecular phylogeny of the frog Ptychadena newtoni gives insights into amphibian colonization of oceanic islands

Aim Amphibians are a model group for studies of the biogeographical origins of salt‐intolerant taxa on oceanic islands. We used the Gulf of Guinea islands to explore the biogeographical origins of island endemism of one species of frog, and used this to gain insights into potential colonization mechanisms. Location São Tomé and Príncipe, two of the four major islands in the Gulf of Guinea, West Africa, are truly oceanic and have an exceptionally high biodiversity. Methods Mitochondrial DNA is used to test the endemic status of a frog from São Tomé and compare it with congeneric taxa from tropical Africa. Existing data on surface currents, surface salinity, atmospheric circulation and bird migration in the Gulf of Guinea are summarized to address hypotheses concerning colonization mechanisms. Results The endemic status of Ptychadena newtoni (Bocage) is supported here by mitochondrial DNA sequences, and analysis of this and other molecular data indicates that an East African species close to Ptychadena mascareniensis (Duméril and Bibron) is its nearest relative. We refute the possibility that this population was anthropogenically introduced, in favour of a natural dispersal mechanism. Main conclusions With six endemic frogs and one caecilian, the Gulf of Guinea islands harbour a diverse amphibian fauna. Five of these species appear to have their closest relatives in East Africa. Insufficient evidence exists for transportation by storms, birds or rafts alone. However, we propose a synergy of rafting, favourable surface currents and a reduction in salinity of surface waters. Catastrophic events, or wet periods in climatic history, could allow freshwater paths to open far enough to enable continental flora and fauna to reach these and other isolated oceanic islands.     

State of the art and perspectives on neotropical fern and lycophyte systematics

For ferns and lycophytes, the Neotropics is a hotspot of diversity (3000–4500 species), and second only to Southeastern Asia in richness and endemism. This paper presents the current state of knowledge on fern and lycophyte systematics in the Neotropics, and emphasizes sampling sufficiency and current taxonomic and phylogenetic knowledge. Plant systematics plays an important role in documenting diversity and geographic distribution patterns that are needed to understand relationships and evolutionary patterns, and a vital role in species conservation. Although in recent decades this field of science has undergone a revolution because of new approaches and techniques, data presented in this work shows that large gaps remain and there is still a long path towards fully understanding fern and lycophyte systematics in Neotropics. Approaches and how to choose areas that should be targeted in order to try to fulfill these knowledge gaps are discussed.     

Equilibrium and non‐equilibrium dynamics simultaneously operate in the Galápagos islands

Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Galápagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Galápagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent‐like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non‐equilibrium and equilibrium ecological paradigms.     

Charting the course of reed‐warblers across the Pacific islands

Aim Deciphering the complex colonization history of island archipelagos is greatly facilitated by comprehensive phylogenies. In this study we investigate the phylogeny and biogeography of the insular reed‐warblers (genus Acrocephalus) of the tropical Pacific Ocean, from Australia to eastern Polynesia. Location Oceania. Methods We used sequences of mitochondrial DNA (cytochrome b, ND2 and ATP8 genes) to infer the colonization patterns of reed‐warblers endemic to Pacific islands and Australia. We sampled all known taxa of Acrocephalus in the Pacific except A. luscinius nijoi, for which no sample was available. Most taxa were represented by toe‐pad samples from museum specimens collected in the 19th and 20th centuries. With a few exceptions, several specimens per taxon were sequenced independently in two institutions (Smithsonian Institution and Natural History Museum of Geneva). Results Our data indicate that Pacific reed‐warblers do not form a monophyletic group, because A. luscinius luscinius from Guam falls outside the main Pacific radiation. The remaining Pacific taxa are divided into two clades: one clade includes all the reed‐warblers from Micronesia (except Guam) and Australia, and two Polynesian taxa from the Line Islands and the southern Marquesas; the other clade includes all remaining Polynesian taxa. The taxa endemic to three archipelagos (Mariana, Marquesas and Society islands) are polyphyletic, suggesting several independent colonizations. Main conclusions Our results provide evidence for a complex pattern of colonization of the Pacific by reed‐warblers. Calibration analyses suggest that reed‐warbler lineages are much younger than the ages of the islands they occupy. Several remote archipelagos were colonized independently more than once. Consequently, we infer that the colonization of reed‐warblers in the Pacific did not follow a regular, stepping‐stone‐like pattern. The phylogeny also suggests a previously undetected case of reverse colonization (from island to continent) for the Australian lineage and indicates that A. luscinius, as currently defined, is not monophyletic. We discuss the supertramp strategy of reed‐warblers in the Pacific and show that, although Pacific reed‐warblers meet some of the supertramp criteria in their aptitude for colonizing remote archipelagos, their life history characteristics do not fit the model.     

Uniform phenotype conceals double colonization by reed-warblers of a remote Pacific archipelago

Aim Remote oceanic islands often provide good illustrations of adaptive radiations, but phylogenetic studies have also demonstrated unexpected multiple colonization events for a given archipelago. In this study we investigate the relationships among endemic populations of the Marquesas reed‐warbler, Acrocephalus mendanae Tristram, 1883, which have colonized nearly all islands of this remote Polynesian archipelago, and which exhibit a very uniform plumage pattern. We study the phylogeny and morphology of all subspecies in the Marquesas, providing an examination of the position of the Marquesas lineages in relation to reed‐warblers distributed across multiple Polynesian archipelagos. Location This study focused on all the main islands of the Marquesas archipelago, along with samples from other Polynesian archipelagos (Society, Tuamotu, Austral, Cook, Kiribati) and Australia. Methods We used mitochondrial DNA markers (cytochrome b and ND2 genes) to develop a phylogeny of the main eastern Polynesian taxa. All subspecies for the Marquesas were investigated, including multiple individuals per island. Phylogenetic analyses using maximum‐likelihood and Bayesian approaches were employed to infer relationships among A. mendanae populations and between the main Polynesian archipelagos. Morphometric analyses based on 110 specimens from museum collections were performed on external characters to investigate the differences between islands, and these results were compared to the phylogeny. Results Our data indicate that the Marquesas reed‐warbler is in fact a polyphyletic taxon including two independent lineages: the northern Marquesas reed‐warbler, closely related to the Tuamotu reed‐warbler, and the southern Marquesas reed‐warbler, sister taxon to that endemic to the Kiribati. Analyses of morphological characters show that the size and shape features of the Marquesas reed‐warblers exhibit high plasticity linked to adaptation to ecological factors, particularly habitat richness (the diversity of vegetation structure that provides suitable resources and habitat for reed‐warblers, simplified here as the number of indigenous plant species). Main conclusions Our results suggest that reed‐warblers have successfully colonized the Marquesas archipelago, one of the most remote groups of islands in the Pacific Ocean, at least twice. Both events occurred more or less simultaneously at ca. 0.6 Ma, and are more recent than the islands' formation. We outline the taxonomic consequences of our phylogeny and discuss the supertramp strategy of reed‐warblers in the Pacific.     

稻族的系统发育及其研究进展

稻族Oryzeae是禾本科Poaceae中包含多种经济植物的重要类群, 现有大约12个属, 广布全球的热带和温带地区。由于其重要的经济价值和在理论研究上的代表性, 稻属Oryza及其近缘属的研究受到了广泛关注。虽然形态学和初步的分子证据表明稻族是一个单系类群, 但稻族内各属的分类处理和属间系统发育关系以及稻族的起源、地理分布式样和机制等方面仍存在许多悬而未决的问题。本文简要回顾了稻族系统学研究的历史, 包括稻族的建立及其在禾本科中的系统位置、稻族的族下划分、稻族各属的界定及其系统发育关系。目前已有的研究结果表明: 稻族是单系类群, 可分为两个主要分支, 相当于传统的两个亚族(Zizaniinae和Oryzinae), 但稻族单性花小穗是多次起源的, 不宜作为划分亚族的依据; 一些单型属(Hydrochloa、Porteresia和Prosphytochloa)的建立得不到分子证据的支持; 根据分子钟原理估计稻族两个主要分支(亚族)的分歧时间在大约2000万年前, 而稻属和近缘属假稻属Leersia的分歧时间为1400万年; 稻属内主要类群的分歧时间在900万年前左右。此外, 本文还对稻族的生物地理学问题进行了初步探讨, 对稻族系统发育和进化研究中存在的问题及未来研究方向进行了讨论。     

Genome size and plastid trnK-matK markers give new insights into the evolutionary history of the genus Lavandula L.

The genus Lavandula L. consists of 39 species distributed from the North Atlantic Islands, across the Mediterranean Basin to India. We analysed 36 taxa of the genus Lavandula representing two of the three subgenera and six of the eight sections according to the most recent classification (Upson & Andrews 2004). We achieved a phylogenetic reconstruction from partial sequences from plastid trnK and matK genes; the genome size was estimated by flow cytometer measurements. The primary aim was to track phylogenetic patterns through the maternal inherited marker at the sectional level and identify possible genome duplications. The cpDNA tree shows the phylogenetic relationships between subgenus, sections and also elucidates for the first time the relationships between the endemic species of Macaronesia, Morocco and Arabia. The ancestral split between the two subgenera could be explained by dispersal followed by an early vicariance event. The C-value shows genome up-sizing within several phylogenetic clades and geographical areas. An ancestral genome-up sizing is characterized at the node of section Dentatae and Lavandula. The cpDNA tree suggests that the taxa L. angustifolia subsp. pyrenaica (DC.) Guinea and L. stoechas subsp. luiseiri are best treated as a distinct species.     

Evidence of taxon cycles in an Indo-Pacific passerine bird radiation (Aves: Pachycephala)

Many insular taxa possess extraordinary abilities to disperse but may differ in their abilities to diversify and compete. While some taxa are widespread across archipelagos, others have disjunct (relictual) populations. These types of taxa, exemplified in the literature by selections of unrelated taxa, have been interpreted as representing a continuum of expansions and contractions (i.e. taxon cycles). Here, we use molecular data of 35 out of 40 species of the avian genus Pachycephala (including 54 out of 66 taxa in Pachycephala pectoralis (sensu lato), to assess the spatio-temporal evolution of the group. We also include data on species distributions, morphology, habitat and elevational ranges to test a number of predictions associated with the taxon-cycle hypothesis. We demonstrate that relictual species persist on the largest and highest islands across the Indo-Pacific, whereas recent archipelago expansions resulted in colonization of all islands in a region. For co-occurring island taxa, the earliest colonists generally inhabit the interior and highest parts of an island, with little spatial overlap with later colonists. Collectively, our data support the idea that taxa continuously pass through phases of expansions and contractions (i.e. taxon cycles).     

Molecular and morphological analysis of the critically endangered Fijian iguanas reveals cryptic diversity and a complex biogeographic history

The Pacific iguanas of the Fijian and Tongan archipelagos are a biogeographic enigma in that their closest relatives are found only in the New World. They currently comprise two genera and four species of extinct and extant taxa. The two extant species, Brachylophus fasciatus from Fiji, Tonga, and Vanuatu and Brachylophus vitiensis from western Fiji, are of considerable conservation concern with B. vitiensis listed as critically endangered. A recent molecular study has shown that Brachylophus comprised three evolutionarily significant units. To test these conclusions and to reevaluate the phylogenetic and biogeographic relationships within Brachylophus, we generated an mtDNA dataset consisting of 1462 base pairs for 61 individuals from 13 islands, representing both Brachylophus species. Unweighted parsimony analyses and Bayesian analyses produced a well-resolved phylogenetic hypothesis supported by high bootstrap values and posterior probabilities within Brachylophus. Our data reject the monophyly of specimens previously believed to comprise B. fasciatus. Instead, our data demonstrate that living Brachylophus comprise three robust and well-supported clades that do not correspond to current taxonomy. One of these clades comprises B. fasciatus from the Lau group of Fiji and Tonga (type locality for B. fasciatus), while a second comprises putative B. fasciatus from the central regions of Fiji, which we refer to here as B. n. sp. Animals in this clade form the sister group to B. vitiensis rather than other B. fasciatus. We herein describe this clade as a new species of Brachylophus based on molecular and morphological data. With only one exception, every island is home to one or more unique haplotypes. We discuss alternative biogeographic hypotheses to explain their distribution in the Pacific and the difficulties of distinguishing these. Together, our molecular and taxonomic results have important implications for future conservation initiatives for the Pacific iguanas.     

New insights into tateid gastropods and their radiation on Fiji based on anatomical and molecular methods (Caenogastropoda: Truncatelloidea)

The South Pacific archipelago of Fiji is characterized by a predominantly Indo‐Malesian flora and fauna. We provide a first systematic study on Fiji's tateid gastropods – previously classified as Hydrobiidae – describing 18 new species, combining morphological, anatomical, and molecular data. The molecular phylogeny of tateid gastropods based on 16S rRNA and cytochrome c oxidase subunit I (COI) showed that the species from Fiji were closer related to New Zealand than to Australian or New Caledonian taxa, which is rather exceptional. Performing an ancestral range reconstruction we inferred the colonization history across the two main islands. The radiation had its origin in southern Viti Levu, with a subsequent dispersal over the western and central parts of the island. The chronology of the radiation over eastern Viti Levu and Vanua Levu remained unresolved because of incomplete lineage sorting, a phenomenon typical for young radiations. © 2014 The Linnean Society of London