A gharial from the Oligocene of Puerto Rico: transoceanic dispersal in the history of a non-marine reptile

The Indian gharial (Gavialis gangeticus) is not found in saltwater, but the geographical distribution of fossil relatives suggests a derivation from ancestors that lived in, or were at least able to withstand, saline conditions. Here, we describe a new Oligocene gharial, Aktiogavialis puertoricensis, from deltaic-coastal deposits of northern Puerto Rico. It is related to a clade of Neogene gharials otherwise restricted to South America. Its geological and geographical settings, along with its phylogenetic relationships, are consistent with two scenarios: (i) that a single trans-Atlantic dispersal event during the Tertiary explains the South American Neogene gharial assemblage and (ii) that stem gharials were coastal animals and their current restriction to freshwater settings is a comparatively recent environmental shift for the group. This discovery highlights the importance of including fossil information in a phylogenetic context when assessing the ecological history of modern organisms.     

A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitution rates of Gnetales （Ephedra, Gnetum, and Welwitschia） has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species （and 7736 aligned nucleotides） to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.     

A fossil‐calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

Abstract Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions (amphitropical range). Great heterogeneity in the substitution rates of Gnetales (Ephedra, Gnetum, and Welwitschia) has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species (and 7736 aligned nucleotides) to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil‐based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long‐distance dispersal, but finer‐scale studies are needed to test this hypothesis.     

Marine incursion into East Asia: a forgotten driving force of biodiversity

Episodic marine incursion has been a major driving force in the formation of present-day diversity. Marine incursion is considered to be one of the most productive ‘species pumps’ particularly because of its division and coalescence effects. Marine incursion events and their impacts on diversity are well documented from South America, North America and Africa; however, their history and impacts in continental East Asia largely remain unknown. Here, we propose a marine incursion scenario occurring in East Asia during the Miocene epoch, 10–17 Ma. Our molecular phylogenetic analysis of Platorchestia talitrids revealed that continental terrestrial populations (Platorchestia japonica) form a monophyletic group that is the sister group to the Northwest Pacific coastal species Platorchestia pacifica. The divergence time between the two species coincides with Middle Miocene high global sea levels. We suggest that the inland form arose as a consequence of a marine incursion event. This is the first solid case documenting the impact of marine incursion on extant biodiversity in continental East Asia. We believe that such incursion event has had major impacts on other organisms and has played an important role in the formation of biodiversity patterns in the region.     

Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China

Background and Aims

The genus Allium comprises more than 800 species, placing it among the largest monocotyledonous genera. It is a variable group that is spread widely across the Holarctic region. Previous studies of Allium have been useful in identifying and assessing its evolutionary lineages. However, there are still many gaps in our knowledge of infrageneric taxonomy and evolution of Allium. Further understanding of its phylogeny and biogeography will be achieved only through continued phylogenetic studies, especially of those species endemic to China that have often been excluded from previous analyses. Earlier molecular studies have shown that Chinese Allium is not monophyletic, so the goal of the present study was to infer the phylogeny and biogeography of Allium and to provide a classification of Chinese Allium by placement of Chinese species in the context of the entire phylogeny.

Methods

Phylogenetic studies were based on sequence data of the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast rps16 intron, analysed using parsimony and Bayesian approaches. Biogeographical patterns were conducted using statistical dispersal–vicariance analysis (S-DIVA).

Key Results

Phylogenetic analyses indicate that Allium is monophyletic and consists of three major clades. Optimal reconstructions have favoured the ancestors of Amerallium, Anguinum, Vvedenskya, Porphyroprason and Melanocrommyum as originating in eastern Asia.

Conclusions

Phylogenetic analyses reveal that Allium is monophyletic but that some subgenera are not. The large genetic distances imply that Allium is of ancient origin. Molecular data suggest that its evolution proceeded along three separate evolutionary lines. S-DIVA indicates that the ancestor of Amerallium, Anguinum, Vvedenskya, Porphyroprason and Melanocrommyum originated from eastern Asia and underwent different biogeographical pathways. A taxonomic synopsis of Chinese Allium at sectional level is given, which divides Chinese Allium into 13 subgenera and 34 sections.     

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.     

Evolution in Aeschynanthus (Gesneriaceae) inferred from ITS sequences

 Aeschynanthus Jack, an epiphytic genus with c.160 species, is widespread in SE Asia. We selected 50 species for ITS nrDNA sequencing, to include all biogeographic areas and all infrageneric groupings, which are currently based on seed morphology. Some species were sequenced directly from PCR product; others cloned because of ITS length polymorphisms. The clone sequences were analysed individually and combined in an elision matrix. Results extend earlier findings that Aeschynanthus is divided into two clades, one occurring primarily in mainland SE Asia and the other in Malesia. This pattern is interpreted as indicating an ancient vicariance event followed by dispersal and plate fusion. Clade I has straight or clockwise spiral orientation of the testa cells and clade II anticlockwise spiral orientation. In clade I some species of section Microtrichium form a basal group with other sections being polyphyletic or paraphyletic. In clade II the monophyletic section Aeschynanthus is nested within the paraphyletic basal Microtrichium. Received February 8, 2001 Accepted June 8, 2001     

Systematic placement of an enigmatic Southeast Asian taxon Eupetes macrocerus and implications for the biogeography of a main songbird radiation, the Passerida

Biogeographic connections between Australia and other continents are still poorly understood although the plate tectonics of the Indo-Pacific region is now well described. Eupetes macrocerus is an enigmatic taxon distributed in a small area on the Malay Peninsula and on Sumatra and Borneo. It has generally been associated with Ptilorrhoa in New Guinea on the other side of Wallace's Line, but a relationship with the West African Picathartes has also been suggested. Using three nuclear markers, we demonstrate that Eupetes is the sister taxon of the South African genus Chaetops, and their sister taxon in turn being Picathartes, with a divergence in the Eocene. Thus, this clade is distributed in remote corners of Africa and Asia, which makes the biogeographic history of these birds very intriguing. The most parsimonious explanation would be that they represent a relictual basal group in the Passerida clade established after a long-distance dispersal from the Australo-Papuan region to Africa. Many earlier taxonomic arrangements may have been based on assumptions about relationships with similar-looking forms in the same, or adjacent, biogeographic regions, and revisions with molecular data may uncover such cases of neglect of ancient relictual patterns reflecting past connections between the continents.     

Molecular phylogeny of the tribe Bovini (Mammalia: Artiodactyla): alternative placement of the Anoa

Noncoding regions from the genes encoding aromatase cytochrome P450 and lactoferrin have been sequenced in ten bovine and one cervid species for an investigation of the evolutionary relationships within the tribe Bovini. The evolutionary rate of DNA-nucleotide alterations along the ancestral bovine lineage amounts to 0.38% per million years, as estimated from this combined 0.478-kb-single copy nuclear (scn) DNA sequence data set. Whereas rate homogenity is apparent within the Bovini, the relative rate test suggests that the boselaphine lineage (as represented by Boselaphus) has evolved at only about one third of the rate found within the Bovini. Consistent with other results, the scnDNA data provide evidence for (i) a monophyletic origin of the Bovini, (ii) a sister group position of the Boselaphini, and (iii) two different clades within the Bovini, the buffaloes (Bubalus and Syncerus) and the cattle (Bos/Bibos and Bison). Surprisingly, the results indicate very clearly that the enigmatic dwarf buffalo of Sulawesi Island (Anoa depressicornis) is most closely related to Boselaphus and that the divergence from the true Bovini occurred close to the base of bovine cladogenesis in the Middle Miocene (≈ 14—12 million years ago).     

Evolution and taxonomic split of the model grass Brachypodium distachyon

Background and Aims

Brachypodium distachyon is being widely investigated across the world as a model plant for temperate cereals. This annual plant has three cytotypes (2n =  10, 20, 30) that are still regarded as part of a single species. Here, a multidisciplinary study has been conducted on a representative sampling of the three cytotypes to investigate their evolutionary relationships and origins, and to elucidate if they represent separate species.

Methods

Statistical analyses of 15 selected phenotypic traits were conducted in individuals from 36 lines or populations. Cytogenetic analyses were performed through flow cytometry, fluorescence in situ hybridization (FISH) with genomic (GISH) and multiple DNA sequences as probes, and comparative chromosome painting (CCP). Phylogenetic analyses were based on two plastid (ndhF, trnLF) and five nuclear (ITS, ETS, CAL, DGAT, GI) genes from different Brachypodium lineages, whose divergence times and evolutionary rates were estimated.

Key Results

The phenotypic analyses detected significant differences between the three cytotypes and demonstrated stability of characters in natural populations. Genome size estimations, GISH, FISH and CCP confirmed that the 2n = 10 and 2n = 20 cytotypes represent two different diploid taxa, whereas the 2n = 30 cytotype represents the allotetraploid derived from them. Phylogenetic analysis demonstrated that the 2n = 20 and 2n = 10 cytotypes emerged from two independent lineages that were, respectively, the maternal and paternal genome donors of the 2n = 30 cytotype. The 2n = 20 lineage was older and mutated significantly faster than the 2n = 10 lineage and all the core perennial Brachypodium species.

Conclusions

The substantial phenotypic, cytogenetic and molecular differences detected among the three B. distachyon sensu lato cytotypes are indicative of major speciation processes within this complex that allow their taxonomic separation into three distinct species. We have kept the name B. distachyon for the 2n = 10 cytotype and have described two novel species as B. stacei and B. hybridum for, respectively, the 2n = 20 and 2n = 30 cytotypes.     

Evolution of the turtle bauplan: the topological relationship of the scapula relative to the ribcage

The turtle shell and the relationship of the shoulder girdle inside or ‘deep’ to the ribcage have puzzled neontologists and developmental biologists for more than a century. Recent developmental and fossil data indicate that the shoulder girdle indeed lies inside the shell, but anterior to the ribcage. Developmental biologists compare this orientation to that found in the model organisms mice and chickens, whose scapula lies laterally on top of the ribcage. We analyse the topological relationship of the shoulder girdle relative to the ribcage within a broader phylogenetic context and determine that the condition found in turtles is also found in amphibians, monotreme mammals and lepidosaurs. A vertical scapula anterior to the thoracic ribcage is therefore inferred to be the basal amniote condition and indicates that the condition found in therian mammals and archosaurs (which includes both developmental model organisms: chickens and mice) is derived and not appropriate for studying the developmental origin of the turtle shell. Instead, among amniotes, either monotreme mammals or lepidosaurs should be used.     

Isolates of Meloidogyne hapla with Distinct Mitochondrial Genomes

Because two conflicting reports of the structure of the Meloidogyne hapla mitochondrial genome exist, we compared the mitochondrial DNA (mtDNA) purified from two isolates of M. hapla: one from San Bernardino County in southern California (BRDO) and the other from England. The authenticity of the BRDO isolate in particular was confirmed by examination of morphological characters, isoenzyme analysis, and differential host range tests. Restriction analysis revealed that mtDNA from the BRDO and English isolates corresponded to only the structure first reported, although significant differences between the two isolates were apparent. Southern blots probed with cloned, cytochrome oxidase I (cox-l) DNA from Romanomermis culicivorax mtDNA confirmed that the analyzed DNA was of mitochondrial origin. Thus, M. hapla has at least two distinct but presumably related mitchondrial genomes, plus at least one very different structure. These data are discussed with reference to recent molecular diagnostic and phylogenetic analyses of Meloidogyne.     

The perils of single gene trees — mitochondrial versus single-copy nuclear DNA variation in white-eyes (Aves: Zosteropidae)

Phylogenetic relationships among animal populations and species commonly have been inferred from patterns of variation observed within a single gene system, most often the mitochondrial genome. Analysis of restriction site variation in the mitochondrial DNA of two species of white-eye ( Zosterops lateralis and Z. lutea ) in Australia produced a single gene tree that does not accurately represent the organismal tree. In contrast, patterns of variation at two anonymous, single-copy nuclear DNA loci revealed a phylogeography consistent with traditional classification of the species. Discordance between mitochondrial DNA and single-copy nuclear DNA variation is probably the result of past hybridization between Z. lateralis and Z. lutea , evidence of which has been lost from the nuclear genome by recombination. This study provides a clear empirical demonstration that single gene genealogies cannot be assumed to accurately represent the true phylogenies, and emphasizes the need for composite genetic analyses.     

Phylogeny and biogeography of wild roses with specific attention to polyploids

Background and Aims The genus Rosa (150–200 species) is widely distributed throughout temperate and sub-tropical habitats from the northern hemisphere to tropical Asia, with only one tropical African species. In order to better understand the evolution of roses, this study examines infrageneric relationships with respect to conventional taxonomy, considers the extent of allopolyploidization and infers macroevolutionary processes that have led to the current distribution of the genus.Methods Phylogenetic relationships among 101 species of the genus Rosa were reconstructed using sequences from the plastid psbA-trnH spacer, trnL intron, trnL-F spacer, trnS-G spacer and trnG intron, as well as from nuclear glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which was used to identify putative allopolyploids and infer their possible origins. Chloroplast phylogeny was used to estimate divergence times and reconstruct ancestral areas.Key Results Most subgenera and sections defined by traditional taxonomy are not monophyletic. However, several clades are partly consistent with currently recognized sections. Allopolyploidy seems to have played an important role in stabilizing intersectional hybrids. Biogeographic analyses suggest that Asia played a central role as a genetic reservoir in the evolution of the genus Rosa.Conclusions The ancestral area reconstruction suggests that despite an early presence on the American continent, most extant American species are the results of a later re-colonization from Asia, probably through the Bering Land Bridge. The results suggest more recent exchanges between Asia and western North America than with eastern North America. The current distribution of roses from the Synstylae lineage in Europe is probably the result of a migration from Asia approx. 30 million years ago, after the closure of the Turgai strait. Directions for a new sectional classification of the genus Rosa are proposed, and the analyses provide an evolutionary framework for future studies on this notoriously difficult genus.     

Age estimates of Frullania (Frullaniaceae,Porellales) main lineages: another example of rapid and recent diversification in liverwort evolution

Frullania Raddi is an extant genus of liverworts (Bryophytes) widespread around the world. It belongs to the family Frullaniaceae Lorch., with a large number of species distributed into several subgenera, sections and subsections according with different morphological classifications. As shown in previous studies, most Frullania sub-generic classifications are supported by molecular data, indicating that morphological characters appear well suitable to discriminate species. However, deep among-clade relationships remain unclear, probably due to the rapid diversification of main clades, paralleling other plant lineages. In this study, we reconstruct Frullania phylogeny based on available molecular data used in previous studies, and we present time estimates for the origin of its main branches. Results supported the monophyly of most subgenera as demonstrated in previous studies and supported a rapid diversification of these main lineages. Time estimates under a relaxed molecular clock and with integrated fossil evidence and nucleotide mutation rates further suggested a Jurassic origin of the genus and a rapid diversification during Palaeogene and Neogene. This may have been influenced by geographical and climate changes during these periods as predicted for most leafy liverworts.     

Cycling of clock genes entrained to the solar rhythm enables plants to tell time: data from arabidopsis

Background and Aims An endogenous rhythm synchronized to dawn cannot time photosynthesis-linked genes to peak consistently at noon since the interval between sunrise and noon changes seasonally. In this study, a solar clock model that circumvents this limitation is proposed using two daily timing references synchronized to noon and midnight. Other rhythmic genes that are not directly linked to photosynthesis, and which peak at other times, also find an adaptive advantage in entrainment to the solar rhythm.Methods Fourteen datasets extracted from three published papers were used in a meta-analysis to examine the cyclic behaviour of the Arabidopsis thaliana photosynthesis-related gene CAB2 and the clock oscillator genes TOC1 and LHY in T cycles and N–H cycles.Key Results Changes in the rhythms of CAB2, TOC1 and LHY in plants subjected to non-24-h light:dark cycles matched the hypothesized changes in their behaviour as predicted by the solar clock model, thus validating it. The analysis further showed that TOC1 expression peaked ∼5·5 h after mid-day, CAB2 peaked close to noon, while LHY peaked ∼7·5 h after midnight, regardless of the cycle period, the photoperiod or the light:dark period ratio. The solar clock model correctly predicted the zeitgeber timing of these genes under 11 different lighting regimes comprising combinations of seven light periods, nine dark periods, four cycle periods and four light:dark period ratios. In short cycles that terminated before LHY could be expressed, the solar clock correctly predicted zeitgeber timing of its expression in the following cycle.Conclusions Regulation of gene phases by the solar clock enables the plant to tell the time, by which means a large number of genes are regulated. This facilitates the initiation of gene expression even before the arrival of sunrise, sunset or noon, thus allowing the plant to ‘anticipate’ dawn, dusk or mid-day respectively, independently of the photoperiod.     

A banned variety was the mother of several major wine grapes

A number of widely grown varieties of Vitis vinifera ssp. sativa, the grape used for wine production, are known to have resulted from crosses between Pinot noir and Gouais blanc, although it is not known which was the maternal parent in these crosses. We have analysed microsatellites and a single nucleotide polymorphism (SNP) in chloroplast DNA from these two varieties and twelve progeny strains, including Chardonnay, Gamay noir and Aligoté. The results demonstrate that Gouais blanc was the maternal parent for nine of these strains, including Chardonnay, Gamay noir and Aligoté. This is a striking conclusion, as Gouais is generally considered a highly inferior variety, and its cultivation was banned for many years in parts of Europe.     

The phylogenetic affinities of Crossley's babbler (Mystacornis crossleyi): adding a new niche to the vanga radiation of Madagascar

Crossley's babbler (Mystacornis crossleyi) is a passerine endemic to Madagascar. Traditionally, it has been classified as a babbler (Timaliidae), although affinities with warblers and vangas have been suggested. We investigated the phylogenetic affinities of Crossley's babbler using sequence data from two nuclear introns (myoglobin intron 2 and beta-fibrinogen intron 5) and one mitochondrial gene (ND2). We present for the first time (to our knowledge) a molecular phylogeny that confidently places this enigmatic species within the vangas (Vangidae). The inclusion of Crossley's babbler within the vangas adds another foraging niche--gleaning small invertebrates from the ground-to this already large adaptive radiation of songbirds.     

Stomatal and pavement cell density linked to leaf internal CO2 concentration

Background and Aims

Stomatal density (SD) generally decreases with rising atmospheric CO₂ concentration, C_a. However, SD is also affected by light, air humidity and drought, all under systemic signalling from older leaves. This makes our understanding of how C_a controls SD incomplete. This study tested the hypotheses that SD is affected by the internal CO₂ concentration of the leaf, C_i, rather than C_a, and that cotyledons, as the first plant assimilation organs, lack the systemic signal.

Methods

Sunflower (Helianthus annuus), beech (Fagus sylvatica), arabidopsis (Arabidopsis thaliana) and garden cress (Lepidium sativum) were grown under contrasting environmental conditions that affected C_i while C_a was kept constant. The SD, pavement cell density (PCD) and stomatal index (SI) responses to C_i in cotyledons and the first leaves of garden cress were compared. ¹³C abundance (δ¹³C) in leaf dry matter was used to estimate the effective C_i during leaf development. The SD was estimated from leaf imprints.

Key Results

SD correlated negatively with C_i in leaves of all four species and under three different treatments (irradiance, abscisic acid and osmotic stress). PCD in arabidopsis and garden cress responded similarly, so that SI was largely unaffected. However, SD and PCD of cotyledons were insensitive to C_i, indicating an essential role for systemic signalling.

Conclusions

It is proposed that C_i or a C_i-linked factor plays an important role in modulating SD and PCD during epidermis development and leaf expansion. The absence of a C_i–SD relationship in the cotyledons of garden cress indicates the key role of lower-insertion CO₂ assimilation organs in signal perception and its long-distance transport.