A synopsis of the endemic plant genera of Borneo

The large, tropical island of Borneo has some of the world's richest habitats for plant life, but faces increasing pressures from anthropogenic activities that threaten its biodiversity. With a good portion of the Bornean flora not critically studied, a comprehensive documentation of the numerous endemic taxa expected for the island is not yet complete. It is not known what the relative significance of endemic genera is compared to Bornean centres of endemism documented or predicted through modelling, and if they can inform current conservation plans. As a first step, we here present a synopsis of the endemic genera of Borneo, based on a comprehensive study of literature, herbarium specimens and distributional data, and an investigation of whether the genera have been included in molecular phylogenetic studies that confirm their monophyly. Such a review is timely since many generic delimitations have been shaped by molecular evidence used to test morphology-based taxonomy, while botanical collection and revisionary efforts continue. Our findings suggest that 65 vascular plant genera from 25 families may be considered endemic to Borneo. More than two-thirds (48) of these genera have had at least one species included in molecular phylogenetic studies, but of these, only 39 have been sufficiently sampled to be considered monophyletic with high confidence, or they are monotypic. Slightly over half (38) of the endemic genera are herbaceous. A majority of the genera have fruits or seeds specialised for dispersal by abiotic vectors, or unspecialised seeds. Almost two-thirds (42) of the endemic genera are monotypic, and some of these could represent relict lineages. We expect the current list of endemic genera to be relatively stable and aligned with recent taxonomic concepts, and that it serves to illuminate an interesting aspect of Borneo's unique assemblage of endemic species.     

The evolution of South American endemic canids: a history of rapid diversification and morphological parallelism

The origin of endemic South American canid fauna has been traditionally linked with the rise of the Isthmus of Panama, suggesting that diversification of the dog fauna on this continent occurred very rapidly. Nevertheless, despite its obvious biogeographic appeal, the tempo of Canid evolution in South America has never been studied thoroughly. This issue can be suitably tackled with the inference of a molecular timescale. In this study, using a relaxed molecular clock method, we estimated that the most recent common ancestor of South American canids lived around 4 Ma, whereas all other splits within the clade occurred after the rise of the Panamanian land bridge. We suggest that the early diversification of the ancestors of the two main lineages of South American canids may have occurred in North America, before the Great American Interchange. Moreover, a concatenated morphological and molecular analysis put some extinct canid species well within the South American radiation, and shows that the dental adaptations to hypercarnivory evolved only once in the South American clade.     

Unravelling the evolutionary history of the polyploid complex Ranunculus parnassiifolius (Ranunculaceae)

Ranunculus L. represents the largest genus within Ranunculaceae, comprising more than 600 species with a worldwide distribution. However, there are still many gaps in our knowledge of the infrageneric taxonomy and evolution of Ranunculus. In this regard, intraspecific variation of the polyploid complex Ranunculus parnassiifolius remains under discussion. To reconstruct the biogeographical history of the polyploid complex R. parnassiifolius, 20 populations distributed throughout the Cantabrian Mountains, Pyrenees, and Alps were investigated. Phylogenetic studies were based on nuclear internal transcribed spacers (ITS) and plastid (rpl32‐trnL, rps16‐trnQ) sequence data, analysed using Bayesian approaches as well as the evolution of morphological characters. Additionally, biogeographical patterns were conducted using statistical dispersal–vicariance analysis. The analyses presented here support the recognition of two evolutionary independent units: R. cabrerensis sensu lato (s.l.) and R. parnassiifolius s.l. Furthermore gradual speciation depending on the biogeographical territory is proposed, and optimal reconstructions have probably favoured the ancestor of Ranunculus parnassiifolius as originating in the Iberian Peninsula. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 477–493.     

Revision of the Boophis majori group (Amphibia: Mantellidae) from Madagascar, with descriptions of five new species

A systematic revision of the Malagasy frogs hitherto attributed to the Boophis difficilis group is presented. The difficilis holotype is not conspecific with other specimens hitherto named Boophis difficilis but belongs to the B. tephraeomystax group based on lack of webbing between fingers and the presence of heterogeneously granular ventral skin. Rhacophorus difficilis Boettger, 1892 is considered as junior synonym of Boophis tephraeomystax. The Boophis difficilis group is dissolved and its species are transferred to a new species group named after Boophis majori , the oldest of the included taxa. All species of the B. majori group, their type specimens, and their geographical distributions are revised based on new morphological, bioacoustic and ecological data. Five new species of the group from the eastern rainforests of Madagascar are described. Morphological differentiation within the B. majori group is low, although some species can be distinguished by characters such as snout-vent length, relative tympanum size, or coloration. The most reliable character for species identification are advertisement calls which are strikingly different between most species of the group. Species diversity in Boophis is highest in central eastern Madagascar and gets lower at the northern and southern borders of the island. Available data do not allow a comprehensive phylogenetic analysis of the B. majori group, but a northern subgroup of small species without red coloration and a southern subgroup of larger species with distinct red pigments can be distinguished. Osteological data for B. miniatus are provided. Within Boophis , representatives of all species groups except the B. tephraeomystax group are characterized by a synapomorphic reduction of the anterolateral hyoidal process.     

A review of Gammaridae (Crustacea: Amphipoda): the family extent,its evolutionary history,and taxonomic redefinition of genera

By molecular analysis of a high number of gammarids, including 29 out‐group genera, we could assure the monophyly of Gammaridae. To avoid the paraphyly of the family, we propose the omission of Pontogammaridae, Typhlogammaridae, and all Baikalian families. Similarly, the genera Fontogammarus, Sinogammarus, Lagunogammarus, Pephredo, Neogammarus, and Laurogammarus may be cancelled. But, tens of Baikal genera, nested within Gammarus, are so diverse that they must be retained, although rendering Gammarus paraphyletic. Besides we propose the polyphyletic Echinogammarus–Chaetogammarus group to be divided into monophyletic genera Echinogammarus s. str., Homoeogammarus, Parhomoeogammarus, Marinogammarus, R elictogammarus gen. nov. , Chaetogammarus, and T richogammarus gen. nov. These solutions made it possible to complete the first analysis of the family evolution in light of its phylogeny. Perimarine clades are mainly basally split clades, whereas in some ancient lakes extremely rich endemic faunas had developed polyphyletically. The troglobiotic Typhlogammarus group from Dinarides and Caucasus formed a monophylum, whereas the troglobiotic assemblage of Gammarus species is highly polyphyletic. Reduction of the uropod III endopodite, which classically distinguishes between the genera Gammarus and Echinogammarus, appeared to be highly polyphyletic. Protective dorsal pleonal projections occur scattered across the family and beyond, whereas lateral projections were limited to species of ancient lakes, so both structures were polyphyletic. The evolutionary history of Gammaridae was investigated with ten different calibration schemes, which produced incompatible results; however, the most probable scenario is a late rise of the family, which can only explain the absence of Gammaridae species around the Indo‐Pacific. © 2015 The Linnean Society of London     

Biogeographic calibrations for the molecular clock

Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.     

Spatio‐temporal scaling of biodiversity in acoustic tropical bird communities

Automated analysis of acoustic communities is a rapidly emerging approach for the characterization and monitoring of biodiversity. To evaluate its utility, we should verify that such ‘bioacoustics’ can accurately detect ecological signal in spatiotemporal acoustic data. Targeting the ‘Biological Dynamics of Forest Fragments Project’ sites in Brazil, we ask: What is the relative contribution of the spatial, temporal and habitat dimension to variation in bird acoustic communities in a previously fragmented tropical rainforest? Does the functional diversity of bird communities scale similarly to space and time as does species diversity, when both are recorded by bioacoustics means? Overall, is the imprint of landscape fragmentation 30 years ago still audible in the present‐day soundscape? We sampled forty‐four sites in secondary forest and 107 sites in old‐growth forest, resulting in 11 000 h of audio recordings. We detected 60 bird species with satisfactory precision and recovered a linear log–log relation between sampling time and species diversity. Sites in primary forest host more species than sites in secondary forest, but the difference decreased with sampling time, as the slope was slightly higher in secondary than primary forests. Functional diversity, as exposed by vocalizing birds, accumulates faster than does species diversity. The similarity among local communities decreases with distance in both time and space, but stability in time is remarkably high: two acoustic samples from the same site one year (or more) apart prove more similar than two samples taken at the same time but from sites situated just a few hundred meters apart. These findings suggest that habitat modification can be heard as a long‐lasting imprint on the soundscape of regenerating habitats and identify soundscape–area and soundscape–time relations as a promising tool for biodiversity research, applied biomonitoring and restoration ecology.     

Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus

Aptostichus simus is a trapdoor spider endemic to the coastal dunes of central and southern California and, on morphological grounds, is recognized as a single species. Mitochondrial DNA 16S rRNA sequences demonstrate that most populations are fixed for the same haplotype and that the population haplotypes from San Diego County, Los Angeles County, Santa Rosa Island, and Monterey County are extremely divergent (6-12%), with estimated separation times ranging from 2 to 6 million years. A statistical cluster analysis of morphological features demonstrates that this genetic divergence is not reflected in anatomical features that might signify ecological differentiation among these lineages. The species status of these divergent populations of A. simus depends upon the species concept utilized. If a time-limited genealogical perspective is employed, A. simus would be separated at the base into two genetically distinct species. This study suggests that species concepts based on morphological distinctiveness, in spider groups with limited dispersal capabilities, probably underestimate true evolutionary diversity.     

Systematics of the Saharo‐Arabian clade of the Palearctic naked‐toed geckos with the description of a new species of Tropiocolotes endemic to Oman

Geckos are one of the most species‐rich, abundant, and widely distributed of all Squamata lineages and present several characteristics that have made them favorite model organisms for biogeographical, ecological, physiological, and evolutionary studies. One of the key aspects of any comparative study is to have a robust, comprehensive phylogeny, and an updated taxonomy. Recently, the Infraorder Gekkota has been the subject of several phylogenetic analyses and taxonomic revisions at different levels. Despite all these phylogenetic and taxonomic advances, there are still some groups whose systematics and taxonomy remain highly problematic. Maybe one of the most poorly resolved groups in spite of decades of intensive research by many herpetologists are the so‐called Palearctic naked‐toed geckos of the family Gekkonidae. This group of nocturnal geckos distributed from Mauritania across North Africa, Arabia, southwestern and central Asia to northern India, western China and southern Mongolia is characterized by the synapomorphy of lack of adhesive subdigital pads. Within the Palearctic naked‐toed geckos, the Saharo‐Arabian clade comprised by the genera Pseudoceramodactylus, Stenodactylus, and Tropiocolotes is the clade with the largest distribution range. At the same time, it is one of the problematic groups, presenting poorly supported phylogenetic relationships, with the genus Tropiocolotes being recovered non‐monophyletic in all analyses despite its morphological uniformity. To reassess the phylogeny of the Palearctic naked‐toed geckos with a special interest in the systematics of Tropiocolotes, we assembled a dataset comprising 298 gecko specimens from 283 different species (including all Tropiocolotes species but one) belonging to 122 of a total of 124 described gecko genera. This dataset included the nuclear c‐mos, ACM4, RAG1, RAG2, and PDC and the mitochondrial ND2 gene. To further investigate the relationships within Tropiocolotes and to revise the systematics of the south Arabian endemic species Tropiocolotes scorteccii, we used an integrative approach including information from the nuclear MC1R and c‐mos, the mitochondrial 12S, 16S, cytb genes, and morphological data from nine of the 10 described Tropiocolotes species. The phylogenetic analyses of the Gekkota dataset recovered a similar topology for the Palearctic naked‐toed geckos to previous studies, but in this case, Tropiocolotes was recovered monophyletic in all analyses, with high support in two of them. The results of the analyses of three datasets specifically assembled to test the effect of both gene sampling and taxon sampling in the monophyly of Tropiocolotes, and the internal relationships of the Palearctic naked‐toed geckos clearly showed that both the number and kind of characters (nuclear or mitochondrial data) and the number of taxa played a fundamental role in recovering the correct phylogenetic relationships. The phylogenetic analyses within Tropiocolotes suggested the existence of high levels of undescribed diversity in the south Arabian T. scorteccii, including a new genetically and morphologically distinct species endemic to Oman (Tropiocolotes confusus sp. nov. ). Our study using a large dataset, including several loci and a dense taxon sampling within Gekkota and especially within Tropiocolotes, has proved a valuable strategy to address the monophyly of Tropiocolotes and the relationships within the Saharo‐Arabian Palearctic naked‐toed geckos. The integrative systematic approach including several samples of south Arabian T. scorteccii based on many years of fieldwork has, once more, uncovered a new species endemic to this region. This highlights the importance of this area of Arabia as a reservoir of reptile endemicity and biodiversity, which is likely linked to the high degree of habitat heterogeneity and the effect of the monsoons. Obviously, based on this and previously published evidence, south Arabia represents an area with still high levels of undiscovered diversity.     

Woody species in resource‐rich microrefugia of granite outcrops display unique functional signatures

Refugia are key environments in biogeography and conservation. Because of their unique eco‐evolutionary formation and functioning, they should display distinct functional trait signatures. However, comparative trait‐based studies of plants in refugia and non‐refugia are lacking. Here, we provide a comparison between resource‐rich (putative microrefugia for species preferring mesic habitats under increasing aridity) and resource‐impoverished woodlands (non‐refugia) around two granite outcrops in south‐western Australia. We measured and compared six functional traits (bark thickness, foliar δ¹³C, foliar C:N, leaf dry matter content, plant height, specific leaf area) in four woody species. We performed multiple‐trait, multiple‐species and single‐trait, within‐species analyses to test whether plants in resource‐rich habitats were functionally distinct and more diverse than those in the surrounding resource‐impoverished woodlands. We found that species in resource‐rich woodlands occupied larger and distinct multiple‐trait functional spaces and showed distinct single‐trait values (for specific leaf area and bark thickness). This suggests that plants in resource‐rich woodlands can deploy unique and more diverse ecological strategies, potentially making these putative microrefugia more resilient to environmental changes. These findings suggest that species in microrefugia may be characterised by unique functional signatures, illustrating the utility of comparative trait‐based approaches to improve understanding of the functioning of refugia.     

中国石松类和蕨类植物的多样性与地理分布

物种编目及其科属系统排列是了解生物多样性的基础, 本文采用Flora of China使用的分类系统, 结合最新分子分类学研究成果以及近几年发表的新资料, 对中国石松类和蕨类植物多样性和地理分布数据进行了统计和分析。结果表明中国共有石松类和蕨类植物40科178属2,147种5个亚种118个变种, 其中特有种839个, 占总种数的39.08%。种数最多的5个科依次为鳞毛蕨科(505种, 含种下单位, 下同)、蹄盖蕨科(323种)、水龙骨科(280种)、凤尾蕨科(266种)和金星蕨科(209种); 种数最多的5个属依次为耳蕨属(Polystichum, 209种)、鳞毛蕨属(Dryopteris, 176种)、蹄盖蕨属(Athyrium, 137种)、双盖蕨属(Diplazium, 98种)和凤尾蕨属(Pteris, 97种)。在地理分布上, 种数排名前5的省份为云南(1,365种)、四川(875种)、贵州(838种)、广西(785种)和台湾(779种)。含中国特有石松类和蕨类植物的科属中, 排前3位的科分别为鳞毛蕨科(257种)、蹄盖蕨科(169种)和凤尾蕨科(113种); 排前3位的属为耳蕨属(140种)、蹄盖蕨属(82种)和鳞毛蕨属(61种)。     

Defining spatial and temporal patterns of phylogeographic structure in Madagascar's iguanid lizards (genus Oplurus)

Understanding the remarkably high species diversity and levels of endemism found among Madagascar’s flora and fauna has been the focus of many studies. One hypothesis that has received much attention proposes that Quaternary climate fluctuations spurred diversification. While spatial patterns of distribution and phylogenetic relationships can provide support for biogeographic predictions, temporal estimates of divergence are required to determine the fit of these geospatial patterns to climatic or biogeographic mechanisms. We use multilocus DNA sequence data to test whether divergence times among Malagasy iguanid lizards of the subfamily Oplurinae are compatible with a hypotheses of Pliocene–Pleistocene diversification. We estimate the oplurine species tree and associated divergence times under a relaxed‐clock model. In addition, we examine the phylogeographic structure and population divergence times within two sister species of Oplurus primarily distributed in the north‐west and south‐west of Madagascar (Oplurus cuvieri and Oplurus cyclurus, respectively). We find that divergence events among oplurine lineages occurred in the Oligocene and Miocene and are thus far older and incompatible with the hypothesis that recent climate fluctuations are related to current species diversity. However, the timing of intraspecific divergences and spatial patterns of population genetic structure within O. cuvieri and O. cyclurus suggest a role for both intrinsic barriers and recent climate fluctuations at population‐level divergences. Integrating information across spatial and temporal scales allows us to identify and better understand the mechanisms generating patterns diversity.     

Taking into account phylogenetic and divergence‐time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae

Aim To examine the biogeographical history of the angiosperm clade Caprifolieae (Caprifoliaceae) using parametric biogeographical reconstruction methods. The existing parametric method was extended to evaluate biogeographical reconstructions over the distribution of dated phylogenies. This method provides a framework for reconstructing large‐scale biogeography with parametric methods, while accounting for uncertainty in the phylogenetic relationships and divergence time. Location Asia, Europe and North America. Methods The biogeographical history of the major lineages of Caprifolieae was reconstructed over the posterior distribution of dated trees generated from Bayesian divergence‐time analyses. Results from a model with no geological constraints were compared with those from one where movement is disallowed across the North Atlantic after the Eocene. The most plausible scenarios were segregated at each node to test whether particular scenarios were reconstructed for particular divergence times. The parametric biogeographical method was also extended to estimate connectivity between areas so that the probability of dispersal between the major areas of the Northern Hemisphere could be explored. Results Phylogenetic results for Caprifolieae agreed with previous estimates using smaller sampling, but uncertainty remained despite efforts to resolve the relationships of the four genera within this clade using multiple markers. In addition to topological uncertainty, there were few fossils available for calibrations, resulting in large confidence intervals for divergence times. Divergence‐time analyses put the diversification of Caprifolieae at between 36 and 51 Ma and showed that Caprifolieae probably originated in Asia, with multiple movements into Europe and western and eastern North America. Main conclusions Newly developed parametric methods for biogeographical reconstruction incorporate more data and better models. Here, the parametric biogeographical reconstruction method has been extended to allow for topological and divergence‐time uncertainty. The analyses of Caprifolieae demonstrated that biogeographical hypotheses can be explored even where there are large confidence intervals on divergence times and uncertainty in topology. These results add to the growing evidence that Asia was an important source of Northern Hemisphere diversity throughout the Cenozoic.     

Phylogenetic relationships of the Cretaceous frog Beelzebufo from Madagascar and the placement of fossil constraints based on temporal and phylogenetic evidence

The placement of fossil calibrations is ideally based on the phylogenetic analysis of extinct taxa. Another source of information is the temporal variance for a given clade implied by a particular constraint when combined with other, well-supported calibrations. For example, the frog Beelzebufo ampinga from the Cretaceous of Madagascar has been hypothesized to be a crown-group member of the New World subfamily Ceratophryinae, which would support a Late Cretaceous connection with South America. However, phylogenetic analyses and molecular divergence time estimates based on other fossils do not support this placement. We derive a metric, Δt, to quantify temporal divergence among chronograms and find that errors resulting from mis-specified calibrations are localized when additional nodes throughout the tree are properly calibrated. The use of temporal information from molecular data can further assist in testing phylogenetic hypotheses regarding the placement of extinct taxa.