MECHANISMS OF LARGE-SCALE EVOLUTIONARY TRENDS

Large-scale evolutionary trends may result from driving forces or from passive diffusion in bounded spaces. Such trends are persistent directional changes in higher taxa spanning significant periods of geological time; examples include the frequently cited long-term trends in size, complexity, and fitness in life as a whole, as well as trends in lesser supraspecific taxa and trends in space. In a driven trend, the distribution mean increases on account of a force (which may manifest itself as a bias in the direction of change) that acts on lineages throughout the space in which diversification occurs. In a passive system, no pervasive force or bias exists, but the mean increases because change in one direction is blocked by a boundary, or other inhomogeneity, in some limited region of the space. Two tests have been used to distinguish these trend mechanisms: (1) the test based on the behavior of the minimum; and (2) the ancestor-descendant test, based on comparisons in a random sample of ancestor-descendant pairs that lie far from any possible lower bound. For skewed distributions, a third test is introduced here: (3) the subclade test, based on the mean skewness of a sample of subclades drawn from the tail of a terminal distribution. With certain restrictions, a system is driven if the minimum increases, if increases significantly outnumber decreases among ancestor-descendant pairs, and if the mean skew of subclades is significantly positive. A passive mechanism is more difficult to demonstrate but is the more likely mechanism if decreases outnumber increases and if the mean skew of subclades is negative. Unlike the other tests, the subclade test requires no detailed phylogeny or paleontological time series, but only terminal (e.g., modern) distributions. Monte Carlo simulations of the diversification of a clade are used to show how the subclade test works. In the empirical cases examined, the three tests gave concordant results, suggesting first, that they work, and second, that the passive and driven mechanisms may correspond to natural categories of causes of large-scale trends.     

Consequences of ignoring spatial variation in population trend when conducting a power analysis

Long‐term, large‐scale monitoring programs are becoming increasingly common to document status and trends of wild populations. A successful program for monitoring population trend hinges on the ability to detect the trend of interest. Power analyses are useful for quantifying the sample size needed for trend detection, given expected variation in the population. Four components of variation (within‐year variation at a given site, interannual variation within a site, variation among sites in the interannual variation, and variation among sites in mean abundance or density) are commonly considered in power analyses for population trend, but a fifth is rarely considered: variation among sites in the local trend. Spatial variation in trend is expected to reduce statistical power, but the magnitude of this reduction has not been fully explored. We used computer simulations to evaluate the consequences of ignoring spatial variation in trend under a variety of sampling designs and wide ranges of other components of variation. The effect of spatial variation in trend on power was minor when other input parameters took extreme values that made the trend either very difficult or very easy to detect. However, at moderate values of the other parameters, spatial variation in trend had a strong effect, reducing statistical power by up to 60%. In some cases, ignoring spatial variation in trend resulted in an 80% probability of a type I error (falsely detecting a trend in a stable population). Spatial variation in trend is therefore an important consideration when designing a long‐term monitoring program for many species, especially those affected by local conditions at sites that are repeatedly surveyed. If variation in trend is ignored, as in many previous power analyses, the recommended sampling design will likely be insufficient to detect the trend of interest and lead to potentially false conclusions of a stable population.     

Patterns of genetic isolation in a widely distributed pelagic fish,the narrow‐barred Spanish mackerel (Scomberomorus commerson)

Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow‐barred Spanish mackerel (Scomberomorus commerson Lacepède, 1800), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo‐West Pacific range using control‐region sequences (including previously published data sets), cytochrome b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo‐Malay‐Papua archipelago (IMPA) and the south‐western Pacific coalesced into a clade (clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (clade I). Such a high level of genetic divergence suggested the occurrence of two sister species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele‐frequency differences were found between local populations in the south‐western Pacific, both at the mitochondrial locus (Φ_st = 0.282–0.609) and at microsatellite loci ( = 0.202–0.313). Clade II consisted of four deeply divergent subclades (9.0–11.8% nucleotide divergence for the control region; 0.3–2.5% divergence at the cytochrome b locus). Mitochondrial subclades within clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within clade II was present throughout the central Indo‐West Pacific: this haplogroup was found to be the sister group to a haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 886–902.     

No evidence for directional evolution of body mass in herbivorous theropod dinosaurs

The correlation between large body size and digestive efficiency has been hypothesized to have driven trends of increasing mass in herbivorous clades by means of directional selection. Yet, to date, few studies have investigated this relationship from a phylogenetic perspective, and none, to our knowledge, with regard to trophic shifts. Here, we reconstruct body mass in the three major subclades of non-avian theropod dinosaurs whose ecomorphology is correlated with extrinsic evidence of at least facultative herbivory in the fossil record—all of which also achieve relative gigantism (more than 3000 kg). Ordinary least-squares regressions on natural log-transformed mean mass recover significant correlations between increasing mass and geological time. However, tests for directional evolution in body mass find no support for a phylogenetic trend, instead favouring passive models of trait evolution. Cross-correlation of sympatric taxa from five localities in Asia reveals that environmental influences such as differential habitat sampling and/or taphonomic filtering affect the preserved record of dinosaurian body mass in the Cretaceous. Our results are congruent with studies documenting that behavioural and/or ecological factors may mitigate the benefit of increasing mass in extant taxa, and suggest that the hypothesis can be extrapolated to herbivorous lineages across geological time scales.     

Molecular phylogenetic analysis of Euphorbiaceae sensu stricto based on plastid and nuclear DNA sequences and ovule and seed character evolution

A phylogenetic analysis of Euphorbiaceae sensu stricto is presented using sequences from rbcL, atpB, matK and 18S rDNA from 85 species and 83 genera. The combined analysis of four molecular markers resulted in only one most parsimonious tree and also generated new supported clades, which include Euphorbioideae + Acalyphoideae s.s., subclades A2 + A3, subclades A5 + A6 and a clade uniting subclades A2–A8 within Acalyphoideae s.s. A palisadal exotegmen is a possible synapomorphy for all the Euphorbiaceae, except for the subfamily Peroideae. The presence of vascular bundles in the inner integument and a thick inner integument were shown to be synapomorphies for the clade of inaperturate and articulated crotonoids and for the large clade of Euphorbioideae, Acalyphoideae s.s., inaperturate and articulated crotonoids, respectively. Characters of the aril and vascular bundles in the outer integument are discussed. The selected embryological characters were seen to be highly correlated with the molecular phylogeny. When the results of molecular phylogenetic analysis of a previous study and this study were adjusted along with the selected embryological characters, all clades within Euphorbiaceae were supported except for a clade comprising Euphorbioideae + Acalyphoideae s.s. + inaperturate crotonoids + articulated crotonoids + Adenoclineae s.l. and a clade uniting subclades A4–A8 within Acalyphoideae s.s. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early‐branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schi‐sandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well‐supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well‐supported eudicot clade, the early‐diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise six well‐supported subclades: (1) Berberidopsidaceae/Aextoxicaceae; (2) Myrothamnaceae/ Gunneraceae; (3) Saxifragales, which are the sister to Vitaceae (including Leea) plus a strongly supported eurosid clade; (4) Santalales; (5) Caryophyllales, to which Dilleniaceae are sister; and (6) an asterid clade. The relationships among these six subclades of core eudicots do not receive strong support. This large data set has also helped place a number of enigmatic angiosperm families, including Podostemaceae, Aphloiaceae, and Ixerbaceae. This analysis further illustrates the tractability of large data sets and supports a recent, phylogenetically based, ordinal‐level reclassification of the angiosperms based largely, but not exclusively, on molecular (DNA sequence) data.     

A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family

Phylogenetic analysis of 330 plastid matK gene sequences, representing 235 genera from 37 of 39 tribes, and four outgroup taxa from eurosids I supports many well-resolved subclades within the Leguminosae. These results are generally consistent with those derived from other plastid sequence data (rbcL and trnL), but show greater resolution and clade support overall. In particular, the monophyly of subfamily Papilionoideae and at least seven major subclades are well-supported by bootstrap and Bayesian credibility values. These subclades are informally recognized as the Cladrastis clade, genistoid sensu lato, dalbergioid sensu lato, mirbelioid, millettioid, and robinioid clades, and the inverted-repeat-lacking clade (IRLC). The genistoid clade is expanded to include genera such as Poecilanthe, Cyclolobium, Bowdichia, and Diplotropis and thus contains the vast majority of papilionoids known to produce quinolizidine alkaloids. The dalbergioid clade is expanded to include the tribe Amorpheae. The mirbelioids include the tribes Bossiaeeae and Mirbelieae, with Hypocalypteae as its sister group. The millettioids comprise two major subclades that roughly correspond to the tribes Millettieae and Phaseoleae and represent the only major papilionoid clade marked by a macromorphological apomorphy, pseudoracemose inflorescences. The robinioids are expanded to include Sesbania and members of the tribe Loteae. The IRLC, the most species-rich subclade, is sister to the robinioids. Analysis of the matK data consistently resolves but modestly supports a clade comprising papilionoid taxa that accumulate canavanine in the seeds. This suggests a single origin for the biosynthesis of this most commonly produced of the nonprotein amino acids in legumes.     

Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII

The ecological importance and diversity of pico/nanoplanktonic algae remains poorly studied in marine waters, in part because many are tiny and without distinctive morphological features. Amongst green algae, Mamiellophyceae such as Micromonas or Bathycoccus are dominant in coastal waters while prasinophytes clade VII, yet not formerly described, appear to be major players in open oceanic waters. The pigment composition of 14 strains representative of different subclades of clade VII was analyzed using a method that improves the separation of loroxanthin and neoxanthin. All the prasinophytes clade VII analyzed here showed a pigment composition similar to that previously reported for RCC287 corresponding to pigment group prasino‐2A. However, we detected in addition astaxanthin for which it is the first report in prasinophytes. Among the strains analyzed, the pigment signature is qualitatively similar within subclades A and B. By contrast, RCC3402 from subclade C (Picocystis) lacks loroxanthin, astaxanthin, and antheraxanthin but contains alloxanthin, diatoxanthin, and monadoxanthin that are usually found in diatoms or cryptophytes. For subclades A and B, loroxanthin was lowest at highest light irradiance suggesting a light‐harvesting role of this pigment in clade VII as in Tetraselmis.     

Comprehensive Genomic Analyses of the OM43 Clade,Including a Novel Species from the Red Sea,Indicate Ecotype Differentiation among Marine Methylotrophs

The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C₁ compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.     

How much can we know about the causes of evolutionary trends?

One of the first questions that paleontologists ask when they identify a large-scale trend in the fossil record (e.g., size increase, complexity increase) is whether it is passive or driven. In this article, I explore two questions about driven trends: (1) what is the underlying cause or source of the directional bias? and (2) has the strength of the directional bias changed over time? I identify two underdetermination problems that prevent scientists from giving complete answers to these two questions.     

Phylogeographic structure and regional history of Lemniscomys striatus (Rodentia: Muridae) in tropical Africa

Aim This study aims to elucidate the phylogeography of the murid rodent Lemniscomys striatus and to evaluate the relative roles of ecological change, habitat patchiness, rivers and geological barriers in structuring patterns of diversity. Location Sub‐Saharan Africa. Methods The extent of phylogeographic patterns and molecular genetic diversity (cytochrome b gene) were addressed in a survey of 128 individuals of L. striatus from 42 localities. Using maximum parsimony, maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intraspecific relationships and tested hypotheses for historical patterns of gene flow within L. striatus. Results Our results identified four major geographical clades within L. striatus: a West African clade, a Benin‐Nigeria clade, a Central African clade, and an East African clade. Several subclades were identified within these four major clades. Restricted gene flow with isolation by distance was recorded, which is congruent with the low dispersal ability of such a small murid rodent. No clear signal of population expansion was detected within clades or subclades. Main conclusions The western rift system and the Volta and Niger rivers may have acted as long‐term extrinsic barriers to gene flow, resulting in the emergence of the four main clades of L. striatus. The observed pattern of mitochondrial variation observed within each clade probably results from late Pleistocene climatic and vegetation changes: during adverse conditions (forest expansion), L. striatus may have survived only in refugia, and then experienced range expansion under favourable conditions (savanna expansion).     

The continuity of microevolution and macroevolution

A persistent debate in evolutionary biology is one over the continuity of microevolution and macroevolution – whether macroevolutionary trends are governed by the principles of microevolution. The opposition of evolutionary trends over different time scales is taken as evidence that selection is uncoupled over these scales. I argue that the paradox inferred by trend opposition is eliminated by a hierarchical application of the ‘geometric‐mean fitness’ principle, a principle that has been invoked only within the limited context of microevolution in response to environmental variance. This principle implies the elimination of well adapted genotypes – even those with the highest arithmetic mean fitness over a shorter time scale. Contingent on premises concerning the temporal structure of environmental variance, selectivity of extinction, and clade‐level heritability, the evolutionary outcome of major environmental change may be viewed as identical in principle to the outcome of minor environmental fluctuations over the short‐term. Trend reversals are thus recognized as a fundamental property of selection operating at any phylogenetic level that occur in response to event severities of any magnitude over all time scales. This ‘bet‐hedging’ perspective differs from others in that a specified, single hierarchical selective process is proposed to explain observed hierarchical patterns of extinction.     

The greening and browning of Alaska based on 1982–2003 satellite data

Aim To examine the trends of 1982–2003 satellite‐derived normalized difference vegetation index (NDVI) values at several spatial scales within tundra and boreal forest areas of Alaska. Location Arctic and subarctic Alaska. Methods Annual maximum NDVI data from the twice monthly Global Inventory Modelling and Mapping Studies (GIMMS) NDVI 1982–2003 data set with 64‐km² pixels were extracted from a spatial hierarchy including three large regions: ecoregion polygons within regions, ecozone polygons within boreal ecoregions and 100‐km climate station buffers. The 1982–2003 trends of mean annual maximum NDVI values within each area, and within individual pixels, were computed using simple linear regression. The relationship between NDVI and temperature and precipitation was investigated within climate station buffers. Results At the largest spatial scale of polar, boreal and maritime regions, the strongest trend was a negative trend in NDVI within the boreal region. At a finer scale of ecoregion polygons, there was a strong positive NDVI trend in cold arctic tundra areas, and a strong negative trend in interior boreal forest areas. Within boreal ecozone polygons, the weakest negative trends were from areas with a maritime climate or colder mountainous ecozones, while the strongest negative trends were from warmer basin ecozones. The trends from climate station buffers were similar to ecoregion trends, with no significant trends from Bering tundra buffers, significant increasing trends among arctic tundra buffers and significant decreasing trends among interior boreal forest buffers. The interannual variability of NDVI among the arctic tundra buffers was related to the previous summer warmth index. The spatial pattern of increasing tundra NDVI at the pixel level was related to the west‐to‐east spatial pattern in changing climate across arctic Alaska. There was no significant relationship between interannual NDVI and precipitation or temperature among the boreal forest buffers. The decreasing NDVI trend in interior boreal forests may be due to several factors including increased insect/disease infestations, reduced photosynthesis and a change in root/leaf carbon allocation in response to warmer and drier growing season climate. Main conclusions There was a contrast in trends of 1982–2003 annual maximum NDVI, with cold arctic tundra significantly increasing in NDVI and relatively warm and dry interior boreal forest areas consistently decreasing in NDVI. The annual maximum NDVI from arctic tundra areas was strongly related to a summer warmth index, while there were no significant relationships in boreal areas between annual maximum NDVI and precipitation or temperature. Annual maximum NDVI was not related to spring NDVI in either arctic tundra or boreal buffers.     

Desert salt flats as oases for the spider Saltonia incerta Banks (Araneae: Dictynidae)

The deserts of southwestern North America have undergone dramatic changes over their recent geological history including large changes in size and connectivity during the Pleistocene glaciopluvial cycles. This study examines the population history of the rare spider Saltonia incerta, once thought to be extinct, to determine the role of past climatological events in shaping the structure of the species. This species is restricted to salt crusts of intermittent or dry lakes, streams or rivers in the desert southwest, a region that was much wetter during glacial periods. We examine the distribution and genetic variability of populations to test whether there is recent dispersal throughout the range of the species. Analyses of mitochondrial and nuclear DNA indicate significant population structure, with one major clade comprising New Mexico localities and one comprising California‐northern Baja California localities. Finer‐scale structure is evident within the California clade, although not all of the subclades are reciprocally monophyletic. However, isolation with migration analysis suggests that migration is very low to non‐existent. These results extend the known distribution of Saltonia, provide genetic evidence of strong isolation among localities within drainage basins and between drainage basins and provide a mechanistic understanding of population connectivity after the aridification of the American southwest. The implication is that although the species' distribution has been fragmented, populations have persisted throughout this area, suggesting that desert salt flats may have served as refugia for at least some terrestrial species.     

The roles of rivers and Pleistocene refugia in shaping genetic diversity in Praomys misonnei in tropical Africa

Aim This study aims to elucidate the phylogeography of the murid rodent Praomys misonnei and to document whether or not rain forest refugia and rivers structure patterns of diversity within this species. Location Tropical Africa, from Ghana to Kenya. Methods Patterns of genetic structure and signatures of population history (cytochrome b gene) were assessed in a survey of 229 individuals from 54 localities. Using maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intra‐specific relationships and tested hypotheses for historical patterns of gene flow within P. misonnei. Results Our phylogenetic analyses reveal a strong phylogeographical structure. We identified four major geographical clades within P. misonnei: one clade in Ghana and Benin, a Nigerian clade, a West Central African clade and a Central and East African clade. Several subclades were identified within these four major clades. A signal of population expansion was detected in most clades or subclades. Coalescence within all of the major clades of P. misonnei occurred during the Middle Pleistocene and/or the beginning of Late Pleistocene. Main conclusions Our results suggest a role for both Pleistocene refugia and rivers in structuring genetic diversity in P. misonnei. This forest‐dwelling rodent may have been isolated in a number of forest fragments during arid periods and expanded its range during wetter periods. Potential forest refugia may have been localized in Benin–Ghana, south‐western Cameroon, southern Gabon, northern Gabon and eastern Democratic Republic of Congo–western Uganda. The Niger and/or the Cross Rivers, the Oubangui‐Congo, Sanaga, Ogooue and/or Ivindo Rivers probably stopped the re‐expansion of the species from relict areas.     

PHYLOGENY OF THE EUGLENOID LORICATE GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) INFERRED FROM NUCLEAR SSU AND LSU rDNA1

Previous studies using the nuclear SSU rDNA and partial LSU rDNA have demonstrated that the euglenoid loricate taxa form a monophyletic clade within the photosynthetic euglenoid lineage. It was unclear, however, whether the loricate genera Trachelomonas and Strombomonas were monophyletic. In order to determine the relationships among the loricate taxa, SSU and LSU nuclear rDNA sequences were obtained for eight Strombomonas and 25 Trachelomonas strains and combined in a multigene phylogenetic analysis. Conserved regions of the aligned data set were used to generate maximum‐likelihood (ML) and Bayesian phylogenies. Both methods recovered a strongly supported monophyletic loricate clade with Strombomonas and Trachelomonas species separated into two sister clades. Taxa in the genus Strombomonas sorted into three subclades. Within the genus Trachelomonas, five strongly supported subclades were recovered in all analyses. Key morphological features could be attributed to each of the subclades, with the major separation being that all of the spine‐bearing taxa were located in two sister subclades, while the more rounded, spineless taxa formed the remaining three subclades. The separation of genera and subclades was supported by 42 distinct molecular signatures (33 in Trachelomonas and nine in Strombomonas). The morphological and molecular data supported the retention of Trachelomonas and Strombomonas as separate loricate genera.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Trend changes in global greening and browning: contribution of short‐term trends to longer‐term change

Field observations and time series of vegetation greenness data from satellites provide evidence of changes in terrestrial vegetation activity over the past decades for several regions in the world. Changes in vegetation greenness over time may consist of an alternating sequence of greening and/or browning periods. This study examined this effect using detection of trend changes in normalized difference vegetation index (NDVI) satellite data between 1982 and 2008. Time series of 648 fortnightly images were analyzed using a trend breaks analysis (BFAST) procedure. Both abrupt and gradual changes were detected in large parts of the world, especially in (semi‐arid) shrubland and grassland biomes where abrupt greening was often followed by gradual browning. Many abrupt changes were found around large‐scale natural influences like the Mt Pinatubo eruption in 1991 and the strong 1997/98 El Niño event. The net global figure – considered over the full length of the time series – showed greening since the 1980s. This is in line with previous studies, but the change rates for individual short‐term segments were found to be up to five times higher. Temporal analysis indicated that the area with browning trends increased over time while the area with greening trends decreased. The Southern Hemisphere showed the strongest evidence of browning. Here, periods of gradual browning were generally longer than periods of gradual greening. Net greening was detected in all biomes, most conspicuously in croplands and least conspicuously in needleleaf forests. For 15% of the global land area, trends were found to change between greening and browning within the analysis period. This demonstrates the importance of accounting for trend changes when analyzing long‐term NDVI time series.     

European freshwater VHSV genotype Ia isolates divide into two distinct subpopulations

Viral haemorrhagic septicaemia (VHS), caused by the novirhabdovirus VHSV, often leads to significant economic losses to European rainbow trout production. The virus isolates are divided into 4 distinct genotypes with additional subgroups including sublineage Ia, isolates of which are the main source of outbreaks in European rainbow trout farming. A significant portion of Danish rainbow trout farms have been considered endemically infected with VHSV since the first disease outbreak was observed in the 1950s. However, following a series of sanitary programs starting in 1965, VHSV has not been detected in Denmark since January 2009. Full-length G-genes of all Danish VHSV isolates that were submitted for diagnostic analyses in the period 2004-2009 were sequenced and analysed. All 58 Danish isolates from rainbow trout grouped with sublineage Ia isolates. Furthermore, VHSV isolates from infected Danish freshwater catchments appear to have evolved into a distinct clade within sublineage Ia, herein designated clade Ia-1, whereas trout isolates originating from other continental European countries cluster in another distinct clade, designated clade Ia-2. In addition, phylogenetic analyses indicate that VHSV Ia-1 strains have caused a few outbreaks in Germany and the UK. It is likely that viruses have been transmitted from infected site(s) out of the Danish environment, although a direct transmission pathway has not been identified. Furthermore, VHSV Ia-2 isolates seem to have been transmitted to Denmark at least once. Interestingly, one viral isolate possibly persisted in a Danish watershed for nearly 4 yr without detection whereas other subclades of VHSV isolates appear to have been eliminated, probably because of implemented eradication procedures.     

On the evolution and diversification of an Andean clade of reptiles: combining morphology and DNA sequences of the palluma group (Liolaemidae: Phymaturus)

Phymaturus comprises 44 species mainly distributed along the south‐west of South America on both sides of the Andes. In this study we present a phylogenetic analysis of Phymaturus of the palluma group, one of its two large clades, including almost all described species. This analysis duplicates the number of in‐group taxa compared with previous contributions. We performed a total‐evidence analysis, combining molecular and morphological characters: sequencing fragments of cytochome b (cytb), 12S, and ND4, for all terminals; describing 45 new morphological characters; and incorporating all DNA sequences available from GenBank. Separate analyses of morphology and DNA partitions are presented and discussed in detail. Seven subclades are recognized here. We named three new subclades and redefined another, found to be paraphyletic. In order to recognize lineages within the traditional Phymaturus palluma group we proposed to treat it as a natural group, containing within it the ranks of clade, subclade, and lineages, respectively. The palluma group is composed by the vociferator and the bibronii clades. The vociferator clade, composed of Chilean and Argentinean species, would be the most basal in the group. Within the bibronii clade, the roigorum subclade includes the Phymaturus verdugo lineage, whereas the mallimaccii subclade would consist of 13 terminal taxa, for which three Chilean species have been added. In this study, morphological apomorphies are identified for all clades and the evolution of ‘male head melanism’ is discussed. © 2015 The Linnean Society of London