Phylogenetic Relationships of the Mutualistic Fungi Associated with Macrotermes subhyalinus in Oman

The symbiotic association between fungus-gardening termites Macrotermes and its fungal symbiont has a moderate degree of specificity-although the symbiotic fungi (Termitomyces) form a monophyletic clade, there is not a one-to-one association between termite species and their fungus-garden associates. Here, we aim to determine the origin and phylogenetic relationships of Termitomyces in Oman. We used sequences of the internal transcribed spacer region (ITS) and the nuclear large subunit ribosomal RNA (LSU rRNA, 25S) gene and analyzed these with sequences of Termitomyces from other geographic areas. We find no evidence for more than a single colonization of Oman by Termitomyces. Unexpectedly, we find Termitomyces in Oman is most closely related to the symbiont of M. subhyalinus in West Africa rather than to those of geographically closer populations in East Africa.

Host phylogeny and ecological associations best explain Wolbachia host shifts in scale insects

Wolbachia are among the most prevalent and widespread endosymbiotic bacteria on Earth. Wolbachia's success in infecting an enormous number of arthropod species is attributed to two features: the range of phenotypes they induce in their hosts, and their ability to switch between host species. Whilst much progress has been made in elucidating their induced phenotypes, our understanding of Wolbachia host-shifting is still very limited: we lack answers to even fundamental questions concerning Wolbachia's routes of transfer and the importance of factors influencing host shifts. Here, we investigate the diversity and host-shift patterns of Wolbachia in scale insects, a group of arthropods with intimate associations with other insects that make them well suited to studying host shifts. Using Illumina multitarget amplicon sequencing of Wolbachia-infected scale insects and their direct associates we determined the identity of all Wolbachia strains. We then fitted a generalized additive mixed model to our data to estimate the influence of host phylogeny and the geographical distribution on Wolbachia strain sharing among scale insect species. The model predicts no significant contribution of host geography but strong effects of host phylogeny, with high rates of Wolbachia sharing among closely related species and a sudden drop-off in sharing with increasing phylogenetic distance. We also detected the same Wolbachia strain in scale insects and several intimately associated species (ants, wasps and flies). This indicates putative host shifts and potential routes of transfers via these associates and highlights the importance of ecological connectivity in Wolbachia host-shifting.

Wolbachia in scale insects: a distinct pattern of infection frequencies and potential transfer routes via ant associates

Wolbachia is one of the most successful endosymbiotic bacteria of arthropods. Known as the 'master of manipulation', Wolbachia can induce a wide range of phenotypes in its host that can have far-reaching ecological and evolutionary consequences and may be exploited for disease and pest control. However, our knowledge of Wolbachia's distribution and the infection rate is unevenly distributed across arthropod groups such as scale insects. We fitted a distribution of within-species prevalence of Wolbachia to our data and compared it to distributions fitted to an up-to-date dataset compiled from surveys across all arthropods. The estimated distribution parameters indicate a Wolbachia infection frequency of 43.6% (at a 10% prevalence threshold) in scale insects. Prevalence of Wolbachia in scale insects follows a distribution similar to exponential decline (most species are predicted to have low prevalence infections), in contrast to the U-shaped distribution estimated for other taxa (most species have a very low or very high prevalence). We observed no significant associations between Wolbachia infection and scale insect traits. Finally, we screened for Wolbachia in scale insect's ecological associates. We found a positive correlation between Wolbachia infection in scale insects and their ant associates, pointing to a possible route of horizontal transfer of Wolbachia.

Turnover of southern cypresses in the post-Gondwanan world: extinction, transoceanic dispersal, adaptation and rediversification

Cupressaceae subfamily Callitroideae has been an important exemplar for vicariance biogeography, but its history is more than just disjunctions resulting from continental drift. We combine fossil and molecular data to better assess its extinction and, sometimes, rediversification after past global change. Key fossils were reassessed and their phylogenetic placement for calibration was determined using trait mapping and Bayes Factors. Five vicariance hypotheses were tested by comparing molecular divergence times with the timing of tectonic rifting. The role of adaptation to fire (serotiny) in its spread across a drying Australia was tested for Callitris. Our findings suggest that three transoceanic disjunctions within the Callitroideae probably arose from long-distance dispersal. A signature of extinction, centred on the end-Eocene global climatic chilling and drying, is evident in lineages-through-time plots and in the fossil record. Callitris, the most diverse extant callitroid genus, suffered extinctions but surviving lineages adapted and re-radiated into dry, fire-prone biomes that expanded in the Neogene. Serotiny, a key adaptation to fire, likely evolved in Callitris coincident with the biome shift. Both extinction and adaptive shifts have probably played major roles in this chronicle of turnover and renewal, but better understanding of biogeographical history requires improved taxonomy of fossils.

A newly recognised species of Cryptes Maskell 1892 (Hemiptera: Coccidae) from Western Australia

Cryptes utzoni Lin, Kondo Cook sp. n. (Hemiptera: Coccidae) is described based on adult female morphology and DNA sequences from mitochondrial and nuclear loci. This Australian endemic species was found on the stem of Acacia aneura (Fabaceae) in Western Australia. All phylogenetic analyses of three independent DNA loci show that C. utzoni is closely related to C. baccatus (Maskell), the type and only species of Cryptes Maskell, 1892. The adult female of C. utzoni is described and illustrated and a table is provided of the characters that differ among adult females of the two species of Cryptes now recognised (C. baccatus and C. utzoni) and a morphologically similar Western Australian species, Austrolichtensia hakearum (Fuller). There is deep genetic divergence in COI among samples of C. baccatus, suggesting the possibility of a species complex in this taxon.

A newly recognised Australian endemic species of Austrolecanium Gullan & Hodgson 1998 (Hemiptera: Coccidae) from Queensland

Austrolecanium cryptocaryae Lin & Cook sp. n. is described based on adult female morphology and DNA sequences from mitochondrial and nuclear loci. This Australian endemic species was found on the underside of leaves of Cryptocarya microneura (Lauraceae) in Queensland. All phylogenetic analyses of four independent DNA loci and a concatenated dataset show that A. cryptocaryae is monophyletic and closely related to A. sassafras Gullan & Hodgson, the type species of Austrolecanium Gullan & Hodgson. The adult female of A. cryptocaryae is described and illustrated and a table is provided of the characters that differ among adult females of the three species of Austrolecanium currently recognised (A. cappari (Froggatt), A. cryptocaryae sp. n. and A. sassafras).

Congruent biogeographical disjunctions at a continent-wide scale: Quantifying and clarifying the role of biogeographic barriers in the Australian tropics

AIM

To test whether novel and previously hypothesized biogeogaphic barriers in the Australian Tropics represent significant disjunction points or hard barriers, or both, to the distribution of plants.

LOCATION

Australian tropics: Australian Monsoon Tropics and Australian Wet Tropics.

METHODS

The presence or absence of 6,861 plant species was scored across 13 putative biogeographic barriers in the Australian Tropics, including two that have not previously been recognised. Randomizations of these data were used to test whether more species showed disjunctions (gaps in distribution) or likely barriers (range limits) at these points than expected by chance.

RESULTS

Two novel disjunctions in the Australian Tropics flora are identified in addition to eleven putative barriers previously recognized for animals. Of these, eleven disjunction points (all within the Australian Monsoon Tropics) were found to correspond to range-ending barriers to a significant number of species, while neither of the two disjunctions found within the Australian Wet Tropics limited a significant number of species' ranges.

MAIN CONCLUSIONS

Biogeographic barriers present significant distributional limits to native plant species in the Australian Monsoon Tropics but not in the Australian Wet Tropics.

A review of the genus Capulinia Signoret (Hemiptera: Coccoidea: Eriococcidae) with description of two new species

The eriococcid genus Capulinia Signoret currently comprises four Neotropical species (the type species C. sallei Signoret, C. crateraformis Hempel, C. jaboticabae Ihering and an undescribed species recognised in the literature) and one species from New Zealand (C. orbiculata Hoy). All species feed on plants in the family Myrtaceae and the undescribed species is a pest of guava, Psidium guajava, in Venezuela and Colombia. Here we describe the pest species based on the adult female and first-instar nymph and name it Capulinia linarosae Kondo & Gullan sp. n. We provide a summary of published information on the biology and pest status of C. linarosae by translating the Spanish literature. We also describe the adult female and first-instar nymph of a new Argentine species that we name as C. luma Kondo & Gullan sp. n. after its host Luma apiculata. In addition, we redescribe the adult female of C. jaboticabae and include notes on C. crateraformis, C. orbiculata and C. sallei. We provide a revised generic diagnosis and keys to all Capulinia species based on adult females and, where available, first-instar nymphs, as well as a revised key to South American eriococcid genera. Phylogenetic analyses of 18S rDNA place Capulinia within the "Gondwanan" clade of eriococcids, mostly likely within the Myrtaceae-feeding group.

Two recently discovered species of Apiomorpha (Hemiptera: Eriococcidae) feeding on eudesmid eucalypts in Western Australia reaffirm host conservatism in this gall-inducing scale insect genus

Gall-inducing insects are relatively host-specific compared with their non-galling relatives. In Australia, there have been at least four origins of gall induction among eriococcid scale insects, with the most species-rich genus, Apiomorpha, inducing galls only on species of Eucalyptus. Here we describe two recently discovered species of Apiomorpha that induce galls on eudesmid eucalypts in Western Australia: Apiomorpha gongylocarpae, sp. nov., which is very similar morphologically to A. pomaphora, and A. jucundacrispi, sp. nov., the adult females of which induce an unusual gall covered in woody protrusions that, when older, have a knobbly appearance. Using molecular, morphological and host-association data, we show that these two species form a monophyletic group with the only other species of Apiomorpha that feed on eudesmid eucalypts (A. hilli and A. pomaphora). We place all four species of eudesmid-feeding Apiomorpha in the A. hilli species group, thus revising the current placement of A. pomaphora by removing it from the A. malleeacola species group. This study highlights additional faunal diversity endemic to Western Australia, with two of the four species being restricted to the globally recognised biodiversity hotspot of the South West Australia Floristic Region. http://zoobank.org/urn:lsid:zoobank.org:pub:D6245EB6-903E-483C-B69B-3ED7EA35AD04.

Key innovation or adaptive change? A test of leaf traits using Triodiinae in Australia

The evolution of novel traits ("key innovations") allows some lineages to move into new environments or adapt to changing climates, whereas other lineages may track suitable habitat or go extinct. We test whether, and how, trait shifts are linked to environmental change using Triodiinae, C4 grasses that form the dominant understory over about 30% of Australia. Using phylogenetic and relaxed molecular clock estimates, we assess the Australian biogeographic origins of Triodiinae and reconstruct the evolution of stomatal and vascular bundle positioning. Triodiinae diversified from the mid-Miocene, coincident with the aridification of Australia. Subsequent niche shifts have been mostly from the Eremaean biome to the savannah, coincident with the expansion of the latter. Biome shifts are correlated with changes in leaf anatomy and radiations within Triodiinae are largely regional. Symplectrodia and Monodia are nested within Triodia. Rather than enabling biome shifts, convergent changes in leaf anatomy have probably occurred after taxa moved into the savannah biome-they are likely to have been subsequent adaptions rather than key innovations. Our study highlights the importance of testing the timing and origin of traits assumed to be phenotypic innovations that enabled ecological shifts.

Three explanations for biodiversity hotspots: small range size, geographical overlap and time for species accumulation. An Australian case study

To understand the generation and maintenance of biodiversity hotspots, we tested three major hypotheses: rates of diversification, ecological limits to diversity, and time for species accumulation. Using dated molecular phylogenies, measures of species' range size and geographical clade overlap, niche modelling, and lineages-through-time plots of Australian Fabaceae, we compared the southwest Australia Floristic Region (SWAFR; a global biodiversity hotspot) with a latitudinally equivalent non-hotspot, southeast Australia (SEA). Ranges of species (real and simulated) were smaller in the SWAFR than in SEA. Geographical overlap of clades was significantly greater for Daviesia in the SWAFR than in SEA, but the inverse for Bossiaea. Lineage diversification rates over the past 10 Myr did not differ between the SWAFR and SEA in either genus. Interaction of multiple factors probably explains the differences in measured diversity between the two regions. Steeper climatic gradients in the SWAFR probably explain the smaller geographical ranges of both genera there. Greater geographical overlap of clades in the SWAFR, combined with a longer time in the region, can explain why Daviesia is far more species-rich there than in SEA. Our results indicate that the time for speciation and ecological limits hypotheses, in concert, can explain the differences in biodiversity.

Systematic review of the Australian ‘bush-coconut’ genus Cystococcus (Hemiptera: Eriococcidae) uncovers a new species from Queensland

Australia houses some unusual biota (insects included), much of which is undescribed. Cystococcus Fuller (Hemiptera : Sternorrhyncha : Coccoidea : Eriococcidae) currently comprises two species, both of which induce galls exclusively on bloodwoods (Myrtaceae: Corymbia Hill & Johnson). These insects display sexual dichronism, whereby females give birth first to sons and then to daughters. Wingless first-instar females cling to their winged adult brothers and are carried out of the maternal gall when the males fly to find mates – a behaviour called intersexual phoresy. Here, we use data from two gene regions, as well as morphology and host-use of the insects, to assess the status of a previously undescribed species. We describe this newly recognised species as Cystococcus campanidorsalis, sp. nov. Semple, Cook & Hodgson, redescribe the two existing species – C. echiniformis Fuller and C. pomiformis (Froggatt), designate a lectotype for C. echiniformis, and provide the first descriptions of adult males, and nymphal males and females for the genus. We have also reinterpreted a key morphological character of the adult females. This paper provides a foundation for further work on the genus, which is widespread across northern Australia and could prove to be useful for studies on biogeography and bloodwood ecosystems. urn:lsid:zoobank.org:pub:3A9DC645-0CBC-48B0-8BD3-5ACC0E2130D1

Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees

BACKGROUND

Estimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimates, especially in lineages with long stems and short crowns ("broom" clades) and no internal calibration. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift occurs on the stem branch of a broom clade. We compare the results of simulations to empirical results from analyses of a real rate-heterogeneous taxon - Australian grass trees (Xanthorrhoea) - whose substitution rate is slower than in its sister groups, as determined by relative rate tests.

RESULTS

In the simulated datasets, the RLC model performed much better than UCLN: RLC correctly estimated the age of the crown node of slow-rate broom clades, whereas UCLN estimates were consistently too young. Similarly, in the Xanthorrhoea dataset, UCLN returned significantly younger crown ages than RLC (mean estimates respectively 3-6 Ma versus 25-35 Ma). In both real and simulated datasets, Bayes Factor tests strongly favored the RLC model over the UCLN model.

CONCLUSIONS

The choice of an unsuitable molecular clock model can strongly bias divergence time estimates. In particular, for data predicted to have more rate variation among than within clades, dating with RLC is much more likely to be accurate than with UCLN. The choice of clocks should be informed by the biology of the study group (e.g., life-form) or assessed with relative rate tests and post-hoc model comparisons.

Rapid chromosomal evolution in a morphologically cryptic radiation

Cryptic species occur within most of the major taxonomic divisions, and a current challenge is to determine why some lineages have more cryptic species than others. It is expected that cryptic species are more common in groups where there are life histories or genetic architectures that promote speciation in the absence of apparent morphological differentiation. Chromosomal rearrangements have the potential to lead to post-zygotic isolation and might be an important factor leading to cryptic species. Here we investigate the potential role of chromosomal change in driving speciation in the karyotypically diverse scale insect genus Apiomorpha, focussing on four species placed in the same species group (the A. minor species group Gullan, 1984). Using mitochondrial and nuclear DNA sequence data, we find that Apiomorpha minor is not monophyletic and consists of at least nine cryptic species. Diploid chromosome counts range from 2n=4 to 2n=84 across the four currently recognized species, and some of the chromosomal variation exists in the absence of other genetic or host use differences, consistent with karyotypic changes being involved in lineage divergence and the generation of cryptic species.

Evolutionary consequences of shifts to bird-pollination in the Australian pea-flowered legumes (Mirbelieae and Bossiaeeae)

BACKGROUND

Interactions with pollinators are proposed to be one of the major drivers of diversity in angiosperms. Specialised interactions with pollinators can lead to specialised floral traits, which collectively are known as a pollination syndrome. While it is thought that specialisation to a pollinator can lead to either an increase in diversity or in some cases a dead end, it is not well understood how transitions among specialised pollinators contribute to changes in diversity. Here, we use evolutionary trait reconstruction of bee-pollination and bird-pollination syndromes in Australian egg-and-bacon peas (Mirbelieae and Bossiaeeae) to test whether transitions between pollination syndromes is correlated with changes in species diversity. We also test for directionality in transitions that might be caused by selection by pollinators or by an evolutionary ratchet in which reversals to the original pollination syndrome are not possible.

RESULTS

Trait reconstructions of Australian egg-and-bacon peas suggest that bee-pollination syndrome is the ancestral form and that there has been replicated evolution of bird-pollination syndromes. Reconstructions indicate potential reversals from bird- to bee-pollination syndromes but this is not consistent with morphology. Species diversity of bird-pollination syndrome clades is lower than that of their bee-pollination syndrome sisters.We estimated the earliest transitions from bee- to bird-pollination syndrome occurred between 30.8 Ma and 10.4 Ma. Geographical structuring of pollination syndromes was found; there were fewer bird-pollination species in the Australian southeast temperate region compared to other regions of Australia.

CONCLUSIONS

A consistent decrease in diversification rate coincident with switches to bird pollination might be explained if greater dispersal by bird pollinators results in higher levels of connectivity among populations and reduced chances of allopatric speciation.The earliest transitions overlap with the early diversification of Australian honeyeaters - the major lineage of pollinating birds in Australia. Our findings are consistent with the idea that environment and availability of pollinators are important in the evolution of pollination syndromes. Changes in flower traits as a result of transitions to bird-pollination syndrome might also limit reversals to a bee-pollination syndrome.

Matsucoccus macrocicatrices (Hemiptera: Matsucoccidae): first report, distribution, and association with symptomatic eastern white pine in the southeastern United States

We provide the first report of Matsucoccus macrocicatrices Richards (Hemiptera: Matsucoccidae) feeding and reproducing on eastern white pine, Pinus strobus L., in the southeastern United States. Until now, M. macrocicatrices had been reported only from the Canadian Atlantic Maritimes, New Hampshire, and Massachusetts. Entomological holdings of 27 major museums in eastern North America have no historical records for M. macrocicatrices from the southeastern region. However, our field surveys and molecular analyses (DNA barcoding) have resulted in the collection and positive identification of M. macrocicatrices in Georgia, North Carolina, South Carolina, Tennessee, Virginia, and West Virginia In addition to the new geographic range, M. macrocicatrices is also being associated with dieback and mortality of all diameter classes of P. strobus leading to concern about a potential shift from its historically nonpestiferous presence on the host tree. On P. strobus, M. macrocicatrices was found embedded in cankers or present on top of the bark with necrotic tissue under their feeding area, indicating that they may be creating wounds for opportunistic pathogenic fungi to infest. Further, we found M. macrocicatrices living outside of the epiphytic mats of its symbiotic fungus, Septobasidium pinicola Snell. This study shows that M. macrocicatrices is now widespread in the southeastern United States, with implications for the future survival and regeneration of P. strobus in eastern North America.

Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes?

Phylogenetic niche conservatism (PNC) is the tendency of lineages to retain their niche-related traits through speciation events. A recent surge in the availability of well-sampled molecular phylogenies has stimulated phylogenetic approaches to understanding ecological processes at large geographical scales and through macroevolutionary time. We stress that PNC is a pattern, not a process, and is found only in some traits and some lineages. At the simplest level, a pattern of PNC is an inevitable consequence of evolution - descent with modification and divergence of lineages - but several intrinsic causes, including physicochemical, developmental and genetic constraints, can lead directly to a marked pattern of PNC. A pattern of PNC can also be caused indirectly, as a by-product of other causes, such as extinction, dispersal limitation, competition and predation. Recognition of patterns of PNC can contribute to understanding macroevolutionary processes: for example, release from constraint in traits has been hypothesized to trigger adaptive radiations such as that of the angiosperms. Given the multiple causes of patterns of PNC, tests should address explicit questions about hypothesized processes. We conclude that PNC is a scientifically useful concept with applications to the practice of ecological research.

Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms

We test the widely held notion that living gymnosperms are 'ancient' and 'living fossils' by comparing them with their sister group, the angiosperms. This perception derives partly from the lack of gross morphological differences between some Mesozoic gymnosperm fossils and their living relatives (e.g. Ginkgo, cycads and dawn redwood), suggesting that the rate of evolution of gymnosperms has been slow. We estimated the ages and diversification rates of gymnosperm lineages using Bayesian relaxed molecular clock dating calibrated with 21 fossils, based on the phylogenetic analysis of alignments of matK chloroplast DNA (cpDNA) and 26S nuclear ribosomal DNA (nrDNA) sequences, and compared these with published estimates for angiosperms. Gymnosperm crown groups of Cenozoic age are significantly younger than their angiosperm counterparts (median age: 32 Ma vs 50 Ma) and have long unbranched stems, indicating major extinctions in the Cenozoic, in contrast with angiosperms. Surviving gymnosperm genera have diversified more slowly than angiosperms during the Neogene as a result of their higher extinction rate. Compared with angiosperms, living gymnosperm groups are not ancient. The fossil record also indicates that gymnosperms suffered major extinctions when climate changed in the Oligocene and Miocene. Extant gymnosperm groups occupy diverse habitats and some probably survived after making adaptive shifts.

Testing the effect of transient Plio-Pleistocene barriers in monsoonal Australo-Papua: did mangrove habitats maintain genetic connectivity in the Black Butcherbird?

Changes in climate and sea level are hypothesized to have promoted the diversification of biota in monsoonal Australia and New Guinea by causing repeated range disjunctions and restricting gene flow between isolated populations. Using a multilocus (one mtDNA locus, five nuclear introns) phylogeographic approach, we test whether populations of the mangrove and rainforest restricted Black Butcherbird (Cracticus quoyi) have diverged across several geographic barriers defined a priori for this region. Phylogeographic structure and estimates of divergence times revealed Plio-Pleistocene divergences and long-term restricted gene flow of populations on either side of four major geographic barriers between and within Australia and New Guinea. Overall, our data are consistent with the hypothesis that mesic-adapted species did not disperse across the open dry woodlands and grasslands that dominated the transient palaeo-landbridges during the Plio-Pleistocene despite the presence of mangrove forests that might have acted as dispersal corridors for mesic-adapted species. Our study offers one of the first multilocus perspectives on the impact of changes in climate and sea level on the population history of widespread species with disjunct ranges in Australia and New Guinea.

Gall-induction in insects: evolutionary dead-end or speciation driver?

Background

The tree of life is significantly asymmetrical - a result of differential speciation and extinction - but general causes of such asymmetry are unclear. Differences in niche partitioning are thought to be one possible general explanation. Ecological specialization might lead to increases in diversification rate or, alternatively, specialization might limit the evolutionary potential of specialist lineages and increase their extinction risk. Here we compare the diversification rates of gall-inducing and non-galling insect lineages. Compared with other insect herbivores feeding on the same host plant, gall-inducing insects feed on plant tissue that is more nutritious and less defended, and they do so in a favorable microhabitat that may also provide some protection from natural enemies. We use sister-taxon comparisons to test whether gall-inducing lineages are more host-specific than non-galling lineages, and more or less diverse than non-gallers. We evaluate the significance of diversity bipartitions under Equal Rates Markov models, and use maximum likelihood model-fitting to test for shifts in diversification rates.

Results

We find that, although gall-inducing insect groups are more host-specific than their non-galling relatives, there is no general significant increase in diversification rate in gallers. However, gallers are found at both extremes - two gall-inducing lineages are exceptionally diverse (Euurina sawflies on Salicaceae and Apiomorpha scale insects on Eucalytpus), and one gall-inducing lineage is exceptionally species-poor (Maskellia armored scales on Eucalyptus).

Conclusions

The effect of ecological specialization on diversification rates is complex in the case of gall-inducing insects, but host range may be an important factor. When a gall-inducing lineage has a host range approximate to that of its non-galling sister, the gallers are more diverse. When the non-galler clade has a much wider host range than the galler, the non-galler is also much more diverse. There are also lineage-specific effects, with gallers on the same host group exhibiting very different diversities. No single general model explains the observed pattern.

Tree thinking for all biology: the problem with reading phylogenies as ladders of progress

Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved "tree thinking" is crucial. The most-serious problem comes from reading trees as ladders from "left to right"--many biologists assume that species-poor lineages that appear "early branching" or "basal" are ancestral--we call this the "primitive lineage fallacy". This mistake causes misleading inferences about changes in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21(st) century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19(th) century notions about the ladder of progress driving evolution.

Relationships among felt scale insects (Hemiptera:Coccoidea:Eriococcidae) of southern beech, Nothofagus (Nothofagaceae), with the first descriptions of Australian species of the Nothofagus-feeding genus Madarococcus Hoy

Species of southern beech (Nothofagus) have been studied extensively because of their importance in understanding southern hemisphere biogeography. Nothofagus species support a diverse assemblage of insect herbivores, including more than 30 described species of felt scales (Eriococcidae). We reconstructed the phylogeny of the Nothofagus-feeding felt scales with nucleotide sequence data and morphology. All but one of the exclusively Nothofagus-feeding species included in the analyses were recovered as a monophyletic group. This clade comprised the genera Chilechiton Hodgson & Miller, Chilecoccus Miller & González, Intecticoccus Kondo, Madarococcus Hoy (except for M. totorae Hoy), Sisyrococcus Hoy and several species of the genus Eriococcus Targioni Tozzetti. The genera Eriococcus and Madarococcus were not recovered as monophyletic. Here we revise Madarococcus. We expand the concept of the genus, provide a key to the adult females of the 31 species of Madarococcus and, for each named species, provide revised synonymies and any new collection or taxonomic information. We recognise the genus from Australia for the first time and describe the adult females of six new Australian species: Madarococcus cunninghamii Hardy & Gullan, sp. nov.; M. meander Hardy & Gullan, sp. nov.; M. megaventris Hardy & Gullan, sp. nov.; M. moorei Hardy & Gullan, sp. nov.; M. occultus Hardy & Gullan, sp. nov., and M. osculus Hardy & Gullan, sp. nov. We also describe the first-instar nymphs of M. cunninghamii, sp. nov., M. meander, sp. nov. and M. moorei, sp. nov. We transfer 17 species into Madarococcus from Eriococcus: M. argentifagi (Hoy), comb. nov.; M. cavellii (Maskell), comb. nov.; M. chilensis (Miller & González), comb. nov.; M. detectus (Hoy), comb. nov.; M. eurythrix (Miller & González), comb. nov.; M. fagicorticis (Maskell), comb. nov.; M. hispidus (Hoy), comb. nov.; M. latilobatus (Hoy), comb. nov.; M. maskelli, (Hoy), comb. nov.; M. montifagi (Hoy), comb. nov.; M. navarinoensis (Miller & González), comb. nov.; M. nelsonensis (Hoy), comb. nov.; M. nothofagi (Hoy), comb. nov.; M. podocarpi (Hoy), comb. nov.; M. raithbyi (Maskell), comb. nov.; M. rotundus (Hoy), comb. nov. and M. rubrifagi (Hoy), comb. nov. We transfer two species from Sisyrococcus into Madarococcus: M. intermedius (Maskell), comb. nov. and M. papillosus (Hoy), comb. nov. One species, M. totarae (Maskell), is excluded from Madarococcus, but cannot at present be placed in another genus and is listed as ‘M.’ totarae incertae sedis. We report the first collection of an eriococcid, M. osculus, sp. nov., on the deciduous beech, Nothofagus gunnii. With respect to biogeography, the results of our phylogenetic analysis are congruent with those obtained from recent analysis of Nothofagus; Australian and New Zealand species of Madarococcus form a monophyletic group to the exclusion of the South American species, suggesting that long-distance dispersal has played an important role in shaping the distributions of both the Nothofagus-feeding felt scales and their hosts.

A congruent molecular signature of vicariance across multiple plant lineages

Explaining disjunct distributions, or why closely related organisms are often separated by apparently severe barriers such as oceans or deserts, is a great challenge for historical biogeography. Competing explanations are long-distance dispersal across a barrier, and vicariance, in which disjunct taxa are descended from an ancestral population that was split by formation of the barrier. Vicariance explanations are testable by their prediction that near-simultaneous speciation should have occurred across multiple lineages of organisms between the disjunct areas because the origin of a barrier would potentially disrupt gene flow within multiple species. To date, there have been few studies providing evidence for multiple synchronous ancient divergences across a barrier whose origin coincides with the timing of the speciation events. Here, we use relaxed molecular-clock dating to investigate the timing of south-western (SW) versus south-eastern (SE) divergences in 23 pairs of plant lineages in southern Australia. Sixteen of the divergences correlate with the origin, 13-14 million years (Myr) ago, of the arid treeless Nullarbor Plain. The Nullarbor Plain currently forms a substantial barrier to SW-SE migration but during the last 45Myr this region has experienced multiple episodes of marine inundation and subaerial exposure. Thus, there have been multiple events that could have caused either isolation and speciation, or secondary contact, among the taxa of southern Australia. The strong molecular signal of coincident speciation in many diverse lineages during a short period provides the best evidence to date linking synchronous speciation to an ancient vicariance event.

Not so ancient: the extant crown group of Nothofagus represents a post-Gondwanan radiation

This study uses a molecular-dating approach to test hypotheses about the biogeography of Nothofagus. The molecular modelling suggests that the present-day subgenera and species date from a radiation that most likely commenced between 55 and 40 Myr ago. This rules out the possibility of a reconciled all-vicariance hypothesis for the biogeography of extant Nothofagus. However, the molecular dates for divergences between Australasian and South American taxa are consistent with the rifting of Australia and South America from Antarctica. The molecular dates further suggest a dispersal of subgenera Lophozonia and Fuscospora between Australia and New Zealand after the onset of the Antarctic Circumpolar Current and west wind drift. It appears likely that the New Caledonian lineage of subgenus Brassospora diverged from the New Guinean lineage elsewhere, prior to colonizing New Caledonia. The molecular approach strongly supports fossil-based estimates that Nothofagus diverged from the rest of Fagales more than 84 Myr ago. However, the mid-Cenozoic estimate for the diversification of the four extant subgenera conflicts with the palynological interpretation because pollen fossils, attributed to all four extant subgenera, were widespread across the Weddellian province of Gondwana about 71 Myr ago. The discrepancy between the pollen and molecular dates exists even when confidence intervals from several sources of error are taken into account. In contrast, the molecular age estimates are consistent with macrofossil dates. The incongruence between pollen fossils and molecular dates could be resolved if the early pollen types represent extinct lineages, with similar types later evolving independently in the extant lineages.

Do early branching lineages signify ancestral traits?

A reverence for ancestors that has pre-occupied humans since time immemorial persists to the present. Reconstructing ancestry is the focus of many biological studies but failure to distinguish between present-day descendants and long-dead ancestors has led to incorrect interpretation of phylogenetic trees. This has resulted in erroneous reconstruction of traits such as morphology and ancestral areas. Misinterpretation becomes evident when authors use the terms 'basal' or 'early diverging' to refer to extant taxa. Here, we discuss the correct interpretation of trees and methods for reconstructing the ancestral features of organisms using recently developed statistical models. These models can be inaccurate unless they use information that is independent of phylogenies, such as genetics, molecular and developmental biology, functional morphology, geological and climatic processes, and the fossil record.

A preliminary phylogeny of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea) based on nuclear small-subunit ribosomal DNA

Scale insects (Hemiptera: Sternorrhyncha: Coccoidea) are a speciose and morphologically specialized group of plant-feeding bugs in which evolutionary relationships and thus higher classification are controversial. Sequences derived from nuclear small-subunit ribosomal DNA were used to generate a preliminary molecular phylogeny for the Coccoidea based on 39 species representing 14 putative families. Monophyly of the archaeococcoids (comprising Ortheziidae, Margarodidae sensu lato, and Phenacoleachia) was equivocal, whereas monophyly of the neococcoids was supported. Putoidae, represented by Puto yuccae, was found to be outside the remainder of the neococcoid clade. These data are consistent with a single origin (in the ancestor of the neococcoid clade) of a chromosome system involving paternal genome elimination in males. Pseudococcidae (mealybugs) appear to be sister to the rest of the neococcoids and there are indications that Coccidae (soft scales) and Kerriidae (lac scales) are sister taxa. The Eriococcidae (felt scales) was not recovered as a monophyletic group and the eriococcid genus Eriococcus sensu lato was polyphyletic.

Extraordinary and extensive karyotypic variation: a 48-fold range in chromosome number in the gall-inducing scale insect Apiomorpha (Hemiptera: Coccoidea: Eriococcidae)

Chromosome number reflects strong constraints on karyotype evolution, unescaped by the majority of animal taxa. Although there is commonly chromosomal polymorphism among closely related taxa, very large differences in chromosome number are rare. This study reports one of the most extensive chromosomal ranges yet reported for an animal genus. Apiomorpha Rübsaamen (Hemiptera: Coccoidea: Eriococcidae), an endemic Australian gall-inducing scale insect genus, exhibits an extraordinary 48-fold variation in chromosome number with diploid numbers ranging from 4 to about 192. Diploid complements of all other eriococcids examined to date range only from 6 to 28. Closely related species of Apiomorpha usually have very different karyotypes, to the extent that the variation within some species-groups is as great as that across the entire genus. There is extensive chromosomal variation among populations within 17 of the morphologically defined species of Apiomorpha indicating the existence of cryptic species-complexes. The extent and pattern of karyotypic variation suggests rapid chromosomal evolution via fissions and (or) fusions. It is hypothesized that chromosomal rearrangements in Apiomorpha species may be associated with these insects' tracking the radiation of their speciose host genus, Eucalyptus.

Extraordinary and extensive karyotypic variation: A 48-fold range in chromosome number in the gall-inducing scale insect Apiomorpha (Hemiptera: Coccoidea: Eriococcidae)

Chromosome number reflects strong constraints on karyotype evolution, unescaped by the majority of animal taxa. Although there is commonly chromosomal polymorphism among closely related taxa, very large differences in chromosome number are rare. This study reports one of the most extensive chromosomal ranges yet reported for an animal genus. Apiomorpha Rübsaamen (Hemiptera: Coccoidea: Eriococcidae), an endemic Australian gall-inducing scale insect genus, exhibits an extraordinary 48-fold variation in chromosome number with diploid numbers ranging from 4 to about 192. Diploid complements of all other eriococcids examined to date range only from 6 to 28. Closely related species of Apiomorpha usually have very different karyotypes, to the extent that the variation within some species- groups is as great as that across the entire genus. There is extensive chromosomal variation among populations within 17 of the morphologically defined species of Apiomorpha indicating the existence of cryptic species-complexes. The extent and pattern of karyotypic variation suggests rapid chromosomal evolution via fissions and (or) fusions. It is hypothesized that chromosomal rearrangements in Apiomorpha species may be associated with these insects' tracking the radiation of their speciose host genus, Eucalyptus.

Key words: Apiomorpha, cytogenetics, chromosomal evolution, holocentric.

The impact of college prematriculation immunization requirements on risk for measles outbreaks

OBJECTIVE

To assess whether prematriculation immunization requirements (PIRs) affect the number of measles cases on college campuses.

DESIGN

We surveyed a stratified random sample of 880 colleges and universities to determine their immunization policies and practices and occurrence of measles outbreaks from 1988 through 1991. We merged national measles surveillance data with survey data by county to determine the risk for measles introduction on college campuses. We used logistic regression methods to estimate the effect of PIRs and assess risk factors for college measles outbreaks.

SETTING

A total of 3205 US colleges and universities listed in standard guides.

RESULTS

Of selected schools, 91 (11%) of the 796 responding schools reported one or more measles cases occurring from 1988 through 1991. Schools with a state-mandated PIR were significantly less likely to report measles outbreaks of two or more cases than other institutions (adjusted relative risk [RR] = 0.30; 95% confidence interval [Cl], 0.11 to 0.84). None of the 14 schools that reported outbreaks of 10 or more cases was subject to state regulation or had a PIR specifying two doses of measles vaccine in place. Of schools with introduction of measles, residential colleges were more likely to report extensive spread of measles (five or more cases) than nonresidential colleges (RR = 35.8; 95% Cl, 2.08 to 617.0). Of public schools, 4-year programs had a higher risk of a large outbreak (five or more cases) than 2-year programs.

CONCLUSIONS

These results strongly support current recommendations for requiring proof of vaccination of college students to decrease the risk for measles outbreaks on college campuses. State regulations mandating PIRs ensure the best protection against widespread measles transmission.

Prematriculation immunization requirements of American colleges and universities

The authors surveyed a stratified sample of 880 colleges and universities in the United States to assess the status and characteristics of their prematriculation immunization requirements (PIRs). On the basis of a 90% return (796 responses), they estimated that 55% of US colleges and universities had implemented a PIR at the time of the survey. Among schools with PIRs, measles vaccine was almost universally required, with 74% requiring two doses, mumps vaccine was required by 70%, and rubella vaccine by 92%. Hepatitis B vaccine was rarely required and was usually recommended only for students in health-profession programs. The strongest determinant of having a PIR was the presence of a state law or regents' policy. PIRs implemented under the aegis of a state law were, on average, less comprehensive but better enforced. Other factors associated with the implementation of a PIR included membership in the American College Health Association (ACHA), the presence of a student health clinic, and availability of record-keeping personnel.

Induced sero-conversion in heifers with a field strain of bovine pestivirus--a comparison of methods and doses

Losses from pestivirus infection in a closed herd of cattle occurred over several years. In order to prevent further losses, controlled exposure of non-pregnant heifers to pestivirus from viraemic carrier animals was undertaken. Two initial experiments were conducted using either intra-nasal EDTA blood or field contact. Subsequently, other yearling heifers were inoculated with various dilutions of serum using subcutaneous, conjunctival and intra-nasal routes. Effective doses were determined. Neither inoculation nor contact infection produced any clinical illness. The highest dilutions of serum at which sero-conversion occurred were conjunctival, undiluted; intranasal, 10(-1) and subcutaneous 10(-5). With the subcutaneous route all heifers sero-converted at 10(-3). The results for the subcutaneous inoculations showed that the 50% infectious dose for cattle was not distinguishable from that determined in cell culture. Inoculation with a field strain of pestivirus in freeze-thawed serum has effectively and safely induced sero-conversion in heifers. Inoculation of all cattle at risk is considered necessary because no secondary transmission from inoculated heifers was observed.