Phylogenetic support for the monophyly of proetide trilobites

The monophyly of the order Proetida, the only trilobite group to survive the end‐Devonian mass extinction, has been regularly questioned since its erection almost three decades ago. Through analysis of a novel phylogenetic data set comprising 114 characters coded for 55 taxa, including both traditional members of the Proetida along with a number of other trilobite groups, the monophyly of proetide trilobites is rigorously tested for the first time. Proetida is shown to be monophyletic, united by the initial compound eye formation in early protaspids occurring at the lateral margin rather than the anterior margin, and the form of the protaspid glabella being tapering with a pre‐glabellar field. A number of adult characters, including the possession of a quadrate or shield‐shaped hypostome with angular posterior margins, the hypostome median body being divided by a deep groove that entirely traverses the median body, the presence of an enlarged thoracic spine on the sixth tergite and a tergite count of between 7 and 10, also define the basal node. Hystricurid and dimeropygoid trilobites are shown to resolve at the base of the group, while the remaining proetide taxa are divided between large proetoid and aulacopleuroid clades. Some taxa previously allied with Aulacopleuroidea, such as rorringtoniids and scharyiids, are retrieved as basal members of the Proetoidea.     

Phylogenetic and biogeographic analysis of the genus Phytoseiulus (Acari: Phytoseiidae)

Kanouh, M., Tixier, M.‐S., Okassa, M. & Kreiter, S. (2010). Phylogenetic and biogeographic analysis of the genus Phytoseiulus (Acari: Phytoseiidae) —Zoologica Scripta, 39, 450–461. The taxonomy of the genus Phytoseiulus (sub‐family Amblyseiinae), has a tumultuous and confused history. This genus currently contains four species, but in previous revisions it contained five, sometimes grouped in two genera. There are no thorough phylogenetic analyses available for the group, analyses against which taxonomic and evolutionary hypotheses could be tested. The present study aims to apply morphological and molecular data to determine phylogenetic relationships among the four species presently included in this genus plus Afroseiulus robertsi, which was previously included in this genus. The new analyses show that the species of the genus Phytoseiulus do not constitute a monophyletic group. A delineation between (i) P. macropilis, P. persimilis, P. fragariae and (ii) P. longipes and A. robertsi is observed. Biogeographic data sets showed that the Neotropical and Afrotropical regions contain the highest diversity of species of Phytoseiulus and of their host plants. Consequently, the western part of Gondwana is hypothesized to be the probable centre of origin for this taxon.     

Phylogenetic and biogeographic implications of chloroplast DNA variation in Picea

Purified chloroplast DNA ( cp DNA) extracts from 31 species of Picea and two species of Pinus (P. sylvestris and P. cembra ) were digested with eight restriction endo-nucleases, separated by electrophoresis and scored for restriction fragment length polymorphisms. The resulting data was analyzed phenetically and cladistically. The phenetic analysis indicated lower levels of cpDNA differentiation within Picea than within Pinus and lower levels of differentiation among Eurasian than among North-American Picea species. The cladistic analysis, using Pinus sylvestris as an outgroup, suggested monophyly for Picea and resolved several monophyletic groups among the 31 species of Picea . An assessment of biogeographic events, based on the cladogram, suggests that Picea originated in North-America and that the colonization of Eurasia occurred through separate, intercontinental migrations.     

Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the Northern Hemisphere

Sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA, the chloroplast ndhF gene, and chloroplast trnL-F regions (trnL intron, and trnL [UAA] 3' exon-trnF [GAA] intergenic spacer) were used for phylogenetic analyses of Rhus, a genus disjunctly distributed in Asia, Europe, Hawaii, North America, and Northern Central America. Both ITS and cpDNA data sets support the monophyly of Rhus. The monophyly of subgenus Rhus was suggested by the combined cpDNA and ITS data, and largely supported in the cpDNA data except that Rhus microphylla of subgenus Lobadium was nested within it. The monophyly of subgenus Lobadium was strongly supported in the ITS data, whereas the cpDNA data revealed two main clades within the subgenus, which formed a trichotomy with the clade of subgenus Rhus plus R. microphylla. The ITS and cpDNA trees differ in the positions of Rhus michauxii, R. microphylla, and Rhus rubifolia, and hybridization may have caused this discordance. Fossil evidence indicates that Rhus dates back to the early Eocene. The penalized likelihood method was used to estimate divergence times, with fossils of Rhus subgenus Lobadium, Pistacia and Toxicodendron used for age constraints. Rhus diverged from its closest relative at 49.1+/-2.1 million years ago (Ma), the split of subgenus Lobadium and subgenus Rhus was at 38.1+/-3.0 Ma. Rhus most likely migrated from North America into Asia via the Bering Land Bridge during the Late Eocene (33.8+/-3.1 Ma). Rhus coriaria from southern Europe and western Asia diverged from its relatives in eastern Asia at 24.4+/-3.2 Ma. The Hawaiian Rhus sandwicensis diverged from the Asian Rhus chinensis at 13.5+/-3.0 Ma. Subgenus Lobadium was inferred to be of North American origin. Taxa of subgenus Lobadium then migrated southward to Central America. Furthermore, we herein make the following three nomenclatural combinations: (1) Searsia leptodictya (Diels) T. S. Yi, A. J. Miller and J. Wen, comb. nov., (2) Searsia pyroides (A. Rich.) T. S. Yi, A. J. Miller and J. Wen, comb. nov., and (3) Searsia undulata (Jacq.) T. S. Yi, A. J. Miller and J. Wen, because our analyses support the segregation of Searsia from Rhus.     

Phylogenetic analysis of Toxicodendron （Anacardiaceae） and its biogeographic implications on the evolution of north temperate and tropical intercontinental disjunctions

Toxicodendron is a genus in the Rhus complex of Anacardiaceae with a disjunct distribution between eastern Asia and North America, extending to southeastern Asia and the neotropics. Nuclear （internal transcribed spacer, external transcribed spacer, and NIA-i3） and chloroplast （ndhF and trnL-F） sequences were used to construct phylogenetic relationships of Toxicodendron. Phylogenetic analysis of these data strongly support Toxieodendron as a monophyletic group distinct from other genera of the Rhus complex, and the phylogeny does not fully corroborate classification at the sectional level. Two temperate disjunct lineages were detected, one from section Toxicodendron and the other between the eastern North American Toxicodendron vernix and the eastern Asian Toxicodendron vernieifluum. Their divergence times were estimated to be 13.46 （7.95-19.42） and 7.53 （2.76-12.86） mya, respectively. The disjunction between section Griffithii （taxa from warm temperate to tropical Asia） and Toxieodendron striatum （from the neotropics） was supported and their divergence time was estimated to be 20.84 （11.1 6-30.52） mya in the early Miocene. Our biogeographic results and the paleontological data support the Bering land bridge as the most likely route to explain the temperate disjunctions, yet the tropical disjunction in Toxicodendron seems to be best explained by the North Atlantic land bridge hypothesis.     

Single-copy DNA-DNA hybridizations among five species ofLaminaria (Phaeophyceae): Phylogenetic and biogeographic implications

DNA-DNA hybridizations between single-copy nuclear DNA fromLaminaria digitata and total DNA fromL. saccharina, L. Hyperborea, L. rodriguezii, L. ochroleuca andChorda filum, respectively, show that these species ofLaminaria are genotypically closely related.Chorda filum is only distantly related withL. digitata. Based on the thermal elution patterns of the DNA hybrids, as quantified by ΔT_m(e) values, it is hypothesized that all five species ofLaminaria evolved at about the same time from their most recent common ancestor some 15–19 Ma ago. This phylogenetic hypothesis is discussed in relation to the history of modern laminarialean distribution patterns. Paper presented at the XIV International Botanical Congress (Berlin, 24 July–1 August, 1987), Symposium 6-15, “Biogeography of marine benthic algae”.     

Phylogenetic and biogeographic complexity of Magnoliaceae in the Northern Hemisphere inferred from three nuclear data sets

This study employs three nuclear genes (PHYA, LFY, and GAI1) to reconstruct the phylogenetic and biogeographic history of Magnoliaceae. A total of 104 samples representing 86 taxa from all sections and most subsections were sequenced. Twelve major groups are well supported to be monophyletic within Magnoliaceae and these groups are largely consistent with the recent taxonomic revision at the sectional and subsectional levels. However, relationships at deeper nodes of the subfamily Magnolioideae remain not well resolved. A relaxed clock relying on uncorrelated rates suggests that the complicated divergent evolution of Magnolioideae began around the early Eocene (54.57mya), concordant with paleoclimatic and fossil evidence. Intercontinental disjunctions of Magnoliaceae in the Northern Hemisphere appear to have originated during at least two geologic periods. Some occurred after the middle Miocene, represented by two well-recognized temperate lineages disjunct between eastern Asia and eastern North America. The others may have occurred no later than the Oligocene, with ancient separations between or within tropical and temperate lineages.     

Phylogenetic and biogeographic analysis of the spear lobsters Linuparus (Decapoda: Palinuridae), with the description of a new species

Linuparus White, 1847 comprises three extant species, Linuparus trigonus (Von Siebold, 1824), L. sordidusBruce, 1965, and L. somniosusBerry and George, 1972, as well as 32 fossil species. Most fossil records are from North America and Europe, but the extant species are all confined to the Indo-West Pacific. Different colour forms in L. trigonus and L. sordidus have been noted, with Northern Hemisphere specimens generally darker in colour for both species. The phylogenetic relationships of the extant Linuparus species, including the colour forms, were investigated using mitochondrial 12S rRNA and COI gene sequence analysis. We found no genetic evidence to differentiate the colour morphs of L. sordidus, but the two colour forms of L. trigonus were clearly distinct at the species level. This is supported morphologically by a consistent difference in the shape of the thoracic sternum between the two forms. The paler coloured Southern Hemisphere form is described as a new species, L. meridionalis. Phylogenetic analysis shows that L. trigonus and L. meridionalis sp. nov. are derived sister taxa, while L. somniosus is basal within the genus. Thus the present results support the previous hypothesis that Linuparus was originated in shallow water.     

Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals

Phylogenetic diversity (PD) captures the shared ancestry of species, and is increasingly being recognized as a valuable conservation currency. Regionally, PD frequently covaries closely with species richness; however, variation in speciation and extinction rates and/or the biogeographic history of lineages can result in significant deviation. Locally, these differences may be pronounced. Rapid recent speciation or high temporal turnover of lineages can result in low PD but high richness. In contrast, rare dispersal events, for example, between biomes, can elevate PD but have only small impact on richness. To date, environmental predictors of species richness have been well studied but global models explaining variation in PD are lacking. Here, we contrast the global distribution of PD versus species richness for terrestrial mammals. We show that an environmental model of lineage diversification can predict well the discrepancy in the distribution of these two variables in some places, for example, South America and Africa but not others, such as Southeast Asia. When we have information on multiple diversity indices, conservation efforts directed towards maximizing one currency or another (e.g. species richness versus PD) should also consider the underlying processes that have shaped their distributions.     

Phylogenetic relationships of rock-wallabies, Petrogale (Marsupialia: Macropodidae) and their biogeographic history within Australia

The rock-wallaby genus Petrogale comprises a group of habitat-specialist macropodids endemic to Australia. Their restriction to rocky outcrops, with infrequent interpopulation dispersal, has been suggested as the cause of their recent and rapid diversification. Molecular phylogenetic relationships within and among species of Petrogale were analysed using mitochondrial (cytochrome oxidase c subunit 1, cytochrome b, NADH dehydrogenase subunit 2) and nuclear (omega-globin intron, breast and ovarian cancer susceptibility gene) sequence data with representatives that encompassed the morphological and chromosomal variation within the genus, including for the first time both Petrogale concinna and Petrogale purpureicollis. Four distinct lineages were identified, (1) the brachyotis group, (2) Petrogale persephone, (3) Petrogalexanthopus and (4) the lateralis-penicillata group. Three of these lineages include taxa with the ancestral karyotype (2n=22). Paraphyletic relationships within the brachyotis group indicate the need for a focused phylogeographic study. There was support for P. purpureicollis being reinstated as a full species and P. concinna being placed within Petrogale rather than in the monotypic genus Peradorcas. Bayesian analyses of divergence times suggest that episodes of diversification commenced in the late Miocene-Pliocene and continued throughout the Pleistocene. Ancestral state reconstructions suggest that Petrogale originated in a mesic environment and dispersed into more arid environments, events that correlate with the timing of radiations in other arid zone vertebrate taxa across Australia.     

Hypostoma of agnostid trilobites

The hypostoma, which is a ventral sclerite that covers the oral region, has recently been discovered in four species of agnostid trilobites. The discovery is significant because the suborder Agnostina is the only major trilobite taxon for which the hypostoma has not been described. The agnostid hypostoma is distinctly different in shape from that of non-agnostid trilobites. Minus its wings, it is widest posteriorly, lacks border furrows, has unusually long wings, and in some species is fenestrate. It is unattached to other sclerites, and presumably was held in place beneath the anterior part of the glabella by muscle tissue. Hypostomal differences probably indicate basic differences in food or feeding habits of agnostid and non-agnostid trilobites. This, along with other evidence, suggests a major divergence in mode of life of these two trilobite groups, and should be given strong consideration in future attempts at trilobite classification.     

Head segmentation of trilobites

Although trilobites have provided research subjects for more than two centuries, their head segmentation has remained unresolved. Four glabellar furrows (SO and S1–S3) marking the segmental boundaries are generally present in the cephalic axis, but there are trilobites with one more pair of furrows, the so‐called S4, in the cephalic axis, causing confusion in understanding trilobite head segmentation. Recent advances in developmental biology and palaeontology have shed light on the arthropod head problem, and thus, trilobite head segmentation can be reviewed in the light of this knowledge. Based on the information from the anatomy of exceptionally preserved trilobites and artiopodans closely related to trilobites, it is inferred that trilobite head contains five segments: the anteriormost ocular segment potentially associated with the hypostome, the antennal segment and the following three segments with walking legs. When present, the S4 furrows are situated where the eye ridges meet the cephalic axis of trilobites, indicating that the furrows are incised ‘within’ the anteriormost segment in trilobites with an anteriorly enlarged frontal lobe. Trilobites of the Order Redlichiida, the most primitive stock, show variable conditions in the frontal glabellar conditions, while in other more derived groups, the condition is rather constant. The frontal glabellar condition, therefore, could provide a clue to elucidate the unresolved Cambrian trilobite phylogeny and the Cambrian roots of the post‐Cambrian trilobites.     

Phylogenetic and biogeographic relationships of the mouse opossum Thylamys (Didelphimorphia,Didelphidae) in southern South America

Nucleotide sequence data from the mitochondrial cytochrome b gene were used to evaluate the phylogenetic relationships among mouse opossum species of the genus Thylamys. Based on approximately 1000 bp in five of the six species of the genus and including different localities for some of the species, we concluded that T. macrura from the subtropical forests of eastern Paraguay is the most primitive taxon. Subsequent radiation of the genus is explained mainly via founder effect speciation. This evolutionary scenario would account for the speciation of T. pusilla, T. venusta, T. pallidior, and T. elegans in the Chaco, southern Bolivia and northern Argentina, the Andean Altiplano, the Coastal Desert of Chile, and coastal Perú, respectively. Calibration of a molecular clock set the Pleistocene as the period for the differentiation of Thylamys species. The molecular results confirm the strong genetic connection between populations that inhabit the "pre-cordillera" of northern Chile (T. pallidior) and the canyons that run through the Atacama Desert to the lowlands in northern Chile. Our results confirm the occurrence of two Thylamys species in Chile, T. pallidior and T. elegans, within and south to the Atacama Desert, respectively.     

Phylogenetic relationships and biogeographic history of the unique Saxifraga sect. Irregulares (Saxifragaceae) from eastern Asia

Saxifraga L. is the largest genus in Saxifragaceae and a characteristic component of the herbaceous flora of the temperate and alpine mountains in the Northern Hemisphere. Section Irregulares is a small group of 15–20 species, representing one of the early‐diverged lineages in the genus characterized with unique zygomorphic flowers. We used both nuclear internal transcribed spacer and chloroplast DNA regions (psbA‐trnH, trnL‐F, and matK) to reconstruct its species relationships, estimate divergence times, and infer its historical biogeography. Our phylogenetic results corroborate the monophyly of sect. Irregulares and its sister relationship to sect. Heterisia from North America. The section was well resolved into two lineages corresponding to their morphological features and biogeographic distributions. One represents ser. Stoloniferae including S. stolonifera Curtis and S. nipponica Makino with long‐creeping stolons/rhizomes and small petals with spots and the other comprises the remaining taxa (ser. Rufescentes) which lack long‐creeping rhizomes. Spots on leaves (abaxially spotted vs. abaxially without spots) and spots on petals (without spots vs. with spots) are inferred to be phylogenetically informative within ser. Rufescentes. Divergence time estimates and ancestral area analysis suggested a western North American origin of sect. Irregulares with migration into East Asia by way of the Bering land bridge in the Middle Oligocene. The development of drying and desertification belt in the late Miocene could have played an important role in the subsequent restriction and separation of the north and south lineages within eastern Asia.     

Phylogenetic analysis ofUlmaceae

A phylogenetic analysis of theUlmaceae, Cannabaceae, Barbeyaceae, andBroussonetia of theMoraceae produced nine equally parsimonious trees with 127 steps. TheUlmoideae (Ulmaceae, sensuGrudzinskaya) are a monophyletic group and distinct from theCeltidoideae. The genusAmpelocera occupies an isolated taxonomic position among the celtidoids. The similarity ofAmpelocera to the fossil celtidoid flowerEoceltis of North America suggests thatAmpelocera posesses an archaic suite of characters, and occupies a primitive position among the celtidoids, theCannabaceae and theMoraceae. The relationships among the other celtidoid taxa,Cannabaceae, andBroussonetia are problematic. TheCannabaceae andBroussonetia of theMoraceae are nested within the celtidoids suggesting that this is a paraphyletic group. The close, but unresolved, relationship of the celtidoids to theMoraceae andCannabaceae observed in this analysis, and the appearance of the celtidoids in the fossil record prior to the ulmoids suggests that the evolutionary relationship of the ulmoids and celtidoids may be more distant than current taxonomic treatments reflect.     

Polyploid speciation inHedera (Araliaceae): Phylogenetic and biogeographic insights based on chromosome counts and ITS sequences

Variation in chromosome number and internal transcribed sequences (ITS) of nrDNA is used to infer phylogenetic relationships of a wide range ofHedera species. Polyploidy was found to be frequent inHedera, with diploid, tetraploid, hexaploid and octoploid populations being detected. Nucleotide additivity occurs in the ITS sequences of one tetraploid (H. hibernica) and two hexaploid species (H. maderensis, H. pastuchovii), suggesting that all three species originated by allopolyploidisation. ITS sequence polymorphism and nucleotide characters may indicate the presence of an ancient genome persistent only in some allopolyploid species. Phylogenetic analyses of ITS sequence data reveal two lineages ofHedera: one containing all sequences belonging to extant diploids plus the tetraploidH. algeriensis, and a second that includes this ancient ITS type and others exclusive to several polyploid species. The origin of the polyploids is evaluated on the basis of morphology, chromosome counts, ITS sequence polymorphism, and phylogenetic analyses. Reconstruction of reticulate evolution inHedera agrees with two allopolyploid areas on both sides of the Mediterranean basin. Morphological, molecular and cytological evidence also suggests an active dispersal ofHedera populations that may account for three independent introductions in Macaronesia.     

Distribution patterns and biogeographic analysis of Austral Polychaeta (Annelida)

Aim We investigate the biogeography of Austral Polychaeta (Annelida) using members of the families Eunicidae, Lumbrineridae, Oenonidae, Onuphidae, Serpulidae and Spionidae and Parsimony Analysis of Endemicity (PAE). We determine whether observed polychaete distribution patterns correspond to traditional shallow-water marine areas of endemism, estimate patterns of endemism and relationships between areas of endemism, and infer the biological processes that have caused these patterns. Location The study is concerned with extant polychaete taxa occupying shallow-water areas derived from the breakup of the Gondwana landmass (i.e. Austral areas). Methods Similarity was assessed using a significance test with Jaccard's indices. Areas not significantly different at 0.99 were combined prior to the PAE. Widespread species and genera (155 taxa) were scored for presence/absence for each area of endemism. PAE was used to derive hypotheses of area relationships. Hierarchical patterns in the PAE trees were identified by testing for congruence with patterns derived from cladistic biogeographic studies of other Gondwanan taxa and with geological evidence. Results The polychaete faunas of four area-pairs were not significantly different and the areas amalgamated: South-west Africa and South Africa, New Zealand South Island and Chatham Islands, Macquarie Island and Antipodean Islands, and West Antarctica and South Georgia. Areas with the highest levels of species endemism were southern Australia (67.0%), South-east South America (53.2%) and South Africa (40.4%). About 60% of species and 7.5% of genera occupied a single area of endemism. The remainder were informative in the PAE. Under a no long-distance dispersal assumption a single minimal-length PAE tree resulted (l=367; ci=0.42); under dispersal allowed, three minimal-length trees resulted (l=278; ci=0.56). In relation to the sister grouping of the New Zealand areas and Australia we find congruence between our minimal-length trees and those derived from a biogeographic study of land plants, and with area relationships predicted by the Expanding Earth Model. Main conclusions The polychaete distribution patterns in this study differ slightly from the classical areas of endemism, most notably in being broader, thereby bringing into question the value of using single provincial system for marine biogeographic studies. The Greater New Zealand region is found to be ‘monophyletic’ with respect to polychaetes, that is comprising a genuine biogeographical entity, and most closely related to the polychaete fauna of southern Australia. This finding is consistent with studies of land plants and with the Expanding Earth model, but disagrees with conventional geology and biogeographic hypothesis involving a ‘polyphyletic’ New Zealand. Both vicariance and concerted range expansion (=biotic dispersion) appear to have played important roles in shaping present-day distribution patterns of Austral polychaetes. Shallow-water ridge systems between the Australian and Greater New Zealand continental landmasses during the Tertiary are thought to have facilitated biotic dispersion.     

Primary and diagenetic microstructures in trilobites

McAllister, John E. & Brand, Uwe 1989 01 15: Primary and diagenetic microstructures in trilobites. Lethaia , Vol. 22, pp. 101–111. Oslo. ISSN 0024–1164.
Ordovician and Devonian trilobites were studied by scanning electron microscopy (SEM) to define primary and diagenetic microstructures. Primary structures such as Osmólska cavities and hexagonal surface openings are present in samples obtained from both shale and limestone lenses in shales. Generally, samples with primary microstructures are also geochemically well preserved. Diagenetic microstructures were found in samples from shales and limestones, but those from limestones are the most geochemically and microstructurally altered. 'Dendritic' patterns and fused matrices were found in the altered cuticles of trilobites of different species and ages and are therefore considered a normal feature of the diagenetic alteration of cuticular calcite. Primary and diagenetic microstructures of trilobite cuticles are independent of size, species and age of the specimens, but are largely controlled by lithology and thus diagenesis. * Trilobita, primary-, diagenetic microstructures, fossil diagenesis .     

Asymmetry of Early Paleozoic trilobites

Asymmetry in fossils can arise through a variety of biological and geological mechanisms. If geological sources of asymmetry can be minimized or factored out, it might be possible to assess biological sources of asymmetry. Fluctuating asymmetry (FA), a general measure of developmental precision, is documented for nine species of lower Paleozoic trilobites. Taphonomic analyses suggest that the populations studied for each taxon span relatively short time intervals that are approximately equal in duration. Tectonic deformation may have affected the specimens studied, since deviations from normal distributions are common. Several measures of FA were applied to 3–5 homologous measures in each taxon. Measurement error was assessed by the analysis of variance (ANOVA) for repeated measurements of individual specimens and by analysis of the statistical moments of the distributions of asymmetry measures. Measurement error was significantly smaller than the difference between measures taken on each side of a specimen. However, the distribution of differences between sides often deviated from a mean of zero, or was skewed or kurtosic. Regression of levels of FA against geologic age revealed no statistically significant changes in levels of asymmetry through time. Geological and taphonomic effects make it difficult to identify asymmetry due to biological factors. Although fluctuating asymmetry is a function of both intrinsic and extrinsic factors, the results suggest that early Cambrian trilobites possessed genetic or developmental mechanisms used to maintain developmental stability comparable to those of younger trilobites. Although the measures are biased by time averaging and deviations from the normal distribution, these data do not lend strong support to 'genomic' hypotheses that have been suggested to control the tempo of the Cambrian radiation.