Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus

Myotragus balearicus was a dwarf artiodactyl endemic to the Eastern Balearic Islands, where it evolved in isolation for more than 5 million years before becoming extinct between 3640 and 2135 cal BC (calibrated years BC). Numerous unusual apomorphies obscure the relationship between Myotragus and the extant Caprinae. Therefore, genetic data for this species would significantly contribute to the clarification of its taxonomic position. In this study, we amplify, sequence, and clone a 338-base pair (bp) segment of the mitochondrial cytochrome b (cyt b) gene from a >9Kyr Myotragus subfossil from la Cova des Gorgs (Mallorca). Our results confirm the phylogenetic affinity of Myotragus with the sheep (Ovis) and the takin (Budorcas). In each tree, the Myotragus branch is long in comparison with the other taxa, which may be evidence of a local change in the rate of evolution in cyt b. This rate change may be due to in part to an early age of first reproduction and short generation time in Myotragus, factors that are potentially related to the extreme reduction in size of the adult Myotragus as compared to the other Caprinae.     

Molecular phylogeny of the extinct cave lion Panthera leo spelaea

To reconstruct the phylogenetic position of the extinct cave lion (Panthera leo spelaea), we sequenced 1 kb of the mitochondrial cytochrome b gene from two Pleistocene cave lion DNA samples (47 and 32 ky B.P.). Phylogenetic analysis shows that the ancient sequences form a clade that is most closely related to the extant lions from Africa and Asia; at the same time, cave lions appear to be highly distinct from their living relatives. Our data show that these cave lion sequences represent lineages that were isolated from lions in Africa and Asia since their dispersal over Europe about 600 ky B.P., as they are not found among our sample of extant populations. The cave lion lineages presented here went extinct without mitochondrial descendants on other continents. The high sequence divergence in the cytochrome b gene between cave and modern lions is notable.     

The Pleistocene easternmost distribution in Eurasia of the species associated with the Eemian Palaeoloxodon antiquus assemblage

• 1 The Palaeoloxodon antiquus large‐mammal assemblage was typical of the late middle and late Pleistocene interglacials in Europe. This review examines the assemblage's origins, dispersal and cohesiveness in Eurasia.
• 2 During the more climatically equable middle‐Pleistocene periods, the Palaeoloxodon assemblage (or closely related) species occurred across central Eurasia almost simultaneously. In Central and Western Europe, these species responded to climatic changes together as an unvarying interglacial assemblage, whereas in Eastern Europe and Siberia, they occurred in diverging assemblages. The boundary of the Palaeoloxodon assemblage can be drawn roughly from Poland to Romania.
• 3 In Central and Western Europe this interglacial assemblage last occurred during the Eemian. During this period many of the Palaeoloxodon assemblage species may also have co‐occurred in south‐eastern Europe and, except for Bubalus murrensis and Hippopotamus amphibius, further eastwards. The extinct species of the Palaeoloxodon assemblage disappeared in Siberia and Central Asia prior to Europe and the Caucasus whereas the extant species were already present in their modern distribution areas.
• 4 A quantitative study of faunal associations across Eurasia, following much‐needed comprehensive systematic reviews, would further elucidate the patterns of faunal change associated with local and global climatic changes during the middle to late Pleistocene.

     

Molecular phylogeny of Armillaria from the Patagonian Andes

A number of species in the plant pathogen genus Armillaria are known from South America where they cause root rot disease on a wide variety of hosts. Knowledge pertaining to phylogenetic relationships of these species with those of other Armillaria species is almost non-existent. In addition, very few cultures representing these species are available, making DNA-based phylogenetic analyses impossible. The aim of this study was to characterise a collection of Armillaria isolates from the Patagonian Andes using DNA sequences and to determine their phylogenetic relationships with other Armillaria species. DNA sequences were obtained from the internal transcribed regions (ITS1, 5.8S and ITS4) and ribosomal large subunit (LSU) gene and used in phylogenetic analyses. Phylogenetic trees generated from the sequences separated the Armillaria isolates into four lineages. Lineages I and II represented A. novae-zelandiae and A. luteobubalina, respectively. Isolates belonging to A. novae-zelandiae from Malaysia, New Zealand, Australia and South America showed considerable intra-clade sub-structure. Lineages III and IV are probably distinct species and are most closely related to A. hinnulea and an unnamed species isolated from New Zealand and Kenya. This is the first comprehensive study of the phylogenetic relationships of Armillaria species from Patagonia and it provides a foundation for future research in this region.     

Island mortality in the past: some evidence from Greece

This paper explores the course of infant and childhood mortality in the Greek island of Paros from the end of the nineteenth until the mid-twentieth century. For this purpose the method of family reconstitution has been applied to two towns on the island. Official population statistics have been used to derive basic mortality estimates for the Cyclades and Greece as a whole. Reference to other studies concerning island mortality is also made. Hence, there appears the chance to compare insular with mainland mortality and realise that insular mortality presented some distinct features. It is shown that island populations presented lower mortality than the national average until the first decades of the twentieth century. However, by the 1950s Greece's infant and childhood mortality had dropped to the same or even to lower levels than those of the islands.     

Vulnerable island carnivores: the endangered endemic dwarf procyonids from Cozumel Island

Insular carnivores represent some of the most critically threatened species, but also the least known. To evaluate the conservation status of these species, thorough abundance estimates are urgently required. To better understand the population biology and conservation status of the endemic and threatened pygmy raccoon (Procyon pygmaeus) and dwarf coati (Nasua nelsoni) on Cozumel Island, Mexico, we worked island-wide to identify the presence of these species, and for the pygmy raccoon we studied several populations in depth during 2001–2003. On Cozumel, trapping was conducted for >6,600 trap nights in 19 locations of varying habitat types. A total of 96 pygmy raccoons (47 males and 49 females) and a single adult, male dwarf coati (N. nelsoni) were captured. Estimated total annual pygmy raccoon population size ± SE was 80 ± 26.1, resulting in an average density of 22 ± 5.1 raccoons/km² for the three small sites where the animals persist. Based in part on the findings of this study that indicate these species have a restricted range and small population numbers, the IUCN recently changed the listing of the pygmy raccoon to Critically Endangered from Endangered. In contrast, the status of the dwarf coati (Endangered) has not been changed, although the taxon is in eminent danger of extinction and in need of immediate conservation action.     

The status of dwarf carnivores on Cozumel Island, Mexico

Cozumel Island in the Mexican Caribbean is inhabited by four carnivores, of which two, the Cozumel coati Nasua nelsoni and pygmy raccoon Procyon pygmaeus, are endemic species. The taxonomic status of a third carnivore, a dwarf gray fox Urocyon cinereoargenteus, is undetermined, but may deserve subspecific or species-level recognition. The fourth species, the kinkajou (Potos flavus), may be a recent introduction. We review the status of these carnivores, report our field observations and results of line transect and trapping efforts, discuss current threats to these taxa, and make recommendations for their conservation. A population density of 0.43 ± 0.27 coatis/km², and a total island population size of 150 ± 95 individuals, was estimated from 386 km of line transects in 1994–1995. Intensive trapping efforts (1479 trap-nights) in 2001 at multiple localities were unsuccessful. Pygmy raccoons were observed in the mangrove and coastal wetland areas of the island and in 2001 we captured 11 individuals with the same sampling efforts as for coatis (8.8 raccoons/1000 trap-nights). The gray fox is also apparently very rare on the island. While a few observations of the animals have been made (1984, 1994 and 2001), no animals were seen along transects and none were trapped. The primary threats to the persistence of these taxa include introduced congeners, introduced predators, parasite and disease spill-over from exotic animals, habitat fragmentation, hunting and collection as pets, and hurricanes. We suggest that the Cozumel coati, pygmy raccoon, and the Cozumel population of the gray fox be considered as Critically Endangered according to the IUCN classification system. Current conservation actions focusing on Cozumel carnivores are extremely limited. We recommend eradication of introduced species, maintenance of habitat connectivity, ex situ conservation programs, explicit public policies on land-use and sustainable development, public awareness campaigns, and continuous scientific research and monitoring.     

Molecular phylogeny of the Entomophthoromycota

The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods.     

Molecular phylogeny of the Rhinotermitidae

Summary. Relationships among genera in the termite family Rhinotermitidae and their relationship to the families Termitidae and Serritermitidae were investigated based on analysis of three mitochondrial genes: COI, COII and 16S rDNA. Maximum Parsimony (MP) bootstrap analysis of each of these genes indicated a low level of phylogenetic incongruence between them, and thus they were combined and analysed by MP and Bayesian analysis. Six main lineages were clearly identified, however relationships among these were not well defined. Tentative support was found for the Rhinotermitid genera Coptotermes, Heterotermes and Reticulitermes being the sister group to the Termitidae, rendering the Rhinotermitidae paraphyletic. The species Serritermes serrifer and Glossotermes oculatus were found to group with strong support, in agreement with the recent transfer of the latter species to the family Serritermitidae based on morphological characteristics. No support was found for the Rhinotermitidae being paraphyletic with respect to the Serritermitidae. A number of disagreements were found between the molecular tree and traditional classifications of genera within subfamilies.Received 20 February 2004; revised 2 April 2004; accepted 19 April 2004.     

Molecular and Morphological Characterization of the Corn Cyst Nematode,Heterodera zeae,from Greece

The corn cyst nematode Heterodera zeae was detected in soil from an organic maize field in northern Greece. In greenhouse studies, reproduction of H. zeae was detected on maize plants (Zeae mays) using soil high in organic matter; the field was under winter fallow at the time of sampling. Maize plants were grown in a greenhouse with soil from the affected field used as inoculum. Females appeared after six weeks incubation, and abundant cysts were present after 12 weeks. Morphological and molecular diagnosis confirmed the presence of H. zeae in the field. Cysts were identified on the basis of cyst shape and characteristics of the cyst terminal cone, including nature of fenestration, presence of bullae, cyst wall pattern, and fenestral diameter. Second-stage juveniles were identified by body and stylet length, the shape of stylet knobs, shape and length of the tail and hyaline tail terminus, and by the number of lateral lines. Molecular analysis included amplification of the ribosomal internal transcribed spacer regions (ITS 1&2 rDNA) 28S large ribosomal subunit (LSU) D2-D3 expansion segment, and partial 18S small ribosomal subunit (SSU). Restriction fragment length polymorphism (RFLP) of ITS rDNA exhibited several unique enzyme patterns that may be diagnostically useful for H. zeae. These findings are in agreement with prior analysis of H. zeae populations from the U.S. and India. Phylogenetic relationships inferred from ITS rDNA are congruent with previous analyses that placed H. zeae in a clade with H. turcomanica, H. salixophila and species of the Humuli group. Phylogenetic trees based upon heat shock protein (Hsp90) coding sequence were in general agreement with a prior study using the same marker. This study represents the first record of H. zeae in Greece and the second report of this nematode in Europe.     

Molecular phylogeny of Pacific Island Colymbetinae: radiation of New Caledonian and Fijian species (Coleoptera, Dytiscidae)

We present a molecular phylogeny and taxonomic review of the Pacific island colymbetine diving beetles, focusing on the Fijian and New Caledonian faunas. Four new species are described: Rhantus monteithi and R. poellerbauerae from New Caledonia, and R. kini and R. bula from Fiji. We also describe the 3rd instar larvae of R. monteithi and R. poellerbauerae spp. nov., assigned to adults using mtDNA sequence data and discuss larval characters in the light of phylogeny. The phylogenetic hypotheses derived from both parsimony and Bayesian inference based on 3508 aligned nucleotides from a combination of mitochondrial (cox1, cob and rrnL‐tRNALeu‐Nad1) and nuclear genes (18S rRNA and H3) reveal a clade comprising R. novaecaledoniae, R. alutaceus, R. pseudopacificus, R. monteithi sp. nov. and R. poellerbauerae sp. nov., which agrees with the R. pacificus group sensu Balke (1993). Carabdytes upin was included within this clade, possibly indicating paraphyly of the genus Rhantus. Rhantus annectens, R. bacchusi, R. supranubicus, R. suturalis, R. simulans, and the Palearctic R. exsoletus, R. latitans and R. bistriatus formed a clade corresponding to the R. suturalis group sensu Balke (2001). Rhantus vitiensis, previously assigned to the R. pacificus group, was included in the R. suturalis clade. We find some support for a scenario where the Pacific was colonized out of the Northern hemisphere only during the past c. 12 million years, rejecting a Gondwanan origin of the morphologically isolated endemics. The new species are all characterized by mtDNA haplotype clusters, the degree of divergence between sister species pairs ranging from 1.3 to 7%, while R. novaecaledoniae individuals from all over New Caledonia apparently form one morphospecies, with moderate genetic diversity (up to 2.3% mtDNA divergence between populations). The sisters R. pollerbauerae sp. nov. + R. monteithi sp. nov. occur sympatrically on Mont Panié but appear ecologically segregated, while the sisters R. vitiensis + R. bula sp. nov. were encountered syntopically on Viti Levu. Comparing genetic and morphological data of Fijian Rhantus and Copelatus diving beetles, we here show that even in island radiations it is not per se possible to know if mitochondrial DNA barcoding would perform well (Rhantus: YES, Copelatus: NO). At the same time we show that fixed cutoff values, as sometimes used to discriminate between barcodes, thus species, might be meaningless. We underpin the importance of morphology for sustainable exploration of global diversity.     

Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf galaxias (G. pusilla)

The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate Southern Australia. We also tested if continental shelf width has influenced connectivity among populations during low sea levels when rivers, now isolated, could have been connected. We addressed these questions by sampling each species across its range using multiple molecular markers (mitochondrial cytochrome b sequences, nuclear S7 intron sequences, and 49 allozyme loci). These data also allowed us to assess species boundaries, to refine phylogenetic affinities, and to estimate species ages. Interestingly, we found compelling evidence for cryptic species in G. pusilla, manifesting as allopatric eastern and western taxa. Our combined phylogeny and dating analysis point to an origin for the genus dating to the early Cenozoic, with three of the four species originating during the Oligocene-Miocene. Each Galaxiella species showed high levels of genetic divergences between all but the most proximate populations. Despite extensive drainage connections during recent low sea levels in southeastern Australia, populations of both species within G. pusilla maintained high levels of genetic structure. All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum. High levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.     

First-year survival of southern elephant seals,Mirounga leonina,at sub-Antarctic Macquarie Island

Juvenile seals branded on the isthmus of Macquarie Island as pups displayed a high degree of philopatry. They returned more often and in greater densities to the northern third of the island within 10 km of their birth sites. Juvenile seals were observed to haul out more frequently and in greater numbers on the east coast as opposed to the west. Juvenile seals typically hauled out on two occasions, once during the winter, and once to moult. The probability of recapturing (resighting) branded and tagged seals was greater during the mid-year haulout. First-year survival estimates were obtained from searches of all Macquarie Island beaches for marked (branded and tagged) seals. From a branded population of 2000 seals, 897 were known to be alive at age 1 year, and minimum first-year survival was calculated at 44.85%. To this minimum estimate was added the number of seals overlooked during systematic and standardised searches of the island, and a revised estimate of 65.60% was calculated. Survival rates calculated using a custom model and a conventional mark-recapture model (MARK) were compared and no differences detected. Actual survival data and probability of sighting estimates were included in the revised estimate of first-year survival of southern elephant seals at Macquarie Island. There were no differences in the number of surviving males and females. Accepted: 25 October 1998     

A new elephant fossil from the late Pleistocene of Alghero: The puzzling question of Sardinian dwarf elephants

Endemic elephants, variously reduced in size, have been reported from a number of Mediterranean islands. Most of these originated from the mainland species Palaeoloxodon antiquus. A few dwarf mammoth remains are recorded from Crete and Sardinia. In Sardinia, a largely incomplete skeleton and a few mammoth teeth have been reported from localities believed to range in age from the late middle to the late Pleistocene. The chronology of colonisation by the ancestral species, the actual persistence through time of Mammuthus lamarmorai on the island, and the morphological and dimensional range of the species are, however, poorly known. This research aims to describe a distal portion of a left tibia of a dwarf elephant found in the Alghero area (NW Sardinia), showing some morphological traits and dimensions consistent with those of the endemic Sardinian mammoth (Mammuthus lamarmorai). The main unanswered questions about chronology, colonisation and population dynamics of endemic Sardinian elephants are highlighted and briefly discussed.     

Molecular phylogeny of the kingdoms Animalia, Plantae, and Fungi

The branching order of the kingdoms Animalia, Plantae, and Fungi has been a controversial issue. Using the transformed distance method and the maximum parsimony method, we investigated this problem by comparing the sequences of several kinds of macromolecules in organisms spanning all three kingdoms. The analysis was based on the large-subunit and small-subunit ribosomal RNAs, 10 isoacceptor transfer RNA families, and six highly conserved proteins. All three sets of sequences support the same phylogenetic tree: plants and animals are sibling kingdoms that have diverged more recently than the fungi. The ribosomal RNA and protein data sets are large enough so that in both cases the inferred phylogeny is statistically significant. The present report appears to be the first to provide statistically conclusive molecular evidence for the phylogeny of the three kingdoms. The determination of this phylogeny will help us to understand the evolution of various molecular, cellular, and developmental characters shared by any two of the three kingdoms. Noting that the large-subunit rRNA sequences have evolved at similar rates in the three kingdoms, we estimated the ratio of the time since the animal-plant split to the time since the fungal divergence to be 0.90.     

Considerations on the potential use of cliffs and caves by the extinct endemic late pleistocene hippopotami and elephants of Cyprus

Most of the fossil mammal sites on Cyprus, as well as on other Mediterranean islands, consist of large quantities of bones found in caves. Of 32 sites with Phanourios minutus and 21 with Elephas cypriotes on Cyprus, 19 were located in caves, two in rock-shelters, and 11 at open-air sites. Fifteen of them were littoral, four coastal, and 13 inland. The purpose of this paper is to examine possible reasons why Phanourios and Elephas remains accumulated mainly in littoral and coastal caves. Based on an analysis of the behavior exhibited by living hippopotami and elephants, we assume that the extinct large mammals of Cyprus entered these caves in search of fresh water and to protect themselves from the heat in the cool and moist cave environment. A further reason may have been that these mammals entered the caves seeking mineral licks to rectify possible mineral deficiencies, to bind secondary plant compounds such as tannins, or to counteract acidosis. By entering caves, or even passing along narrow paths through cliffs, they were at risk of becoming trapped in natural traps, such as caves with their openings facing upwards, sinkholes, and mire traps. There is no evidence that Phanourios and Elephas remains were accumulated by natural predators because on the island there were no predators large enough to carry such large mammals. The only exception are the remains in the Akrotiri Aetokremnos rock shelter on the Akrotiri peninsula, where there is evidence that the 218,459 Phanourios and 330 Elephas remains were accumulated by the first human settlers of Cyprus, about 10,000 years BP.