Species Diversity, Biogeography, and the Evolution of Biotas

SYNOPSIS. A central scientific problem for ecologists and systematistshas been to explain spatiotemporal patterns of species diversity.One aspect of this question is how to understand the taxonomicassembly of biotas and their included ecosystems and communities.Four processes add or subtract species from a region: speciation,extinction, biotic dispersion, and long-distance dispersal.Speciation and biotic dispersion are postulated to result inhistorically structured (hierarchical) species assemblages,whereas long-distance dispersal results in assemblages thatwould be expected to be historically unstructured (nonhierarchical).Continental biotas, as exemplified by the Australian avifauna,are historically structured: they are segregated into areasof endemism having hierarchical relationships that presumablyarose as a result of their history being dominated by cyclesof biotic dispersion and vicariance. It is also proposed thatthese latter two processes are necessary, and in many casesprobably sufficient, to explain the taxonomic composition ofcommunities within these areas of endemism. Long-distance dispersalappears to play a much more minor role in the assembly of eithercontinental biotas or their communities than current ecologicaltheory would predict.     

The Impact of Ecology and Biogeography on Legume Diversity,Endemism, and Phylogeny in the Caribbean Region: A New Direction in Historical Biogeography

The legume family is so well represented in the Caribbean that if a preserve was needed somewhere on earth to harbor all of the primary lineages in this family, the flora of just Cuba would suffice. Molecular phylogenetic, biogeographic, and evolutionary rates analysis all suggest that legume diversity and endemism in the Caribbean are mostly of recent origin and are likely a function of the abundance of seasonally dry tropical forests (SDTFs) throughout the neotropics. Legumes have a strong ecological affinity for SDTFs, and the Caribbean basin is well covered by this forest type. Rate-variable molecular clock analysis suggests that the majority of worldwide island lineages of legumes have ages of much less than 30 Ma. Singular historical events invoking land bridges or mobile continental plates are thus not needed to explain Caribbean legume diversity and endemism. The Greater Antilles are large islands located close to the American continent. They are therefore expected to fairly represent the diverse continental lineages of legumes. Yet, they are distant enough to be dispersal limited. As such, island lineages can speciate and diversify over evolutionary time unimpeded by high rates of immigration from the mainland. Vicariance and other standard phylogenetic methods of historical biogeography are likely to be replaced by those of ecological and island biogeography. This is because model selection approaches derived from the neutral concept of isolation by distance will be able to quantify patterns of alpha and beta diversity and detect niche assembly and phylogenetic niche conservatism within and among metacommunities that are hypothesized to constrain phylogeny.     

Biogeography, Evolution, and Diversity of Epibionts in Phototrophic Consortia

Motile phototrophic consortia are highly regular associations in which numerous cells of green sulfur bacteria surround a flagellated colorless β-proteobacterium in the center. To date, seven different morphological types of such consortia have been described. In addition, two immotile associations involving green sulfur bacteria are known. By employing a culture-independent approach, different types of phototrophic consortia were mechanically isolated by micromanipulation from 14 freshwater environments, and partial 16S rRNA gene sequences of the green sulfur bacterial epibionts were determined. In the majority of the lakes investigated, different types of phototrophic consortia were found to co-occur. In all cases, phototrophic consortia with the same morphology from the same habitat contained only a single epibiont phylotype. However, morphologically indistinguishable phototrophic consortia collected from different lakes contained different epibionts. Overall, 19 different types of epibionts were detected in the present study. Whereas the epibionts within one geographic region were very similar (Dice coefficient, 0.582), only two types of epibionts were found to occur on both the European and North American continents (Dice coefficient, 0.190). None of the epibiont 16S rRNA gene sequences have been detected so far in free-living green sulfur bacteria, suggesting that the interaction between epibionts and chemotrophic bacteria in the phototrophic consortia is an obligate interaction. Based on our phylogenetic analysis, the epibiont sequences are not monophyletic. Thus, the ability to form symbiotic associations either arose independently from different ancestors or was present in a common ancestor prior to the radiation of green sulfur bacteria and the transition to the free-living state in independent lineages. The present study thus demonstrates that there is great diversity and nonrandom geographical distribution of phototrophic consortia in the natural environment.     

Description of a Well Preserved Fetus of the European Eocene Equoid Eurohippus messelensis

The early Middle Eocene locality of Grube Messel, near Darmstadt (Germany), is famous for its complete vertebrate skeletons. The degree of preservation of soft tissues, such as body silhouettes, internal organs and gut contents, is frequently remarkable. The present specimen was analyzed for remnants of the reproductive system. Classic anatomy and osteology and high-resolution micro-x-ray were applied to describe the fetus of the European Eocene equoid Eurohippus messelensis. Scanning electronic microscopy (SEM) was used for determination of soft tissue remnants. The fetus is the earliest and best-preserved fossil specimen of its kind. The postcranial fetal skeleton is almost complete and largely articulated, allowing the conclusion that the pregnant mare was in late gestation. The apparent intrauterine position of the fetus is normal for the phase of pregnancy. Death of mare and fetus were probably not related to problems associated with parturition. Soft tissue interpreted as the uteroplacenta and a broad uterine ligament are preserved due to bacterial activity and allow considerations on the evolutionary development of the structures.     

Description of three new Triaenodes species from Fiji (Trichoptera,Leptoceridae)

The following three new species are illustrated and described from Fiji: Triaenodes rebellus Eriksson & Johanson, sp. n., Triaenodes oscitus Müller & Johanson, sp. n., and Triaenodes forcipatus Puranen Li & Johanson, sp. n. All species are endemic to Viti Levu. A key to the male Triaenodes species of Fiji is provided. With this report, the number of Triaenodes species known from Fiji is doubled.     

Caudal Pneumaticity and Pneumatic Hiatuses in the Sauropod Dinosaurs Giraffatitan and Apatosaurus

Skeletal pneumaticity is found in the presacral vertebrae of most sauropod dinosaurs, but pneumaticity is much less common in the vertebrae of the tail. We describe previously unrecognized pneumatic fossae in the mid-caudal vertebrae of specimens of Giraffatitan and Apatosaurus. In both taxa, the most distal pneumatic vertebrae are separated from other pneumatic vertebrae by sequences of three to seven apneumatic vertebrae. Caudal pneumaticity is not prominent in most individuals of either of these taxa, and its unpredictable development means that it may be more widespread than previously recognised within Sauropoda and elsewhere in Saurischia. The erratic patterns of caudal pneumatization in Giraffatitan and Apatosaurus, including the pneumatic hiatuses, show that pneumatic diverticula were more broadly distributed in the bodies of the living animals than are their traces in the skeleton. Together with recently published evidence of cryptic diverticula—those that leave few or no skeletal traces—in basal sauropodomorphs and in pterosaurs, this is further evidence that pneumatic diverticula were widespread in ornithodirans, both across phylogeny and throughout anatomy.     

Biogeography and Landscape-Scale Diversity of the Dominant Crenarchaeota of Soil

We surveyed the diversity of soil Archaea across a large scale elevational gradient of ecosystem types, from foothills forest to alpine tundra in the Front Range of the Rocky Mountains. We used a dilution technique to sequence the single most abundant archaeal 16S rDNA sequence in each of the 40 soil cores distributed across the gradient to compare our results to those of typical 16S clone library studies.We found a greater diversity of sequences than has typically been found in clone library studies from a single site or core, identifying sequences both from the Terrestrial Group and the FFSB Group at several sites. We did not observe any significant environmental correlates with the dominant sequence type, nor was there any relationship between the spatial distance between samples and the phylogenetic similarity of the dominant sequence types. Despite using a very different methodology, our collective results are in remarkably good agreement with other studies of soil Crenarchaeota in terms of the diversity and relative abundance of sequence types identified. We are able to identify two instances of very tightly clustered sequences which we suggest are the results of global selective sweeps—one closely related to SCA1145, an abundant globally distributed group within the Terrestrial Group of Crenarchaeota, and another nested within the more basal FFSB group of sequences. We replicated our sequence results at two levels: first, by repeating the dilution and PCR processes from the same soil core DNA extraction, and second, by performing a replicate DNA extraction from the same homogenized soil core sample. Pairs of sequences produced by the dilution replicates were significantly more similar than the pairs of sequences produced by the extraction replicates, suggesting that soil Crenarchaeota exists in highly localized and discrete clonal populations.     

New Mid-Cretaceous (Latest Albian) Dinosaurs from Winton,Queensland, Australia

Background

Australia''s dinosaurian fossil record is exceptionally poor compared to that of other similar-sized continents. Most taxa are known from fragmentary isolated remains with uncertain taxonomic and phylogenetic placement. A better understanding of the Australian dinosaurian record is crucial to understanding the global palaeobiogeography of dinosaurian groups, including groups previously considered to have had Gondwanan origins, such as the titanosaurs and carcharodontosaurids.

Methodology/Principal Findings

We describe three new dinosaurs from the late Early Cretaceous (latest Albian) Winton Formation of eastern Australia, including; Wintonotitan wattsi gen. et sp. nov., a basal titanosauriform; Diamantinasaurus matildae gen. et sp. nov., a derived lithostrotian titanosaur; and Australovenator wintonensis gen. et sp. nov., an allosauroid. We compare an isolated astragalus from the Early Cretaceous of southern Australia; formerly identified as Allosaurus sp., and conclude that it most-likely represents Australovenator sp.

Conclusion/Significance

The occurrence of Australovenator from the Aptian to latest Albian confirms the presence in Australia of allosauroids basal to the Carcharodontosauridae. These new taxa, along with the fragmentary remains of other taxa, indicate a diverse Early Cretaceous sauropod and theropod fauna in Australia, including plesiomorphic forms (e.g. Wintonotitan and Australovenator) and more derived forms (e.g. Diamantinasaurus).     

Origins,Diversity and Relationships of Lemurs

I review new evidence on origins and adaptive radiation of Malagasy lemurs, a remarkably diverse group containing 13% of living primate species. The number of recognized lemur species has increased significantly, partly due to research revealing specific subdivisions within known populations but mainly because of discovery of new populations through fieldwork. Some species feared to be extinct have also been rediscovered. Specific numbers have increased particularly in small-bodied, cryptic genera for which continued research will surely reveal even more species.Adaptative radiation of lemurs has been essentially confined to Madagascar. The high density of lemur species on that island, associated with very small geographical ranges, has major implications both for their evolutionary divergence and for conservation. Reconstructions of phylogenetic relationships among primates have been considerably enhanced by DNA sequence data. Sufficient data are now available from both nuclear and mitochondrial sequences to examine relationships among and within the major groups of living primates. Most studies have confirmed that lemurs constitute a monophyletic sister-group of the lorisiform clade and all exclude a specific relationship between cheirogaleids and lorisiforms repeatedly inferred from morphological evidence. However, some analyses indicate that the aye-aye may have branched away before the divergence between other lemurs and lorisiforms. DNA sequence analyses have also yielded a broad consensus for relationships between Eulemur, Hapalemur, Lemur and Varecia: Varecia branched away first, while Lemur is more closely related to Hapalemur than to Eulemur. As debate about phylogenetic relationships among lemurs and other primates seems to have been settled in favor of lemur monophyly (possibly excluding the aye-aye), only a single invasion of Madagascar is required; but it must still be explained how ancestral lemurs could have migrated there at an appropriate time. Separation between Madagascar and Africa was apparently complete by about 120 Ma, too far in the past for direct overland migration. A recent hypothesis suggested that uplifted land in the Mozambique Channel assisted colonization of Madagascar 26-45 Ma, seemingly agreeing with an estimated date of about 40 Ma for divergence of lemurs from other primates. However, mounting evidence suggests that divergence occurred significantly earlier. Because the earliest known fossil representatives of several modern orders of placental mammals (including primates) are dated no earlier than the early Tertiary, it is widely accepted that their divergence took place after the Cretaceous/Tertiary mass extinction. Yet the known fossil record can only yield minimum divergence times; if sampling is poor and/or biased there may be a considerable discrepancy between minimum and actual dates. There is, for example, virtually no known fossil record for lemurs in Madagascar and the earliest known representatives are subfossil lemurs, so in this case a direct reading of the fossil record would indicate that the lemurs first originated just a few thousand years ago! Examination of underestimation of times of origin because of poor sampling in the fossil record has confirmed previous suggestions that primates originated considerably earlier than generally believed. Several recent phylogenetic reconstructions based on DNA sequence data and using calibration dates derived from groups other than primates provide independent support for this inference. Overall, it now seems that primates originated at around 90 Ma rather than the 55 Ma indicated by direct reading of the known fossil record. Hence, colonization of Madagascar by lemurs would have taken place at about 80 Ma, double the date usually accepted, and should be interpreted in terms of contemporary continental relationships.     

Description of the Blueberry Root-knot Nematode,Meloidogyne carolinensis n. sp.

Meloidogyne carolinensis n. sp. is described from cultivated highbush blueberry (cultivars derived from hybrids of Vaccinium corymbosum L. and V. lamarckii Camp) in North Carolina. The perineal pattern of the female has a large cuticular ridge that surrounds the perivulval area, and the excretory pore is near the level of the base of the stylet. The stylet is 15.9 μm long and the knobs gradually merge with the shaft. The head shape and stylet morphology of the male are quite variable. The typical head and four variants, as well as the typical stylet and two variants, are described. The labial disc, medial lips, and lateral lips of second-stage juveniles are fused and in the same contour. The head region is not annulated. Mean juvenile length is 463.7 μm, stylet length is 11.9 μm, and tail length is 42.5 μm.     

Description of Trichodryas slipinskii sp. n. from China (Coleoptera,Dermestidae, Trinodinae)

Trichodryas slipinskiisp. n. from Yunnan Province of China is described and illustrated. A key to the known species of this genus is provided.     

Systematics,Taxonomy, and the New Flora of the Bahamian Archipelago

A history of botanical exploration in the Bahama Archipelago is given, and is presented in three sections. The first section begins with the earliest botanical collections in 1700 by Thomas Walker and describes, in chronological order, botanical collections made up to 1920, when Britton and Millspaugh published the first Bahama flora. The second section chronicles botanical research in the archipelago after 1920, up until the publication by Correll and Correll of the Flora of the Bahama Archipelago in 1982. The third section describes plant research in the archipelago between 1982 and the present day. Following a brief rationale for the need for a new flora, the present research toward the flora is discussed, and an example of changes in the flora since 1982 is presented, with changes in the fern flora tabulated.     

New Data on Dinosaurs of the Crimean Peninsula

Reexamination of the holotype of Riabininohadros weberae from the Upper Cretaceous (upper Maastrichtian) of the Crimean Peninsula (Besh-Kosh) allowed determination of previously unknown elements of the femur, astragalus, and calcaneus. This taxon shows a set of primitive characters observed in iguanodontids and basal ornithischians and is referred to as Styracosterna indet. The second dinosaur specimen from Crimea (Aleshino) is a fragmentary skeleton, including cervical and dorsal vertebrae. It possibly belongs to advanced iguanodontids or primitive hadrosauroids. Thus, in the Maastrichtian of the Crimean Peninsula, at least two dinosaur species coexisted.     

Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity,Ecology, and Evolution

New questions about microbial ecology and diversity combined with significant improvement in the resolving power of molecular tools have helped the reemergence of the field of prokaryotic biogeography. Here, we show that biogeography may constitute a cornerstone approach to study diversity patterns at different taxonomic levels in the prokaryotic world. Fundamental processes leading to the formation of biogeographic patterns are examined in an evolutionary and ecological context. Based on different evolutionary scenarios, biogeographic patterns are thus posited to consist of dramatic range expansion or regression events that would be the results of evolutionary and ecological forces at play at the genotype level. The deterministic or random nature of those underlying processes is, however, questioned in light of recent surveys. Such scenarios led us to predict the existence of particular genes whose presence or polymorphism would be associated with cosmopolitan taxa. Furthermore, several conceptual and methodological pitfalls that could hamper future developments of the field are identified, and future approaches and new lines of investigation are suggested.     

The Diversity and Biogeography of Western Indian Ocean Reef-Building Corals

This study assesses the biogeographic classification of the Western Indian Ocean (WIO) on the basis of the species diversity and distribution of reef-building corals. Twenty one locations were sampled between 2002 and 2011. Presence/absence of scleractinian corals was noted on SCUBA, with the aid of underwater digital photographs and reference publications for species identification. Sampling effort varied from 7 to 37 samples per location, with 15 to 45 minutes per dive allocated to species observations, depending on the logistics on each trip. Species presence/absence was analyzed using the Bray-Curtis similarity coefficient, followed by cluster analysis and multi-dimensional scaling. Total (asymptotic) species number per location was estimated using the Michaelis-Menten equation. Three hundred and sixty nine coral species were named with stable identifications and used for analysis. At the location level, estimated maximum species richness ranged from 297 (Nacala, Mozambique) to 174 (Farquhar, Seychelles). Locations in the northern Mozambique Channel had the highest diversity and similarity, forming a core region defined by its unique oceanography of variable meso-scale eddies that confer high connectivity within this region. A distinction between mainland and island fauna was not found; instead, diversity decreased radially from the northern Mozambique Channel. The Chagos archipelago was closely related to the northern Mozambique Channel region, and analysis of hard coral data in the IUCN Red List found Chagos to be more closely related to the WIO than to the Maldives, India and Sri Lanka. Diversity patterns were consistent with primary oceanographic drivers in the WIO, reflecting inflow of the South Equatorial Current, maintenance of high diversity in the northern Mozambique Channel, and export from this central region to the north and south, and to the Seychelles and Mascarene islands.     

Actinobacteria Cyclophilins: Phylogenetic Relationships and Description of New Class- and Order-Specific Paralogues

Cyclophilins are folding helper enzymes belonging to the class of peptidyl-prolyl cis-trans isomerases (PPIases; EC 5.2.1.8) that catalyze the cis-trans isomerization of peptidyl-prolyl bonds in proteins. They are ubiquitous proteins present in almost all living organisms analyzed to date, with extremely rare exceptions. Few cyclophilins have been described in Actinobacteria, except for three reported in the genus Streptomyces and another one in Mycobacterium tuberculosis. In this study, we performed a complete phylogenetic analysis of all Actinobacteria cyclophilins available in sequence databases and new Streptomyces cyclophilin genes sequenced in our laboratory. Phylogenetic analyses of cyclophilins recovered six highly supported groups of paralogy. Streptomyces appears as the bacteria having the highest cyclophilin diversity, harboring proteins from four groups. The first group was named "A" and is made up of highly conserved cytosolic proteins of approximately 18 kDa present in all Actinobacteria. The second group, "B," includes cytosolic proteins widely distributed throughout the genus Streptomyces and closely related to eukaryotic cyclophilins. The third group, "M" cyclophilins, consists of high molecular mass cyclophilins ( approximately 30 kDa) that contain putative membrane binding domains and would constitute the only membrane cyclophilins described to date in bacteria. The fourth group, named "C" cyclophilins, is made up of proteins of approximately 18 kDa that are orthologous to Gram-negative proteobacteria cyclophilins. Ancestral character reconstruction under parsimony was used to identify shared-derived (and likely functionally important) amino acid residues of each paralogue. Southern and Western blot experiments were performed to determine the taxonomic distribution of the different cyclophilins in Actinobacteria.     

Environmental Mapping of Paracoccidioides spp. in Brazil Reveals New Clues into Genetic Diversity,Biogeography and Wild Host Association

BackgroundParacoccidioides brasiliensis and Paracoccidioides lutzii are the etiological agents of Paracoccidioidomycosis (PCM), and are easily isolated from human patients. However, due to human migration and a long latency period, clinical isolates do not reflect the spatial distribution of these pathogens. Molecular detection of P. brasiliensis and P. lutzii from soil, as well as their isolation from wild animals such as armadillos, are important for monitoring their environmental and geographical distribution. This study aimed to detect and, for the first time, evaluate the genetic diversity of P. brasiliensis and P. lutzii for Paracoccidioidomycosis in endemic and non-endemic areas of the environment, by using Nested PCR and in situ hybridization techniques.Conclusions/SignificanceData may reflect the actual occurrence of Paracoccidioides species in their saprobic habitat, despite their absence/non-detection in seven armadillos evaluated in regions with high prevalence of PCM infection by P. lutzii. These results may indicate a possible ecological difference between P. brasiliensis and P. lutzii concerning their wild hosts.