Phanerozoic marine diversity: rock record modelling provides an independent test of large-scale trends

Sampling bias created by a heterogeneous rock record can seriously distort estimates of marine diversity and makes a direct reading of the fossil record unreliable. Here we compare two independent estimates of Phanerozoic marine diversity that explicitly take account of variation in sampling—a subsampling approach that standardizes for differences in fossil collection intensity, and a rock area modelling approach that takes account of differences in rock availability. Using the fossil records of North America and Western Europe, we demonstrate that a modelling approach applied to the combined data produces results that are significantly correlated with those derived from subsampling. This concordance between independent approaches argues strongly for the reality of the large-scale trends in diversity we identify from both approaches.     

The fossil record and taphonomy of butterflies and moths (Insecta,Lepidoptera): implications for evolutionary diversity and divergence-time estimates

Background

It is conventionally accepted that the lepidopteran fossil record is significantly incomplete when compared to the fossil records of other, very diverse, extant insect orders. Such an assumption, however, has been based on cumulative diversity data rather than using alternative statistical approaches from actual specimen counts.

Results

We reviewed documented specimens of the lepidopteran fossil record, currently consisting of 4,593 known specimens that are comprised of 4,262 body fossils and 331 trace fossils. The temporal distribution of the lepidopteran fossil record shows significant bias towards the late Paleocene to middle Eocene time interval. Lepidopteran fossils also record major shifts in preservational style and number of represented localities at the Mesozoic stage and Cenozoic epoch level of temporal resolution. Only 985 of the total known fossil specimens (21.4%) were assigned to 23 of the 40 extant lepidopteran superfamilies. Absolute numbers and proportions of preservation types for identified fossils varied significantly across superfamilies. The secular increase of lepidopteran family-level diversity through geologic time significantly deviates from the general pattern of other hyperdiverse, ordinal-level lineages.

Conclusion

Our statistical analyses of the lepidopteran fossil record show extreme biases in preservation type, age, and taxonomic composition. We highlight the scarcity of identified lepidopteran fossils and provide a correspondence between the latest lepidopteran divergence-time estimates and relevant fossil occurrences at the superfamily level. These findings provide caution in interpreting the lepidopteran fossil record through the modeling of evolutionary diversification and in determination of divergence time estimates.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0290-8) contains supplementary material, which is available to authorized users.     

Phylogeny and adaptive diversity of rodents of the family Ctenomyidae (Caviomorpha): delimiting lineages and genera in the fossil record

Differentiation of genera of the modern (Late Miocene to Recent) South American rodent family Ctenomyidae would have been linked to the acquisition of disparate adaptations to digging and life underground. In accordance with this hypothesis, the delimitation of lineages and genera in the ctenomyid fossil record is evaluated here following an adaptation-rooted criterion that involves both an assessment of the monophyly and of the adaptive profiles of recognized clades. The application of such a criterion, including morphofunctional information, delimited four cohesive lineages among crown ctenomyids (i.e. euhypsodont species of the Late Miocene to Recent): Eucelophorus (Early Pliocene–Middle Pleistocene), Xenodontomys-Actenomys (Late Miocene–Pliocene), Praectenomys (Pliocene) and Ctenomys (including Paractenomys ; Pliocene–Recent); in addition, the results supported the status of Xenodontomys as a paraphyletic ancestor of Actenomys . The cladogenesis that gave rise to the crown group would have occurred immediately after the acquisition of euhypsodonty in a Xenodontomys simpsoni -like ancestor during the Late Miocene. This putative ancestor would have had fossorial habits and moderate digging specializations, an adaptive profile maintained in Xenodontomys-Actenomys . Eucelophorus and Ctenomys would have independently evolved subterranean habits at least since the Pliocene. Although the earliest history of the only living representative, Ctenomys , is known only fragmentarily, remains from Esquina Blanca (Uquía Formation), in north-western Argentina, suggest a minimum age of around 3.5 Ma (Early–Late Pliocene) for the differentiation of the genus. This date agrees with recent molecular estimates.     

Rarity in the tropics: biogeography and macroecology of the primates

Aim To describe rarity and elucidate its biology in a tropical mammalian order, the Primates. Location Africa, Central and South America, Asia, Madagascar. Methods A review of the literature, with some additional analyses using data from the literature. A variety of definitions of rarity are used in order to describe it and to investigate its biology by correlating the degree of rarity with a variety of biological traits indicative of resource use (e.g. size of annual home range), reproductive rate (e.g. birth interval)and specialization (e.g. number of habitat types used). Results Few primate taxa occur outside the tropics, and most taxa are rare (small geographical range size or latitudinal extent, low density or both). Latitudinal extent is narrower at lower latitudes in Africa and Asia, but the potential resultant packing of taxa appears not to explain the taxonomic diversity gradient. Whilst primate species do not show the common, positive density by range size relationship, primate genera show a significant shallow slope, and primate families/subfamilies a strongly positive slope. Rare taxa are specialized, but neither use more resources nor breed more slowly than common taxa. The correlation of rarity and specialization is via geographical range: taxa with small ranges, or small ranges for their density, are specialized, but not taxa at low density. Common taxa are generalized because they consist of more differently specialized subtaxa, not because each subtaxon is generalized. Main conclusions Most primate taxa are rare, in which case most are presumably likely to go extinct. Rare primates are specialized, but do not necessarily use more resources, nor breed more slowly. Specialization as an explanation for rarity appears to work via constriction of range size, not of density. Common primates might be common (large range size) not because subtaxa or individuals are generalized, but because they are composed of more subtaxa. A consequence could be that persistence of even common taxa will depend on conservation of several populations scattered across the taxon's geographical range.     

The earliest fossil record of a modern-type piciform bird from the late Oligocene of Germany

Summary Presented here is a record of a piciform bird from a late Oligocene fissure filling from Germany. This is the earliest known fossil record of a modern-type piciform bird and the only one from deposits earlier than Miocene. The specimen, an isolated tarsometatarsus, is similar in size and proportions to the tarsometatarsus of the recent Cardinal-Woodpecker (Dendropicos fuscescens, Picidae). However, owing to its fragmented state a reliable assignment to any of the recent piciform families is not possible.

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Der älteste Nachweis eines modernen Spechtvogels aus dem späten Oligozän Deutschlands

Zusammenfassung Ein Nachweis eines Spechtvogels wird aus einer spätoligozänen Spaltenfüllung Deutschlands beschrieben. Es ist der bisher älteste Nachweis eines modernen Spechtvogels und der einzige aus vor-miozänen Ablagerungen. Das Exemplar, ein isolierter Tarsometatarsus, ähnelt in Größe und Proportionen dem Tarsometatarsus des rezenten Kardinalspechts (Dendropicos fuscescens, Picidae). Aufgrund seiner fragmentarischen Erhaltung ist jedoch keine zuverlässige Zuordnung zu einer der rezenten Familien spechtartiger Vögel möglich.

     

Museum samples provide novel insights into the taxonomy and genetic diversity of Irish red grouse

The taxonomic status of red grouse in Ireland has been the subject of considerable debate over the past century. Irish red grouse are usually classified as Lagopus lagopus scoticus, which is the same subspecies as that found in Britain, but some ornithologists believe that native Irish red grouse constitute an endemic subspecies, namely L. lagopus hibernicus. The considerable decline of Irish red grouse over the past century, along with possible hybridization with introduced grouse from Britain, have highlighted the need to resolve their taxonomic status as part of a biodiversity management plan. However, genetic analysis of samples from a single point in time will provide limited insight into potentially confounding historical events such as hybridization and introgression. We therefore compared mtDNA sequences from both current and historical samples of the two putative subspecies, scoticus and hibernicus, to see if they are or were genetically distinct. Red grouse from Britain and Ireland shared mitochondrial haplotypes, and our historical data suggest that this is unlikely to be the result of recent hybridization and introgression. These findings, combined with a general lack of documented differences in behaviour and ecology, suggest that Irish red grouse should remain classified as L. lagopus scoticus. At the same time, we found evidence that a significant amount of genetic diversity has been lost from Irish red grouse over the past century, presumably as a result of diminishing population sizes and fragmentation of extant populations. A loss of habitat, combined with the declining numbers and genetic diversity of Irish red grouse, justify their designation as an All-Ireland Priority (Red List) species and a Northern Ireland Priority Species for conservation.     

Preface: The phylogeny, fossil record and ecological diversity of ostracod crustaceans

After more than two centuries of research, more than 65,000 living and fossil ostracod species have been described and studied, yet much remains to be learned about this ancient, widespread and diverse group of bivalved arthropods. Their higher classification and phylogeny are subjects of vigorous debate, as is their position in the broader picture of crustacean phylogeny. At the same time, major advances in our understanding of ostracod lineages and their relationships are resulting from the application of innovative approaches and techniques. This preface provides a contextual overview of the 15 contributions to this volume, which resulted from the 14th International Symposium on Ostracoda (ISO2001) held in 2001at Shizuoka, Japan. As such it provides a cross-section of topics at the forefront of research on the evolution and diversity of Ostracoda, and indicates directions for future work.     

Morphological design and fossil record of the podocopid ostracod naupliar eye

The naupliar eye of podocopid ostracods is a useful character for considering evolution in photic environments. Based on external morphologies and histological observations, naupliar eyes are here categorized into six types. The fossil record demonstrates that the major evolutionary changes in podocopid naupliar eyes occured after the Ordovician. Eye types 1 and 2 are not joined to the carapace by the hypodermal cells, and these two types are found in Palaeozoic ostracods. Eye type 3, 4, 5 and 6 are extended on eye stalks, tightly joined to the carapace by the hypodermal cells, and use the carapace as the refractive cuticle lens. Eye type 3 appeared in the Permian, and eye types 4, 5 and 6 appeared in the Early Jurassic. The design of the podocopid naupliar eye diversified in the Early Jurassic.     

Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys

The prokaryotic diversity of culturable thermophilic communities of deep-sea hydrothermal chimneys was analysed using a continuous enrichment culture performed in a gas-lift bioreactor, and compared to classical batch enrichment cultures in vials. Cultures were conducted at 60 degrees C and pH 6.5 using a complex medium containing carbohydrates, peptides and sulphur, and inoculated with a sample of a hydrothermal black chimney collected at the Rainbow field, Mid-Atlantic Ridge, at 2,275 m depth. To assess the relevance of both culture methods, bacterial and archaeal diversity was studied using cloning and sequencing, DGGE, and whole-cell hybridisation of 16S rRNA genes. Sequences of heterotrophic microorganisms belonging to the genera Marinitoga, Thermosipho, Caminicella (Bacteria) and Thermococcus (Archaea) were obtained from both batch and continuous enrichment cultures while sequences of the autotrophic bacterial genera Deferribacter and Thermodesulfatator were only detected in the continuous bioreactor culture. It is presumed that over time constant metabolite exchanges will have occurred in the continuous enrichment culture enabling the development of a more diverse prokaryotic community. In particular, CO(2) and H(2) produced by the heterotrophic population would support the growth of autotrophic populations. Therefore, continuous enrichment culture is a useful technique to grow over time environmentally representative microbial communities and obtain insights into prokaryotic species interactions that play a crucial role in deep hydrothermal environments.     

Linking taphonomy to community-level abundance: Insights into compositional fidelity of the Upper Triassic shell concentrations (Eastern Alps)

Although actualistic live/dead comparisons lead to robust estimates of fidelity of modern death assemblages, quantitative evaluation of fidelity of fossil assemblage remains uncertain. In this paper, effects of storm reworking on compositional fidelity of the Upper Triassic shell concentrations (Eastern Alps, Austria) are evaluated. An exploratory approach is based on comparison of reworked and non-reworked assemblages in ordination analyses. Non-reworked assemblages of one or more communities provide a baseline for evaluation of fidelity of reworked assemblages. In siliciclastic-rich intervals of the Kössen Formation, shell concentrations are represented by (1) packstones with small, shallow infaunal bivalves, (2) floatstones and pavements with large semi-infaunal bivalves, and (3) bioclastic marlstones. In carbonate-rich intervals, bioclastic floatstones with bivalves and brachiopods occur. Analyzing all shell concentrations, eight sample groups sharing similar species composition are discriminated. Limited effect of storm reworking on composition of shell concentrations is indicated by (1) a general persistence of six sample groups when only non-reworked assemblages are analyzed, (2) similarity in composition between reworked and non-reworked assemblages within sample groups, and (3) compositional segregation between non-reworked assemblages of distinctive sample groups, mostly without any reworked assemblages of intermediate composition.Depth-related variations in dead-shell production, shell destruction and body size governed preservation and distribution of the shell concentrations along onshore-offshore gradient in the Kössen Basin. First, at times when environmental conditions were unfavorable for shell producers, coupled with high background shell destruction rates, limestone beds formed during storm events were shell-poor. Second, less common shell concentrations in upper than in lower parts of siliciclastic intervals can be related to higher environmental stress in shallower habitats. Third, the difference between shell concentrations dominated by small and large bivalves is driven by between-habitat differences in body size and is not due to a differential sorting of small and large shells. Combining community analysis based on species abundances with taphonomic analysis can thus be helpful in tracking fidelity of fossil assemblages.     

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.     

The behavioural diversity of Atlantic cod: insights into variability within and between individuals

Cod (Gadus morhua) are an iconic fish species of cultural, historical and economical significance across the Atlantic and adjacent seas. Among many scholarly investigations, this interest has prompted behavioural research, rendering cod one of the few commercially harvested marine fishes for which behaviour has been studied in a comprehensive manner. In our review of this behavioural work, we examine the variability in cod behaviour across five functional domains: foraging, predation, social interactions, migration and reproduction. Research to date suggests a high level of behavioural sophistication in cod that is underpinned by complex learning strategies and long-term memory. Cod also demonstrate substantial variability in how they respond to different ecological circumstances. Considerable variation is evident both within and between individuals, and in some instances, between populations. There are a number of pathways from which this variation appears to arise, such as asocial and social learning, environmental control of phenotypic plasticity and genetic control, but there are no known examples of behaviours that are purely the result of one of these mechanisms. Behavioural variation is therefore likely to result from a combination of these factors, underscoring the need for a quantitative, multivariate approach to understand behavioural variation in cod.     

Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record

Diatoms, unicellular eukaryotic algae with a siliceous skeleton, offer the rare advantage of displaying both an extensive fossil record and numerous extant species, thus providing the opportunity of confronting molecular and paleontological data in a protist group. A portion of the 28S ribosomal RNA was sequenced from 5 diatoms, the divergence times of which are well known. The nucleotide substitution rate was estimated in these unicellular eukaryotes and compared with the rate of multicellular eukaryotes, using a broad data base comprising metazoans and metaphytes. When using fossil record derived divergence times, our results show that the nucleotide substitution rate is about 5 times faster in diatoms than in chordates. But, when using the relative rate test, it is observed that, over a long time period, the nucleotide substitution rate may in fact have been slightly slower in diatoms than in chordates. For this contradiction, two possible explanations are proposed: (i) a failure of the relative rate test, (ii) a gap in the pre-Jurassic diatom fossil record. We have checked that our results concerning the relative rate test were valid. Thus, the second hypothesis, which implies pre-Jurassic diatom evolution, in fact already suggested by some non-molecular evidences, is favoured. Decoupling of morphological differentiation from genetic speciation also appears to have occurred and may account in part for the underestimation of the dates of recent cladogenesis events.     

The effects of pollen diversity on plant reproduction: insights from apple

For many plants, the number of pollen genotypes deposited on a flower’s stigma is positively related to fruit maturation and seed number; however, the mechanisms underlying this effect are less understood. Here we examined whether diversity of pollen (1, 3, or 5 donors) affects reproductive success in self-incompatible apple (Malus × domestica). Using paternity analysis, we then assessed the siring rate of individual donors to test whether diversity effects are related to the presence of a superior pollen donor or to donor × donor interactions. Increasing the diversity of compatible pollen enhanced seed number and reduced seed abortion in some but not all recipient genotypes. This effect was associated with an increased number of sires per fruit and non-random siring success among pollen donors. Two donors had consistently high siring rates, regardless of recipient genotype; however, the siring success of pollen donors was not correlated with their siring success in single-donor pollinations. Rather, siring success was affected by the identity of other pollen genotypes present on the stigma. Our results therefore suggest that the effects of pollen diversity are variable but may enhance fecundity by fostering interactions between pollen donors.     

Genome-wide genetic diversity of Holstein Friesian cattle reveals new insights into Australian and global population variability, including impact of selection

Past breeding strategies for dairy cattle have been very effective in producing rapid genetic gain to achieve industry targets and raise profitability. Such gains have been largely facilitated by intense selection of sires combined with the use of artificial insemination. However, this practice can potentially limit the level of genetic diversity through inbreeding and selection plateaus. The rate of inbreeding in Australia is increasing, primarily as a result of semen importation from a small number of prominent bulls from the USA. The effect of this genetic influx in the Australian dairy cattle population is poorly understood both in terms of diversity and local adaptation/divergence. This study uses 845 genome-wide SNP genetic markers and 431 bulls to characterize the level of genetic diversity and genetic divergence within the Australian and international Holstein Friesian dairy population. No significant differences in genetic diversity (as measured by heterozygosity [H(o)] and allelic richness [A]) were observed over the 25-year time period (1975-1999) for bulls used in Australia. The importation of foreign semen into Australia has increased the effective population size until it was in effect a sub-sample of the global population. Our data indicate that most individuals are equally closely related to one another, regardless of country of origin and year of birth. In effect, the global population can be considered as one single population unit. These results indicate that inbreeding, genetic drift and selection has had little effect at reducing genetic diversity and differentiating the Australian Holstein Friesian population at a genome-wide level.     

The identification of fossil angiosperm pollen and its bearing on the time and place of the origin of angiosperms

Studies in the 1970's reporting the occurrence of fossil pollen types in the Cretaceous, coupled with surveys of extant pollen morphology of primitive flowering plants, laid the foundation for proposing a Lower Cretaceous origin of angiosperms. Over the last 30 years, morphological, ultrastructural, and ontogenetic studies of both extant and fossil pollen have provided an array of new characters, as well as greater resolution in defining character polarities. Moreover, a range of fossil pollen types exhibiting angiosperm characters occur in low frequency within Triassic and Jurassic sediments. The pollen data provide evidence of a pre-Cretaceous origin of angiosperms. Speciation and extinction rates were likely equal during the Triassic and Jurassic, resulting in the paucity of angiosperm pollen types from different geographic areas in the Atlantic – South American/African rift zone. It was not until the Lower Cretaceous that origination rates exceed extinction rates, resulting in the subsequent diversification of angiosperms and the origin of the eudicots.     

Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota

The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.     

The relationship between the concepts of genetic diversity and differentiation

Summary Diversity as a measure of individual variation within a population is widely agreed to reflect the number of different types in the population, taking into account their frequencies. In contrast, differentiation measures variation between two or more populations, demes or subpopulations. As such, it is based on the relative frequencies of types within these subpopulations and, ideally, measures the average distance of subpopulations from their respective lumped remainders. This concept of subpopulation differentiation can be applied consistently to a single population by regarding each individual as a deme (subpopulation) of its own, and it results in a measure of population differentiation _T which depends on the relative frequencies of the types and the population size. _T corresponds to several indices of variation frequently applied in population genetics and ecology, and it verifies these indices as measures of differentiation rather than diversity. For any particular frequency distribution of types, the diversity is then shown to be the size of a hypothetical population in which each type is represented exactly once, i. e. for which _T =1. Hence, the diversity of a population is its differentiation effective number of types. This uniquely specifies the link between the two concepts. Moreover, again corresponds to known measures of diversity applied in population genetics and ecology. While population differentiation can always be estimated from samples, the diversity of a population, particularly if it is large, may not be. In such cases, it is recommended that population differentiation is estimated and the corresponding sample diversity merely computed. Finally, a solution to the problem of measuring multi-locus diversities is provided.