Diversity biases in terrestrial mammalian assemblages and quantifying the differences between museum collections and published accounts: A case study from the Miocene of Nevada

Understanding diversity through time in the fossil record has primarily relied on the raw count of species within a given time interval, or species richness. These estimates are often derived from published fossil data, and standardized for sample size or geographic area. However, most methods that standardize richness by sample size are sensitive to changes in evenness, which introduces a potential problem with relying on published records: published accounts could be more even than the museum collections from which they are drawn. We address this bias in the context of mammalian paleodiversity, comparing published and museum collections of the Hemphillian Thousand Creek fauna to those of the Barstovian Virgin Valley fauna. We rarified specimen data, both number of identified specimens (NISP) and minimum number of individuals (MNI), and presence/absence data to compare published and museum data within and between faunas. Within faunas, published numbers of specimens are more even than museum samples, but the difference for localities in Virgin Valley is not significant. Neither published nor museum numbers of specimens indicate a significant difference between faunas, but the diversity pattern is reversed between the two data sets. Presence/absence rarefactions show no differences between sources; here, published data adequately sample the underlying museum records. Specimen-based evenness is not accurate in the published sample, and therefore we suggest that future studies of diversity in terrestrial mammalian assemblages must assess unpublished collections. Additionally, NISP data for Thousand Creek are more even than MNI data, suggesting that relying solely on NISP for assessing species diversity can also be misleading. Because publication bias alters richness and evenness, diversity estimates using published data must be circumspect about data sources.     

Variation in larval chaetotaxy in Orthosia gothica (Lepidoptera: Noctuidae): effects of mother,sex and side,and implications for systematics

Insect larval characteristics, including chaetotaxy, are used widely in systematics, including for classification and phylogenetic reconstruction. Despite their common use, basic aspects of larval morphology, including intraspecific variation, effects of relatedness between individuals, sex and asymmetry, are little investigated. In the larvae of the noctuid moth Orthosia gothica, properties of shape and size were separated to examine their effects separately. Siblings were found not to cover the entire variation of a population, and therefore specimens originating from a single female do not represent independent samples. This methodological bias may potentially lead to wrong conclusions regarding species characteristics. We observed slight differences between the left and right sides of the specimens studied, implying that one side should be examined consistently in studying larval chaetotaxy. We found no differences between sexes, but this may apply only to the species examined here; in general, sex should be determined and accounted for. We discovered considerable variation in seta numbers, which further emphasizes the importance of sufficient material, particularly in cladistic analyses in which setal counts are often used as characters.     

The Hemiptera (Insecta) of Canada: Constructing a Reference Library of DNA Barcodes

DNA barcode reference libraries linked to voucher specimens create new opportunities for high-throughput identification and taxonomic re-evaluations. This study provides a DNA barcode library for about 45% of the recognized species of Canadian Hemiptera, and the publically available R workflow used for its generation. The current library is based on the analysis of 20,851 specimens including 1849 species belonging to 628 genera and 64 families. These individuals were assigned to 1867 Barcode Index Numbers (BINs), sequence clusters that often coincide with species recognized through prior taxonomy. Museum collections were a key source for identified specimens, but we also employed high-throughput collection methods that generated large numbers of unidentified specimens. Many of these specimens represented novel BINs that were subsequently identified by taxonomists, adding barcode coverage for additional species. Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna. We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance. The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided.     

Methods of studying the distribution, diversity and abundance of birds in East Africa—some quantitative approaches

In this paper we compare the use of transect counts with a simpler method of investigating bird diversity and numbers, particularly in terrestrial habitats, both natural and non‐natural. Transect Counts (TCs) have long been widely used, whereas Timed Species Counts (TSCs), which estimate relative abundance, are comparatively untried. We find that TSCs give results which are comparable to those from TCs in most respects, except that they can only be used indirectly for estimating population densities, and they give different measures of diversity. However, TSCs generate data on many more species much faster than do TCs and are therefore more cost‐effective in most situations. In particular, TSCs are useful for community studies. We show, for example, that in natural habitats bird populations are positively correlated with the amount of woody vegetation, but not with rainfall. Diversity too increases with woody vegetation. Because TSCs are simple, more of them can be made for a given input of time, and hence more distributional data are obtained as an additional benefit.     

Habiline variation: A new approach using STET

The problem of whether the hominid fossil sample of habiline specimens is comprised of more than one species has received much attention in paleoanthropology. The core of this debate has critical implications about when and how variation can be explained by taxonomy. In this paper, we examine the problem of whether the observed variation in habiline samples reflects species differences. We test the null hypothesis of no difference by examining the degree of variability in habiline sample in comparison with other single-species early hominid fossil samples from Sterkfontein and Swartkrans (Sterkfontein is earlier than the habiline sample, Swartkrans may be within the habiline time span). We developed a new method for this examination, which we call STandard Error Test of the null hypothesis of no difference (STET). Our sampling statistic is based on the standard error of the slope of regressions between pairs of specimens, relating all of the homologous measurements that each pair shares. We show that the null hypothesis for the habiline sample cannot be rejected. The similarities of specimen pairs within the habiline sample are not more than those observed between the specimens in the australopithecine samples we analyzed.     

MOTUs, Morphology, and Biodiversity Estimation: A Case Study Using Nematodes of the Suborder Criconematina and a Conserved 18S DNA Barcode

DNA barcodes are increasingly used to provide an estimate of biodiversity for small, cryptic organisms like nematodes. Nucleotide sequences generated by the barcoding process are often grouped, based on similarity, into molecular operational taxonomic units (MOTUs). In order to get a better understanding of the taxonomic resolution of a 3' 592-bp 18S rDNA barcode, we have analyzed 100 MOTUs generated from 214 specimens in the nematode suborder Criconematina. Previous research has demonstrated that the primer set for this barcode reliably amplifies all nematodes in the Phylum Nematoda. Included among the Criconematina specimens were 25 morphologically described species representing 12 genera. Using the most stringent definition of MOTU membership, where a single nucleotide difference is sufficient for the creation of a new MOTU, it was found that an MOTU can represent a subgroup of a species (e.g. Discocriconemella limitanea), a single species (Bakernema inaequale), or a species complex (MOTU 76). A maximum likelihood phylogenetic analysis of the MOTU dataset generated four major clades that were further analyzed by character-based barcode analysis. Fourteen of the 25 morphologically identified species had at least one putative diagnostic nucleotide identified by this character-based approach. These diagnostic nucleotides could be useful in biodiversity assessments when ambiguous results are encountered in database searches that use a distance-based metric for nucleotide sequence comparisons. Information and images regarding specimens examined during this study are available online.     

Cloned endangered species takin (Budorcas taxicolor) by inter-species nuclear transfer and comparison of the blastocyst development with yak (Bos grunniens) and bovine

Interspecies cloning might be used as an effective method to conserve endangered species and to support the study of nuclear-cytoplasm interaction. In this study, we describe the development of takin-bovine embryos in vitro produced by fusing takin ear fibroblasts with enucleated bovine oocytes and examine the fate of mitochondrial DNA in these embryos. We also compare the blastocyst development of takin-bovine embryos with yak-bovine and bovine-bovine embryos and compare the cell numbers of the blastocyst. Our results indicate that: (1) takin-bovine cloned embryos can develop to the blastocyst stage in vitro (5%), (2) blastocyst mitochondria DNA are derived primarily from bovine oocytes in spite of a little takin donor cell mitochondrial DNA, (3) using the same cloned protocol, development efficiency is significantly different between bovine-bovine cloning, yak-bovine, and takin-bovine cloning (48 vs. 28% vs. 5%, P < 0.01), and (4) cell numbers in the blastocysts of the three species of embryos were not different. These results suggest that the bovine oocytes can reprogram the takin, yak, and bovine fibroblast nuclei. However, the development efficiency of intra-species cloning tends to be higher than inter-species cloning; the more close the species of the donor cell is to the recipient oocyte (yak versus takin), the greater the blastocyst development in vitro.     

Measurement of grey parrot (Psittacus erithacus) trachea via magnetic resonance imaging,dissection, and electron beam computed tomography

To produce a model to explain the acoustic properties of human speech sounds produced by Grey parrots (Psittacus erithacus) and to compare these properties across species (e.g., with humans, other psittacine and nonpsittacine mimics), researchers need adequate measurements of the chambers that constitute the parrot vocal tract. Various methods can provide such data. Here we compare results for tracheal measurements provided by a) magnetic resonance imaging (MRI) of a live bird, b) caliper measurements of four preserved specimens, and c) electron beam computed tomography (EBCT) of three of these preserved specimens. We find that EBCT scans provide data that correspond to the inner area of the dissected trachea, whereas MRI results correspond to area measurements that include tracheal ring thickness. We briefly discuss how these data may predict formant values for Grey parrot reproduction of human vowels. Our results suggest how noninvasive techniques can be used for cross-species comparisons, including the coevolution of structure and function in avian mimicry. J. Morphol. 238:81–91, 1998. © 1998 Wiley-Liss, Inc.     

Lessons learned from microsatellite development for nonmodel organisms using 454 pyrosequencing

Microsatellites, also known as simple sequence repeats (SSRs), are among the most commonly used marker types in evolutionary and ecological studies. Next Generation Sequencing techniques such as 454 pyrosequencing allow the rapid development of microsatellite markers in nonmodel organisms. 454 pyrosequencing is a straightforward approach to develop a high number of microsatellite markers. Therefore, developing microsatellites using 454 pyrosequencing has become the method of choice for marker development. Here, we describe a user friendly way of microsatellite development from 454 pyrosequencing data and analyse data sets of 17 nonmodel species (plants, fungi, invertebrates, birds and a mammal) for microsatellite repeats and flanking regions suitable for primer development. We then compare the numbers of successfully lab‐tested microsatellite markers for the various species and furthermore describe diverse challenges that might arise in different study species, for example, large genome size or nonpure extraction of genomic DNA. Successful primer identification was feasible for all species. We found that in species for which large repeat numbers are uncommon, such as fungi, polymorphic markers can nevertheless be developed from 454 pyrosequencing reads containing small repeat numbers (five to six repeats). Furthermore, the development of microsatellite markers for species with large genomes was also with Next Generation Sequencing techniques more cost and time‐consuming than for species with smaller genomes. In this study, we showed that depending on the species, a different amount of 454 pyrosequencing data might be required for successful identification of a sufficient number of microsatellite markers for ecological genetic studies.     

陕西蓝田锡水洞遗址大型哺乳动物保存特征与古人类行为分析

陕西蓝田锡水洞中产出许多中更新世哺乳类化石,这些标本残破者较多。对880件标本作埋藏学分析后发现:其中只有376件较完好,可供分类鉴定;根据身体大小,这些可鉴定的标本可分为较大、中等及较小3类,大个体动物的骨骼保存越破碎;98%的骨骼的风化级别为0—2,只有2%的风化较强,达3—5级;属草食动物的骨骼占97.6%,而食肉类的仅占1.7%;以青羊为例,死亡年龄以中青年为主,为灾变死亡;头骨残破,肢骨近端破碎严重,而远端肢梢几乎完好。种种迹象表明,与古人类活动有关。当时居住在锡水洞中的古人类以草食动物为主要猎取对象,敲骨吸髓,还可用骨作器。     

Integrating DNA data and traditional taxonomy to streamline biodiversity assessment: an example from edaphic beetles in the Klamath ecoregion, California, USA

Conservation and land management decisions may be misguided by inaccurate or misinterpreted knowledge of biodiversity. Non‐systematists often lack taxonomic expertise necessary for an accurate assessment of biodiversity. Additionally, there are far too few taxonomists to contribute significantly to the task of identifying species for specimens collected in biodiversity studies. While species level identification is desirable for making informed management decisions concerning biodiversity, little progress has been made to reduce this taxonomic deficiency. Involvement of non‐systematists in the identification process could hasten species identification. Incorporation of DNA sequence data has been recognized as one way to enhance biodiversity assessment and species identification. DNA data are now technologically and economically feasible for most scientists to apply in biodiversity studies. However, its use is not widespread and means of its application has not been extensively addressed. This paper illustrates how such data can be used to hasten biodiversity assessment of species using a little‐known group of edaphic beetles. Partial mitochondrial cytochrome oxidase I was sequenced for 171 individuals of feather‐wing beetles (Coleoptera: Ptiliidae) from the Klamath ecoregion, which is part of a biodiversity hotspot, the California Floristic Province. A phylogram of these data was reconstructed via parsimony and the strict consensus of 28,000 equally parsimonious trees was well resolved except for peripheral nodes. Forty‐two voucher specimens were selected for further identification from clades that were associated with many synonymous and non‐synonymous nucleotide changes. A ptiliid taxonomic expert identified nine species that corresponded to monophyletic groups. These results allowed for a more accurate assessment of ptiliid species diversity in the Klamath ecoregion. In addition, we found that the number of amino acid changes or percentage nucleotide difference did not associate with species limits. This study demonstrates that the complementary use of taxonomic expertise and molecular data can improve both the speed and the accuracy of species‐level biodiversity assessment. We believe this represents a means for non‐systematists to collaborate directly with taxonomists in species identification and represents an improvement over methods that rely solely on parataxonomy or sequence data.     

The identification of Cryptosporidium species (protozoa) in Ifsahan, Iran by PCR-RFLP analysis of the 18S rRNA gene

Cryptosporidium is an important protozoan that cause diarrheal illness in humans and animals. Different species of Cryptosporidium have been reported and it is believed that species characteristics are an important factor to be considered in strategic planning for control. We therefore analyzed oocysts from human and animal isolates of Cryptosporidium by PCR-RFLP to determine strain variation in Isfahan. In total, 642 human fecal samples from children under five years of age, immunocompromised patients, and high risk persons and 480 randomly selected rectal specimens of cows and calves in Isfahan were examined. Microscopic examination showed that 4.7% (30/642) of human samples and 6.2% (30/480) of animal samples were infected with Cryptosporidium. After identification of the samples infected with the parasite, oocysts were purified and their DNA was extracted. We used PCR-RFLP analysis of a 1750-bp region of 18S rRNA gene to identify Cryptosporidium species. The human samples were infected with Cryptosporidium parvum II, C. muris, C. wrairi, and a new genotype of Cryptosporidium (GenBank accession numbers: DQ520951). The cattle samples were identified as C. parvum II, C. muris, C. wrairi, C. serpentis, C. baileyi, and a new genotype of Cryptosporidium (GenBank accession numbers: DQ520952). Also we found a new genotype infecting both human and cattle samples (GenBank accession numbers: DQ520950). In addition to demonstrating the widespread occurrence of most species of Cryptosporidium, C. parvum, we also observed extensive polymorphism within species. Furthermore, the occurrence of the same species of parasite in both animal and human samples shows the importance of the animal-human cycle.     

Barcoding,molecular taxonomy,and exploration of the diversity of shrews (Soricomorpha: Soricidae) on Mount Nimba (Guinea)

We tested the efficiency of cytochrome oxidase I (COI)‐barcoding as a taxonomic tool to discriminate and identify sympatric shrew species on Mount Nimba (Guinea). We identified 148 specimens at the species level using morphological characters and comparison with type specimens, including several taxa from Mount Nimba. We identified ten morphospecies and tested aspects of genetic diversity and monophyly using genetic data from three mitochondrial (16S, cytochrome b, and COI) and one nuclear marker (the breast cancer gene, BRCA). Nine morphospecies were validated under the phylogenetic and genetic species concepts, including the recently diverged species Crocidura buettikoferi, Crocidura theresae, and Crocidura grandiceps. Under the same concepts, our analyses revealed the presence of two cryptic species amongst animals identified as Crocidura muricauda. We then tested the efficiency of barcoding thanks to commonly used phenetic methods, with the 148 specimens representing 11 potentially valid species based on morphological and molecular data. We show that COI‐barcoding is a powerful tool for shrew identification and can be used for taxonomic surveys. The comparison of genetic divergence values shows the presence of a barcoding gap (i.e. difference between the highest intraspecific and the lowest interspecific genetic divergence values). Given that only a few COI sequences are available for Afrotropical shrews, our work is an important step forward toward their enrichment. We also tested the efficiency of the three other sequenced markers and found that cytochrome b is as efficient as COI for barcoding shrews. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 672–687.     

Making endangered species safe: the case of the kokako of North Island, New Zealand

The theory of population regulation predicts that threatened species are safest at high population numbers, partly because density-dependent compensatory mechanisms counteract unpredictable disturbances. We illustrate this principle using data from the endemic kokako (Callaeas cinerea wilsoni) populations in the North Island, New Zealand. First we calculate the fledging rate per female (production) necessary to stabilise the population and thereby the residual numbers of nest predators, namely ship rats and possums, which have to be achieved to reach this production. Both predator species must be reduced to low densities to exceed this threshold production. At these low predator densities kokako numbers increase rapidly, and we predict that the population will at some stage experience density-dependent negative feedback producing a declining rate of increase. We review evidence for such feedback at Mapara. More research is required to verify and understand these density-dependent causes of loss at high density, particularly the role of territoriality and intra-specific and inter-specific competition, and to generalise across species. In addition to the increased resilience of a threatened species when at high numbers, the degree of predator removal can be relaxed. Consequently, the cost of management will also decline.     

Contributions of Speed and Accuracy to Translational Selection in Bacteria

Among bacteria, we have previously shown that species that are capable of rapid growth have stronger selection on codon usage than slow growing species, and possess higher numbers of rRNA and tRNA genes. This suggests that fast-growers are adapted for fast protein synthesis. There is also considerable evidence that codon usage is influenced by accuracy of translation, and some authors have argued that accuracy is more important than speed. Here we compare the strength of the two effects by studying the codon usages in high and low expression genes and on conserved and variable sites within high expression genes. We introduce a simple statistical method that can be used to assess the significance and the strength of the two types of bias in the same sets of sequences. We compare our statistical measure of codon bias to the common used codon adaptation index, and show that the new measure is preferable for three reasons for the purposes of this analysis. Across a large sample of bacterial genomes, both effects from speed and accuracy are clearly visible, although the speed effect appears to be much stronger than the accuracy effect and is found to be significant in a larger proportion of genomes. It is also difficult to explain the correlation of codon bias in the high expression genes with growth rates and numbers of copies of tRNA and rRNA genes on the basis of selection for accuracy. Hence we conclude that selection for translational speed is a dominant effect in driving codon usage bias in fast-growing bacteria, with selection for accuracy playing a small supplementary role.     

Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip

Genome-wide association studies are revolutionizing the search for the genes underlying human complex diseases. The main decisions to be made at the design stage of these studies are the choice of the commercial genotyping chip to be used and the numbers of case and control samples to be genotyped. The most common method of comparing different chips is using a measure of coverage, but this fails to properly account for the effects of sample size, the genetic model of the disease, and linkage disequilibrium between SNPs. In this paper, we argue that the statistical power to detect a causative variant should be the major criterion in study design. Because of the complicated pattern of linkage disequilibrium (LD) in the human genome, power cannot be calculated analytically and must instead be assessed by simulation. We describe in detail a method of simulating case-control samples at a set of linked SNPs that replicates the patterns of LD in human populations, and we used it to assess power for a comprehensive set of available genotyping chips. Our results allow us to compare the performance of the chips to detect variants with different effect sizes and allele frequencies, look at how power changes with sample size in different populations or when using multi-marker tags and genotype imputation approaches, and how performance compares to a hypothetical chip that contains every SNP in HapMap. A main conclusion of this study is that marked differences in genome coverage may not translate into appreciable differences in power and that, when taking budgetary considerations into account, the most powerful design may not always correspond to the chip with the highest coverage. We also show that genotype imputation can be used to boost the power of many chips up to the level obtained from a hypothetical “complete” chip containing all the SNPs in HapMap. Our results have been encapsulated into an R software package that allows users to design future association studies and our methods provide a framework with which new chip sets can be evaluated.     

Identifying species of moths (Lepidoptera) from Baihua Mountain,Beijing, China,using DNA barcodes

DNA barcoding has become a promising means for the identification of organisms of all life‐history stages. Currently, distance‐based and tree‐based methods are most widely used to define species boundaries and uncover cryptic species. However, there is no universal threshold of genetic distance values that can be used to distinguish taxonomic groups. Alternatively, DNA barcoding can deploy a “character‐based” method, whereby species are identified through the discrete nucleotide substitutions. Our research focuses on the delimitation of moth species using DNA‐barcoding methods. We analyzed 393 Lepidopteran specimens belonging to 80 morphologically recognized species with a standard cytochrome c oxidase subunit I (COI) sequencing approach, and deployed tree‐based, distance‐based, and diagnostic character‐based methods to identify the taxa. The tree‐based method divided the 393 specimens into 79 taxa (species), and the distance‐based method divided them into 84 taxa (species). Although the diagnostic character‐based method found only 39 so‐identifiable species in the 80 species, with a reduction in sample size the accuracy rate substantially improved. For example, in the Arctiidae subset, all 12 species had diagnostics characteristics. Compared with traditional morphological method, molecular taxonomy performed well. All three methods enable the rapid delimitation of species, although they have different characteristics and different strengths. The tree‐based and distance‐based methods can be used for accurate species identification and biodiversity studies in large data sets, while the character‐based method performs well in small data sets and can also be used as the foundation of species‐specific biochips.     

Gender differences and regionalization of the cultural significance of wild mushrooms around La Malinche volcano, Tlaxcala, Mexico

The purpose of this study was to determine the cultural significance of wild mushrooms in 10 communities on the slopes of La Malinche volcano, Tlaxcala. The frequency and order of mention of each mushroom species in interviews of 200 individuals were used as indicators of the relative cultural significance of each species. A X(2) analysis was used to compare the frequency of mention of each species between males and females, and a Mann-Whitney U test was used to compare the difference in the total number of fungi mentioned by either gender. Traditional names for mushroom species were documented and frequency of mention assessed through multivariate statistics. The fungi with highest frequency of mention were Amanita basii, Lyophyllum decastes, Boletus pinophilus, Gomphus floccosus and Cantharellus cibarius complex. We found significant differences in the frequency of mention of different fungi by males and females but no significant difference was found for the total number of fungi mentioned by either gender. Principal component analysis suggested a cultural regionalization of La Malinche volcano communities based on preferences for consumption and use of traditional names. We observed two groups: one formed by communities on the eastern part of the volcano (with mixed cultures) and the other including communities on the western slope (ethnic Nahua towns). San Isidro Buensuceso is the most distinct community, according to the criteria in this study.