Evaluating the use of pairwise dissimilarity metrics in paleoanthropology

Questions of alpha taxonomy are best addressed by comparing unknown specimens to samples of the taxa to which they might belong. However, analysis of the hominin fossil record is riddled with methods that claim to evaluate whether pairs of individual fossils belong to the same species. Two such methods, log se_m and the related STET method, have been introduced and used in studies of fossil hominins. Both methods attempt to quantify morphological dissimilarity for a pair of fossils and then evaluate a null hypothesis of conspecificity using the assumption that pairs of fossils that fall beneath a predefined dissimilarity threshold are likely to belong to the same species, whereas pairs of fossils above that threshold are likely to belong to different species. In this contribution, we address (1) whether these particular methods do what they claim to do, and (2) whether such approaches can ever reliably address the question of conspecificity. We show that log se_m and STET do not reliably measure deviations from shape similarity, and that values of these measures for any pair of fossils are highly dependent upon the number of variables compared. To address these issues we develop a measure of shape dissimilarity, the Standard Deviation of Logged Ratios (s_LR). We suggest that while pairwise dissimilarity metrics that accurately measure deviations from isometry (e.g., s_LR) may be useful for addressing some questions that relate to morphological variation, no pairwise method can reliably answer the question of whether two fossils are conspecific.     

Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period

Background  

This study analyzes metabolomic data from a rice tillering (branching) developmental profile to define a set of biomarker metabolites that reliably captures the metabolite variance of this plant developmental event, and which has potential as a basis for rapid comparative screening of metabolite profiles in relation to change in development, environment, or genotype. Changes in metabolism, and in metabolite profile, occur as a part of, and in response to, developmental events. These changes are influenced by the developmental program, as well as external factors impinging on it. Many samples are needed, however, to characterize quantitative aspects of developmental variation. A biomarker metabolite set could benefit screening of quantitative plant developmental variation by providing some of the advantages of both comprehensive metabolomic studies and focused studies of particular metabolites or pathways.     

PHYLOGENY, REPRODUCTIVE ISOLATION AND KIN RECOGNITION IN THE SOCIAL AMOEBA DICTYOSTELIUM PURPUREUM

Little is known about the population structure of social microorganisms, yet such studies are particularly interesting for the ways that genetic variation impacts their social evolution. Dictyostelium , a eukaryotic microbe widely used as a developmental model, has a social fruiting stage in which some formerly independent individuals die to help others. To assess genetic variation within the social amoeba Dictyostelium purpureum , we sequenced ∼4000 base pairs of ribosomal DNA (rDNA) from 37 isolates collected in Texas, Virginia, and Japan. Our analysis showed extensive genetic variation between populations and clear evidence of phylogenetic structure. We identified three major phylogenetic groups that were more different than other accepted species pairs. Tests using pairs of clones showed that both sexual macrocyst and asexual fruiting body formation were influenced by genetic divergence. Macrocysts were less likely to form between pairs of clones from different groups than from the same group. There was also a correlation between the genetic divergence of a pair of clones and their degree of mixing within fruiting bodies. These observations suggest that cryptic species might occur within D. purpureum and, more importantly, reveal how genetic variation impacts social interactions.     

Karyotypes of two rare rodents, Hapalomys delacouri and Typhlomys cinereus (Mammalia, Rodentia), from Vietnam

Karyotypes of Hapalomys delacouri (Rodentia, Muridae) and Typhlomys cinereus (Rodentia, Platacanthomyidae) from Vietnam are described for the first time. The diploid karyotype of Hapalomys delacouri is 38 (NFa=48), consisting of six pairs of bi-armed and 12 pairs of acrocentric autosomes decreasing in size; plus a large metacentric X chromosome and Y chromosome, also metacentric, that is equal in size to the largest pair of acrocentric autosomes. The newly described karyotype differs significantly from that reported for Hapalomys delacouri from northern Thailand. The latter record very likely represents a different species of Hapalomys, possibly the taxon Hapalomys pasquieri described from north-central Laos.The diploid karyotype of Typhlomys cinereus is 38 (NF=48), consisting of five pairs of meta- to submetacentric and 14 pairs of acrocentric chromosomes varying in size from large to small; sex chromosomes were not defined.     

Avian reproductive failure in response to an extreme climatic event

Recently, climate change research has emphasized the potential increase in the frequency and severity of climatic extremes. We compared the reproductive effort and output among four species of passerine birds in coastal southern California, USA, a semi-arid region, during a normal precipitation year (2001) and the driest year in a 150-year climate record (2002). Both reproductive effort and output differed dramatically between years. Mean reproductive output among the four species was 2.37 fledglings/pair in 2001 and 88.4% of all pairs observed attempted at least one nest. The birds attempted a mean of 1.44 nests per pair and were successful in 47.7% of those attempts. In 2002, only 6.7% of the pairs even attempted a nest and only 1.8% were successful, for a total output of 0.07 fledglings per pair. The abundance of suitable arthropod prey items in the environment was also much lower in 2002, suggesting that low food availability was the proximal cause of the reproductive failure. The data for one of these species, the rufous-crowned sparrow (Aimophila ruficeps), were combined with reproductive and rainfall data from a previous 3-year study (1997–1999) in the same sites. The combined data sets suggest that the response of reproduction to rainfall variation is linear, and that the low end of the precipitation range brings the population near reproductive failure. Any change in climate that would increase the frequency of extreme dry conditions would likely endanger populations of these species.     

DEVELOPMENTAL STABILITY OF RAINBOW TROUT HYBRIDS: GENOMIC COADAPTATION OR HETEROZYGOSITY?

I compare the developmental stability of first generation hybrids between hatchery strains of rainbow trout (Salmo gairdneri) to that of the three pure parental strains raised in a common environment. Two of three reciprocal hybrid pairs show significantly less fluctuating asymmetry of four meristic characters than is found in parental strains. In contrast, the third hybrid pair shows reduced but not significantly lower developmental stability compared to pure strains. These hybrids had previously been found to develop slower than their maternal parental strains, indicating divergence of parental regulatory mechanisms controlling early ontogeny. A significant positive association between the degree of relative delay in hybrid developmental rate and their degree of developmental instability supports this view. For example, the only hybrid pair with decreased developmental stability also had the largest relative delay in development time of all hybrids. Neither absolute developmental rate nor enzyme heterozygosity at 42 loci alone can explain the degree of fluctuating asymmetry in these hybrids. The developmental stability of hybrids is apparently a result of the interaction between the developmental divergence between parental strains and their genomic heterozygosity due to hybridization.     

Developmental trajectories and breakdown in F1 interpopulation hybrids of Tribolium castaneum

When hybrid inviability is an indirect by‐product of local adaptation, we expect its degree of severity between pairs of populations to vary and to be sensitive to the environment. While complete reciprocal hybrid inviability is the outcome of the gradual process of local adaptation, it is not representative of the process of accumulation of incompatibility. In the flour beetle, Tribolium castaneum, some pairs of populations exhibit complete, reciprocal F1 hybrid incompatibility while other pairs are fully or partially compatible. We characterize this naturally occurring variation in the degree and timing of expression of the hybrid incompatible phenotype to better understand the number of genes or developmental processes contributing to speciation. We assessed the morphological and developmental variation in four Tribolium castaneum populations and their 12 possible F1 hybrids at each life‐history stage from egg to adult. We find that the rate of hybrid larval development is affected in all interpopulation crosses, including those eventually producing viable, fertile adults. Hybrid incompatibility manifests early in development as changes in the duration of instars and diminished success in the transition between instars are relative to the parent populations. Parent populations with similar developmental profiles may produce hybrids with disrupted development. The degree and timing of expression of hybrid inviability depends upon populations crossed, direction of the cross, and environment in which hybrids are raised. Our findings suggest that the coordinated expression of genes involved in transitional periods of development is the underlying cause of hybrid incompatibility in this species.     

Characterization of microRNAs from sheep (<Emphasis Type="Italic">Ovis aries</Emphasis>) using computational and experimental analyses

Ovis aries is one of the most important agricultural livestock for meat production, and also is an ideal model organism for biological and comparative genomics studies. Many miRNAs have been reported for their important roles in developmental processes in various animals, but there is limited information about O. aries miRNAs. In this study, combining a computational method based on expressed sequence tag (EST) analysis with experimental identification based on small RNA cDNA library, we identified 31 miRNAs belong to 24 families in sheep, 2 of which were novel miRNAs which had never been previously identified in any species. Especially, we cloned 12 miRNAs from the sheep skeletal muscle, which were good candidate miRNAs to be studied about the miRNA-dependant regulated process of muscle development, and we identified four pairs of miRNA/miRNA* and one pair of miRNA-3p/miRNA-5p from sheep EST sequences. Expression analysis indicated that some miRNAs were expressed in a specific tissue, and the pair of miRNA-3p/miRNA-5p and one pair of miRNA/miRNA* had a similar relative expression pattern in some tissues, respectively. Further, we predicted 120 potential target genes of 31 oar-miRNAs on the 3′UTR of O. aries genes. Gene ontology analysis showed that most of these genes took part in the cellular process and metabolic process. Our results enriched the O. aries miRNA database and provided useful information for investigating biological functions of miRNAs and miRNA* in sheep.     

Dual Function of Chip Calls Depending on Changing Call Rate Related to Risk Level in Territorial Pairs of White‐Eared Ground‐Sparrows

Different mechanisms have been proposed for encoding information into vocalizations: variation of frequency or temporal characteristics, variation in the rate of vocalization production, and use of different vocalization types. We analyze the effect of rate variation on the dual function of chip calls (contact and alarm) produced by White‐eared Ground‐sparrows (Melozone leucotis). We conducted an acoustic playback experiment where we played back 1 min of four chip call rates (12, 36, 60, 84 calls/min). We measured the response of territorial pairs using behavioral responses, and fine structural features of calls produced in response to those playbacks. White‐eared Ground‐sparrows showed more intense behavioral responses to higher than lower call rate playbacks. Both individuals of the pair approached the source of the playback stimulus faster, produced the first vocalization faster, produced more vocalizations, and spent more time close to the stimulus in higher call rate than in lower call rate playbacks. Frequency and duration characteristics of calls (chip and tseet) were similar in response to all call rate playbacks. Our playback experiment elicited different intensity of behavioral responses, suggesting that risk‐based information is encoded in call rate. Our results suggest that variation in the rate of chip call production serves a dual function in this species; calls are used at lower rates for pair contact and at higher rates for alarm/mobbing signals.     

Variable extent of parallelism in respiratory,circulatory, and neurological traits across lake whitefish species pairs

Parallel adaptive radiation events provide a powerful framework for investigations of ecology's contribution to phenotypic diversification. Ecologically driven divergence has been invoked to explain the repeated evolution of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis) species in multiple lakes in eastern North America. Nevertheless, links between most putatively adaptive traits and ecological variation remain poorly defined within and among whitefish species pairs. Here, we examine four species pairs for variation in gill, heart, and brain size; three traits predicted to show strong phenotypic responses to ecological divergence. In each of the species pairs, normals exhibited larger body size standardized gills compared to dwarfs – a pattern that is suggestive of a common ecological driver of gill size divergence. Within lakes, the seasonal hypoxia experienced in the benthic environment is a likely factor leading to the requirement for larger gills in normals. Interestingly, the morphological pathways used to achieve larger gills varied between species pairs from Québec and Maine, which may imply subtle non‐parallelism in gill size divergence related to differences in genetic background. There was also a non‐significant trend toward larger hearts in dwarfs, the more active species of the two, whereas brain size varied exclusively among the lake populations. Taken together, our results suggest that the diversification of whitefish has been driven by parallel and non‐parallel ecological conditions across lakes. Furthermore, the phenotypic response to ecological variation may depend on genetic background of each population.     

Species delimitation and biogeography of two fir species (Abies) in central China: cytoplasmic DNA variation

It remains unclear how speciation history might contribute to species-specific variation and affect species delimitation. We examined concordance between cytoplasmic genetic variation and morphological taxonomy in two fir species, Abies chensiensis and A. fargesii, with overlapping distributions in central China. Range-wide genetic variation was investigated using mitochondrial (mt) and plastid (pt) DNA sequences, which contrast in their rates of gene flow. Four mtDNA haplotypes were recovered and showed no obvious species' bias in terms of relative frequency. In contrast, a high level of ptDNA variation was recorded in both species with 3 common ptDNA haplotypes shared between them and 21 rare ptDNA haplotypes specific to one or other species. We argue that the lack of concordance between morphological and molecular variation between the two fir species most likely reflects extensive ancestral polymorphism sharing for both forms of cytoplasmic DNA variation. It is feasible that a relatively fast mutation rate for ptDNA contributed to the production of many species-specific ptDNA haplotypes, which remained rare due to insufficient time passing for their spread and fixation in either species, despite high levels of intraspecific ptDNA gene flow. Our phylogeographic analyses further suggest that polymorphisms in both organelle genomes most likely originated during and following glacial intervals preceding the last glacial maximum, when species distributions became fragmented into several refugia and then expanded in range across central China.     

Effect of specific and generic sex attractant blends on pheromone trap captures of four leafroller species in mid-Atlantic apple orchards

The responses of tufted apple bud moth, Platynota idaeusalis (Walker), the leafroller P. flavedana Clemens, redbanded leafroller, Argyrotaenia velutinana (Walker), and obliquebanded leafroller, Choristoneura rosaceana (Harris), to the pheromone blends of each, as well as to 3 putative generic blends (two- and three-component blends containing pheromone elements of each of the 4 species) were evaluated in small orchard plots. P. idaeusalis and P. flavedana, and A. velutinana and C. rosaceana comprise 2 pairs of species, each pair with broad overlap in pheromone blend, and quite different from one another. Each generic blend suppressed trap captures of all 4 species. The blends for P. idaeusalis and P. flavedana each reduced captures for these species. Furthermore, the blend for P. idaeusalis also suppressed captures of A. velutinana. The P. flavedana blend did not reduce captures of A. velutinana; in fact, at times captures increased. This study determines relative abilities of several sex attractant blends to reduce captures of 4 leafroller species in pheromone traps, presumably reflecting the ability of a blend to reduce orientation of males to females in a large block situation. This is a requisite 1st step in the development of a multispecies mating disruption blend.     

Characterization of the macronuclear DNA of different species ofTetrahymena

Summary The macronuclear DNAs from 20 different species ofTetrahymena were characterized using alternating Orthogonal Field (AOF) gel electrophoresis. Each species has approximately 300 different macronuclear DNA molecules that range in size from about 100–2000 kb pairs. Although the individual macronuclear DNA molecules are not well resolved on an AOF gel, most species have a unique profile of macronuclear DNA. The sequences that hybridize with histone H4 (Tetrahymena) and ubiquitin (yeast) genes were identified on the separated macronuclear DNA molecules of the different species. All species have 2 histone H4 genes located on macronuclear DNA molecules of different sizes. This is consistent with the duplication of the histone H4 gene prior to the speciation events leading to the various species ofTetrahymena. The number and sizes of the macronuclear DNA molecules that hybridize with the ubiquitin probe vary from species to species. A grouping of the different species ofTetrahymena based on this hybridization pattern paralels groupings of the species based on ribosomal RNA sequences and isoenzymes. Some intraspecific variation among different strains ofTetrahymena thermophila was detected using ubiquitin and 5S ribosomal RNA as probes.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

Effect of the Nematode Contortylenchus brevicomi on Gallery Construction and Fecundity of the Southern Pine Beetle

Field-collected Dendroctonus frontalis were reared in a controlled environment. Male-female beetle pairs retrieved from galleries 1, 2, or 5 wk after introduction into pine bolts were examined for nematode parasites. Data were obtained for each pair on gallery length, egg niche construction, egg viability, and progeny survival. In a separate study, beetle pairs were reared under laboratory conditions for 10 wk. The number of emerged adult progeny of each pair was recorded. Contortylenchus brevicomi, a nematode parasite, was found in 25% of all beetles that established galleries. After 2 and 3 wk, female beetles infected with the nematode had produced fewer eggs and shorter galleries than did uninfected females. Uninfected females mated with nematode-infected males showed similar trends, although the differences in the 2- and 3-wk tests were not significant. Progeny survival or egg viability was not affected by nematode parasitism of either parent beetle. Unikaryon minutum, a microsporidian parasite found in 65% of all colonizing beetles, had no effect on measured variables. The lower fecundity of beetles parasitized by C. brevicomi continued throughout the insect''s reproductive cycle. After 10 wk, nematode-infected beetle pairs produced fewer emerged adult progeny than did uninfected pairs.     

Thermal biology,population fluctuations and implications of temperature extremes for the management of two globally significant insect pests

The link between environmental temperature, physiological processes and population fluctuations is a significant aspect of insect pest management. Here, we explore how thermal biology affects the population abundance of two globally significant pest fruit fly species, Ceratitis capitata (medfly) and C. rosa (Natal fruit fly), including irradiated individuals and those expressing a temperature sensitive lethal (tsl) mutation that are used in the sterile insect technique. Results show that upper and lower lethal temperatures are seldom encountered at the field sites, while critical minimum temperatures for activity and lower developmental thresholds are crossed more frequently. Estimates of abundance revealed that C. capitata are active year-round, but abundance declines markedly during winter. Temporal autocorrelation of average fortnightly trap captures and of development time, estimated from an integrated model to calculate available degree days, show similar seasonal lags suggesting that population increases in early spring occur after sufficient degree-days have accumulated. By contrast, population collapses coincide tightly with increasing frequency of low temperature events that fall below critical minimum temperatures for activity. Individuals of C. capitata expressing the tsl mutation show greater critical thermal maxima and greater longevity under field conditions than reference individuals. Taken together, this evidence suggests that low temperatures limit populations in the Western Cape, South Africa and likely do so elsewhere. Increasing temperature extremes and warming climates generally may extend the season over which these species are active, and could increase abundance. The sterile insect technique may prove profitable as climates change given that laboratory-reared tsl flies have an advantage under warmer conditions.     

Diversity of juvenile Chinook salmon life history pathways

Life history variability includes phenotypic variation in morphology, age, and size at key stage transitions and arises from genotypic, environmental, and genotype-by-environment effects. Life history variation contributes to population abundance, productivity, and resilience, and management units often reflect life history classes. Recent evidence suggests that past Chinook salmon (Oncorhynchus tshawytscha) classifications (e.g., ‘stream’ and ‘ocean’ types) are not distinct evolutionary lineages, do not capture the phenotypic variation present within or among populations, and are poorly aligned with underlying ecological and developmental processes. Here we review recently reported variation in juvenile Chinook salmon life history traits and provide a refined conceptual framework for understanding the causes and consequences of the observed variability. The review reveals a broad continuum of individual juvenile life history pathways, defined primarily by transitions among developmental stages and habitat types used during freshwater rearing and emigration. Life history types emerge from discontinuities in expressed pathways when viewed at the population scale. We synthesize recent research that examines how genetic, conditional, and environmental mechanisms likely influence Chinook salmon life history pathways. We suggest that threshold models hold promise for understanding how genetic and environmental factors influence juvenile salmon life history transitions. Operational life history classifications will likely differ regionally, but should benefit from an expanded lexicon that captures the temporally variable, multi-stage life history pathways that occur in many Chinook salmon populations. An increased mechanistic awareness of life history diversity, and how it affects population fitness and resilience, should improve management, conservation, and restoration of this iconic species.     

Multiple hypotheses explain variation in extra‐pair paternity at different levels in a single bird family

Extra‐pair paternity (EPP), where offspring are sired by a male other than the social male, varies enormously both within and among species. Trying to explain this variation has proved difficult because the majority of the interspecific variation is phylogenetically based. Ideally, variation in EPP should be investigated in closely related species, but clades with sufficient variation are rare. We present a comprehensive multifactorial test to explain variation in EPP among individuals in 20 populations of nine species over 89 years from a single bird family (Maluridae). Females had higher EPP in the presence of more helpers, more neighbours or if paired incestuously. Furthermore, higher EPP occurred in years with many incestuous pairs, populations with many helpers and species with high male density or in which males provide less care. Altogether, these variables accounted for 48% of the total and 89% of the interspecific and interpopulation variation in EPP. These findings indicate why consistent patterns in EPP have been so challenging to detect and suggest that a single predictor is unlikely to account for the enormous variation in EPP across levels of analysis. Nevertheless, it also shows that existing hypotheses can explain the variation in EPP well and that the density of males in particular is a good predictor to explain variation in EPP among species when a large part of the confounding effect of phylogeny is excluded.     

Polyploidy affects the seed,dormancy and seedling characteristics of a perennial grass,conferring an advantage in stressful climates

• Polyploidy (the state of having more than two genome copies) is widely distributed in flowering plants and can vary within species, with polyploid races often associated with broad ecological tolerances. Polyploidy may influence within‐species variation in seed development, germination and establishment. We hypothesized that interactions between polyploidy and the seed developmental environment would affect subsequent dormancy, germination and early growth traits, particularly in stressful environments.
• Using seeds developed in a common garden under ambient and warmed conditions, we conducted germination trials under drought and temperature stress, and monitored the subsequent growth of seedlings. The study species, Themeda triandra, is a widespread, keystone, Australian native grass and a known polyploid complex.
• Tetraploid plants produced heavier, more viable seeds than diploids. Tetraploids were significantly more dormant than diploids, regardless of seed developmental environment. Non‐dormant tetraploids were more sensitive to germination stress compared to non‐dormant diploids. Finally, tetraploid seedlings were larger and grew faster than diploids, usually when maternal plants were exposed to developmental temperatures atypical to the source environment.
• Seed and seedling traits suggest tetraploids are generally better adapted to stressful environments than diploids. Because tetraploid seeds of T. triandra are more dormant they are less likely to germinate under stress, and when they do germinate, seedling growth is rapid and independent of seed developmental environment. These novel results demonstrate that polyploidy, sometimes in interaction with developmental environment and possibly also asexuality, can have within‐species variation in seed and seedling traits that increase fitness in stressful environments.