funrar: An R package to characterize functional rarity

Emphasis has been put in recent ecological research on investigating phylogenetic, functional and taxonomic facets of biological diversity. While a flourishing number of indices have been proposed for assessing functional diversity, surprisingly few options are available to characterize functional rarity. Functional rarity can play a key role in community and ecosystem dynamics. We introduce here the funrar R package to quantify functional rarity based on species trait differences and species frequencies at local and regional scales. Because of the increasing availability of big datasets in macroecology and biogeography, we optimized funrar to work with large datasets of thousands of species and sites. We illustrate the use of the package to investigate the functional rarity of North and Central American mammals.     

A search for quantitative trait loci for ovulation rate in cattle

Seventy-seven polymorphic microsatellites were analysed in offspring of three elite sires that were part of the foundation of an experimental population selected for twinning rate at the US Meat Animal Research Center, Clay Center, Nebraska. All females were assessed for ovulation rate by rectal palpation of corpora lutea over 8–10 consecutive oestrous cycles from approximately 12 to 18 months of age, and associations between ovulation rate and sire allele were examined in each of the three sire groups. A preliminary analysis was performed using selectively genotyped daughters of each sire. Markers found significant or approaching significance were also genotyped in all daughters, sons and granddaughters of these sires. A test of marker associations limited to the granddaughter data provided an independent confirmation of marker effect and significance relative to the initial test with daughter data. Putative ovulation rate quantitative trait loci were detected on chromosomes 7 and 23. Marker UWCA20 on chromosome 7 was associated with an effect in excess of one phenotypic standard deviation and accounted for approximately 10% of phenotypic variation ovulation rate. Marker CYP21 (steroid 21-hydroxylase) on chromosome 23 was associated with an effect of slightly less than half a phenotypic standard deviation and accounted for approximately 4% of phenotypic variation.     

Individualistic responses of forest herb traits to environmental change

• Intraspecific trait variation (ITV; i.e. variability in mean and/or distribution of plant attribute values within species) can occur in response to multiple drivers. Environmental change and land‐use legacies could directly alter trait values within species but could also affect them indirectly through changes in vegetation cover. Increasing variability in environmental conditions could lead to more ITV, but responses might differ among species. Disentangling these drivers on ITV is necessary to accurately predict plant community responses to global change.
• We planted herb communities into forest soils with and without a recent history of agriculture. Soils were collected across temperate European regions, while the 15 selected herb species had different colonizing abilities and affinities to forest habitat. These mesocosms (384) were exposed to two‐level full‐factorial treatments of warming, nitrogen addition and illumination. We measured plant height and specific leaf area (SLA).
• For the majority of species, mean plant height increased as vegetation cover increased in response to light addition, warming and agricultural legacy. The coefficient of variation (CV) for height was larger in fast‐colonizing species. Mean SLA for vernal species increased with warming, while light addition generally decreased mean SLA for shade‐tolerant species. Interactions between treatments were not important predictors.
• Environmental change treatments influenced ITV, either via increasing vegetation cover or by affecting trait values directly. Species’ ITV was individualistic, i.e. species responded to different single resource and condition manipulations that benefited their growth in the short term. These individual responses could be important for altered community organization after a prolonged period.

     

Unequivocal determination of sire allele origin for multiallelic microsatellites when only the sire and progeny are genotyped

The effect of a segregating economic trait locus (ETL) can be detected with the aid of a linked genetic marker, if specific alleles of each locus are in association among the individuals genotyped for the genetic marker. For dairy cattle this can be achieved by application of the ‘granddaughter design’. If only the sires and their sons are genotyped for the genetic markers, then the allele origin of sons having the same genotypes as their sires cannot be determined. Seven sires and 101 sons were genotyped for five microsatellites. The mean frequency of heterozygous sires was 77%. The mean number of alleles per locus was 8.2. Frequency of informative sons per locus ranged from 60% to 80% with a mean of 72%. With highly polymorphic microsatellites, at least 60% more grandsire families can be included in the analysis, and the number of sons assayed can be reduced by 40%, as compared to diallelic markers.     

Quantitative trait locus mapping using sets of near-isogenic lines: relative power comparisons and technical considerations

 The power to detect QTL using near-isogenic line (NIL) comparisons versus recombinant inbred (RI) populations was assessed. The power to detect QTL was found to be generally greater when using RI populations than when using NIL contrasts. Power to detect QTL with NIL contrasts never exceeded that of RI populations when the number of RI lines is maximized relative to replication of lines for a given number of experimental units. The relative power of NIL contrasts is highest for traits with high heritability and when a gain in precision is realized due to increased replication of entries. Although NIL populations are generally less powerful than RI populations of similar size, some practical considerations may enhance the value of these materials. Availability of NILs allows the genetic effect of a specific chromosome region to be determined by comparing two lines; all RI lines in a population need to be rescored for each new trait even if the effect of a specific chromosome region is suspected. NIL comparisons may allow genetic differences to be detected by visual inspection; genetic effects can only be expressed as means and variances with recombinant inbred populations. In summary, RI populations generally, and in some cases, substantially, provide better power for QTL detection than NIL comparisons. Practical considerations, however, indicate that many factors need to be considered when choosing a population structure to meet an experimental objective. Received: 12 December 1996 / Accepted: 21 March 1997