Global population divergence and admixture of the brown rat (Rattus norvegicus)

Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes

Variation in brown rat cranial shape shows directional selection over 120 years in New York City

Urbanization exposes species to novel environments and selection pressures that may change morphological traits within a population. We investigated how the shape and size of crania and mandibles changed over time within a population of brown rats (Rattus norvegicus) living in Manhattan, New York, USA, a highly urbanized environment. We measured 3D landmarks on the cranium and mandible of 62 adult individuals sampled in the 1890s and 2010s. Static allometry explained approximately 22% of shape variation in crania and mandible datasets, while time accounted for approximately 14% of variation. We did not observe significant changes in skull size through time or between the sexes. Estimating the P-matrix revealed that directional selection explained temporal change of the crania but not the mandible. Specifically, rats from the 2010s had longer noses and shorter upper molar tooth rows, traits identified as adaptive to colder environments and higher quality or softer diets, respectively. Our results highlight the continual evolution to selection pressures. We acknowledge that urban selection pressures impacting cranial shape likely began in Europe prior to the introduction of rats to Manhattan. Yet, our study period spanned changes in intensity of artificial lighting, human population density, and human diet, thereby altering various aspects of rat ecology and hence pressures on the skull

Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications

The evolutionary origins of the multitude of duplicate genes in the plant genomes are still incompletely understood. To gain an appreciation of the potential selective forces acting on these duplicates, we phylogenetically inferred the set of metabolic gene families from 10 flowering plant (angiosperm) genomes. We then compared the metabolic fluxes for these families, predicted using the Arabidopsis thaliana and Sorghum bicolor metabolic networks, with the families' duplication propensities. For duplications produced by both small scale (small-scale duplications) and genome duplication (whole-genome duplications), there is a significant association between the flux and the tendency to duplicate. Following this global analysis, we made a more fine-scale study of the selective constraints observed on plant sodium and phosphate transporters. We find that the different duplication mechanisms give rise to differing selective constraints. However, the exact nature of this pattern varies between the gene families, and we argue that the duplication mechanism alone does not define a duplicated gene's subsequent evolutionary trajectory. Collectively, our results argue for the interplay of history, function, and selection in shaping the duplicate gene evolution in plants

Variability in total project and per sample genotyping costs under varying study designs including with microsatellites or SNPs to answer conservation genetic questions

The field of conservation genetics is in the midst of transitioning from microsatellites to single nucleotide polymorphisms (SNPs) as part of a broader transition from genetic to genomic studies. Genomics offers the potential for more accurate estimation of individual and population parameters but at higher project costs. I calculated cost curves for multi-locus genotypes to describe how total project and per sample costs varied between microsatellite and SNP genotyping. Cost curves were calculated varying multiple parameters which influenced costs, including: number of microsatellite loci, primer multiplexing, number of samples pooled per library, sequencing costs, and variation in laborer salaries. Sequencing costs had the greatest effect on total project costs for both markers, suggesting a way to achieve the greatest savings. For microsatellites, increasing loci number had a small effect on increasing costs, although using an increasing number of multiplex panels had a significant effect. For SNPs, increasing the number of samples pooled per genotyping library resulted in the greatest cost savings; however, this was tempered somewhat by species genome size and study design parameters which could decrease per locus sequencing depth below thresholds needed for robust SNP calling. Thus, this study highlights multiple parameters to consider when designing conservation genotyping studies to maximize information while minimizing costs. I also surveyed studies that compared microsatellites and SNPs. SNPs had greater accuracy than microsatellites when SNP loci were 3–2800 fold greater. Cost curves are provided as changing parameter assumptions effects estimates

Puckett_etal-mtDNA_HaplotypeList

List of samples and the identified mitochondrial haplotype. See GenBank accessions: AY334363–AY334367 (Onorato et al 2004), FJ619652–FJ619659 (Van Den Bussche et al 2009), KJ406324-KJ406336 (Puckett et al 2014), and KM230048-KM230113 (this paper)

Puckett_etal-MaxEntInput

Geographic coordinates used as input in MaxEnt species distribution model

Brown rat demography reveals pre-commensal structure in eastern Asia prior to expansion into Southeast Asia

ABSTRACTFossil evidence indicates that the globally-distributed brown rat (Rattus norvegicus) originated in northern China and Mongolia. Historical records report the human-mediated invasion of rats into Europe in the 1500s, followed by global spread due to European imperialist activity during the1600s-1800s. We analyzed 14 genomes representing seven previously identified evolutionary clusters and tested alternative demographic models to infer patterns of range expansion, divergence times, and changes in effective population (Ne) size for this globally important pest species. We observed three range expansions from the ancestral population that produced the Pacific (~4.8kya), eastern China (diverged ~0.55kya), and Southeast (SE) Asia (~0.53kya) lineages. Our model shows a rapid range expansion from SE Asia into the Middle East then continued expansion into central Europe 537 years ago (1478 AD). We observed declining Ne within all brown rat lineages from 150-1kya, reflecting population contractions during glacial cycles. Ne increased since 1kya in Asian and European, but not Pacific, evolutionary clusters. Our results support the hypothesis that northern Asia was the ancestral range for brown rats. We suggest that southward human migration across China between 800-1550s AD resulted in the introduction of rats to SE Asia, from which they rapidly expanded via existing maritime trade routes. Finally, we discovered that North America was colonized separately on both the Atlantic and Pacific seaboards, yet by evolutionary clusters of vastly different ages and genomic diversity levels. Our results should stimulate discussions among historians and zooarcheologists regarding the relationship between humans and rats.</jats:p

Evolution of degrees of carnivory and dietary specialization across Mammalia and their effects on speciation

AbstractConflation between omnivory and dietary generalism limits ecological and evolutionary analyses of diet, including estimating contributions to speciation and diversification. Additionally, categorizing species into qualitative dietary classes leads to information loss in these analyses. Here, we constructed two continuous variables – degree of carnivory (i.e., the position along the continuum from complete herbivory to complete carnivory) and degree of dietary specialization (i.e., the number and variety of food resources utilized) – to elucidate their histories across Mammalia, and to tease out their independent contributions to mammalian speciation. We observed that degree of carnivory significantly affected speciation rate across Mammalia, whereas dietary specialization did not. We further considered phylogenetic level in diet-dependent speciation and saw that degree of carnivory significantly affected speciation in ungulates, carnivorans, bats, eulipotyphlans, and marsupials, while the effect of dietary specialization was only significant in carnivorans. Across Mammalia, omnivores had the lowest speciation rates. Our analyses using two different categorical diet variables led to contrasting signals of diet-dependent diversification, and subsequently different conclusions regarding diet’s macroevolutionary role. We argue that treating variables such as diet as continuous instead of categorical reduces information loss and avoids the problem of contrasting macroevolutionary signals caused by differential discretization of biologically continuous traits.</jats:p

Spatial patterns of genetic diversity in eight bear (Ursidae) species

Many of the 8 extant bear species have large ranges, yet range-wide studies of genetic diversity are often impractical because of logistic challenges or focus on local questions. However, understanding the levels of diversity among populations of a species can be useful for conservation and management. Bear researchers were at the forefront of using microsatellites to study the demographics and diversity of populations, such that 3 species have complete sampling and 3 others are represented across their range breadth. Yet there has not been a synthesis of these data within or among species because of difficulties comparing microsatellites. We extracted microsatellite summary statistics from 104 papers that sampled 284 populations of any species within Ursidae, then yardstick-transformed the data for direct comparison. Studies had a median of 2 geographic sites, 30 individuals sampled per site, and 12 loci genotyped. We identified 193 loci genotyped in bears and argue this is a limitation within and among species comparisons. Tremarctos ornatus had the lowest average range-wide genetic diversity (Ar = 2.5; He = 0.43), although ascertainment bias may affect the results, whereas Ursus arctos had the highest diversity (Ar = 6.4; He = 0.69). We argue that at the spatial scale of a species\u27 range, variation due to phylogeography and anthropogenically influenced diversity will overwhelm accuracy issues between studies and reveal broad spatial patterns. Further, by comparing allelic richness to heterozygosity across the range of a species, managers may identify populations in need of genetic management. We end by summarizing what is known about within-species lineages and genetic diversity and identify priority areas for future studies