Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis

Knowledge of how animal species use food resources available in the environment can increase our understanding of many ecological processes. However, obtaining this information using traditional methods is difficult for species feeding on a large variety of food items in highly diverse environments. We amplified the DNA of plants for 306 scat and 40 soil samples, and applied an environmental DNA metabarcoding approach to investigate food preferences, degree of diet specialization and diet overlap of seven herbivore rodent species of the genus Ctenomys distributed in southern and midwestern Brazil. The metabarcoding approach revealed that these species consume more than 60% of the plant families recovered in soil samples, indicating generalist feeding habits of ctenomyids. The family Poaceae was the most common food resource retrieved in scats of all species as well in soil samples. Niche overlap analysis indicated high overlap in the plant families and molecular operational taxonomic units consumed, mainly among the southern species. Interspecific differences in diet composition were influenced, among other factors, by the availability of resources in the environment. In addition, our results provide support for the hypothesis that the allopatric distributions of ctenomyids allow them to exploit the same range of resources when available, possibly because of the absence of interspecific competition.     

Accumulation of Dobzhansky-Muller incompatibilities within a spatially structured population

Abstract.— A simple, deterministic analysis predicts that accumulation of Dobzhansky-Muller incompatibilities by a spatially structured population strongly depends on the number of negative interactions of an allele. If an allele can be incompatible with alleles at only one locus, incompatibilities accumulate linearly with time. In contrast, if an allele can participate in multiple pairwise incompatibilities with alleles at different loci, the expected number of incompatibilities eventually increases quadratically.     

New sea urchin phylogeography reveals latitudinal shifts associated with speciation

Where do new species arise? When do they form and how do they diverge from a common ancestor? A new comprehensive study of Arbacia sea urchins provides surprising answers to these questions. By combining mtDNA phylogeographic markers with a nuclear locus (encoding the sperm acrosomal protein bindin) known to be susceptible to high rates of adaptive codon evolution, Lessios et al. (2012) show that new species and lineages arose relatively recently, most often in association with latitudinal shifts between the temperate zones and the tropics, and in one case, in association with a significant geological barrier to gene flow (the rise of the Isthmus of Panama). In addition to the ‘where’ and ‘when’ of Arbacia speciation, these new data resolve an important question about ‘who’Arbacia species are by revealing extensive allele sharing at both loci between a pair of broadly sympatric nominal species (that should perhaps be considered a single taxon). ‘How’Arbacia diverge from each other is less easily resolved: there is no evidence for reinforcement (via selection on bindin) as an important source of divergence between nominal species, and there are few other data to decide among the alternative hypotheses to explain Arbacia speciation.     

Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin. We investigated biogeographical variation in highly recombining genes to determine the extent of clustering between genomes from geographically distinct Campylobacter populations. Whole‐genome sequences from 294 Campylobacter isolates from North America and the UK were analysed. Isolates from within the same country shared more recently recombined DNA than isolates from different countries. Using 15 UK/American closely matched pairs of isolates that shared ancestors, we identify regions that have frequently and recently recombined to test their correlation with geographical origin. The seven genes that demonstrated the greatest clustering by geography were used in an attribution model to infer geographical origin which was tested using a further 383 UK clinical isolates to detect signatures of recent foreign travel. Patient records indicated that in 46 cases, travel abroad had occurred <2 weeks prior to sampling, and genomic analysis identified that 34 (74%) of these isolates were of a non‐UK origin. Identification of biogeographical markers in Campylobacter genomes will contribute to improved source attribution of clinical Campylobacter infection and inform intervention strategies to reduce campylobacteriosis.     

Hybridization and the inheritance of female colour polymorphism in two ischnurid damselflies (Odonata: Coenagrionidae)

Female‐limited polychromatism is frequent in many species of Odonata. Ischnura elegans has three colour morphs: one male‐like coloured (androchrome) and two additional gynochrome brown morphs (infuscans and rufescens‐obsoleta morphs). A total of 19 progenies obtained from once‐mated females were reared in the laboratory in three generations. Results indicate that the colour morphs are controlled by the same genetic system as previously described for I. graellsii, i.e. an autosomal locus with female‐limited expression and with three alleles with a hierarchy of dominance (p^a > pⁱ > p°). Five interspecific crossings between female I. graellsii and male I. elegans, five crossings between hybrid females and male I. elegans and one crossing between female I. graellsii and a hybrid male further confirmed that the genetic system is the same in both species. A survey of morph frequencies in north‐west Spain revealed that I. elegans shows high variability in androchrome frequency (4–91%) between nearby populations, whereas in I. graellsii androchromes never are the majority morph (5–40%). The highest androchrome frequency in I. graellsii was found in populations closest to a locality where both species have hybridized, and that now has the highest androchrome frequency of I. elegans. We hypothesize that I. elegans genes have been incorporated into the genome of I. graellsii resulting in increased androchrome frequency in the latter species. Low androchrome frequency in I. elegans seems also related to the influence of I. graellsii genes. Therefore, we suggest that hybridization between both taxa is contributing to the temporal maintenance of contrasting androchrome frequencies in nearby populations. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85 , 471–481.     

Increased genetic divergence between two closely related fir species in areas of range overlap

Because of introgressive hybridization, closely related species can be more similar to each other in areas of range overlap (parapatry or sympatry) than in areas where they are geographically isolated from each other (allopatry). Here, we report the reverse situation based on nuclear genetic divergence between two fir species, Abies chensiensis and Abies fargesii, in China, at sites where they are parapatric relative to where they are allopatric. We examined genetic divergence across 126 amplified fragment length polymorphism (AFLP) markers in a set of 172 individuals sampled from both allopatric and parapatric populations of the two species. Our analyses demonstrated that AFLP divergence was much greater between the species when comparisons were made between parapatric populations than between allopatric populations. We suggest that selection in parapatry may have largely contributed to this increased divergence.     

Phylogeography of Agathistoma (Turbinidae,Tegulinae) snails in tropical and southwestern Atlantic

The rocky intertidal gastropods Agathistoma viridulum and A. hotessierianum occur from the Caribbean to southern Brazil, with a gap in the equatorial region, giving them an anti-tropical distribution. We used sequences from mitochondrial genes to elucidate the phylogeography of A. viridulum and A. hotessierianum and to infer their relationships to other species of Agathistoma. For A. hotessierianum, haplotype networks and phylogenetic analyses split samples into two distinct groups: one (A. hotessierianum) in the Caribbean region (Greater and Lesser Antilles; Venezuela: Sucre and Isla Margarita) and a new species that we describe from northeastern Brazil. For A. viridulum, genetic analyses split the samples into three groups (Caribbean, northeastern Brazil and southeastern Brazil), but genetic divergence among these was too low for them to be considered species, and morphological differences were not significant. The mtDNA tree identified two clades of eastern Pacific Agathistoma, but many lower-level relationships within Agathistoma were not well resolved, suggesting that more complete taxon sampling and additional genetic data will be needed to establish more robust relationships among Tegulinae.