Population-level Structure Research Articles

First Insights into Population Structure and Genetic Diversity Versus Host Specificity in Trypanorhynch Tapeworms Using Multiplexed Shotgun Genotyping.

Theory predicts relaxed host specificity and high host vagility should contribute to reduced genetic structure in parasites while strict host specificity and low host vagility should increase genetic structure. Though these predictions are intuitive, they have never been explicitly tested in a population genomic framework. Trypanorhynch tapeworms, which parasitize sharks and rays (elasmobranchs) as definitive hosts, are the only order of elasmobranch tapeworms that exhibit considerable variability in their definitive host specificity. This allows for unique combinations of host use and geographic range, making trypanorhynchs ideal candidates for studying how these traits influence population-level structure and genetic diversity. Multiplexed shotgun genotyping (MSG) data sets were generated to characterize component population structure and infrapopulation diversity for a representative of each trypanorhynch suborder: the ray-hosted Rhinoptericola megacantha (Trypanobatoida) and the shark-hosted Callitetrarhynchus gracilis (Trypanoselachoida). Adults of R. megacantha are more host-specific and less broadly distributed than adults of C. gracilis, allowing correlation between these factors and genetic structure. Replicate tapeworm specimens were sequenced from the same host individual, from multiple conspecific hosts within and across geographic regions, and from multiple definitive host species. For R. megacantha, population structure coincided with geography rather than host species. For C. gracilis, limited population structure was found, suggesting a potential link between degree of host specificity and structure. Conspecific trypanorhynchs from the same host individual were found to be as, or more, genetically divergent from one another as from conspecifics from different host individuals. For both species, high levels of homozygosity and positive FIS values were documented.

The representation of context in mouse hippocampus is preserved despite neural drift

The hippocampus is thought to mediate episodic memory through the instantiation and reinstatement of context-specific cognitive maps. However, recent longitudinal experiments have challenged this view, reporting that most hippocampal cells change their tuning properties over days even in the same environment. Often referred to as neural or representational drift, these dynamics raise questions about the capacity and content of the hippocampal code. One such question is whether and how these long-term dynamics impact the hippocampal code for context. To address this, we image large CA1 populations over more than a month of daily experience as freely behaving mice participate in an extended geometric morph paradigm. We find that long-timescale changes in population activity occur orthogonally to the representation of context in network space, allowing for consistent readout of contextual information across weeks. This population-level structure is supported by heterogeneous patterns of activity at the level of individual cells, where we observe evidence of a positive relationship between interpretable contextual coding and long-term stability. Together, these results demonstrate that long-timescale changes to the CA1 spatial code preserve the relative structure of contextual representation.

Mitochondrial genome diversity and population mitogenomics of polar cod (Boreogadus saida) and Arctic dwelling gadoids

High-latitude fish typically exhibit a narrow thermal tolerance window, which may pose challenges when coping with temperatures that shift outside of a species’ range of tolerance. Due to its role in aerobic metabolism and energy balance, the mitochondrial genome is likely critical for the acclimation and adaptation to differing temperature regimes in marine ectotherms. As oceans continue to warm, there is growing need to understand the ability of organisms to respond to changing environmental conditions given evidence that some species, in particular cold-water species, may already be experiencing difficulties. To assess how Arctic gadids in Alaska have responded to differential thermal preferences in the past and how regions are interconnected, we sequenced complete mitochondrial genomes for four Arctic gadids to determine the distribution of mitochondrial diversity and population-level structure as well as to detect signatures of selection acting on the mitochondrial genome. We found little population-level structure within all four species with the clear exception of Gulf of Alaska saffron cod (Eleginus gracilis). Northern localities exhibited higher levels of genetic diversity and primarily northern lineages were observed within polar cod (Boreogadus saida) and saffron cod, likely reflecting asymmetrical dispersal and potentially admixture of distinct lineages via ocean currents. The main evolutionary force shaping the evolution of the mitogenome appears to be purifying selection, but we also identified potential positive selection of candidate amino acid replacements primarily in complex I (ND genes) in polar cod. The high levels of mitochondrial diversity observed in our study and large population size may provide this species with the ability to respond evolutionarily (i.e. long-term) to a changing environment.

Genetic structure associated with habitat diversification supports the independent evolution of ecomorphs in Bradypodion pumilum

ABSTRACTThere are notable examples of repeated evolution of ecomorphs within groups of closely related species, these are typically viewed as remarkable cases of natural selection. In most cases, directional selection for certain phenotypic traits under specific (and differing) environmental conditions is implicated. Differing ecomorphological forms for closely related species (or for populations within a species) have been documented for several lineages of South African dwarf chameleons (Bradypodion), although this pattern is not ubiquitous across the genus. Within one species, Bradypodion pumilum, two ecomorphs have been observed, these differ in terms of morphology, performance, ecology and habitat, yet genetic differences (mtDNA) were not apparent, with shared haplotypes across the ecomorphs. We investigated whether more sensitive genetic markers (eight microsatellite loci) would show population level structure between ecomorphs, which could indicate lack of gene flow across the ecological (habitat) boundary. Our results suggest that the two ecomorphs are distinct at a population level, implying that gene flow is absent or reduced and that the two ecomorphs are on separate evolutionary trajectories. Given that mtDNA could not detect population structure, we infer that the ecological boundary between ecomorphs is relatively recent in evolutionary history. The two ecomorphs are distinctive in terms of their morphology, ecology, habitat and functional traits, these differences are likely driven and maintained by reproductive isolation across the habitat boundary.

Cultural selection shapes network structure.

Cultural evolution relies on the social transmission of cultural traits along a population's social network. Research indicates that network structure affects information spread and thus the capacity for cumulative culture. However, how network structure itself is driven by population-culture co-evolution remains largely unclear. We use a simple model to investigate how populations negotiate the trade-off between acquiring new skills and getting better at existing skills and how this trade-off shapes social networks. We find unexpected eco-evolutionary feedbacks from culture onto social networks and vice versa. We show that selecting for skill generalists results in sparse networks with diverse skill sets, whereas selecting for skill specialists results in dense networks and a population that specializes on the same few skills on which everyone is an expert. Our model advances our understanding of the complex feedbacks in cultural evolution and demonstrates how individual-level behavior can lead to the emergence of population-level structure.

Phylogeographic Analysis and Genetic Structure of an Endemic Sino-Japanese Disjunctive Genus Diabelia (Caprifoliaceae).

The Sino-Japanese Floristic Region (SJFR) is a key area for plant phylogeographical research, due to its very high species diversity and disjunct distributions of a large number of species and genera. At present, the root cause and temporal origin of the discontinuous distribution of many plants in the Sino-Japanese flora are still unclear. Diabelia (Caprifoliaceae; Linnaeoideae) is a genus endemic to Asia, mostly in Japan, but two recent discoveries in China raised questions over the role of the East China Sea (ECS) in these species' disjunctions. Chloroplast DNA sequence data were generated from 402 population samples for two regions (rpl32-trnL, and trnH-psbA) and 11 nuclear microsatellite loci were screened for 549 individuals. Haplotype, population-level structure, combined analyses of ecological niche modeling, and reconstruction of ancestral state in phylogenies were also performed. During the Last Glacial Maximum (LGM) period after the Tertiary, Diabelia was potentially widely distributed in southeastern China, the continental shelf of the East China Sea and Japan (excluding Hokkaido). After LGM, all populations in China have disappeared except those in Zhejiang which may represent a Glacial refuge. Populations of Diabelia in Japan have not experienced significant bottleneck effects, and populations have maintained a relatively stable state. The observed discontinuous distribution of Diabelia species between China and Japan are interpreted as the result of relatively ancient divergence. The phylogenetic tree of chloroplast fragments shows the characteristics of multi-origin evolution (except for D. sanguinea). STRUCTURE analysis of nuclear Simple Sequence Repeat (nSSR) showed that the plants of the Diabelia were divided into five gene pools: D. serrata, D. spathulata, D. sanguinea, D. ionostachya (D. spathulata var. spathulata-Korea), and populations of D. ionostachya var. ionostachya in Yamagata prefecture, northern Japan. Molecular evidence provides new insights of Diabelia into biogeography, a potential glacial refuge, and population-level genetic structure within species. In the process of species differentiation, ECS acts as a corridor for two-way migration of animals and plants between China and Japan during glacial maxima, providing the possibility of secondary contact for discontinuously distributed species between China and Japan, or as a filter (creating isolation) during glacial minima. The influence of the ECS in speciation and biogeography of Diabelia in the Tertiary remains unresolved in this study. Understanding origins, evolutionary histories, and speciation will provide a framework for the conservation and cultivation of Diabelia.

The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data

Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization.

Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus).

Species ranges that span different geographic landscapes frequently contain cryptic species- or population-level structure. Identifying these possible diversification factors can often be accomplished under a comparative phylogeographic framework. However, comparisons suffer if previous studies are limited to a particular group or habitat type. In California, a complex landscape has led to several phylogeographic breaks, primarily in terrestrial species. However, two sister taxa of freshwater fish, riffle sculpin (Cottus gulosus) and Pit sculpin (Cottus pitensis), display ranges based on morphological identifications that do not coincide with these breaks. Using a comprehensive sampling and nuclear, mitochondrial and microsatellite markers, we hypothesized that proposed species ranges are erroneous based on potential hybridization/gene flow between species. Results identified a phylogeographic signature consistent with this hypothesis, with breaks at the Coast Range Mountains and Sacramento/San Joaquin River confluence. Coastal locations of C.gulosus represent a unique lineage, and 'true' C.gulosus were limited to the San Joaquin basin, both regions under strong anthropogenic influence and potential conservation targets. C.pitensis limits extended historically throughout the Sacramento/Pit River basin but currently are restricted to the Pit River. Interestingly, locations in the Sacramento River contained low levels of ancestral hybridization and gene flow from C.gulosus but now appear to be a distinct population. The remaining population structure was strongly correlated with Sierra Nevada presence (high) or absence (low). This study stresses the importance of testing phylogeographic breaks across multiple taxa/habitats before conservation decisions are made, but also the potential impact of different geographic landscapes on evolutionary diversification.

Transmission Biases in Linguistic Epidemiology

AbstractThere is growing interest in approaching research on language contact and change through an epidemiological, population-based model which takes 'linguistic items' or equivalent as a key unit of analysis. This paper explores a number of elements of such a model, with particular attention to a set of biases which may act as conduits or filters for the transmission of linguistic items in populations. These include a number of such biases introduced in recent models of cultural transmission: a threshold bias, a sociometric bias, a model bias, a conformity bias, and a frequency bias. A further bias is of particular relevance to language, but is argued to be equally important for models of cultural transmission in general. This is a context bias, which takes into account the kind of structural context which a given item or variant presupposes for its function. The presence or absence of a relevant structural context will determine the likelihood that the item will be transmitted, and if so to what degree of faithfulness. These biases may help toward characterising an anatomy of cultural epidemiology which makes explicit the relation between individual cognition, social processes, and population-level structure.