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1. Tooth transposition prevalence and type among sub‐Saharan Africans

   https://doi.org/10.1002/ajhb.23329  

   Irish, Joel D. ( September 2019 , American Journal of Human Biology)

   Although rare, tooth transposition—an exchange in location of two teeth—is a frequent topic of study. Clinical and, to a much lesser extent, dental anthropological research have focused predominantly on prevalence (0.03%‐0.74% in several world populations) and case studies, albeit on a restricted spatiotemporal scale. Many regions have received little attention, including sub‐Saharan Africa, while premodern data are few. Here, the aim is to supplement both fields of dental research by reviewing previous publications, and newly reporting transposition rates, types, and co‐occurring abnormalities in time‐successive samples across the subcontinent.

   Dental data in 51 sub‐Saharan samples (>2500 individuals) dating >10 000 BC to 20th century were recorded. Of these, 36 are of modern and 15 premodern age, comprising males and females ≥12‐years of age. Transposition presence, quadrant, and type were tabulated, cases described, and prevalence presented. In the latter case, Poisson 95% confidence intervals were calculated to better discern true population rates at various geographic levels.

   Overall, six of 1886 modern individuals (0.32%) and one of premodern age evidence Mx.C.P1, an exchange of the maxillary canine and first premolar. Various associated dental abnormalities are also evident, including retained deciduous teeth, reduced permanent crowns, and agenesis.

   This study provides additional insight into the geographic distribution, features, and time depth of transposition, along with hints supporting a genetic etiology and, potentially, some indications of diachronic change from an initial Mx.C.P1 to several types more recently based on premodern evidence. It is of clinical concern today, but is not just a modern anomaly.

    

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2. Phenotypic differentiation despite gene flow: Beak morphology, bite performance, and population genetics of Loggerhead Shrikes ( Lanius ludovicianus )

   https://doi.org/10.1002/ece3.11079  

   Sustaita, Diego ; Wulf, Gwendalyn K. ; Sethuraman, Arun ( March 2024 , Ecology and Evolution)

   Previous studies of Loggerhead Shrikes (Laniidae:Lanius ludovicianus) in North America have indicated considerable intraspecific genetic and phenotypic differentiation, but the congruence between genetic and phenotypic differentiation remains obscure. We examined phenotypic differences in beak shape and bite force among geographic groupings across a 950 km range, from the lower Imperial Valley to the upper Central Valley of California, USA. We integrated these analyses with a population genetic analysis of six microsatellite markers to test for correspondence between phenotypic and genetic differences among geographic groups. We found significant phenotypic differentiation despite a lack of significant genetic differentiation among groups. Pairwise beak shape and bite force distances nevertheless were correlated with genetic (F_ST) distances among geographic groups. Furthermore, the phenotypic and genetic distance matrices were correlated with pairwise geographic distances. Takentogether, these results suggest that phenotypic differences might be influenced by neutral processes, inbreeding (as indicated by high heterozygosity deficiencies we observed), local adaptation, and/or phenotypic plasticity.

    

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3. Testing main Amazonian rivers as barriers across time and space within widespread taxa

   https://doi.org/10.1111/jbi.13676  

   Pirani, Renata M. ; Werneck, Fernanda P. ; Thomaz, Andréa T. ; Kenney, Mariah L. ; Sturaro, Marcelo J. ; Ávila‐Pires, Teresa C. S. ; Peloso, Pedro L. V. ; Rodrigues, Miguel T. ; Knowles, L. Lacey ( September 2019 , Journal of Biogeography)

   Present Amazonian diversity patterns can result from many different mechanisms and, consequently, the factors contributing to divergence across regions and/or taxa may differ. Nevertheless, the river‐barrier hypothesis is still widely invoked as a causal process in divergence of Amazonian species. Here we use model‐based phylogeographic analyses to test the extent to which major Amazonian rivers act similarly as barriers across time and space in two broadly distributed Amazonian taxa.

   Amazon rain forest.

   The lizardGonatodes humeralis(Sphaerodactylidae) and the tree frogDendropsophus leucophyllatus(Hylidae).

   We obtained RADseq data for samples distributed across main river barriers, representing main Areas of Endemism previously proposed for the region. We conduct model‐based phylogeographic and genetic differentiation analyses across each population pair.

   Measures of genetic differentiation (based onF_STcalculated from genomic data) show that all rivers are associated with significant genetic differentiation. Parameters estimated under investigated divergence models showed that divergence times for populations separated by each of the 11 bordering rivers were all fairly recent. The degree of differentiation consistently varied between taxa and among rivers, which is not an artifact of any corresponding difference in the genetic diversities of the respective taxa, or to amounts of migration based on analyses of the site‐frequency spectrum.

   Taken together, our results support a dispersal (rather than vicariance) history, without strong evidence of congruence between these species and rivers. However, once a species crossed a river, populations separated by each and every river have remained isolated—in this sense, rivers act similarly as barriers to any further gene flow. This result suggests differing degrees of persistence and gives rise to the seeming contradiction that the divergence process indeed varies across time, space and species, even though major Amazonian rivers have acted as secondary barriers to gene flow in the focal taxa.

    

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4. Worldwide relationships in the fern genus Pteridium (bracken) based on nuclear genome markers

   https://doi.org/10.1002/ajb2.1365  

   Wolf, Paul G. ; Rowe, Carol A. ; Kinosian, Sylvia P. ; Der, Joshua P. ; Lockhart, Peter J. ; Shepherd, Lara D. ; McLenachan, Patricia A. ; Thomson, John A. ( September 2019 , American Journal of Botany)

   Spore‐bearing plants are capable of dispersing very long distances. However, it is not known if gene flow can prevent genetic divergence in widely distributed taxa. Here we address this issue, and examine systematic relationships at a global geographic scale for the fern genusPteridium.

   We sampled plants from 100 localities worldwide, and generated nucleotide data from four nuclear genes and two plastid regions. We also examined 2801 single nucleotide polymorphisms detected by a restriction site‐associatedDNAapproach.

   We found evidence for two distinct diploid species and two allotetraploids between them. The “northern” species (Pteridium aquilinum) has distinct groups at the continental scale (Europe, Asia, Africa, and North America). The northern European subspeciespinetorumappears to involve admixture among all of these. A sample from the Hawaiian Islands contained elements of both North American and AsianP. aquilinum. The “southern” species,P. esculentum, shows little genetic differentiation between South American and Australian samples. Components of African genotypes are detected on all continents.

   We find evidence of distinct continental‐scale genetic differentiation inPteridium. However, on top of this is a clear signal of recent hybridization. Thus, spore‐bearing plants are clearly capable of extensive long‐distance gene flow; yet appear to have differentiated genetically at the continental scale. Either gene flow in the past was at a reduced level, or vicariance is possible even in the face of long‐distance gene flow.

    

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5. Spatial population genomics of the brown rat ( Rattus norvegicus ) in New York City

   https://doi.org/10.1111/mec.14437  

   Combs, Matthew ; Puckett, Emily E. ; Richardson, Jonathan ; Mims, Destiny ; Munshi‐South, Jason ( December 2017 , Molecular Ecology)

   Human commensal species such as rodent pests are often widely distributed across cities and threaten both infrastructure and public health. Spatially explicit population genomic methods provide insights into movements for cryptic pests that drive evolutionary connectivity across multiple spatial scales. We examined spatial patterns of neutral genomewide variation in brown rats (Rattus norvegicus) across Manhattan, New York City (NYC), using 262 samples and 61,401SNPs to understand (i) relatedness among nearby individuals and the extent of spatial genetic structure in a discrete urban landscape; (ii) the geographic origin ofNYCrats, using a large, previously published data set of global rat genotypes; and (iii) heterogeneity in gene flow across the city, particularly deviations from isolation by distance. We found that rats separated by ≤200 m exhibit strong spatial autocorrelation (r = .3,p = .001) and the effects of localized genetic drift extend to a range of 1,400 m. Across Manhattan, rats exhibited a homogeneous population origin from rats that likely invaded from Great Britain. While traditional approaches identified a single evolutionary cluster with clinal structure across Manhattan, recently developed methods (e.g., fineSTRUCTURE,sPCA,EEMS) provided evidence of reduced dispersal across the island's less residential Midtown region resulting in fine‐scale genetic structuring (F_ST = 0.01) and two evolutionary clusters (Uptown and Downtown Manhattan). Thus, while some urban populations of human commensals may appear to be continuously distributed, landscape heterogeneity within cities can drive differences in habitat quality and dispersal, with implications for the spatial distribution of genomic variation, population management and the study of widely distributed pests.

    

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