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1. Old divergence and restricted gene flow between torrent duck ( Merganetta armata ) subspecies in the Central and Southern Andes

   https://doi.org/10.1002/ece3.5538  

   Alza, Luis ; Lavretsky, Philip ; Peters, Jeffrey L. ; Cerón, Gerardo ; Smith, Matthew ; Kopuchian, Cecilia ; Astie, Andrea ; McCracken, Kevin G. ( August 2019 , Ecology and Evolution)

   To investigate the structure and rate of gene flow among populations of habitat‐specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction.

   Peruvian and Argentine Andes.

   Two subspecies of torrent duck (Merganetta armata).

   We sampled 156 individuals in Peru (M. a. leucogenis;Chillón River,n = 57 and Pachachaca River,n = 49) and Argentina (M. a. armata;Arroyo Grande River,n = 33 and Malargüe River,n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine‐scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru,n = 10 and Argentina,n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z‐linked double‐digest restriction‐associated DNA sequences.

   Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species‐level differences (Φ_STmtDNA = 0.82; Φ_STautosomal = 0.30; Φ_STZ chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using∂a∂i(isolation‐with‐migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal∂a∂i = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well‐differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country.

   We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure.

    

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2. Examination of runs of homozygosity in relation to height in an endogamous Namibian population

   https://doi.org/10.1002/ajpa.24660  

   Swinford, Natalie ; Gallagher, Brenna ; Sheehama, Jacob ; Lin, Meng ; Prall, Sean ; Scelza, Brooke ; Henn, Brenna M. ( November 2022 , American Journal of Biological Anthropology)

   Height is a complex, highly heritable polygenic trait subject to both genetic composition and environmental influences. Recent studies suggest that a large proportion of height heritability is determined by the cumulative effect of many low allele frequency variants across the genome. Previous research has also identified an inverse relationship between height and runs of homozygosity (ROH); however, this has yet to be examined within African populations. We aim to identify this association within the Himba, an endogamous Namibian population who are recently bottlenecked, resulting in elevated haplotype sharing and increased homozygosity.

   Here, we calculate the fraction of the genome composed of long runs of homozygosity (F_ROH) in a sample of 245 adults and use mixed effects models to assess its effect on height.

   We find that Himba adults exhibit increased homozygosity. However, in contrast to previous studies in other populations, we do not find a significant effect ofF_ROHon height within the Himba. We further estimated heritability of height, noting both an enrichment of distant relatives and greater developmental homogeneity across households; we find that (SE ± 0.146), comparable to estimates reported in Europeans.

   Our results may be due to other environmental variables we were not able to include, measurement error, or low statistical power, but may also imply that phenotypic expression resulting from increased homozygosity may vary from population to population.

    

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3. Genetic diversity and selection in Puerto Rican horses

   https://doi.org/10.1038/s41598-021-04537-5  

   Wolfsberger, Walter W. ; Ayala, Nikole M. ; Castro-Marquez, Stephanie O. ; Irizarry-Negron, Valerie M. ; Potapchuk, Antoliy ; Shchubelka, Khrystyna ; Potish, Ludvig ; Majeske, Audrey J. ; Oliver, Luis Figueroa ; Lameiro, Alondra Diaz ; et al ( January 2022 , Scientific Reports)

   Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the “Criollo”) horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the “gait-keeper”DMRT3mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the “gait-keeper”DMRT3allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant “gait-keeper” allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing theDMRT3locus to this day. The lack of the detectable signature of selection associated with theDMRT3in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (includingCHRM5, CYP2E1, MYH7, SRSF1, PAM, PRNand others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.

    

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4. Genotyping‐by‐sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen ( Populus tremuloides )

   https://doi.org/10.1002/ece3.6214  

   Bagley, Justin C. ; Heming, Neander M. ; Gutiérrez, Eliécer E. ; Devisetty, Upendra K. ; Mock, Karen E. ; Eckert, Andrew J. ; Strauss, Steven H. ( April 2020 , Ecology and Evolution)

   Populus tremuloidesis the widest‐ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome‐wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics ofP. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal–Cascades (cluster 1), east‐slope Cascades–Sierra Nevadas–Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of theP. tremuloidesrange, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the “stable‐edge hypothesis” that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited “trailing‐edge” dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the “inland dispersal hypothesis” predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific‐coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable‐edge, refugial locations, and postglacial expansion withinP. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific‐coastal genetic lineage of quaking aspen.

    

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5. Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida scrub jays , Aphelocoma coerulescens

   https://doi.org/10.1111/eva.13421  

   Nguyen, Tram N. ; Chen, Nancy ; Cosgrove, Elissa J. ; Bowman, Reed ; Fitzpatrick, John W. ; Clark, Andrew G. ( June 2022 , Evolutionary Applications)

   Understanding the genomic consequences of population decline is important for predicting species' vulnerability to intensifying global change. Empirical information about genomic changes in populations in the early stages of decline, especially for those still experiencing immigration, remains scarce. We used 7834 autosomal SNPs and demographic data for 288 Florida scrub jays (Aphelocoma coerulescens; FSJ) sampled in 2000 and 2008 to compare levels of genetic diversity, inbreeding, relatedness, and lengths of runs of homozygosity (ROH) between two subpopulations within dispersal distance of one another but have experienced contrasting demographic trajectories. At Archbold Biological Station (ABS), the FSJ population has been stable because of consistent habitat protection and management, while at nearby Placid Lakes Estates (PLE), the population declined precipitously due to suburban development. By the onset of our sampling in 2000, birds in PLE were already less heterozygous, more inbred, and on average more related than birds in ABS. No significant changes occurred in heterozygosity or inbreeding across the 8‐year sampling interval, but average relatedness among individuals decreased in PLE, thus by 2008 average relatedness did not differ between sites. PLE harbored a similar proportion of short ROH but a greater proportion of long ROH than ABS, suggesting one continuous population of shared demographic history in the past, which is now experiencing more recent inbreeding. These results broadly uphold the predictions of simple population genetic models based on inferred effective population sizes and rates of immigration. Our study highlights how, in just a few generations, formerly continuous populations can diverge in heterozygosity and levels of inbreeding with severe local population decline despite ongoing gene flow.

    

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