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Figure 3 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)

Figure 3. Thirty-seven warbling vireo populations genotyped at 14 microsatellite loci. Colours correspond to the four genetic groups from STRUCTURE: eastern (red), north-western (green), south-western (blue) and the Black Hills (orange) (see Fig. 2). The eastern (Medicine Hat, M HAT; left circle) and north-western (Cypress Hills, C HILLS; right circle) groups from the SEAB population are shown separately. Refer to Table 1 for population abbreviations and sample sizes.

Figure 2 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)

Figure 2. Hierarchical STRUCTURE plots (K = 2) based on genotypes from 14 microsatellite loci. Populations with additional hierarchical structure are in yellow. Each bar represents a single individual, and the Q value is the percent ancestry of that individual to each genetic group. (A) All populations (red = eastern group), (B) western populations and the Black Hills (orange), (C) remaining western populations (north-western = green; south-western = blue). Refer to Table 1 for population abbreviations and sample sizes.

Figure 1 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)

Figure 1. Range distributions of the three warbling vireo subspecies in this study based on Phillips (1991) and American Ornithologists' Union (1998) in gray scale on the map. Circles on the map show sampling locations included in the cyt b analysis (top inset). Black circles are eastern haplotypes, whereas white circles are western haplotypes. The eastern (Medicine Hat, M HAT; left circle) and western (Cypress Hills, C HILLS; right circle) groups from the SEAB population are shown separately. The ATPase 6 and 8 results are not on the map (bottom inset) and do not include the eastern group. Colours in the haplotype networks correspond to our microsatellite genetic groups: eastern (black), north-western (grey), south-western (white) and the Black Hills (striped). Each circle is a haplotype, and its size is proportional to how many individuals share that haplotype. Cross hatches in the haplotype networks represent more than one nucleotide difference. Refer to Table 1 for population abbreviations and sample sizes.

Figure 6 in Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)

Figure 6. Contemporary ecological niche models for three of the four warbling vireo microsatellite genetic groups (Black Hills are not included): north-western (top), south-western (middle) and eastern (bottom). The logarithmic scale on the left depicts the percent likelihood of habitat suitability based on climate variables.

Hybridization and low genetic diversity in the endangered Alabama Red-Bellied Turtle (Pseudemys alabamensis)

Pseudemys alabamensis is one of the most endangered freshwater turtle species in the United States due to its restricted geographic distribution in coastal Alabama and Mississippi. Populations of P. alabamensis are geographically isolated from one another by land and salt water, which could act as barriers to gene flow. It is currently unknown how differentiated these isolated populations are from one another and whether they have experienced reductions in population size. Previous work found morphological differences between Alabama and Mississippi populations, suggesting that they may be evolutionarily distinct. Other Pseudemys turtles such as P. concinna and P. floridana occur naturally within the same geographic area as P. alabamensis and are known to hybridize with each other. These more abundant species could threaten the unique genetic identity of P. alabamensis through introgression. In order to evaluate the endangered status of P. alabamensis and the level of hybridization with other species, we used mitochondrial and nuclear microsatellite markers to assess genetic variation within and among populations of P. alabamensis throughout its range and estimate admixture with co-occurring Pseudemys species. In P. alabamensis, we found no variation in mitochondrial DNA and observed an excess of homozygosity in the microsatellite data. Our results indicate evidence of genetic differentiation between Alabama and Mississippi populations of P. alabamensis, and low estimated breeding sizes and inbreeding for two populations (Fowl River, Alabama and Biloxi, Mississippi). Our results also support admixture of P. alabamensis with P. concinna/P. floridana. Based on our results, P. alabamensis is highly endangered throughout its range and threatened by both low population sizes and hybridization. In order to improve the species' chances of survival, focus should be placed on habitat preservation, maintenance of genetic diversity within both Mississippi and Alabama populations, and regular population monitoring activities such as nest surveillance and estimates of recruitment.

opencc-by-4.0May 2022View details →

A pilot study evaluating consumer motivations, perceptions, and responses to direct-to-consumer (DTC) canine genetic test results

Survey responses exported from Qualtrics XM platform used for data analysis. The objectives of the study were to evaluate the user experience of current Wisdom Panel customers and evaluate their motivations to pursue canine genetic services, their perceptions of the services and test(s) used, and their response to the canine genetic test results. The file format provided is for Excel. Data analysis was completed using SPSS version 28. Please contact the author directly with any questions about the data.

Dispersal ability and its consequences for population genetic differentiation and diversification

Dispersal ability is known to influence geographic structuring of genetic variation within species, with a direct relationship between low vagility and population genetic structure, which can potentially give rise to allopatric speciation. However, our general understanding of the relationship between dispersal ability, population differentiation and lineage diversification is limited. To address this issue, we sampled mitochondrial DNA variation within lineages of beetles and spiders across the Canary Islands to explore the relationships between dispersal ability, differentiation within lineages and diversification. We found positive relationships between population genetic structure and diversification for both beetles and spiders. Comparisons between dispersive and non-dispersive lineages revealed significant differences for both lineage differentiation and diversification. For both taxa, non-dispersive lineages had stronger population genetic structure. Genus-level endemic species richness and proxies for diversification rate within genera were higher in non-dispersive taxa for both beetles and spiders. Comparisons of average and maximum node divergences within genera suggest that species turnover may be higher in non-dispersive genera. Our results reveal a model where dispersal limitation may shape the diversity of lineages across evolutionary time scales by positively influencing intraspecific and species diversity, moderated by higher extinction rates compared to more dispersive lineages.

opencc-by-4.0Sep 2022View details →

Western redcedar single nucleotide polymorphism (SNP) genotyping data for genomic selection and population genetics

Western redcedar (Thuja plicata) Single Nucleotide Polymorphism (SNP) data in Variant Call Format (VCF) for genomic selection training and target populations, genomic selection parents, and self-fertilized (selfing) lines, comprising 4,833 trees. Targeted sequencing-based genotyping was done by Capture-Seq methodology at Rapid Genomics (Neves est al. 2013). A set of 57,000 probes as designed for initial marker discovery, from which a panel of 20,858 probes was selected for genotyping. A set of transcriptomes (Shalev et al. 2018) (PRJNA704616) was aligned to the reference genome to identify SNPs. Candidate probes (120 nt) were initially designed in silico and 57,000 selected by removing candidates with poor base composition for hybridization (GC content <0.2 and >0.6, high G content >0.2 and long homopolymers >7), followed by removing probes aligning to more than one position on the reference genome (≥90% identity and length). The 57,000 probes represent 14,517 scaffolds (average 3.9 probes/scaffold), with 37,275 targeting at least one SNP and 19,725 mapping to intergenic regions not containing pre-identified SNPs. A set of 128 individuals were selected to validate the 57,000 probe panel and associated polymorphisms. Genomic DNA (0.5 ug) was fragmented (mean size 300 bp), followed by repair of ends, phosphorylation, adenylation, ligation of Illumina compatible adapters containing 8bp indexes and 5’ T-overhang, and 10 cycles PCR amplification with universal primers to produce sequencing-ready libraries. Libraries were quantified using PicoGreen. Libraries from 16 samples were pooled, hybridized to the 120 nt RNA probes following Agilent’s SureSelect Target Enrichment System (Agilent Technologies) and sequenced on an Illumina HiSeq X machine with paired-end 150bp cycle for an average sequencing depth per sample of 15X. Sequence data were aligned to the reference genome with BWA-MEM (http://arxiv.org/abs/1303.3997) and sets of four samples were combined to increase sequencing depth for identifying markers. Putative SNPs were identified using Freebayes (http://arxiv.org/abs/1207.3907) in 150bp on either side of the 57,000 probes and filtered probes that had more than 17 SNPs per 420 bp target region (150bp + 120bp + 150bp). The sequencing depth of the probes was used to select the final set of 20,885 probes, removing probes on both sides of the distribution (low and high sequencing depth), for Capture-Seq on the remainder of the samples.

Population genetic and environmental data for Chamaecrista fasciculata

Chamaecrista fasciculata is a widely distributed, phenotypically variable species in the eastern U.S. Whereas studies have demonstrated genetic structure and local adaptation in northern areas of its distribution, there has been no comparison of genetic variability among populations at the southern extent where phenotypic variation is more complex. We characterized genetic variation at 14 microsatellite loci for populations in Mississippi and Alabama and compared this to variation in a phenotypic trait, leaf pubescence. Geographic distance, climatic variables, and elevation were evaluated as factors to explain the observed patterns of genetic diversity. A significant amount of variation (19%) resided among populations, but most variation (68%) was among individuals. Assignment of individuals into genetic groups suggests two primary clusters, but these groups are not concordant with known geographical or ecological breaks, nor phenotypic variants. Genetic structure at a regional scale can be characterized as isolation by distance, while environmental factors may play a secondary role in limiting gene flow at local scales. Mean population FST is strongly associated with allelic diversity and heterozygosity, suggesting that genetic drift influences population variation. Despite the presence of genetic and phenotypic variation in southern populations of C. fasciculata, the lack of concordant patterns between these types of variation indicate that they are not driven by the same factors. This study demonstrates how local factors differentially influence the maintenance of intraspecific variation and suggest the southern distributional range is an active area of evolution for C. fasciculata

Life-history stage and the population genetics of the tiger mosquito Aedes albopictus at a fine spatial scale

As a widespread vector of disease, the mosquito species Aedes albopictus Skuse (Diptera: Culicidae) is a high priority for both public health and invasive species research and management. Like all mosquitoes, A. albopictus has a complex life history with aquatic egg, larval, and pupal stages and a terrestrial adult stage. This requires targeted management strategies for each life stage, coordinated across time and space. Researchers use population genetics to inform control of A. albopictus. However, these studies do not consider the impact on life stage on population genetic characteristics and subsequent conclusions. Our objective was to examine whether the life stage impacted patterns of A. albopictus genetic diversity and differentiation at a spatial scale relevant to management efforts. We first conducted a literature review of field-caught A. albopictus population genetic papers and identified 74 peer-reviewed publications, none of which compared results between life stages. We them examined population genetic patterns of egg and adult A. albopictus at five sites in Wake County, North Carolina USA using 8,425 single nucleotide polymorphisms. We found that level of genetic diversity and connectivity between sites varied between adults and eggs. This warrants further study and is critical for research aimed at informing local management.

Historical connections between Atlantic Forest and Amazonia drove genetic and ecological diversity in Lithobates palmipes (Anura, Ranidae)

The Atlantic and Amazon rainforests have a shared but unclear past, with intermittent connections resulting from historical climate change. We investigate these connections by studying the phylogeography and climatic niche of the disjunct distributed frog Lithobates palmipes. We sequenced two fragments of mitochondrial DNA from Atlantic Forest (AtF) and Amazonia (AmF) individuals and evaluated how genetic diversity is distributed in space and whether past demographic changes occurred. Also, we evaluated the existence of past suitable connections between biomes for L. palmipes through ecological niche models (ENM) and tested for niche divergence. The AtF group is nested within the AmF group and closely related to individuals from eastern Amazonia, a pattern recovered in many species that used northeast connection routes. We found evidence of recurrent use of connections in different directions and time during the Pleistocene, resulting in genetic structure between biomes, with no signal of demographic change and evidence of niche divergence across both genetic groups. ENMs indicated suitable areas connecting forests throughout northeastern Brazil during the Pleistocene. Mitochondrial lineages do not match biomes exactly. One lineage is composed of AtF populations and eastern Amazonia individuals. The other is composed of western Amazonia individuals, suggesting an effect of past climatic heterogeneity within the Amazonia forest. This is the first evidence that this route drove genetic and ecological diversity for amphibians recently, a group with habits and ecological requirements different from other vertebrates that have been shown to use this putative corridor.

Restoring faith in conservation action: maintaining wild genetic diversity through the Tasmanian devil insurance program

Conservation breeding programs aim to maintain 90% wild genetic diversity, but rarely assess functional diversity. Here, we compare both genome-wide and functional diversity (in over 500 genes) of Tasmanian devils (Sarcophilus harrisii) within the insurance metapopulation and across the species' range (64,519 km2). Populations have declined by 80% since 1996 due to a contagious cancer, devil facial tumour disease (DFTD). However, predicted local extinctions have not occurred. Recent suggestions of selection for "resistance" alleles in the wild precipitated concerns that insurance population devils may be unsuitable for translocations. Using 830 wild samples collected at 31 locations between 2012-2021, and 553 insurance metapopulation devils, we show that the insurance metapopulation is representative of current wild genetic diversity. Allele frequencies at DFTD-associated loci were not substantially different between captive and wild devils. Methods presented here are valuable for others investigating evolutionary potential in threatened species, particularly ones under significant selective pressures.

Genotype data for: Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex

Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species A. alosa, which disperses greater distances compared to the iteroparous species, A. fallax. Individuals caught at sea were assigned at the river level for A. fallax and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: A. agone in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species' populations and their hybridization should be carefully considered while implementing conservation programs.

Population genetic and geographic data of six Neotropical plant species

We examined population genetic structure and fine-scale spatial genetic structure (FSGS) in six perennial understory angiosperms in Andean cloud forests of northwestern Ecuador. Species belong to three families (Gesneriaceae, Melastomataceae, and Rubiaceae), and within each family we paired one insect-pollinated with one hummingbird-pollinated species, predicting that insect-pollinated species have greater population differentiation (as quantified with the FST statistic) and stronger FSGS (as quantified with the SP statistic) than hummingbird-pollinated species.

FIGURE 97 in Mitochondrial genetics of Ophiderini, with a new species from the Eudocima phalonia species group (Lepidoptera: Noctuidae: Calpinae)

FIGURE 97. Type localities and localities for DNA sequence vouchers in the Phyllodes imperialis complex (white stars=type localities; red circles=first haplotype; yellow square=second haplotype).

FIGURE 85. Strict consensus tree from a in Mitochondrial genetics of Ophiderini, with a new species from the Eudocima phalonia species group (Lepidoptera: Noctuidae: Calpinae)

FIGURE 85. Strict consensus tree from a parsimony analysis of Calpinae COI 5' mtDNA sequences (part): Eudocima clade (part).

FIGURE 82. Strict consensus tree from a in Mitochondrial genetics of Ophiderini, with a new species from the Eudocima phalonia species group (Lepidoptera: Noctuidae: Calpinae)

FIGURE 82. Strict consensus tree from a parsimony analysis of Calpinae COI 5' mtDNA sequences (part): Eudocima clade (part).

FIGURE 80. Strict consensus tree from a in Mitochondrial genetics of Ophiderini, with a new species from the Eudocima phalonia species group (Lepidoptera: Noctuidae: Calpinae)

FIGURE 80. Strict consensus tree from a parsimony analysis of Calpinae COI 5' mtDNA sequences (part): Gonodonta and Xylophylla+Eudocima formosa+Huebnerius+Gloriana clades.

FIGURE 84. Strict consensus tree from a in Mitochondrial genetics of Ophiderini, with a new species from the Eudocima phalonia species group (Lepidoptera: Noctuidae: Calpinae)

FIGURE 84. Strict consensus tree from a parsimony analysis of Calpinae COI 5' mtDNA sequences (part): Eudocima clade (part).

FIGURE 81. A–B in Mitochondrial genetics of Ophiderini, with a new species from the Eudocima phalonia species group (Lepidoptera: Noctuidae: Calpinae)

FIGURE 81. A–B: Strict consensus tree from a parsimony analysis of Calpinae COI 5' mtDNA sequences (part): Miniophyllodes +Minioides+Lobophyllodes clade; C: Phyllodes clade recovered on some but not all equally parsimonious trees.