An official website of the United States government
The common bottlenose dolphin (Tursiops truncatus) is a key marine mammal species in the Gulf of Mexico, playing an essential role as a top predator. This study investigates the genetic diversity and population structure of bottlenose dolphins stranded in the Mississippi Sound from 2010 to 2021. Tissue samples (muscle, liver, lung, kidney, and brain) were collected from 511 stranded dolphins, and mitochondrial DNAs (mtDNA) were extracted for analysis. A total of 417 samples were successfully amplified and sequenced using high throughput sequencing, yielding 386 complete mitogenomes. Genetic diversity metrics, such as nucleotide and haplotype diversity, were calculated, and population structure was inferred for both mitochondrial control region (mtCR) and whole mitogenome sequences. Using the whole mitogenome, the study identified four genetically distinct populations within the Mississippi Sound, demonstrating regional variation in dolphin populations. Notably, two stranded individuals likely originated from populations outside the sampled area. The use of whole mitogenomes allowed for improved resolution of genetic diversity and population differentiation compared to previous studies using partial mtDNA sequences. These findings enhance our understanding of bottlenose dolphin population structure in the region and underscore the value of stranded animals for population genetic studies.
more »
« less
Predictors of genomic diversity within North American squamates
Abstract Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for 2 mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; 4 individuals and 6,820 to 44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (phylogenetically independent contrasts: R2 = 0.31, P = 0.007) and GBS diversity (R2 = 0.21; P = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across species’ ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups.
more »
« less
- Award ID(s):
- 2112946
- PAR ID:
- 10427918
- Editor(s):
- Ruane, Sara
- Date Published:
- Journal Name:
- Journal of Heredity
- Volume:
- 114
- Issue:
- 2
- ISSN:
- 0022-1503
- Page Range / eLocation ID:
- 131 to 142
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Lopez, Jose (Ed.)Abstract Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.more » « less
-
Lohmueller, Kirk (Ed.)Abstract To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.more » « less
-
Abstract The Mallard (Anas platyrhynchos) duck is a ubiquitous and socio-economically important game bird in North America. Despite their generally abundant midcontinent population, Mallards in eastern North America are declining, which may be partially explained by extensive hybridization with human-released domestically derived game-farm Mallards. We investigated the genetic composition of Mallards in the middle and lower Mississippi flyway, key wintering regions for the species. We found that nearly 30% of wild Mallards carried mitochondrial (mtDNA) haplotypes derived from domestic Mallards present in North America, indicating that the individuals had female game-farm Mallard lineage in their past; however, nuclear results identified only 4% of the same sample set as putative hybrids. Recovering 30% of samples with Old World (OW) A mtDNA haplotypes is concordant with general trends across the Mississippi flyway and this percentage was stable across Mallards we sampled a decade apart. The capture and perpetuation of OW A mtDNA haplotypes are likely due to female breeding structure, whereas reversal of the nuclear signal back to wild ancestry is due to sequential backcrossing and lower and/or declining admixture with game-farm Mallards. Future studies of wild ancestry of Mississippi flyway Mallards will benefit from coupling molecular and spatial technology across flyways, seasons, and years to search for potential transitions of Mallard populations with different genetic ancestry, and whether the genetic ancestry is somehow linked to an individual’s natal and subsequent breeding location.more » « less
-
DNA metabarcoding is a popular methodology for biodiversity assessment and increasingly used for community level analysis of intraspecific genetic diversity. The evolutionary history of hundreds of specimens can be captured in a single collection vial. However, the method is not without pitfalls, which may inflate or misrepresent recovered diversity metrics. Nuclear pseudogene copies of mitochondrial DNA (numts) have been particularly difficult to control because they can evolve rapidly and appear deceptively similar to true mitochondrial sequences. While the problem of numts has long been recognized for traditional sequencing approaches, the issues they create are particularly evident in metabarcoding in which the identity of individual specimens is generally not known. In this issue ofMolecular Ecology Resources, Andújar et al. (2021) provide an easy to implement bioinformatic approach to reduce erroneous sequences due to numts and residual noise in metabarcoding data sets. The metaMATE software designates input sequences as authentic (mtDNA haplotypes) or nonauthentic (numts and erroneous sequences) by comparison to reference data and by analysing nucleotide substitution patterns. Filtering is applied over a range of abundance thresholds and the choice to proceed with a more rigid or less strict sequence removal strategy is at the researchers’ discretion. This is a valuable addition to a growing number of complementary tools for improving the reliability of modern biodiversity monitoring.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/jhered/esad001
