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
RAD‐tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)
Abstract Obovaria olivariais a species of freshwater mussel native to the Mississippi River and Laurentian Great Lakes‐St. Lawrence River drainages of North America. This mussel has experienced population declines across large parts of its distribution and is imperiled in many jurisdictions.Obovaria olivariauses the similarly imperiledAcipenser fulvescens(Lake Sturgeon) as a host for its glochidia. We employed mitochondrial DNA sequencing and restriction site‐associated DNA sequencing (RAD‐seq) to assess patterns of genetic diversity and population structure ofO. olivariafrom 19 collection locations including the St. Lawrence River drainage, the Great Lakes drainage, the Upper Mississippi River drainage, the Ohioan River drainage, and the Mississippi Embayment. Heterozygosity was highest in Upper Mississippi and Great Lakes populations, followed by a reduction in diversity and relative effective population size in the St. Lawrence populations. PairwiseFSTranged from 0.00 to 0.20, and analyses of genetic structure revealed two major ancestral populations, one including all St. Lawrence River/Ottawa River sites and the other including remaining sites; however, significant admixture and isolation by river distance across the range were evident. The genetic diversity and structure ofO. olivariais consistent with the existing literature onAcipenser fulvescensand suggests that, although northern and southernO. olivariapopulations are genetically distinct, genetic structure inO. olivariais largely clinal rather than discrete across its range. Conservation and restoration efforts ofO. olivariashould prioritize the maintenance and restoration of locations whereO. olivariaremain, especially in northern rivers, and to ensure connectivity that will facilitate dispersal ofAcipenser fulvescensand movement of encysted glochidia.
more »
« less
- Award ID(s):
- 1831512
- PAR ID:
- 10364962
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Ecology and Evolution
- Volume:
- 12
- Issue:
- 1
- ISSN:
- 2045-7758
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Specialist insects are especially susceptible to loss of genetic diversity in the face of habitat destruction and fragmentation. Implementing effective conservation practices for specialist insects will benefit from knowledge of population structure and genetic diversity. Because insects are hyper-diverse, characterizing the population structure of all species within the insect community is untenable, even if focused within a particular habitat type. Thus, concentrating on a single species specialized to a particular habitat type is needed to infer general trends. Here, we investigate the range-wide population genetics ofTetraopes texanusHorn 1878 (Coleoptera: Cerambycidae), which provides a useful model of grassland insects due to its’ habitat specificity and unique biology.Tetraopes texanusoccurs primarily in Texas and Oklahoma, into Northern Mexico, and possibly into eastern New Mexico but also occurs in Black Belt prairies of Mississippi and Alabama. Mitochondrial and nuclear DNA (RAD-seq) analysis identified two distinct population clusters ofT. texanuscorresponding to the Texas and Oklahoma population and the Mississippi and Alabama population. Demographic models indicate ongoing, though incomplete, isolation of the two populations, with estimated dates of divergence in the mid-Pleistocene, coinciding with the end of a glacial period and a shift in glacial interval. These results can inform conservation of grassland adapted insects and offers insight to the biogeography of the Gulf Coastal Plain.more » « less
-
Abstract The round goby ( Neogobius melanostomus ) is a successful invader of the Great Lakes–St Lawrence River basin that harbours a number of local parasites. The most common are metacercariae of the genus Diplostomum . Species of Diplostomum are morphologically difficult to distinguish but can be separated using molecular techniques. While a few species have been sequenced from invasive round gobies in this study system, their relative abundance has not been documented. The purpose of this study was to determine the species composition of Diplostomum spp. and their relative abundance in round gobies in the St Lawrence River by sequencing the barcode region of cytochrome c oxidase I. In 2007–2011, Diplostomum huronense (= Diplostomum sp. 1) was the most common, followed in order by Diplostomum indistinctum (= Diplostomum sp. 4) and Diplostomum indistinctum sensu Galazzo, Dayanandan, Marcogliese & McLaughlin (2002). In 2012, the most common species infecting the round goby in the St Lawrence River was D. huronense , followed by D. indistinctum and Diplostomum gavium (= Diplostomum sp. 3). The invasion of the round goby in the St Lawrence River was followed by a decline of Diplostomum spp. in native fishes to low levels, leading to the previously published hypothesis that the presence of the round goby has led to a dilution effect. Herein, it is suggested that despite the low infection levels in the round goby, infections still may lead to spillback, helping to maintain Diplostomum spp. in native fishes, albeit at low levels.more » « less
-
The use of environmental DNA (eDNA) to assess aquatic biodiversity is a growing field with great potential for monitoring and managing threatened species, like freshwater mussel (Unionidae) populations. Freshwater mussels are globally imperiled and serve essential roles in aquatic systems as a food source and as a natural water filter making their management essential for ecosystem health. Unfortunately, mussel populations are often understudied, and challenges exist to accurately and efficiently describe the full suite of species present. Multispecies eDNA approaches may also be more challenging where freshwater mussel populations are most diverse due to ongoing and significant taxonomic restructuring that has been further complicated by molecular phylogenies using mitochondrial genes. For this study, we developed a microfluidic metabarcoding array that targets a wide range of species, from invertebrates to fishes, with an emphasis on detecting unionid mussels known to be present in the Sipsey River, Alabama. We compared mussel species diversity across six sites with well-studied mussel assemblages using eDNA surveys and traditional quadrat surveys in 2016. We examined how factors such as mussel population density, biomass and location in the river substrate impacted our ability to detect certain species; and investigated unexpected eDNA detections through phylogenetic analysis. Our eDNA results for fish and mussel species were broadly consistent with the data from traditional electrofishing and quadrat-based field surveys, although both community eDNA and conventional sampling detected species unique to that method. Our phylogenetic analysis agreed with other studies that treat Pleurobema decisum and P. chattanoogaense as synonymous species; however, they are still listed as unique species in molecular databases which complicates their identity in a metabarcoding assay. We also found that Fusconaia flava and F. cerina are indistinguishable from one another using a portion of the NADH dehydrogenase Subunit 1 (ND1) marker, which may warrant further investigation into whether or not they are synonymous. Our results show that many factors impacted our ability to detect and correctly identify Unionidae mussel species. Here we describe the obstacles we faced, including the murky phylogeny of Unionidae mussels and turbid river conditions, and our development of a potentially impactful freshwater mussel monitoring eDNA assay.more » « less
-
Abstract AimArctic plants survived the Pleistocene glaciations in unglaciated refugia. The number, ages, and locations of these refugia are often unclear. We use high‐resolution genomic data from present‐day and Little‐Ice‐Age populations of Arctic Bell‐Heather to re‐evaluate the biogeography of this species and determine whether it had multiple independent refugia or a single refugium in Beringia. LocationCircumpolar Arctic and Coastal British Columbia (BC) alpine. TaxonCassiope tetragonaL., subspeciessaximontanaandtetragona, outgroupC. mertensiana(Ericaceae). MethodsWe built genotyping‐by‐sequencing (GBS) libraries usingCassiope tetragonatissue from 36 Arctic locations, including two ~250‐ to 500‐year‐old populations collected under glacial ice on Ellesmere Island, Canada. We assembled a de novo GBS reference to call variants. Population structure, genetic diversity and demography were inferred from PCA, ADMIXTURE, fastsimcoal2, SplitsTree, and several population genomics statistics. ResultsPopulation structure analyses identified 4–5 clusters that align with geographic locations. Nucleotide diversity was highest in Beringia and decreased eastwards across Canada. Demographic coalescent analyses dated the following splits with Alaska: BC subspeciessaximontana(5 mya), Russia (~1.4 mya), Europe (>200–600 kya), and Greenland (~60 kya). Northern Canada populations appear to have formed during the current interglacial (7–9 kya). Admixture analyses show genetic variants from Alaska appear more frequently in present‐day than historic plants on Ellesmere Island. ConclusionsPopulation and demographic analyses support BC, Alaska, Russia, Europe and Greenland as all having had independent Pleistocene refugia. Northern Canadian populations appear to be founded during the current interglacial with genetic contributions from Alaska, Europe and Greenland. We found evidence, on Ellesmere Island, for continued recent gene flow in the last 250–500 years. These results suggest that a re‐analysis of other Arctic species with shallow population structure using higher resolution genomic markers and demographic analyses may help reveal deeper structure and other circumpolar glacial refugia.more » « less
