Andrew T Fields

Stony Brook University | Stony Brook · School of Marine and Atmospheric Sciences

The presence of cryptic species can hinder effective conservation planning and implementation, as has been the case for speciose groups of freshwater fishes that are difficult to differentiate due to conserved morphologies. The West Texas shiner Notropis megalops and the Texas shiner Notropis amabilis are a cryptic pair of leuciscids (minnows) that...

The Leuciscidae (minnows, shiners and relatives) is a diverse family of freshwater fishes with many species endangered due to anthropogenic stressors. Notropis oxyrhynchus and Notropis buccula are two shiners found only in the upper Brazos River basin in Texas, USA and listed as endangered due to contracted habitat. The complete mitochondrial genom...

While dorsal-ventrally compressed chondrichthyans are among the most imperiled fishes in the world, there is still limited knowledge of the biology of many of these species, even in well-studied ocean basins. In the western North Atlantic Ocean, the population structure of the Atlantic angel shark (Squatina dumeril) is not fully understood; therefo...

Patterns of genetic variation reflect interactions among microevolutionary forces that vary in strength with changing demography. Here, patterns of variation within and among samples of the mouthbrooding gafftopsail catfish (Bagre marinus, Family Ariidae) captured in the U.S. Atlantic and throughout the Gulf of Mexico were analyzed using genomics t...

Age estimates are essential for fisheries assessment and management, but deepwater (>200 m) fishes are often difficult to age using traditional techniques. Therefore, age-predictive epigenetic clocks were developed for a model deepwater reef fish, blackbelly rosefish Helicolenus dactylopterus, using two tissue types (fin clips and muscle; n = 61 in...

Globally, many pond turtles (Family Emydidae) are of conservation concern due to contracting ranges, increasingly fragmented habitats, and declining populations. One of these turtles, the diamondback terrapin (Malaclemys terrapin), is of concern within the United States, but surveying potential estuarine habitat for the presence of the species requ...

Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and has direct implications for the spatial scal...

Developing‐world shark fisheries are typically not assessed or actively managed for sustainability; one fundamental obstacle is the lack of species and size‐composition catch data. We tested and implemented a new and potentially widely applicable approach for collecting these data: mandatory submission of low‐value secondary fins (anal fins) from l...

The silky shark is the second most common shark in Southeast Asia’s dried fin markets and is managed in the Atlantic Ocean by the International Commission for the Conservation of Atlantic Tuna (ICCAT) and by three Indo-Pacific regional fisheries management organizations (RMFOs). ICCAT reports ~ 7% of global silky landings but there is a moratorium...

Fins from highly mobile shark species entering large shark fin trade hubs can originate from various geographical locations and stocks. Tracing fins from internationally regulated species to their starting point in the supply chain can have important implications for the monitoring and enforcement of international laws intended to protect threatene...

Species-specific monitoring through large shark fin market surveys has been a valuable data source to estimate global catches and international shark fin trade dynamics. Hong Kong and Guangzhou, mainland China, are the largest shark fin markets and consumption centers in the world. We used molecular identification protocols on randomly collected pr...

There is an urgent need for population‐specific trade information for overexploited sharks, as international trade regulations are becoming an important tool for their conservation [i.e., listings on the Convention on International Trade in Endangered Species (CITES)]. We tested a genetic stock identification (GSI) workflow to quantify the relative...

Trade‐driven overexploitation threatens many sharks. Twelve of the world's most vulnerable shark species have been listed on the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) to regulate internationally traded products such as meat and dried fins. CITES records indicate that Hong Kong was the world's top le...

Sawfishes (Family Pristidae) constitute one of the most threatened families of marine fish, and substantial management efforts are required to stabilize and recover their populations worldwide. Philopatry is common in marine animals, including sharks and rays, and can be a key driver of population structure, which in turn determines the most approp...

The shark fin trade is a major driver of shark exploitation in fisheries all over the world, most of which are not managed on a species‐specific basis. Species‐specific trade information highlights taxa of particular concern and can be used to assess the efficacy of management measures and anticipate emerging threats. The species composition of the...

Protecting sharks from overexploitation has become global priority after widespread population declines have occurred. Tracking catches and trade on a species-specific basis has proven challenging, in part due to difficulties in identifying processed shark products such as fins, meat, and liver oil. This has hindered efforts to implement regulation...

Compound character attributes (cCA) for CITES-listed shark species. (XLSX)

Number of nucleotide differences between species of the Carcharhinus genus in samples from Guangzhou, China, at the Shark150 region (above diagonal) and Shark474 region (below diagonal). Highlighted cells and number in bold depict two or less nucleotide differences. (XLSX)

Alignment of the Shark150 and Shark474 for common Carcharhinus spp. found in Asian shark fin markets. (TXT)

Carcharhinus samples used to design Shark474F. (DOCX)

Population structure and lineage diversification within a small, non-dispersive hammerhead shark species, the bonnethead shark Sphyrna tiburo, was assessed. Sphyrna tiburo is currently described as one continuously distributed species along the Atlantic continental margins of North, Central and South America, but recent genetic analysis of an insul...

Shark populations around the world are threatened by the high demand for their fins in Asian countries. The molecular identification of processed shark products has proven to be challenging, due to the level of degradation of the DNA. This lack of detailed species-specific data has hindered the adoption of management regulations of the shark trade...

Facultative parthenogenesis - the ability of sexually reproducing species to sometimes produce offspring asexually - is known from a wide range of ordinarily sexually reproducing vertebrates in captivity, including some birds, reptiles and sharks [1-3]. Despite this, free-living parthenogens have never been observed in any of these taxa in the wild...

The white shark, Carcharodon carcharias, is both one of the largest apex predators in the world and among the most heavily protected marine fish. Population genetic diversity is in part shaped by recent demographic history and can thus provide information complementary to more traditional population assessments, which are difficult to obtain for wh...

There is a growing need to identify shark products in trade, in part due to the recent listing of five commercially important species on the Appendices of the Convention on International Trade in Endangered Species (CITES; porbeagle, Lamna nasus, oceanic whitetip, Carcharhinus longimanus scalloped hammerhead, Sphyrna lewini, smooth hammerhead, S. z...

Genetic diversity, population genetic structure and isolation by distance (IBD) were assessed in a viviparous coastal shark (the lemon shark Negaprion brevirostris) across 8 western Atlantic samples spaced between ~150 and 7000 km apart. Juveniles (N = 325) were sequenced at 2 mitochondrial loci (1729 bp) and typed at 9 nuclear encoded microsatelli...

Lucilia Robineau-Desvoidy (Diptera: Calliphoridae) is a blow fly genus of forensic, medical, veterinary, and agricultural importance. This genus is also famous because of its beneficial uses in maggot debridement therapy (MDT). Although the genus is of considerable economic importance, our knowledge about microbes associated with these flies and ho...

We announce the complete genome sequence for Proteus mirabilis strain BB2000, a model system for self recognition. This opportunistic pathogen contains a single, circular chromosome (3,846,754 bp). Comparisons between this genome and that of strain HI4320 reveal genetic variations corresponding to previously unknown physiological and self-recogniti...

We announce the complete genome sequence for Proteus mirabilis strain BB2000, a model system for self recognition. This opportunistic pathogen contains a single, circular chromosome (3,846,754 bp). Comparisons between this genome and that of strain HI4320 reveal genetic variations corresponding to previously unknown physiological and self-recogniti...

Flies transport specific bacteria with their larvae that provide a wider range of nutrients for those bacteria. Our hypothesis was that this symbiotic interaction may depend on interkingdom signaling. We obtained Proteus mirabilis from the salivary glands of the blow fly Lucilia sericata; this strain swarmed significantly and produced a strong odor...

Genes within 1 kb of a peak variant, excluding the Chr. 2 centromere. (0.47 MB TXT)

Differentiation of all chromosomes. The diffStat is shown for each variant that had higher or lower allele frequencies in the large-selected lines compared to the small-selected lines. Color coding indicates estimated starting allele frequency: black = all variants, gold = variants with an average control frequency <0.05; red = peak variants. Left...

False discovery rates for each allele frequency class at various thresholds for the X chromosome. (0.02 MB PDF)

Functional clustering of GO terms generated by DAVID. (0.46 MB XLS)

Significant GO Terms, as generated by DAVID. (0.20 MB XLS)

Examples of significantly differentiated genes. The diffStat is shown for each variant at each locus; colors are as in figure S2. A: At EGFR several polymoprhisms are significantly differentiated across 25-kb, B: At dally, a large region of differentiation encompassed multiple genes and many polymoprhisms. For the candidate gene at each locus, the...

Low bias introduced by estimating starting allele frequency. A: the proportion of variants with average frequency of 0.40–0.60, depending on starting frequency. B: Distribution of expected allele frequency differentiation for alleles which have a final average frequency between 0.45–0.50 in the two control populations; colors indicate starting alle...

Significance of anatomical measurements. (0.04 MB PDF)

All peak variants. (0.41 MB XLS)

Read coverage of genome partitions using reads with alignment qualities greater than 15. A: Chromosomes X, 2, and 3; B: centromeric regions, C: mitochondria, D: Y chromosome, E: U and Uextra (unplaced regions). Females were sequenced, so Y coverage is expected to be near zero for unique alignments, though some male DNA could be present if females w...

False discovery rates for each allele frequency class at various thresholds for autosomes. (0.02 MB PDF)

Differentiation of all chromosomes. The diffStat is shown for each variant that had higher or lower allele frequencies in the large-selected lines compared to the small-selected lines. Color coding indicates significance: black = nonsignificant variants, blue = significant variants at the permissive FDR threshold (FDR<10%); gold = significant varia...

Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype m...