Worldwide phylogeography and local population structure of the rough-toothed dolphin (Steno bredanensis)

Several dolphin species have global distributions. The extent of their radiation and limits to gene flow are presumably a product of oceanographic features both recent and historical, behavioral specializations and social organization. Rough-toothed dolphins (Steno bredanensis) are globally distributed in tropical and subtropical waters and are generally found in depths greater than 1,500 meters making them challenging to comprehensively sample. Although it has been assumed that pelagic dolphins range widely due to the lack of apparent barriers and unpredictable prey distribution, recent evidence suggests rough-toothed dolphins exhibit fidelity to some oceanic islands. A small number of photo-identification and genetic studies conducted to date on rough-toothed dolphins show regional population structure and stable associations in groups, with some individuals observed repeatedly in the same groups over several years. The aim of this dissertation is to describe patterns of phylogeography over evolutionary time on a global scale and expand studies of population and social structure on a regional level. The dataset contains 351 rough-toothed dolphin biopsies, tissue and teeth samples collected from the Pacific and Atlantic Oceans and limited samples from the Indian Ocean. To evaluate the phylogeography and test for possible species or subspecies level delineation between oceans, I used mitochondrial DNA sequences from the control region (350 bp) and 12 concatenated protein-coding genes from the whole mitogenome, as well as six nuclear introns. Although I found support for two Pacific clades and a private North Atlantic clade in the whole mitogenome, there were no genealogical patterns consistent across multiple loci, allowing me to reject species level delineation. To further evaluate the amount of gene flow and test for divisions below the species level, I used population level indices and found significant genetic differentiation for rough-toothed dolphins between the Atlantic Ocean with both the Indian/Western Pacific and Central/Eastern Pacific for both the mitochondrial datasets and the intron dataset. Significant differentiation between the Indian/Western Pacific Ocean and Eastern Pacific Ocean was found for the mitochondrial but not nuclear datasets. From these results I recommended the Atlantic Ocean basin be considered a separate evolutionary significant unit. This reflects that these populations are on independent evolutionary trajectories, but are not diagnosable species or subspecies. To further evaluate population structure on a regional scale, I used a subset of these samples from three archipelagos in the Central Pacific Ocean including the Hawaiian Islands, the Society Island of French Polynesia and the Samoan Islands. Using a 450bp portion of the mtDNA control region and 15 microsatellite loci, an overall AMOVA indicated strong genetic differentiation among islands within the main Hawaiian Islands (mtDNA F[subscript ST]=0.165; p<0.001; microsatellite F[subscript ST]=0.043 p<0.001) and the Society Islands of French Polynesia (F[subscript ST]=0.499; p<0.001; microsatellite F[subscript ST]=0.079 p<0.001) as well as among the three archipelagos (mtDNA F[subscript ST]=0.299; p<0.001; microsatellite F[subscript ST]=0.055 p<0.001). My results corroborate the photo-identification and the genetic studies for three archipelagos, confirming population structure on the regional level. Lastly, to test the hypothesis that social structure observed in rough-toothed dolphins is kinship based, as in other delphinid species such as killer whales, I used a subset of the main dataset from groups of living and mass stranded dolphins. I found multiple matrilines in more than half the groups, allowing me to reject a strictly matrilineal group structure, such as that observed in some killer whales. Instead I found rough-toothed dolphin groups showed weak matrilineality, where some groups are more matrilineal than expected by chance. Although group structure is stable, is not determined primarily by kin-based relationships. These analyses provide new insights into a little studied species. The use of worldwide datasets allowed me to evaluate population structure on different temporal, spatial and regional scales and delineate populations for future conservation and management.Keywords: microsatellites, dolphin, genomics, phylogeography, genetics, population structur

Implementation and evaluation of a harm-reduction model for clinical care of substance using pregnant women

<p>Abstract</p> <p>Background</p> <p>Methamphetamine (MA) use during pregnancy is associated with many pregnancy complications, including preterm birth, small for gestational age, preeclampsia, and abruption. Hawaii has lead the nation in MA use for many years, yet prior to 2007, did not have a comprehensive plan to care for pregnant substance-using women. In 2006, the Hawaii State Legislature funded a pilot perinatal addiction clinic. The Perinatal Addiction Treatment Clinic of Hawaii was built on a harm-reduction model, encompassing perinatal care, transportation, child-care, social services, family planning, motivational incentives, and addiction medicine. We present the implementation model and results from our first one hundred three infants (103) seen over 3 years of operation of the program.</p> <p>Methods</p> <p>Referrals came from community health centers, hospitals, addiction treatment facilities, private physician offices, homeless outreach services and self-referral through word-of-mouth and bus ads. Data to describe sample characteristics and outcome was obtained prospectively and retrospectively from chart abstraction and delivery data. Drug use data was obtained from the women's self-report and random urine toxicology during the pregnancy, as well as urine toxicology at the time of birth on mothers, and urine and meconium toxicology on the infants. Post-partum depression was measured in mothers with the Edinburgh Post-Partum depression scale. Data from Path clinic patients were compared with a representative cohort of women delivering at Kapiolani Medical Center for Women and Children during the same time frame, who were enrolled in another study of pregnancy outcomes. Ethical approval for this study was obtained through the University of Hawaii Committee for Human Studies.</p> <p>Results</p> <p>Between April 2007 and August 2010, 213 women with a past or present history of addiction were seen, 132 were pregnant and 97 delivered during that time. 103 live-born infants were delivered. There were 3 first-trimester Spontaneous Abortions, two 28-week intrauterine fetal deaths, and two sets of twins and 4 repeat pregnancies. Over 50% of the women had lost custody of previous children due to substance use. The majority of women who delivered used methamphetamine (86%), either in the year before pregnancy or during pregnancy. Other drugs include marijuana (59.8%), cocaine (33%), opiates (9.6%), and alcohol (15.2%). Of the women served, 85% smoked cigarettes upon enrollment. Of the 97 women delivered during this period, all but 4 (96%) had negative urine toxicology at the time of delivery. Of the 103 infants, 13 (12.6%) were born preterm, equal to the state and national average, despite having many risk factors for prematurity, including poverty, poor diet, smoking and polysubstance use. Overwhelmingly, the women are parenting their children, > 90% retained custody at 8 weeks. Long-term follow-up showed that women who maintained custody chose long-acting contraceptive methods; while those who lost custody had a very high (> 50%) repeat pregnancy rate at 9 months post delivery.</p> <p>Conclusion</p> <p>Methamphetamine use during pregnancy doesn't exist is isolation. It is often combined with a multitude of other adverse circumstances, including poverty, interpersonal violence, psychiatric comorbidity, polysubstance use, nutritional deficiencies, inadequate health care and stressful life experiences. A comprehensive harm reduction model of perinatal care, which aims to ameliorate some of these difficulties for substance-using women without mandating abstinence, provides exceptional birth outcomes and can be implemented with limited resources.</p

Haplotype frequencies of Steno bredanensis in the Central Pacific Ocean

Haplotype frequencies of Steno bredanensis in the Central Pacific Ocean. The islands where data was collected include Kauai, Hawaii, Oahu, Northwest Hawaiian Islands, Moorea, Raiatea (French Polynesia), Savaii, Upolo, Tutuila. The 23 haplotype sequences are available on Genbank

Worldwide Phylogeography of Rough-Toothed Dolphins (steno Bredanensis) Provides Evidence for Subspecies Delimitation

Rough-toothed dolphins ( Steno bredanensis ) have a global tropical and subtropical distribution with oceanic, neritic, and island-associated populations. To inform conservation and management for this species, we used sequences from the mtDNA control region ( n = 360 ), mitogenomes ( n = 19 ), and six nuclear introns (n = 35) to provide multiple lines of evidence to critically evaluate the potential taxonomic status of rough-toothed dolphins. Using samples from the Pacific, Indian, and Atlantic Oceans, we examined the null hypothesis that rough-toothed dolphins are one panmictic species and the alternate hypothesis of oceanic subspecies. Phylogenetic analyses of mitogenomes revealed a private Atlantic clade sister to a larger cosmopolitan clade including individuals from all tropical and subtropical oceans. We dated the split between the Atlantic clade and the cosmopolitan clade to 890,000 years ago. We determined that Atlantic rough-toothed dolphins could be correctly diagnosed with 98% accuracy with the mtDNA control region and calculated the net nucleotide divergence as 0.02. Population level analyses revealed significant genetic differentiation using mtDNA among most regions, while significant differentiation using nuclear markers occurred only between the Atlantic and the Indian/Pacific regions. Therefore, the oceanic divergence and diagnosability of rough-toothed dolphins in the Atlantic and the Indian/Pacific Oceans meet proposed criteria for recognition as two subspecies

Data from: Staying close to home? Genetic differentiation of rough-toothed dolphins near oceanic islands in the central Pacific Ocean

Rough-toothed dolphins have a worldwide tropical and subtropical distribution, yet little is known about the population structure and social organization of this typically open-ocean species. Although it has been assumed that pelagic dolphins range widely due to the lack of apparent barriers and unpredictable prey distribution, recent evidence suggests rough-toothed dolphins exhibit fidelity to some oceanic islands. Using the most comprehensively extensive dataset for this species to date, we assess the isolation and interchange of rough-toothed dolphins at the regional and oceanic scale within the central Pacific Ocean. Using mtDNA and microsatellite genotyping (nDNA), we analyzed samples of insular communities from the main Hawaiian (Kaua‘i n = 93, O‘ahu n = 9, Hawai‘i n = 57), French Polynesian (n = 70) and Samoan (n = 16) archipelagos, and pelagic samples off the Northwestern Hawaiian Islands (n = 18). An overall AMOVA indicated strong genetic differentiation among islands (mtDNA FST = 0.265; p < 0.001; nDNA FST = 0.038; p < 0.001), as well as among archipelagos (mtDNA FST = 0.299; p < 0.001; nDNA FST = 0.055; p < 0.001). Shared haplotypes (n = 4) between the archipelagos may be a product of a relatively recent divergence and/or periodic exchange from poorly understood pelagic populations. Analyses using STRUCTURE and GENELAND identified four separate management units among archipelagos and within the Hawaiian Islands. These results confirm the presence of multiple insular populations within the Pacific and island-specific genetic isolation among populations attached to islands in each archipelago. Insular populations seem most prevalent where oceanographic conditions indicate high local productivity or a discontinuity with surrounding oligotrophic areas. Our findings have important implications for a little studied species that faces increasing anthropogenic threats around oceanic islands