Nest parasitism, promiscuity, and relatedness among wood ducks

Nest parasitism is a common reproductive strategy used by many species of cavity nesting birds. Among these, the wood duck (Aix sponsa) is known to have evolved very specific strategies of when and whom to parasitize that is often based on population and/or environmental queues. Here, we investigated the genetic relationship of two female wood ducks competing over an artificial nesting box in Delaware, including the continued incubation of one female despite the death and body remains of the other female throughout the incubation process. We test whether such an extreme case of nest parasitism can be explained by relatedness, egg lineage composition, or a combination of other factors. To do so, we extracted genomic DNA from blood and tissue of the females, as well as chorioallantoic membranes of all viable and inviable eggs. Subsequently, we assessed relatedness among females and eggs based on hundreds of nuclear loci and the mitochondrial control region. We concluded that (1) the two incubating females were entirely unrelated, (2) the single clutch is in fact represented by a minimum of four unrelated females, and (3) a single female can lay eggs sired by different males. The latter finding is the first direct evidence for successful extra-pair copulation in wood ducks. With decreasing costs and increasing effectiveness, genomic methods have the potential to provide important insights into more complex ecological and evolutionary tactics of such populations.

Phylogenetic relationships, population connectivity, and development of genetic assignment testing in Buller's Albatross (Thalassarche bulleri ssp.)

<p>The Diomedeidae (Albatrosses) family is comprised of 22 recognised species, 13 are of high conservation concern because they are experiencing population declines. The taxonomy of albatrosses has always been problematic, which makes it difficult to estimate the number and size of breeding groups within a species. The Northern Buller’s Albatross (Thalassarche bulleri platei) and Southern Buller’s Albatross (Thalassarche bulleri bulleri) (Robertson & Nunn 1998; Turbott 1990) were recognised as separate species until 2006. A review of morphological data provided a basis for defining them as one species (Thalassarche bulleri); a result that was supported by international conservation agreements. However, there was no genetic data available at the time to corroborate the taxonomic change. The species status of Buller’s Albatross ssp. is an important issue because they are consistently recorded in the top five observed seabird interactions with commercial fishing vessels within New Zealand's Exclusive Economic Zone. Despite their prevalence in fisheries interactions, the relative impact of commercial fishing activity on northern and southern populations is unknown. Incidental mortality of albatrosses in commercial fisheries is recognised as a primary source of population disturbance. The overall goal of this thesis research was to investigate the genetic differences between the two sub-species of Buller’s Albatross. DNA was isolated from blood samples collected from a total of 73 birds from two Northern Buller’s Albatross colonies (n = 26) and two Southern Buller’s Albatross colonies (n = 47). The degree of genetic differentiation between the Northern and Southern taxa was estimated using DNA sequences from a 221 bp fragment of the mitochondrial control region, Domain II (CRII). The genetic differentiation between regional colony groups was high (pairwise ΦST = 0.621, p < 0.00001). Two haplogroups were identified within Northern Buller’s Albatross, while Southern Buller’s Albatross samples composed a single haplogroup. An analysis of molecular variance did not find any significant population structuring at the colony level. All individuals sampled from fisheries bycatch (n = 97) were assigned with maximum probability to either Northern (n = 19) or Southern Buller’s Albatross (n = 78; P = 1.00). The DNA sequences differences found in the mitochondrial control region can be used to assign provenance of T. bulleri ssp. samples, which will be a useful conservation management tool. In addition, a genome wide set of markers was obtained using a Genotyping by Sequencing approach. DNA was digested using restriction enzymes, fragments were labeled adaptor sequences, and shotgun sequenced on an Illumina platform by AgResearch. The Stacks pipeline was used to filter the sequences and obtain a set of single nucleotide polymorphism (SNP) markers across the genome. Estimates of genetic diversity and gene flow were conducted for 26 319 putative loci comprised of 54,061 single nucleotide polymorphisms. Estimates of genetic diversity were consistent across datasets with both taxa exhibiting similar levels of nucleotide diversity (Northern π ≈ 0.002 – 0.004; Southern π ≈ 0.002 – 0.003). However, estimates of genetic differentiation increased slightly as filtering protocols became increasingly restrictive (FST ≈ 0.019 – 0.048). This low level of differentiation was supported by admixture analyses, which identified two distinct ‘clusters’, one corresponding to T. b. platei and the second to T. b. bulleri. The results of this research demonstrate that Northern and Southern Buller’s Albatrosses are two genetically distinct groups.</p>

Phylogenetic relationships, population connectivity, and development of genetic assignment testing in Buller's Albatross (Thalassarche bulleri ssp.)

<p>The Diomedeidae (Albatrosses) family is comprised of 22 recognised species, 13 are of high conservation concern because they are experiencing population declines. The taxonomy of albatrosses has always been problematic, which makes it difficult to estimate the number and size of breeding groups within a species. The Northern Buller’s Albatross (Thalassarche bulleri platei) and Southern Buller’s Albatross (Thalassarche bulleri bulleri) (Robertson & Nunn 1998; Turbott 1990) were recognised as separate species until 2006. A review of morphological data provided a basis for defining them as one species (Thalassarche bulleri); a result that was supported by international conservation agreements. However, there was no genetic data available at the time to corroborate the taxonomic change. The species status of Buller’s Albatross ssp. is an important issue because they are consistently recorded in the top five observed seabird interactions with commercial fishing vessels within New Zealand's Exclusive Economic Zone. Despite their prevalence in fisheries interactions, the relative impact of commercial fishing activity on northern and southern populations is unknown. Incidental mortality of albatrosses in commercial fisheries is recognised as a primary source of population disturbance. The overall goal of this thesis research was to investigate the genetic differences between the two sub-species of Buller’s Albatross. DNA was isolated from blood samples collected from a total of 73 birds from two Northern Buller’s Albatross colonies (n = 26) and two Southern Buller’s Albatross colonies (n = 47). The degree of genetic differentiation between the Northern and Southern taxa was estimated using DNA sequences from a 221 bp fragment of the mitochondrial control region, Domain II (CRII). The genetic differentiation between regional colony groups was high (pairwise ΦST = 0.621, p < 0.00001). Two haplogroups were identified within Northern Buller’s Albatross, while Southern Buller’s Albatross samples composed a single haplogroup. An analysis of molecular variance did not find any significant population structuring at the colony level. All individuals sampled from fisheries bycatch (n = 97) were assigned with maximum probability to either Northern (n = 19) or Southern Buller’s Albatross (n = 78; P = 1.00). The DNA sequences differences found in the mitochondrial control region can be used to assign provenance of T. bulleri ssp. samples, which will be a useful conservation management tool. In addition, a genome wide set of markers was obtained using a Genotyping by Sequencing approach. DNA was digested using restriction enzymes, fragments were labeled adaptor sequences, and shotgun sequenced on an Illumina platform by AgResearch. The Stacks pipeline was used to filter the sequences and obtain a set of single nucleotide polymorphism (SNP) markers across the genome. Estimates of genetic diversity and gene flow were conducted for 26 319 putative loci comprised of 54,061 single nucleotide polymorphisms. Estimates of genetic diversity were consistent across datasets with both taxa exhibiting similar levels of nucleotide diversity (Northern π ≈ 0.002 – 0.004; Southern π ≈ 0.002 – 0.003). However, estimates of genetic differentiation increased slightly as filtering protocols became increasingly restrictive (FST ≈ 0.019 – 0.048). This low level of differentiation was supported by admixture analyses, which identified two distinct ‘clusters’, one corresponding to T. b. platei and the second to T. b. bulleri. The results of this research demonstrate that Northern and Southern Buller’s Albatrosses are two genetically distinct groups.</p>

Interspecific hybridization in natural sturgeon populations of the Eastern Black Sea: the consequence of drastic population decline?

The eastern part of the Black Sea and its tributaries are suitable habitats for several sturgeon species, among which Acipenser gueldenstaedtii, A. stellatus, A. nudiventris, A. persicus, A. sturio, and H. huso are well documented. However, different threats have led these species to a dramatic decline, all of them are currently listed as Critically Endangered, and some Locally Extinct, in that area. We tested 94 wild sturgeon samples from the Black Sea and Rioni River by analyzing the mitochondrial Control Region and nuclear markers for hybrid identification. The data analyses (1) assessed mitochondrial diversity among samples, (2) identified their species, as well as (3) indicated instances of hybridization. The data collected, besides confirming a sharp decrease of catches of Beluga and Stellate sturgeon in recent years, also revealed four juvenile hybrids between Russian and Stellate sturgeon, providing the first evidence of natural interspecific hybridization in the Rioni. The present communication raises concerns about the status of sturgeon species in this area and underlines the urgent need for conservation programs to restore self-sustaining populations.

Genetic hypervariability of a Northeastern Atlantic venomous rockfish

Background Understanding the interplay between climate and current and historical factors shaping genetic diversity is pivotal to infer changes in marine species range and communities’ composition. A phylogeographical break between the Atlantic and the Mediterranean has been documented for several marine organisms, translating into limited dispersal between the two basins. Methods In this study, we screened the intraspecific diversity of 150 individuals of the Madeira rockfish (Scorpaena maderensis) across its distributional range (seven sampling locations in the Atlantic and Mediterranean basins) using the mitochondrial control region and the nuclear S7 first intron. Results The present work is the most comprehensive study done for this species, yielding no genetic structure across sampled locations and no detectable Atlantic-Mediterranean break in connectivity. Our results reveal deep and hyper-diverse bush-like genealogies with large numbers of singletons and very few shared haplotypes. The genetic hyper-diversity found for the Madeira rockfish is relatively uncommon in rocky coastal species, whose dispersal capability is limited by local oceanographic patterns. The effect of climate warming on the distribution of the species is discussed.

Shedding Light on the Dark Ages: Sketching Potential Trade Relationships in Early Medieval Romania through Mitochondrial DNA Analysis of Sheep Remains

Southeast Europe has played an important role in shaping the genetic diversity of sheep due to its proximity to the Danubian route of transport from the Near East into Europe, as well as its possible role as a post-domestication migration network and long tradition of sheep breeding. The history of Romania and, in particular, the historical province of Dobruja, located on the shore of the Black Sea, has been influenced by its geographical position at the intersection between the great powers of the Near East and mainland Europe, with the Middle Ages being an especially animated time in terms of trade, migration, and conflict. In this study, we analyzed the mitochondrial control region of five sheep originating from the Capidava archaeological site (Dobruja, Southeast Romania), radiocarbon dated to the Early Middle Ages (5th–10th century AD), in order to better understand the genetic diversity of local sheep populations and human practices in relation to this particular livestock species. The analyses illustrate high haplotype diversity in local medieval sheep, as well as possible genetic continuity in the region. A higher tendency for North to South interaction, rather than East to West, is apparent, together with a lack of interaction along the Asian route. Continuous interaction between the First Bulgarian Empire, which occupied Dobruja starting with the 7th century AD, and the Byzantine Empire is indicated. These results might suggest expanding trade in Southeast Romania in the Early Middle Ages.

Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software

Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.