Genetic Differentiation of the Steppe Field Mouse Sylvaemus witherbyl Populations: Results of the Mitochondrial Control Region Analysis

The mitochondrial control region has been the first choice for examining the population structure but hypervariability and homoplasy have reduced its suitability. We analysed eight populations using control region for examining the population structure ofHilsa. Although the control region analysis revealed broad structuring between the Arabian Sea and Bay of Bengal (FST 0.0441,p<0.001) it was unable to detect structure among riverine populations. These results suggest that the markers used must be able to distinguish populations and control region has led to an underestimation of genetic differentiation among populations ofHilsa.

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High similarity of genetic population structure in the false clown anemonefish (Amphiprion ocellaris) found in microsatellite and mitochondrial control region analysis

Conservation Genetics ◽

10.1007/s10592-012-0318-1 ◽

2012 ◽

Vol 13 (3) ◽

pp. 693-706 ◽

Cited By ~ 19

Author(s):

J. Timm ◽

S. Planes ◽

M. Kochzius

Keyword(s):

Population Structure ◽

Control Region ◽

Mitochondrial Control Region ◽

Genetic Population Structure ◽

High Similarity ◽

Genetic Population ◽

Region Analysis

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

10.26686/wgtn.17060534.v1 ◽

2021 ◽

Author(s):

◽

Jana Wold

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Control Region ◽

Dna Sequences ◽

Mitochondrial Control Region ◽

Morphological Data ◽

Management Tool ◽

Commercial Fishing ◽

Single Nucleotide ◽

Fishing Vessels

<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>

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First comprehensive insights into nuclear and mitochondrial DNA based population structure of Near East mountain brook newts (Salamandridae: genus Neurergus) suggest the resurrection of Neurergus derjugini

Amphibia-Reptilia ◽

10.1163/15685381-00002939 ◽

2014 ◽

Vol 35 (2) ◽

pp. 173-187 ◽

Cited By ~ 5

Author(s):

Ralf Hendrix ◽

Jürgen Fleck ◽

Willi Schneider ◽

Christoph Schneider ◽

Daniel Geller ◽

...

Keyword(s):

Mitochondrial Dna ◽

Genetic Differentiation ◽

Control Region ◽

Near East ◽

Nuclear Gene ◽

Mitochondrial Control Region ◽

Original Description ◽

Nuclear Genes ◽

High Genetic Diversity ◽

Geographic Ranges

Due to their extraordinary coloration, mountain brook newts of the genus Neurergus found in the Near East have fascinated herpetologists since their initial description more than 150 years ago. Although the monophyly of Neurergus newts within the Salamandridae has been unambiguously shown for mitochondrial genes, and recent comprehensive molecular phylogenies placed Neurergus as a sister taxon of banded newts (genus Ommatotriton), we know almost nothing about the structure and relatedness of populations at the intraspecific level. In this study, we therefore analysed sequence variation of a mitochondrial DNA segment (covering a partial region of the control region and the 12S ribosomal RNA) from more than 100 individuals and of two nuclear genes (KIAA and SACS) for a representative subset of individuals originating from nine distinct populations, representing N. strauchii, N. crocatus and N. microspilotus. We also studied individuals of N. derjugini, a taxon that has long been synonymized as N. crocatus, and of which individuals have not been accessible to the scientific community since its original description in 1916. Our results suggest high genetic diversity of populations within species for the mitochondrial DNA marker, while the resolution of applied nuclear genes did not go beyond the level of species. For N. strauchii and N. crocatus, two species that inhabit the largest geographic ranges within the genus, we found a high proportion of diversity both within and between populations for the mitochondrial control region. Individuals of N. microspilotus and N. derjugini only displayed considerable genetic differentiation for one nuclear gene (SACS), while only very little or none genetic differentiation could be found for the mitochondrial control region and the KIAA gene, respectively. As both taxa are also morphologically not well differentiated, we suggest on the basis of the current dataset to taxonomically synonymize N. microspilotus due to priority reasons as N. derjugini. It can be therefore concluded that the most accurate taxonomy of the genus Neurergus should consider N. crocatus, N. strauchii, N. kaiseri and N. derjugini as valid taxonomic units at the species level.

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

10.26686/wgtn.17060534 ◽

2021 ◽

Author(s):

◽

Jana Wold

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Control Region ◽

Dna Sequences ◽

Mitochondrial Control Region ◽

Morphological Data ◽

Management Tool ◽

Commercial Fishing ◽

Single Nucleotide ◽

Fishing Vessels

<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>

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