Mitochondrial DNA Control Region Sequences Research Articles

Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes.

The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.

Comparison of Patterns of Genetic Variation and Demographic History in the Greater Sage-Grouse (Centrocercus urophasianus): Relevance for Conservation

The greater sage-grouse (Centrocercus urophasianus) was once widespread in western North America but its range has contracted by an uncertain degree owing to anthropogenic and natural causes. Concern over population declines has led to its proposed listing as threatened under the U.S. Endangered Species Act. Detailed genetic and demographic analyses of this species throughout its range are available but heretofore have not been compared. Reduced genetic variability is often taken as a proxy for declining populations, but rarely are there quantitative population estimates with which to compare. I compared published mitochondrial DNA (mtDNA) control region sequences, microsatellite allele frequencies at seven loci, and estimates of numbers of males per lek, number of active leks, percent decline in the best population models, and the probability (P) of Ne < 50 in 30 years and P(Ne < 500) in 100 years, at two spatial scales, 45 local population samples and 16 larger aggregates of samples. When excluding the populations from the Columbia Basin, which show little genetic diversity and are statistical outliers, there were no consistent relationships between estimates of genetic variation and demographic trends across the remainder of the range at either spatial scale. A measure of inbreeding derived from microsatellite data was also not related to population trends. Thus, despite habitat reduction and range fragmentation, the greater sage-grouse does not exhibit expected genetic signatures of declining populations. Possibly, the mtDNA and microsatellite data are insufficiently sensitive to detect population declines that have occurred over the span of a half century. Alternatively, only when populations are reduced to the levels seen in the Columbia Basin will genetic effects be seen, suggesting that the bulk of the range of the greater sage-grouse is not currently in genetic peril.

Nuclear and mitochondrial genetic structure in the Eurasian beaver (Castor fiber) - implications for future reintroductions.

Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conducting postrelease monitoring. In this study, we use a panel of 306 SNP (single nucleotide polymorphism) markers and 487–489 base pairs of mitochondrial DNA control region sequence data to examine 321 individuals from possible source populations of the Eurasian beaver for a reintroduction to Scotland. We use this information to reassess the phylogenetic history of the Eurasian beavers, to examine the genetic legacy of past reintroductions on the Eurasian landmass and to assess the future power of the genetic markers to conduct ongoing monitoring via parentage analysis and individual identification. We demonstrate the capacity of medium density genetic data (hundreds of SNPs) to provide information suitable for applied conservation and discuss the difficulty of balancing the need for high genetic diversity against phylogenetic best fit when choosing source population(s) for reintroduction.

Genetic Structure and Cryptic Genealogy of the Bonin Flying FoxPteropus pselaphonRevealed by Mitochondrial DNA and Microsatellite Markers

The Bonin flying fox (Pteropus pselaphon) is endemic to the Ogasawara Islands, a collection of small oceanic islands in the Pacific Ocean. It inhabits only five islands: Chichi-jima, Haha-jima, Kita-iwo, Iwo, and Minami-iwo (arranged from north to south). Hahajima and Kita-iwo, the most widely spaced islands, are separated by a distance of about 160 km. The islands have different histories in the modern era with respect to human activity. At present, P. pselaphon population sizes exceed 100 on Chichi-jima and Minamiiwo, but the species is rare on the other three islands. Loss of genetic diversity is of concern because of the small population sizes. We obtained samples from three of the five islands — Chichi-jima, Kita-iwo, and Minami-iwo — and investigated species genetic diversity and genetic structure based on mitochondrial DNA (mtDNA) control region sequences and microsatellite markers. Different mtDNA haplotypes were found in each island population. Based on the mtDNA sequence data, P. pselaphon displayed a cryptic genealogy, as haplotypes on each island did not cluster together. The microsatellite marker data, however, revealed a clear genetic structure among the island populations, suggesting the absence of recent inter-island gene flow. Based on these results, we propose that the individual island populations are not evolutionarily significant units, but should be conserved collectively as a single management unit.

Genetic isolation among the northwestern, southwestern and central-eastern Indian Ocean populations of the pronghorn spiny lobster Panulirus penicillatus.

The pronghorn spiny lobster Panulirus penicillatus is a highly valuable species which is widely distributed in Indo-West Pacific and Eastern Pacific regions. Mitochondrial DNA control region sequences (566–571 bp) were determined to investigate the population genetic structure of this species in the Indian Ocean. In total, 236 adult individuals of Panulirus penicillatus were collected from five locations in the Indian Ocean region. Almost all individuals had a unique haplotype. Intrapopulation haplotype (h) and nucleotide (π) diversities were high for each locality, ranging from h = 0.9986–1.0000 and π = 0.031593–0.043441. We observed distinct genetic isolation of population located at the northwestern and southwestern edge of the species range. Gene flow was found within localities in the central and eastern region of the Indian Ocean, probably resulting from an extended planktonic larval stage and prevailing ocean currents.

Nuclear and mitochondrial patterns of population structure in North Pacific false killer whales (Pseudorca crassidens).

False killer whales (Pseudorca crassidens) are large delphinids typically found in deep water far offshore. However, in the Hawaiian Archipelago, there are 2 resident island-associated populations of false killer whales, one in the waters around the main Hawaiian Islands (MHI) and one in the waters around the Northwestern Hawaiian Islands (NWHI). We use mitochondrial DNA (mtDNA) control region sequences and genotypes from 16 nuclear DNA (nucDNA) microsatellite loci from 206 individuals to examine levels of differentiation among the 2 island-associated populations and offshore animals from the central and eastern North Pacific. Both mtDNA and nucDNA exhibit highly significant differentiation between populations, confirming limited gene flow in both sexes. The mtDNA haplotypes exhibit a strong pattern of phylogeographic concordance, with island-associated populations sharing 3 closely related haplotypes not found elsewhere in the Pacific. However, nucDNA data suggest that NWHI animals are at least as differentiated from MHI animals as they are from offshore animals. The patterns of differentiation revealed by the 2 marker types suggest that the island-associated false killer whale populations likely share a common colonization history, but have limited contemporary gene flow.

Colonization of Brazil by the cattle egret (Bubulcus ibis) revealed by mitochondrial DNA

The cattle egret (Bubulcus ibis) has recently colonized Brazil. This process offers an excellent opportunity for the study of colonization and dispersal patterns across extensive areas by non-native birds. The aims of the present investigation were a) to determine the genetic diversity of the cattle egret in Brazil and Africa, b) evaluate genetic differentiation between populations in different regions of Brazil and Africa, and c) detect genetic signs of demographic expansion in these two areas. Mitochondrial DNA (mtDNA) Control Region (CR) sequences were obtained from 112 cattle egrets in four Brazilian and four African (Kenya, Ghana and Nigeria) populations. Genetic diversity (H, h, θ s ) and population structure (AMOVA, Fst) were assessed and the populations were tested for signs of recent demographic expansion. A total of 35 haplotypes were found: 22 exclusive to Africa, 10 exclusive to Brazil and three shared by both samples. The degree of genetic diversity, determined by mtDNA analysis, was similar between Brazil and Africa, demonstrating that the successful colonization of the non-native area occurred with no significant loss of diversity. The pairwise Fst values among the Brazilian and African populations were all significantly different. The population in southern Brazilian exhibited the lowest degree of differentiation with respect to the African population, followed by the southeastern and northeastern populations of the country. The genetic differentiation data suggest that the colonization of Brazil by the cattle egret began in the southern region and expanded to the southeastern and northeastern regions of the country. This genetic differentiation pattern is in accordance with the higher number of cattle per grazing area in southern Brazil, which may have favored the onset of the successful establishment of the species. The findings indicate that mtDNA genetic diversity was retained during the colonization process and colonization began in the southern region of the country. Moreover, signs of demographic expansion were detected in the African sample.

Population genetic diversity of the northern snakehead (Channa argus) in China based on the mitochondrial DNA control region and adjacent regions sequences

Genetic variation and population structure of northern snakehead (Channa argus) from eight locations in China were investigated using mitochondrial DNA control region and adjacent regions sequences. Sequence analysis showed that there were 105 haplotypes in 260 individuals, 48 unique haplotypes and 57 shared haplotypes, but no common haplotype shared by all populations. As a whole, the haplotype diversity was high (h = 0.989), while the nucleotide diversity was low (π = 0.00482). AMOVA analysis detected significant genetic differentiation among all eight populations (FST = 0.328, p < 0.01) and 66.17% of the total variance was resulted from intra-population differentiation. UPGMA analysis indicated that the eight populations could be divided into four major clusters, which was consistent with that the eight sampled locations were belonged to four isolated river systems. The neutrality and mismatch distribution tests suggested that the eight populations of C. argus in the sampling locations underwent recent population expansion. Among the eight populations, the Erhai Lake population may represent a unique genetic resource and therefore needs to be conserved.

Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe.

After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000 years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.

Remarkably low genetic diversity and strong population structure in common bottlenose dolphins (Tursiops truncatus) from coastal waters of the Southwestern Atlantic Ocean

Knowledge about the ecology of bottlenose dolphins in the Southwestern Atlantic Ocean is scarce. Increased by-catch rates over the last decade in coastal waters of southern Brazil have raised concerns about the decline in abundance of local dolphin communities. Lack of relevant data, including information on population structure and connectivity, have hampered an assessment of the conservation status of bottlenose dolphin communities in this region. Here we combined analyses of 16 microsatellite loci and mitochondrial DNA (mtDNA) control region sequences to investigate genetic diversity, structure and connectivity in 124 biopsy samples collected over six communities of photographically identified coastal bottlenose dolphins in southern Brazil, Uruguay and central Argentina. Levels of nuclear genetic diversity were remarkably low (mean values of allelic diversity and heterozygosity across all loci were 3.6 and 0.21, respectively), a result that possibly reflects the small size of local dolphin communities. On a broad geographical scale, strong and significant genetic differentiation was found between bottlenose dolphins from southern Brazil–Uruguay (SB–U) and Bahia San Antonio (BSA), Argentina (AMOVA mtDNA ΦST = 0.43; nuclear FST = 0.46), with negligible contemporary gene flow detected based on Bayesian estimates. On a finer scale, moderate but significant differentiation (AMOVA mtDNA ΦST = 0.29; nuclear FST = 0.13) and asymmetric gene flow was detected between five neighbouring communities in SB–U. Based on the results we propose that BSA and SB–U represent two distinct evolutionarily significant units, and that communities from SB–U comprise five distinct Management Units (MUs). Under this scenario, conservation efforts should prioritize the areas in southern Brazil where dolphins from three MUs overlap in their home ranges and where by-catch rates are reportedly higher.

Mitochondrial control region variation in a Korean population sample

Mitochondrial DNA (mtDNA) control region (16024-576) sequences were generated from 281 individuals from South Korea. Robotic liquid handling, a redundant sequencing strategy, and a series of quality control checks were implemented to ensure the high quality of the dataset. This population sample showed a low random match probability (0.25 %) and high genetic diversity (0.9933). The haplogroup breakdown was consistent with previous studies describing Korean mtDNA variation. The 224 unique haplotypes (33 shared) presented will supplement the data already publically available.

Noninvasive sampling and genetic variability, pack structure, and dynamics in an expanding wolf population

Abstract After centuries of population decline and range contraction, gray wolves (Canis lupus) are now expanding in Europe. Understanding wolf social structure and population dynamics and predicting their future range expansion is mandatory to design sound conservation strategies, but field monitoring methods are difficult or exceedingly expensive. Noninvasive genetic sampling offers unique opportunities for the reliable monitoring of wolf populations. We conducted a 9-year-long monitoring program in a large area (approximately 19,171 km2) in northern Italy, aiming to identify individuals, estimate kinship, reconstruct packs, and describe their dynamics. Of 5,065 biological samples (99% scats), we genotyped and sexed 44% reliably using 12 unlinked autosomal microsatellites, 4 Y-linked microsatellites, and a diagnostic mitochondrial DNA control-region sequence. We identified 414 wolves, 88 dogs, and 16 wolf × dog hybrids. Wolves in the study area belonged to at least 42 packs. We reconstructed the genealo...

Irritable Bowel Syndrome May Be Associated with Maternal Inheritance and Mitochondrial DNA Control Region Sequence Variants

Mitochondrial dysfunction has been implicated in various functional disorders that are co-morbid to irritable bowel syndrome (IBS) such as migraine, depression and chronic fatigue syndrome. The aim of the current case-control pilot study was to determine if functional symptoms in IBS show a maternal inheritance bias, and if the degree of this maternal inheritance is related to mitochondrial DNA (mtDNA) polymorphisms. Pedigrees were obtained from 308 adult IBS patients, 102 healthy controls, and 36 controls with inflammatory bowel disease (IBD), all from Caucasian heritage, to determine probable maternal inheritance. Two mtDNA polymorphisms (16519T and 3010A), which have previously been implicated in other functional disorders, were assayed in mtDNA haplogroup H IBS subjects and compared to genetic data from 344 published haplogroup H controls. Probable maternal inheritance was found in 17.5 % IBS, 2 % healthy controls and 0 % IBD controls (p < .0001). No difference was found between IBS and control for 3010A, and a trend was found for 16519T (p = 0.05). IBS with maternal inheritance were significantly more likely to have the 16519T than controls (OR 5.8; 95 % CI 1.5-23.1) or IBS without maternal inheritance (OR 5.2; 95 % CI 1.2-22.6). This small pilot study shows that a significant minority (1/6) of IBS patients have pedigrees suggestive of maternal inheritance. The mtDNA polymorphism 16519T, which has been previously implicated in other functional disorders, is also associated with IBS patients who display maternal inheritance. These findings suggest that mtDNA-related mitochondrial dysfunction may constitute a sub-group within IBS. Future replication studies in larger samples are needed.

Genetic monitoring of pilot whales, Globicephala spp. (Cetacea: Delphinidae), stranded on French coasts

We used mitochondrial DNA control region sequences to genetically identify to the species level 23 pilot whales (genus Globicephala) that stranded on the French coasts between 1996 and 2011. Genetic analysis complemented morphological diagnoses, often hampered by an overlap in morphological characters between the two species or incomplete measurements. Mitochondrial DNA data allowed identification of 21 long-finned pilot whales (Globicephala melas) and two unusual stranding events of the more tropical species (Globicephala macrorhynchus). In pilot whales as in most cetaceans, shifts in species range are expected to occur due to global climate change. In this context, our study contributes to the long-term monitoring of pilot whale stranding events, providing indirect information on species occurrence.

A new PCR-based method shows that blue crabs (Callinectes sapidus (Rathbun)) consume winter flounder (Pseudopleuronectes americanus (Walbaum)).

Winter flounder (Pseudopleuronectes americanus) once supported robust commercial and recreational fisheries in the New York (USA) region, but since the 1990s populations have been in decline. Available data show that settlement of young-of-the-year winter flounder has not declined as sharply as adult abundance, suggesting that juveniles are experiencing higher mortality following settlement. The recent increase of blue crab (Callinectes sapidus) abundance in the New York region raises the possibility that new sources of predation may be contributing to juvenile winter flounder mortality. To investigate this possibility we developed and validated a method to specifically detect winter flounder mitochondrial control region DNA sequences in the gut contents of blue crabs. A survey of 55 crabs collected from Shinnecock Bay (along the south shore of Long Island, New York) in July, August, and September of 2011 showed that 12 of 42 blue crabs (28.6%) from which PCR-amplifiable DNA was recovered had consumed winter flounder in the wild, empirically supporting the trophic link between these species that has been widely speculated to exist. This technique overcomes difficulties with visual identification of the often unrecognizable gut contents of decapod crustaceans, and modifications of this approach offer valuable tools to more broadly address their feeding habits on a wide variety of species.

Irritable Bowel Syndrome May Be Associated with Maternal Inheritance and Mitochondrial DNA Control Region Sequence Variants

Irritable Bowel Syndrome May Be Associated with Maternal Inheritance and Mitochondrial DNA Control Region Sequence Variants

Range-wide phylogeography and conservation genetics of a narrowly endemic stream salamander, Pachyhynobius shangchengensis (Caudata, Hynobiidae): implications for conservation

The Shangcheng stout salamander (Pachyhynobius shangchengensis) is an endangered amphibian endemic to the Dabie Mountains, southeast China, and is currently threatened by habitat loss and illegal poaching. Here we used the mitochondrial DNA control region sequence (768 bp) to conduct a comprehensive investigation of genetic diversity, phylogeographic pattern, and demographic history of the species across its geographic distribution to assist its conservation. We concluded that the levels of genetic variation are relatively low in all four populations. Analysis of molecular variance indicated that the most likely phylogeographic pattern is [JGT] [KHJ] [TM, BYM]. Two distinct clades were identified in the phylogenetic tree of 28 haplotypes, corresponding to the two southern populations (TM, BYM) and two northern populations (JGT, KHJ). Significant population differentiation (FST) was detected among all populations. Among the four populations, historical demographic analyses (e.g., the g parameter, the Tajima D test, and the Fu Fs test) did not reveal definite information on population expansion except for the BYM population, which had undergone a strong population expansion event. Based on the analysis of a Bayesian skyline plot, the total population underwent a significant population fluctuation around 20 kya. This may have been triggered by the end of the last glacial maximum. In conclusion, the existence of three evolutionarily significant units (BMY-TM, KHJ, and JGT) and four management units (BMY, TM, KHJ, and JGT) is supported by our study.

Matrilineal Genetic Structure of Domestic Geese

In contrast to other farm animals, the matrilineal structure of domestic goose has remained an open question. In this study, we analyzed mitochondrial DNA control region sequence variation of 245 domestic geese to discern the main matrilineal c omponents and their phylogeneticrelationships. The result of phylogeneticanalysis indic ated the distinct lineage of clade II and the result of network analysis further suggested the major group of Chinese native goose breeds (subclade S) and introgressive goose breeds (subclade G). Except Yili geese, all Chinese domestic goose breeds were clustered in S, whereas clade II were widely distributed in 2 European breeds, Yili geese as well as 3 domesticGraylag geese. The results support that Chinese domesticgoose breeds (except the Yili breed) originated from Swan goose (Anser cygnoides) while European goose breeds originated from Graylag goose (Anser anser). In total, 17 Landoise and 16 White Roman geese were clustered in subclade G together with 1 domestic goose (A. anser, AY112966), which supported the previous finding that European geese originated from Graylag goose (A. anser). But 9 unanticipated samples of two Chinese domestic goose breeds including 7 Lion-head geese and 1 Zhedong White goose in haplotype H9 were also clustered in subclade G as well as 3 Lion-head geese in haplotypes H13, H15 and H16 and 2 Zhedong White geese in haplotypes H18 and H19, which may be caused by the potential gene introgressions between swan goose breeds and graylag breeds with a directional contribution towards graylag geese.

Patterns of avian diversification in Borneo: The case of the endemic Mountain Black-eye (Chlorocharis emiliae)

The Mountain Black-eye (Chlorocharis emiliae) is an endemic white-eye (Zosteropidae) of Borneo with a unique ‘‘sky island’’ distribution. We compared mitochondrial ND2, ND3, Cytb, and control region DNA sequences (2,194 nucleotides) to study the phylogeographic relationships of five populations of this species that span its range: Mounts Kinabalu, Trus Madi, Murud, Mulu, and Pueh. These comparisons showed that black-eyes are divided into two main clades that correspond generally to subspecific morphological groups: one in Sabah, Malaysia (Kinabalu and Trus Madi), and one in Sarawak, Malaysia (Murud, Mulu, and Pueh). The genetic and morphologic subdivision of black-eyes disputes the expected merging of populations during the Last Glacial Maximum (LGM), when montane forest presumably expanded and provided the opportunity for currently isolated populations to intermingle. Instead the genetic aging of black-eye populations indicates they diversified long before the LGM, and either did not expand sufficiently in range during the LGM to reach one another, or were reproductively isolated by the time of the LGM and thus prevented from interbreeding. Moreover, the subdivision between black-eyes in Sabah and Sarawak means that this species (and probably several other montane species) has a phylogeographic structure remarkably similar to Borneo’s lowland bird populations, which are presumed to have evolved under different paleo-geographic conditions. The similar phylogeographic pattern found in both montane and lowland species requires that we rethink the causes of bird population diversification on the island of Borneo.

梧州繁殖中心圈养黑叶猴遗传多样性分析和野外放归种源选择

Mitochondrial DNA (mtDNA) control region and microsatellite DNA sequences were used to analyze genetic diversity, origins, and relationships of captive langur ( Trachypithecus francoisi ) individuals. Sequencing of the 355-bp mtDNA control region for 52 individuals uncovered 35 variable nucleotide sites, including 3 transitions (ts), 29 transversions (tv), and 3 insertion/deletions, with 13 defined haplotypes. A haplotype diversity of 0.627 and a nucleotide diversity of 0.027 were calculated. Eleven microsatellite loci showing good amplification were also assayed in the 52 individuals. A total of 47 alleles were detected, with an average of 4.18 per locus. Mean polymorphic information content ( PIC ) was 0.566. Expected heterozygosity ( He ) and observed heterozygosity ( Ho ) were 0.559 and 0.551. Compared with other endangered primates, we found that the genetic diversity of the captive T. francoisi population was not low. Based on phylogenetic analysis of haplotypes of wild and captive T. francoisi individuals, we inferred that the captive T. francoisi individuals came from Guangxi, near the Vietnamese border. Using genetic distance relationships, we selected three male and seven female captive langurs to establish three family units for reintroduction.