Region Haplotypes Research Articles

Dopamine D1 receptor (DRD1) 5′ region haplotypes significantly affect transcriptional activity in vitro

The role of dopamine D1 receptor (DRD1) gene promoter polymorphisms in schizophrenia remains controversial. We aimed to characterize the polymorphisms in the promoter region because little is known about the extent of variance in this region and potential roles in gene transcription activity. In a previous case-control study, we amplified and genotyped the polymorphisms of DRD1 gene. According to its haplotype estimation, we identified eight SNPs and confirmed ten different haplotypes by cloning and sequencing the fragment spanning −1990 to +10. The promoter activity of these haplotypes was analyzed using dual luciferase assays in SH-SY5Y and HEK293 cells. Compared with the reference haplotype, the constructed haplotypes containing different variation sites could significantly alter the luciferase activity. Additionally, the prediction of the transcription factor binding sites was performed. Our examination could provide the informative reference for the role of DRD1 gene promoter in schizophrenia.

SEQUENCE POLYMORPHISM OF MITOCHONDRIAL DNA HYPERVARIABLE REGIONS I AND II IN MALAY POPULATION OF MALAYSIA

The analysis of the control region of human mitochondrial genome (mtDNA) especially hypervariable regions I (HVI) and II (HVII) segments have been proven to be useful for human identification. For forensic application of mtDNA profiling in Malaysia, a comprehensive database on both HVI and HVII regions are essential. In order to identify polymorphic positions and to determine their frequency in the Malay population, mtDNA HVI and HVII regions of 103 maternally unrelated individuals were amplified ,sequenced and compared with Cambridge reference sequence (CRS). Sequence comparison led to the identification of a total of 446 and 604 location polymorphisms in mtDNA HVI and HVII regions respectively. This polymorphisms defined by 88 haplotypes (81 unique) in the HVI and 78 haplotypes (64 unique) in the HVII regions. In combined HVI and HVII defined 101 haplotypes (99 unique) was defined. In the HVII region All the individuals in HVII showed nucleotide transition event from A G at nucleotide position 073 and 263 and an insertion of cytosine (315.1C) at nucleotide position 315. The genetic diversity and probability of random match in combined HVI and HVII of 103 Malay individuals was found to be 0.9996 and 0.0101 respectively.Scientific World, Vol. 12, No. 12, September 2014, page 24-29

Sharing of chloroplast haplotypes among red oak species suggests interspecific gene flow between neighboring populations

The North American red oak species Quercus rubra L., Quercus ellipsoidalis E. J. Hill, Quercus velutina Lam., and Quercus coccinea Münchh. are morphologically similar and showed very low interspecific differentiation at most nuclear genetic markers in our earlier analyses (<10%). However, a few genetic markers showed interspecific differentiation values (up to 84%) above neutral expectations, a pattern of genomic divergence consistent with models of ecological speciation in the face of gene flow and strong divergent selection. Accordingly, these interfertile species are predicted to maintain differential adaptations to drought, while neutral regions of the genome appear to be homogenized by interspecific gene flow. According to this model of maintenance of species integrity by divergent selection with gene flow, we expect a sharing of chloroplast haplotypes between interspecific population pairs. We analyzed maternally inherited chloroplast DNA markers for the first time in interspecific populations of the red oaks (section Lobatae) to provide additional evidence for contemporary gene flow between Q. rubra and Q. ellipsoidalis and between Q. velutina and Q. ellipsoidalis. Very low interspecific differentiation (GST= 0.023), but pronounced genetic differentiation among populations from different regions (GST= 0.277) across species, and sharing of regional chloroplast haplotypes between species in sympatric and neighboring populations provided strong evidence for contemporary interspecific gene flow. The pattern of divergence at chloroplast DNA markers in red oaks suggests interspecific gene flow that resulted in a sharing of chloroplast types while the ecological and morphological distinctness of species was maintained.

Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies.

Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facilitates the positive identification of that strain and reveals its relatedness to other strains. The presence of these alternate haplotype regions affects phenotype scoring and gene expression measurements. Here, we present a rich set of genetic differences as a community resource to allow researchers to more accurately conduct and interpret their experiments with Chlamydomonas.

Mitochondrial DNA Diversity and Phylogeography ofLucania interiorisInform Biodiversity Conservation in the Cuatro Ciénegas Basin, México

Abstract. The Cuatro Cienegas killifish Lucania interioris is an endemic fundulid in the Chihuahuan Desert valley of Cuatro Cienegas, Coahuila, Mexico. It occurs in 3 major drainage regions of the basin and is limited primarily to naturally fragmented and physicochemically severe habitats of the valley floor. We assessed mitochondrial DNA variation and population genetic structure in L. interioris from 8 populations representative of the entire geographic range of this species, including its distribution within and among major drainage regions (western, central, and southeastern) of the valley. Five populations were invariant, including both populations in the western region (Haplotype A only), whereas 2 haplotypes were observed in each of the remaining populations. Haplotype diversity was low in the central basin (HD = 0.10 and HD = 0.19) and moderate in the southeastern basin (HD = 0.52). Low levels of divergence among haplotypes (0.3%–0.9%), together with high levels of genetic differentiation among re...

Molecular understanding of Indian untransfused thalassemia intermedia.

The term thalassemia intermedia describe a form of thalassemia of intermediate severity, between the major transfusion-dependent forms of the disease and the symptomless carrier states. The phenotypic diversity of β-thalassemia results from its underlying genetic diversity. The wide clinical variability of these conditions leads to major difficulties in their management. The molecular basis of thalassemia intermedia is very heterogeneous. The clinical and hematological course of β-thalassemia intermedia is influenced by a number of genetic factors. The main aim of the study was to evaluate the effect of globin and nonglobin genetic modifiers on clinical severity of the disease. The study group consisted of 66 homozygous patients with β-thalassemia [40 transfusion-dependent thalassemia (TDT), 26 nontransfusion-dependent thalassemia (NTDT)]. Hepatosplenomegaly was pronounced in the NTDT group. The presence of associated α-thalassemia was significantly higher in untransfused patients (P < 0.05). The milder β-thalassemia mutations, such as Cap site +1 (A → C), -88 (C → T), and -87 (C → G), were observed mainly in the NTDT group (9.61%) as against patients with TDT (1.25%). The cis-DNA haplotypes, motifs, or polymorphisms around the gamma-globin genes [(AT)x (T)y motif (38.4%), XmnI (76.92%)and the Aγ-δ intergenic region haplotype T (73.07%) and Pre Gγ globin gene haplotype TAG (46.15%)] contributed significantly in amelioration of the disease severity. Our study emphasizes the complexity of genetic interactions that underlie the phenotype of β-thalassemia and highlights the importance of epistatic factors and the regulation of HbF production in β-thalassemia syndromes.

First data on genetic diversity of burbot (Lota lota L.) in the Western Siberian

Analysis of genetic diversity of burbot (Lota lota Linneus, 1758) mitochondrial control region (mtCR) haplotypes from geographically distant localities in the Ob-Irtysh River basin in comparison with distribution of known burbot haplotypes was conducted. mtCR fragments from burbot samples, obtained in two localities (longitudinal part of the Irtysh near Tobolsk and the Sob River, a left-bank tributary of the Ob River), were sequenced.

Estimation of chimpanzee community size and genetic diversity in Kahuzi-Biega National Park, Democratic Republic of Congo.

A small chimpanzee habitat in the montane forest of Kahuzi-Biega National Park, Democratic Republic of Congo, is connected with the lowland forest of this park through a corridor, which is affected by human encroachment. To assess the conservation status of the chimpanzee population in this small habitat, we estimated the size of the community and evaluated its genetic diversity by using 279 fecal samples collected in the montane forest of Kahuzi. Using autosomal microsatellite (or short tandem repeat, STR) loci, we identified 32 individuals, comprising 19 females and 13 males. Samples from 24 individuals were collected at least twice and a genetic mark-recapture analysis estimated that the community size was 36 (range: 32-42). Data on nest site sharing confirmed that all the samples belonged to the same community. Nest site sharing information may be useful in population studies of unhabituated chimpanzees. The genetic structure and diversity of the 32 genotyped individuals was assessed using Y-chromosomal short tandem repeat (Y-STR) loci and mitochondrial D-loops. One dominant Y-STR haplotype was found, whereas there was no dominant haplotype in the mitochondrial region, reflecting a female-biased dispersal pattern, which is typical of chimpanzees. The genetic diversity for three markers in Kahuzi chimpanzees was comparable to that in other eastern chimpanzee populations. A relatively high heterozygosity and negative inbreeding coefficient (FIS ) for STR loci suggests that the study community belongs to an outbreeding chimpanzee population. These findings suggest that individuals of the study community may have reproductive contact with other chimpanzee individuals from neighboring communities in Kahuzi-Biega National Park, at least in the recent past. Am. J. Primatol. 77:1015-1025, 2015. © 2015 Wiley Periodicals, Inc.

Beta-globin gene evolution in the ruminants: evidence for an ancient origin of sheep haplotype B.

Domestic sheep (Ovis aries) can be divided into two groups with significantly different responses to hypoxic environments, determined by two allelic beta-globin haplotypes. Haplotype A is very similar to the goat beta-globin locus, whereas haplotype B has a deletion spanning four globin genes, including beta-C globin, which encodes a globin with high oxygen affinity. We surveyed the beta-globin locus using resequencing data from 70 domestic sheep from 42 worldwide breeds and three Ovis canadensis and two Ovis dalli individuals. Haplotype B has an allele frequency of 71.4% in O. aries and was homozygous (BB) in all five wild sheep. This shared ancestry indicates haplotype B is at least 2-3 million years old. Approximately 40 kb of the sequence flanking the ~37-kb haplotype B deletion had unexpectedly low identity between haplotypes A and B. Phylogenetic analysis showed that the divergent region of sheep haplotype B is remarkably distinct from the beta-globin loci in goat and cattle but still groups with the Ruminantia. We hypothesize that this divergent ~40-kb region in haplotype B may be from an unknown ancestral ruminant and was maintained in the lineage to O. aries, but not other Bovidae, evolving independently of haplotype A. Alternatively, the ~40-kb sequence in haplotype B was more recently acquired by an ancestor of sheep from an unknown non-Bovidae ruminant, replacing part of haplotype A. Haplotype B has a lower nucleotide diversity than does haplotype A, suggesting a recent bottleneck, whereas the higher frequency of haplotype B suggests a subsequent spread through the global population of O. aries.

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.

We report a novel high-throughput method to empirically quantify individual-specific regulatory element activity at the population scale. The approach combines targeted DNA capture with a high-throughput reporter gene expression assay. As demonstration, we measured the activity of more than 100 putative regulatory elements from 95 individuals in a single experiment. In agreement with previous reports, we found that most genetic variants have weak effects on distal regulatory element activity. Because haplotypes are typically maintained within but not between assayed regulatory elements, the approach can be used to identify causal regulatory haplotypes that likely contribute to human phenotypes. Finally, we demonstrate the utility of the method to functionally fine map causal regulatory variants in regions of high linkage disequilibrium identified by expression quantitative trait loci (eQTL) analyses.

A cytosine-thymine (CT)-rich haplotype in intron 4 of SNCA confers risk for Lewy body pathology in Alzheimer's disease and affects SNCA expression

IntroductionWe recently showed that tagging single-nucleotide polymorphisms across the SNCA locus were significantly associated with increased risk for Lewy body (LB) pathology in Alzheimer's disease (AD) cases. However, the actual genetic variant(s) that underlie the observed associations remain elusive. MethodsWe used a bioinformatics algorithm to catalog structural variants in a region of SNCA intron 4, followed by phased sequencing. We performed a genetic association analysis in autopsy series of LB variant of Alzheimer's disease (LBV/AD) cases compared with AD-only controls. We investigated the biological functions by expression analysis using temporal-cortex samples. ResultsWe identified four distinct haplotypes within a highly polymorphic low-complexity cytosine-thymine (CT)-rich region. We showed that a specific haplotype conferred risk to develop LBV/AD. We demonstrated that the CT-rich site acts as an enhancer element, where the risk haplotype was significantly associated with elevated levels of SNCA messenger RNA. DiscussionWe have discovered a novel haplotype in a CT-rich region in SNCA that contributes to LB pathology in AD patients, possibly via cis-regulation of the gene expression.

A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea.

We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23–47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea.

Morphological and genetic characterization of Sardinian trout Salmo cettii Rafinesque, 1810 and their conservation implications

The morphological and genetic structure of Western Mediterranean trout Salmo cettii inhabiting basins in Sardinia was completed to assist the design of its conservation programmes. Genetic analysis of protein-coding LDH-C1 plus sequencing mitochondrial control region gene and analyses of morphological characters described 253 specimens from seven localities in two basins in Southwest Sardinia. Nuclear and mitochondrial analyses revealed all of the fish were pure-bred native S. cettii, with no introgression from allochthonous S. trutta. The novel 18 mtDNA control region haplotypes were clustered in an ‘insular’ clade, strictly related to the Adriatic haplogroup, and depicted a radial network around two ancestral haplotypes. Completion of discriminant analysis using data on body pigmentation and quantitative morphologic parameters revealed three phenotypic groups within the fish. Each population and phenotype, characterised by high values of nucleotide and haplotype diversity, were not genetically differentiated and not geographically structured according to the two hydrological basins. Geometric morphometric analysis, based on 15 landmarkers, revealed pronounced and highly significant differences in body shape morphology between populations, suggesting S. cettii is locally adapting to extreme environmental conditions and so future management plans for these populations should treat the two basins as distinct morphological units.

Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago.

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.

Haplotype phasing and inheritance of copy number variants in nuclear families.

DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.

Wide-ranging phylogeographic structure of invasive red lionfish in the Western Atlantic and Greater Caribbean

The red lionfish (Pterois volitans) is an invasive predatory marine fish that has rapidly expanded its presence in the Western Hemisphere. We collected 214 invasive red lionfish samples from nine countries and territories, including seven unpublished locations. To more comprehensively evaluate connectivity, we compiled our d-loop sequence data with 846 published sequences, resulting in 1,060 samples from 14 locations. We found low nucleotide diversity (π = 0.003) and moderate haplotype diversity (h = 0.59). Using haplotype population pairwise ΦST tests, we analyzed possible phylogeographic breaks that were previously proposed based on other reef organisms. We found support for the Bahamas/Turks/Caicos versus Caribbean break (ΦST = 0.12) but not for the Northwestern Caribbean, Eastern Caribbean, or US East Coast versus Bahamas breaks. The Northern Region had higher variation and more haplotypes, supporting introductions of at least five haplotypes to the region. Our wide-ranging samples showed that a lower-frequency haplotype in the Northern Region dominated the Southern Region and suggested multiple introductions, possibly to the south. We tested multiple scenarios of phylogeographic structure with analyses of molecular variance and found support for a Northern and Southern Region split at the Bahamas/Turks/Caicos versus Caribbean break (percentage of variation among regions = 8.49 %). We found that Puerto Rico clustered with the Southern Region more strongly than with the Northern Region, as opposed to previous reports. We also found the rare haplotype H03 for the first time in the southern Caribbean (Panama), indicating that either secondary releases occurred or that the low-frequency haplotypes have had time to disperse to extreme southern Caribbean locations.

Haplotype analysis of the 4p16.3 region in Portuguese families with Huntington's disease.

Huntington's disease (HD) is a neurodegenerative disorder characterized by involuntary choreic movements, cognitive impairment, and behavioral changes, caused by the expansion of an unstable CAG repeat in HTT. We characterized the genetic diversity of the HD mutation by performing an extensive haplotype analysis of ∼1Mb region flanking HTT in over 300 HD families of Portuguese origin. We observed that haplotype A, marked by HTT delta2642, was enriched in HD chromosomes and carried the two largest expansions reported in the Portuguese population. However, the most frequent HD haplotype B carried one of the largest (+12 CAGs) expansions, which resulted in an allele class change to full penetrance. Despite having a normal CAG distribution skewed to the higher end of the range, these two core haplotypes had similar expanded CAG repeat sizes compared to the other major core haplotypes (C and D) and there was no statistical difference in transmitted repeat instability across haplotypes. We observed a diversity of HTT region haplotypes in both normal and expanded chromosomes, representative of more than one ancestral chromosome underlying HD in Portugal, where multiple independent events on distinct chromosome 4 haplotypes have given rise to expansion into the pathogenic range. © 2015 Wiley Periodicals, Inc.

Native Fusarium head blight resistance from winter wheat cultivars ‘Lyman,’ ‘Overland,’ ‘Ernie,’ and ‘Freedom’ mapped and pyramided onto ‘Wesley’-Fhb1 backgrounds

Pyramiding QTL from multiple sources for FHB resistance presents an opportunity to enhance the FHB resistance of elite wheat germplasm. Mapping FHB resistance QTL directly in wheat breeding populations would eliminate the need for purpose-built mapping populations and thus accelerate marker-assisted pyramiding efforts. In this study, we demonstrate that multiple QTL for FHB resistance can be mapped directly in early-generation breeding populations by application of identical-by-descent (IBD)-based linkage mapping. IBD-based linkage analysis was conducted using 565 segregating F1 progeny derived from 28 four-way crosses among Fhb1 donor lines and multiple native sources of resistance including Lyman, Overland, Ernie, and Freedom. A total of 15 QTL for FHB resistance were mapped on chromosomes 1A, 1B, 2A, 3A, 3B, 4A, 4B, 4D, 5A, 6A, 6D, and 7D, including known loci Fhb1, Fhb5, and Rht-B1. QTL conferring native resistance in the cultivars Lyman and Overland are mapped for the first time in this study, including a QTL on chromosome 1AS (Qfhb.sdsu-1A) explaining between 4.5 and 9.9 % of the phenotypic variance in all evaluations. Marker haplotypes for these QTL regions can be used to conduct marker-assisted selection and fixation of resistance alleles in subsequent generations of these breeding populations.

Multiple Fusarium head blight resistance loci mapped and pyramided onto elite spring wheat Fhb1 backgrounds using an IBD-based linkage approach

Pyramiding QTL for FHB resistance from multiple sources presents an opportunity to enhance the Fhb1 derived resistance of elite spring wheat germplasm. Conventionally, pyramiding QTL using a marker assisted-selection approach requires preliminary mapping studies to identify the resistance QTL from each parental line and validation studies to assess the QTL effects in multiple genetic backgrounds. This study evaluates IBD-based linkage analysis for the purpose of mapping, validation and marker-assisted pyramiding of resistance QTL simultaneously in breeding populations. Eight hundred and twenty nine segregating F1 progeny from 43 four-way crosses among multiple sources of resistance were evaluated in the greenhouse and in field-based progeny tests. IBD-based linkage analysis was conducted using a mixed model extension of Haseman-Elston sib-pair regression. QTL for FHB resistance were identified on chromosomes 2A, 2B, 3B and 7B, cumulatively explaining 18–21 % of the variance for FHB severity in different evaluations. The QTL on chromosome 3B corresponded with Fhb1, and the QTL on chromosomes 2B and 7B are corroborated by previous mapping studies. The QTL mapped to chromosome 2A potentially represents a novel source of resistance derived from elite North American spring wheat germplasm. Marker haplotypes for these QTL regions are being used for marker-assisted selection of resistance alleles in subsequent generations of these breeding populations.

Polyphyletic ancestry of historic gray wolves inhabiting U.S. Pacific states

Given the recent re-colonization of gray wolves (Canis lupus) to the Pacific northwest, USA, and subsequent migration into northern California, understanding how well natural migration has restored historic diversity can inform management decisions. In this study, we report the mitochondrial DNA control region haplotypes of nine museum specimens that curators identified as C. lupus from Oregon, Nevada, and California. Among the nine samples currently available for genetic analysis of historic genetic diversity of C. l. spp. in the U.S. Pacific states, we found six previously described haplotypes including two domestic dog (C. l. familiaris) haplotypes. Notably, we present the first evidence of Mexican wolf (C. l. baileyi) ancestry in southern California while the northern Californian specimen, as well as one individual from Nevada, present a haplotype common to wolves from the historic American West and extant Canadian wolf populations. Finally, the three Oregon specimens shared a haplotype that is only observed in extant wolves from coastal British Columbia (the “coastal rainforest” wolf ecotype), indicating that the historical range of this haplotype reached as far south as southwestern Oregon. In conclusion, our results indicate that the genetic composition of historic wolf populations in the Pacific northwest and southwest states was polyphyletic and included wolves that share maternal ancestry with current populations from adjacent regions. These findings, in addition with future nuclear analyses, reveal more accurate historic range delimitations, which is critical information when designing appropriate management plans for wolves naturally re-colonizing the U.S. Pacific northwest and southwest regions.