Haplotype Phylogeny Research Articles

Molecular markers for analyses of intraspecific genetic diversity in the Asian Tiger mosquito, Aedes albopictus.

BackgroundThe dramatic worldwide expansion of Aedes albopictus (the Asian tiger mosquito) and its vector competence for numerous arboviruses represent a growing threat to public health security. Molecular markers are crucially needed for tracking the rapid spread of this mosquito and to obtain a deeper knowledge of population structure. This is a fundamental requirement for the development of strict monitoring protocols and for the improvement of sustainable control measures.MethodsWild population samples from putative source areas and from newly colonised regions were analysed for variability at the ribosomal DNA internal transcribed spacer 2 (ITS2). Moreover, a new set of 23 microsatellite markers (SSR) was developed. Sixteen of these SSRs were tested in an ancestral (Thailand) and two adventive Italian populations.ResultsSeventy-six ITS2 sequences representing 52 unique haplotypes were identified, and AMOVA indicated that most of their variation occurred within individuals (74.36%), while only about 8% was detected among populations. Spatial analyses of molecular variance revealed that haplotype genetic similarity was not related to the geographic proximity of populations and the haplotype phylogeny clearly indicated that highly related sequences were distributed across populations from different geographical regions. The SSR markers displayed a high level of polymorphism both in the ancestral and in adventive populations, and FST estimates suggested the absence of great differentiation. The ancestral nature of the Thai population was corroborated by its higher level of variability.ConclusionsThe two types of genetic markers here implemented revealed the distribution of genetic diversity within and between populations and provide clues on the dispersion dynamics of this species. It appears that the diffusion of this mosquito does not conform to a progressive expansion from the native Asian source area, but to a relatively recent and chaotic propagule distribution mediated by human activities. Under this scenario, multiple introductions and admixture events probably play an important role in maintaining the genetic diversity and in avoiding bottleneck effects. The polymorphic SSR markers here implemented will provide an important tool for reconstructing the routes of invasion followed by this mosquito.

Phylogeny of seven Bulinus species originating from endemic areas in three African countries, in relation to the human blood fluke Schistosoma haematobium.

BackgroundSnails species belonging to the genus Bulinus (Planorbidae) serve as intermediate host for flukes belonging to the genus Schistosoma (Digenea, Platyhelminthes). Despite its importance in the transmission of these parasites, the evolutionary history of this genus is still obscure. In the present study, we used the partial mitochondrial cytochrome oxidase subunit I (cox1) gene, and the nuclear ribosomal ITS, 18S and 28S genes to investigate the haplotype diversity and phylogeny of seven Bulinus species originating from three endemic countries in Africa (Cameroon, Senegal and Egypt).ResultsThe cox1 region showed much more variation than the ribosomal markers within Bulinus sequences. High levels of genetic diversity were detected at all loci in the seven studied species, with clear segregation between individuals and appearance of different haplotypes, even within same species from the same locality. Sequences clustered into two lineages; (A) groups Bulinus truncatus, B. tropicus, B. globosus and B. umbilicatus; while (B) groups B. forskalii, B. senegalensis and B. camerunensis. Interesting patterns emerge regarding schistosome susceptibility: Bulinus species with lower genetic diversity are predicted to have higher infection prevalence than those with greater diversity in host susceptibility.ConclusionThe results reported in this study are very important since a detailed understanding of the population genetic structure of Bulinus is essential to understand the epidemiology of many schistosome parasites.

Differences in population genetic structure of two ethnomedicinal herbs of the genus Phyllanthus from India: a consequence of anthropogenic intervention?

Phyllanthus amarus and Phyllanthus fraternus are important ethnomedicinal herbs used as traditional medicines in many parts of the world. The increasing popularity of these green medicines and almost no studies on structuring of genetic diversity in these herbs, led to this investigation. Keeping this in view, our main objective was to analyze the structuring of chloroplast DNA diversity in wild populations of the two herbs from Northern India, using chloroplast DNA (cpDNA) markers. PCR–RFLP of cpDNA regions was carried out to detect intraspecific polymorphisms. The study revealed differences in cpDNA diversity in the two ethnomedicinal herbs. Lower cpDNA diversity, lesser number of haplotypes and absence of correlation between phylogeny and geographical distribution of haplotypes were observed in P. amarus. Absence of phylogeographic structure in P. amarus may be attributed partly to higher anthropogenic intervention, owing to its commercialization for export and raw drug trade. The investigation identified populations with high haplotype diversity and unique haplotypes in both the herbs, which will be useful while formulating future conservation strategies. As there are comparatively less number of studies on structure of cpDNA diversity in annuals, the present analyses also add to the available data on population genetic structure in annual plants.

Genetic structure and colonization history of the fruit fly Bactrocera tau (Diptera: Tephritidae) in China and Southeast Asia.

Bactrocera tau (Walker), a major invasive pest worldwide, was first described in Fujian (China) in 1849 and has dispersed to tropical and subtropical Asia and the South Pacific region. Few data are available on its colonization history and expansion processes. This pilot study attempted to reconstruct the colonization history and pathways of this pest in China and neighboring Southeast Asian countries based on mitochondrial DNA. Results of the study showed six genetic groups corresponding to geographical characteristics, although the pattern was relatively weak. Homogeneous genetic patterns were observed within southern and central China, and northern Vietnam. Continuous colonization from the coast of southern China to inland regions of China and northern Vietnam was suggested. Strong genetic structure was observed in western China, Thailand, and Laos. The isolation of four of the six groups was most probably attributable to major topographical barriers of western China. Yunnan acted as a contact zone of B. tau in China and neighboring Southeast Asia. The absence of isolation by distance and the overall low phylogeographic structure of B. tau suggested that long distance dispersal events and human activities could play a major role in the colonization and expansion patterns of B. tau. By analyzing the genetic diversity, gene flow, haplotype phylogeny, and demographic history of 23 fly populations, we hypothesized that B. tau could have been introduced long ago in southern China, from which it further expanded or that southern China could correspond to the native range of this species.

Morphological, ecological and mtDNA sequence variation in coregonid fish from the Baunt Lake system (the Vitim River basin)

We performed morphological, ecological and genetic analyses of taxonomically complex sympatric whitefi sh forms inhabiting the Baunt Lake system in the Vitim River basin, Transbaikalia. It was shown that the whitefi sh forms in this system clearly differed based on morphological traits, growth rate and diet. The most signifi cant differences were based on the number of gill rakers, while the number of lateral line scales was similar. These whitefi sh had distinct diets, namely euryphagous and planktivorous diets. We developed a phylogeny of mtDNA haplotypes among the whitefi sh species and populations from the Baunt Lake system and the headwater regions of the Ob and Yenisei River basins. A morphologically homogeneous cisco-like whitefi sh sample revealed two distinct mitochondrial lineages. A strong genetic divergence between the fi rst mitochondrial lineage of cisco-like whitefi sh and all of the studied whitefi sh forms was revealed. We analyzed alternative hypotheses regarding the ori gin of cisco-like whitefi sh and the densely rakered whitefi sh form from the Baunt Lake system.

Evolutionary Analysis of the Contact System Indicates that Kininogen Evolved Adaptively in Mammals and in Human Populations

Activation of the contact system leads to the cleavage of kininogen by plasma kallikrein resulting in kinin release and in the initiation of the intrinsic pathway of coagulation. Proteolysis of kininogen also generates antimicrobial peptides (AMPs) and can be induced by diverse pathogens. Thus, the contact system is regarded as a branch of innate immunity. We performed an evolutionary analysis of contact system genes by analyzing both inter- and intraspecies diversity. Results indicated that mammalian kininogen genes evolved adaptively. Positively selected sites are located in all protein domains with the exclusion of the bradykinin region and also involve AMP sequences (including the highly effective NAT26 peptide); positively selected sites also occur at alternative cleavage sites for neutrophil-released kinins. Population genetic analysis in humans indicated that a region of the kininogen gene (KNG1) has been a target of long-standing multiallelic balancing selection and that the coalescence time of the haplotype phylogeny dates back to the split between the humans and chimpanzees. No selection signature was detected in the Pan troglodytes KNG1 gene or in human genes encoding other components of the contact system. The selection targets in human KNG1 might be accounted for by variants with transcriptional regulatory activity. Results herein indicate a continuum in selective pressure acting on different timescales and targeting KNG1. This is in line with evidences suggesting a central role for kininogen in modulating of immune response and with its being a target of an extremely diverse array of pathogen species.

Analysis of Human Mitochondrial DNA Polymorphisms in the Japanese Population

The highly polymorphic nature and high amplification efficiency of mitochondrial DNA (mtDNA) is valuable for the analysis of biological evidence in forensic casework, such as the identification of individuals and assignment of race/ethnicity. To be useful, a mtDNA polymorphism database for the Japanese population requires an understanding of the range of haplotype variation and phylogenies of mtDNA sequences. To extend current knowledge on the haplotypes in the Japanese population, this study defines new lineages and provides more detail about some of those previously described. We compared the hypervariable regions (HVRs) of 270 healthy, unrelated Japanese individuals and demonstrated 192 haplotypes. Combining HVR1 and HVR2, the genetic diversity was 0.9935, thus providing a high level of identification capability. Haplogroup status was defined for 160 individuals using HVR1, HVR2, and particular coding region polymorphisms; these individuals belonged to 94 haplotypes, four of which were new lineages. The complete mtDNA sequence was also determined from seven individuals.

Pelvic-fin brooding in a new species of riverine ricefish (Atherinomorpha: Beloniformes: Adrianichthyidae) from Tana Toraja, Central Sulawesi, Indonesia

A new species of ricefi sh is described from a hill stream in Tana Toraja, Sulawesi. Oryzias eversi, new species, is distinguished from all other adrianichthyids in Sulawesi by having a low number of fi n rays in anal (17-18 (19)) and dorsal (10-12) fi ns, only 33-36 scales in lateral midline, ½14 transverse scale rows at dorsal fi n origin, 30-32 (33) vertebrae, small eyes (28.2-35.5% of head length), a conspicuous blackish male courtship colouration, and brooding behaviour similar to lacustrine ricefi shes. Female Oryzias eversi carry the eggs until the embryos hatch, and show a conspicuous abdominal concavity and extended fi ns, accommodating and holding the clutch of eggs. The eggs are connected to the female for the whole time of development by attaching fi laments that protrude from the female's urogenital pore. A mitochondrial haplotype phylogeny suggests that the new species is closely related to another pelvic the lake-dwelling O. sarasinorum from Lake Lindu in Central Sulawesi. However, the haplotype group of O. eversi and O. sarasinorum is nested within a clade of egg-depositing Oryzias from central, southwest, and southeast Sulawesi, whereas another brooder, Adrianichthys oophorus from Lake Poso, forms a distinct, second lineage of Sulawesi's ricefi shes. Accordingly, the brooding strategy has probably evolved more than once and may be realised in river habitats, which represents a new evolutionary trajectory in the radiation of ricefi shes in Sulawesi. The present discovery adds another new ricefi sh species to Sulawesi's still only partially known ichthyofauna, and highlights the island's role as hotspot of adrianichthyid diversity.

Genetic analysis of Black Tiger shrimp (Penaeus monodon) across its natural distribution range reveals more recent colonization of Fiji and other South Pacific islands

The Black Tiger shrimp (Penaeus monodon) has a natural distribution range from East Africa to the South Pacific Islands. Although previous studies of Indo-Pacific P. monodon have found populations from the Indian Ocean and Australasia to differ genetically, their relatedness to South Pacific shrimp remains unknown. To address this, polymorphisms at eight shared microsatellite loci and haplotypes in a 418-bp mtDNA-CR (control region) sequence were examined across 682 P. monodon from locations spread widely across its natural range, including the South Pacific islands of Fiji, Palau, and Papua New Guinea (PNG). Observed microsatellite heterozygosities of 0.82–0.91, allele richness of 6.85–9.69, and significant mtDNA-CR haplotype variation indicated high levels of genetic diversity among the South Pacific shrimp. Analysis of microsatellite genotypes using a Bayesian STRUCTURE method segregated Indo-Pacific P. monodon into eight distinct clades, with Palau and PNG shrimp clustering among others from Southeast Asia and eastern Australia, respectively, and Fiji shrimp clustering as a distinct group. Phylogenetic analyses of mtDNA-CR haplotypes delineated shrimp into three groupings, with shrimp from Fiji again being distinct by sharing no haplotypes with other populations. Depending on regional location, the genetic structures and substructures identified from the genotyping and mtDNA-CR haplotype phylogeny could be explained by Metapopulation and/or Member–Vagrant type evolutionary processes. Neutrality tests of mutation-drift equilibrium and estimation of the time since population expansion supported a hypothesis that South Pacific P. monodon were colonized from Southeast Asia and eastern Australia during the Pleistocene period over 60,000 years ago when land bridges were more expansive and linked these regions more closely.

Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene

BackgroundMUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD) within this gene in Chinese indigenous breeds and Western commercial breeds.ResultsA total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb) in Western commercial breeds. The significant positive Tajima’D, and Fu and Li’s D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process.ConclusionsChinese and Western breeds have similar nucleotide diversity but evolve divergently in the MUC4 region. Western breeds exhibited unusual low LD extent at the MUC4 locus, reflecting the complexity of nucleotide variability of pig genome. The finding suggests that high density (e.g. 1SNP/10 kb) markers are required to capture the underlying causal variants at such regions.

Invasion History of the Oriental Fruit Fly, Bactrocera dorsalis, in the Pacific-Asia Region: Two Main Invasion Routes

The oriental fruit fly, Bactrocera dorsalis, was initially recorded in Taiwan Island in 1912, and has dispersed to many areas in the Pacific-Asia region over the last century. The area of origin of the species may be confidently placed in South-East China. However, routes of range expansion to new areas and underlying population processes remain partially unclear, despite having been the subject of several studies. To explore the invasion history of this species, a partition of the cox1 gene of mitochondrial DNA was used to investigate genetic diversity, haplotype phylogeny and demographic history of 35 populations, covering China and South-East Asia and including marginal populations from Pakistan and Hawaii. Based on neighbor-joining tree analysis and the distribution of haplotypes, two main invasion routes are inferred: one from South-East China to Central China, another from South-East China to South-East Asia, with both routes probably coinciding in Central China. Populations in Taiwan Island and Hainan Island might have originated in South-East China. The marginal populations in Pakistan and Hawaii might have undergone founding events or genetic bottlenecks. Possible strategies for the control of this species are proposed based on the invasion history and reconstructed expansion routes.

An evolutionary history of the selectin gene cluster in humans

Molecules involved in leukocyte trafficking have a central role in the development of inflammatory and immune responses. We performed F(ST) analysis of the selectin cluster, as well as of SELPLG, ICAM1 and VCAM1. Peaks of significantly high population genetic differentiation were restricted to two regions in SELP and one in SELPLG. Resequencing data indicated that the region covering SELP exons 11-13 displays high nucleotide diversity in Africans and Europeans (CEU), and a high level of within-species diversity compared with inter-specific divergence. Analysis of inferred haplotypes revealed a complex phylogeny with two deeply separated clades that coalesce at ~3.5 million years (MY) plus a minor clade with a TMRCA (time to the most recent common ancestor) of ~2.2 MY. A splicing assay indicated no haplotype-specific effect on SELP exon 14 inclusion. These data are consistent with a model of multiallelic balancing selection; single-nucleotide polymorphism analysis indicated that the Val640Leu variant represents a likely selection target. In populations of Asian ancestry a distinct haplotype, possibly carrying regulatory variants, has been driven to high frequency by positive selection. No deviation from neutrality was observed for the SELPLG region. Resequencing of SELP in chimpanzees revealed a haplotype phylogeny with extremely deep basal branches, suggesting either long-standing balancing selection or ancestral population structure. Thus, SELP has experienced a complex selective history, possibly as a result of local adaptation. Variants in the gene have been associated with autoimmune and cardiovascular diseases. Association studies would benefit from both taking the complex SELP haplotype structure into account and from analysis of possible regulatory variants in the gene.

First mitochondrial DNA analysis of the spectacled porpoise (Phocoena dioptrica) from Tierra del Fuego, Argentina

The spectacled porpoise (Phocoena dioptrica, Lahille, 1912) is one of the cetacean species about which least is known. Most information on the biology and ecology of this species has been obtained from stranded specimens and sightings at sea. In this study, analysis of 380bp fragment of mitochondrial DNA (mtDNA) control region sequences (N=50) was performed to provide a preliminary assessment of the genetic variation in spectacled porpoise specimens found stranded or by caught on the coast of Tierra del Fuego, Argentina. Results showed high levels of mtDNA diversity, as expected in large size and stable populations, and similar to other species of porpoises. The star-like shape phylogeny of haplotypes indicates a recent population expansion. This is the first report on the genetic variation of this species. Other lines of evidence (microsatellite loci, single-nucleotide polymorphism (SNPs)) are needed to improve our knowledge on the molecular biology of the spectacled porpoise.

Variants in SNAP25 are targets of natural selection and influence verbal performances in women.

Descriptions of genes that are adaptively evolving in humans and that carry polymorphisms with an effect on cognitive performances have been virtually absent. SNAP25 encodes a presynaptic protein with a role in regulation of neurotransmitter release. We analysed the intra-specific diversity along SNAP25 and identified a region in intron 1 that shows signatures of balancing selection in humans. The estimated TMRCA (time to the most recent common ancestor) of the SNAP25 haplotype phylogeny amounted to 2.08 million years. The balancing selection signature is not secondary to demographic events or to biased gene conversion, and encompasses rs363039. This SNP has previously been associated to cognitive performances with contrasting results in different populations. We analysed this variant in two Italian cohorts in different age ranges and observed a significant genotype effect for rs363039 on verbal performances in females alone. Post hoc analysis revealed that the effect is driven by differences between heterozygotes and both homozygous genotypes. Thus, heterozygote females for rs363039 display higher verbal performances compared to both homozygotes. This finding was replicated in a cohort of Italian subjects suffering from neuromuscular diseases that do not affect cognition. Heterozygote advantage is one of the possible reasons underlying the maintenance of genetic diversity in natural populations. The observation that heterozygotes for rs363039 display higher verbal abilities compared to homozygotes perfectly fits the underlying balancing selection model. Although caution should be used in inferring selective pressures from observed signatures, SNAP25 might represent the first description of an adaptively evolving gene with a role in cognition.

Species Limits Based on mtDNA and Morphological Data in the Polytypic Species Plestiodon brevirostris (Squamata: Scincidae)

The Mexican Plestiodon brevirostris species group (Squamata: Scincidae) is composed of seven nominal species. The wide-ranging P. brevirostris is a polytypic species composed of five subspecies: P. b. brevirostris, P. b. bilineatus, P. b. dicei, P. b. indubitus, and P. b. pineus. A tree-based approach for species delimitation with mtDNA data was used to test the traditional species-level taxonomy of P. brevirostris preliminarily. A haplotype phylogeny for all of the species and subspecies in the P. brevirostris group, except P. colimensis, was inferred. The mtDNA data consisted of sequences encompassing the genes encoding 16S rRNA (part), ND1, and associated tRNAs (1355 base pairs), which were analyzed with Bayesian methods. Then, a search for diagnostic morphological characters for the putative species delimited by this approach was performed. The results indicate that the P. brevirostris group is paraphyletic with respect to P. lynxe, and that P. brevirostris actually is composed of at least five distinct lineages disguised by traditional taxonomy: P. b. brevirostris, P. b. bilineatus, P. b. dicei, and the eastern populations of P. b indubitus (from Morelos, Guerrero, and Mexico) represent distinct species, whereas the western populations of P. b. indubitus (from Colima and Jalisco) represent an undescribed species. The data cannot resolve whether P. b. pineus is conspecific with P. b. dicei or P. b. dicei is a paraphyletic (5nonexclusive) species relative to an exclusive P. b. pineus. Thus, the status of P. b. pineus remains uncertain. The haplotype phylogeny also suggests that P. b. brevirostris may represent more than one species.

Population genetic structure and implications for natal philopatry of nesting green turtles Chelonia mydas in the Yaeyama Islands, Japan

ESR Endangered Species Research Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials ESR 14:141-148 (2011) - DOI: https://doi.org/10.3354/esr00355 Population genetic structure and implications for natal philopatry of nesting green turtles Chelonia mydas in the Yaeyama Islands, Japan Hideaki Nishizawa1,*, Osamu Abe2, Junichi Okuyama1, Masato Kobayashi2, Nobuaki Arai1 1Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto, 606-8501, Japan 2Ishigaki Tropical Station, Seikai National Fisheries Research Institute, Fisheries Research Agency, Fukaiohta 148-446, Ishigaki, Okinawa 907-0451, Japan *Email: nishizawa0311@gmail.com ABSTRACT: Patterns of mitochondrial DNA (mtDNA) variation and microsatellite genotyping were used to analyze the population genetic structure of nesting green turtles Chelonia mydas (n = 67) in the Yaeyama Islands of Japan, which represent the northern limit of green turtle nesting in the western Pacific Ocean. The composition of a mixture of 6 mtDNA haplotypes from 3 rookeries, southwestern (SW) Iriomote Island (n = 26), eastern (E) Ishigaki Island (n = 29), and northwestern (NW) Ishigaki Island (n = 12), produced genetic diversity values (haplotype diversity h = 0.582 to 0.638, nucleotide diversity π = 0.0138 to 0.0244) within the high end of the range found in previous studies. The phylogeny of haplotypes, representing 3 distinct clades, indicated historical introgressions by individuals with divergent haplotypes from both Pacific colonies and Indian and Southeast Asian colonies. Significant genetic differentiation, at least between SW Iriomote Island and Ishigaki Island in which samples from E and NW Ishigaki were combined, was observed based on mtDNA; this indicated precise female natal philopatry compared to other Pacific and Indian regions, although microsatellite analyses of 4 markers revealed no significant genetic differentiation. Further studies are needed to clarify the precision of natal philopatry and male-mediated gene flow; however, this study provides valuable insights about the phylogeography of green turtles in Japan. Our results also underscore the need for green turtle conservation in the northwest Pacific Ocean. KEY WORDS: Sea Turtle · Pacific Ocean · mtDNA · Phylogeography · Conservation · Microsatellite · Chelonia mydas Full text in pdf format PreviousNextCite this article as: Nishizawa H, Abe O, Okuyama J, Kobayashi M, Arai N (2011) Population genetic structure and implications for natal philopatry of nesting green turtles Chelonia mydas in the Yaeyama Islands, Japan. Endang Species Res 14:141-148. https://doi.org/10.3354/esr00355 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in ESR Vol. 14, No. 2. Online publication date: July 07, 2011 Print ISSN: 1863-5407; Online ISSN: 1613-4796 Copyright © 2011 Inter-Research.

Morphology and mitochondrial DNA variation of the Siberian whitefish Coregonus lavaretus pidschian (Gmelin) in the upstream water bodies of the Ob and Yenisei Rivers

Combining morphological, ecological and genetic analyses, we compared patterns of diversification within and among populations of the southern Siberian whitefish species Coregonus lavaretus pidschian (Gmelin) to illuminate their evolutionary history. Using sequencing data from 1,930 bp of NADH dehydrogenase subunit 1 (ND1) mitochondrial DNA regions, we documented phylogeographic relationships among populations and developed a phylogeny of mtDNA haplotypes. We found significant differences in the perforated lateral-line scale numbers within and between some populations. Clear differences in the number of gill rakers on the first branchial arch were only exhibited between populations of C. l. pidschian and Coregonus lavaretus pravdinellus Dulkeit. Concordance between different morphological groups based on two meristic traits and mtDNA patterns was also tested.

Eastern fox squirrel (Sciurus niger) lacks phylogeographic structure: recent range expansion and phenotypic differentiation

The eastern fox squirrel (Sciurus niger) occurs naturally over most of eastern North America. The striking patterns of geographic variation in size and coat color displayed by this species are consistent with a hypothesis of southward range contraction and isolation in 2 refugia (in Texas and Florida) during the Last Glacial Maximum, followed by northward range expansion after the glaciers receded. Similar hypotheses have been proposed to explain the patterns in phylogeographic structure exhibited by many plants and animals in eastern North America. We analyzed DNA sequence variation in a 402–base-pair segment of the mitochondrial cytochrome-b gene in populations throughout the species’ range. Despite our broad geographic sampling, we failed to detect any phylogeographic structure. Unique haplotypes differed from high-frequency haplotypes by only 1 or 2 base pairs, producing a starlike phylogeny of haplotypes. Genetic variation within populations and the species as a whole was characterized by high haplotype diversity and low nucleotide diversity. Taken together, our data indicate that the eastern fox squirrel underwent a rapid range expansion and rapid morphological divergence within the past 14,000 years. DOI: 10.1644/09-MAMM-A-266.1.

Regional Variation in mtDNA of the Lesser Prairie-Chicken

Cumulative loss of habitat and long-term decline in the populations of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) have led to concerns for the species' viability throughout its range in the southern Great Plains. For more efficient conservation past and present distributions of genetic variation need to be understood. We examined the distribution of mitochondrial DNA (mtDNA) variation in the Lesser Prairie-Chicken across Kansas, Colorado, Oklahoma, and New Mexico. Throughout the range we found little genetic differentiation except for the population in New Mexico, which was significantly different from most other populations. We did, however, find significant isolation by distance at the rangewide scale (r = 0.698). We found no relationship between haplotype phylogeny and geography, and our analyses provide evidence for a post-glacial population expansion within the species that is consistent with the idea that speciation within Tympanuchus is recent. Conservation actions that increase the likelihood of genetically viable populations in the future should be evaluated for implementation.

Genetic diversity, structure, and demographic change in tanoak, Lithocarpus densiflorus (Fagaceae), the most susceptible species to sudden oak death in California

Knowledge of population genetic structure of tanoak (Lithocarpus densiflorus) is of interest to pathologists seeking natural variation in resistance to sudden oak death disease, to resource managers who need indications of conservation priorities in this species now threatened by the introduced pathogen (Phytophthora ramorum), and to biologists with interests in demographic processes that have shaped plant populations. We investigated population genetic structure using nuclear and chloroplast DNA (cpDNA) and inferred the effects of past population demographic processes and contemporary gene flow. Our cpDNA results revealed a strong pattern of differentiation of four regional groups (coastal California, southern Oregon, Klamath mountains, and Sierra Nevada). The chloroplast haplotype phylogeny suggests relatively deep divergence of Sierra Nevada and Klamath populations from those of coastal California and southern Oregon. A widespread coastal California haplotype may have resulted from multiple refugial sites during the Last Glacial Maximum or from rapid recolonization from few refugia. Analysis of nuclear microsatellites suggests two major groups: (1) central coastal California and (2) Sierra Nevada/Klamath/southern Oregon and an area of admixture in north coastal California. The low level of nuclear differentiation is likely to be due to pollen gene flow among populations during postglacial range expansion.