Northern Haplotypes Research Articles

Genetic characterisation of oyster populations along the north-eastern coast of Tunisia

The taxonomy of oysters has been traditionally based on characteristics of the shell. More recently, the analysis of protein and DNA polymorphism has provided a means to overcome difficulties in distinguishing the different species of oysters based solely on shell morphology. In order to identify oysters of the Tunisian north-east coast, we sequenced a 16S rRNA mitochondrial fragment from 68 oysters sampled from the Bizert Lagoon and the Gulf of Hammamet in northern Tunisia. Comparison of oyster 16S rRNA sequences available in GenBank showed the presence of both Ostreola stentina and Crassostrea gigas in our samples, which could not be detected on the basis of shell morphology only. These data confirmed that C. gigas, a non-native species, is now naturalised in the Bizert Lagoon. Furthermore, significant levels of genetic divergence among the 16S rRNA haplotypes from O. stentina populations have been observed. Specifically, the haplotypes found in the Bizert Lagoon are closer to those previously detected from Morocco and Portugal, whereas those in the Gulf of Hammamet are closer to the haplotypes from the south of Tunisia, with a divergence ranging from 2.1% to 2.7% between the northern and eastern Tunisian haplotypes. The possible impact of the Siculo-Tunisian Strait on the phylogeography of O. stentina is discussed.

Mitochondrial DNA‐inferred population structure and demographic history of the mitten crab (Eriocheir sensu stricto) found along the coast of mainland China

The mitten crab, Eriocheir sensu stricto, is economically important in East Asia, although it is an invasive species in Europe and North America. Little is known about its population structure and historical demography in its native range, especially along the Pacific coast of China. We collected mitochondrial cytochrome oxidase subunit II and cytochrome b sequences from 154 individuals distributed in the rivers along the Chinese coast and 15 individuals from Japan. Phylogenetic analysis resulted in three major monophyletic groups: northern China, southern China and Japan. Negligible migration was detected among those groups by coalescent analysis. Hence, we support the recognition of three species: Eriocheir hepuensis in southern China, Eriocheir sinensis in northern China and Eriocheir japonica in Japan. The populations in the middle (the Oujiang and Minjiang Rivers) possess a mixture of haplotypes similar to either the northern or the southern haplotypes. We believe that secondary intergradation as the most likely cause of the clinal variation based on examining the genetic variation in the latitudinal space. The estimated divergence time between E. sinensis and E. hepuensis is 2.24 million years ago (Ma), while the divergence time between E. japonica and E. sinensis is 1.83 Ma. Both are in the late Pliocene, suggesting that land bridges associated with low sea level during that time might have severed as vicariant barriers for speciation. The divergence of the northern population and the 'northern haplotypes' in the middle population was estimated at 0.12 Ma, while the time separating the southern population and the 'southern haplotypes' in the middle populations was estimated as 0.16 Ma, implicating possible secondary contact in the late Pleistocene.

Strait of Gibraltar: an effective gene‐flow barrier for wind‐pollinated Carex helodes (Cyperaceae) as revealed by DNA sequences, AFLP, and cytogenetic variation

The Strait of Gibraltar is the most important barrier disconnecting the landmasses of Europe and Africa on the western Mediterranean extreme. Carex helodes is a wind-pollinated species endemic to the western Mediterranean. Because molecular and cytogenetic data allow the inference of its evolutionary history, we analyzed variations in chromosome number, including meiotic chromosome behavior, amplified fragment length polymorphism (AFLP) fingerprints, and nucleotide substitutions in plastid and nuclear DNA sequences. Cytogeographic results showed that the African populations have stabilized at a single chromosome number of 2n = 74, whereas the most frequent cytotype in Iberia is 2n = 72. Phylogenetic reconstructions of 17 sequences from nine closely related species revealed that C. helodes is monophyletic and that the Moroccan populations are embedded in the Iberian lineages. The haplotype network is also consistent with a European origin of the northern African haplotype. AFLP analysis also revealed hierarchical levels of genetic variation compatible with a founder effect process responsible for the African populations. All sources of evidence support the hypothesis that the Strait of Gibraltar has been an effective gene-flow barrier, generating two isolated evolutionary lineages after their dispersal. Recent connections between the two lineages appear unlikely, whereas active gene flow occurs among populations within the two lineages.

Molecular phylogeography of the viperine snake Natrix maura (Serpentes: Colubridae): Evidence for strong intraspecific differentiation

The molecular phylogeography of the viperine snake, Natrix maura (Linnaeus, 1758), was investigated using complete sequences of the mitochondrial cytochrome b gene and genomic ISSR-PCR fingerprinting. In a total of 120 samples, 44 unique cytochrome b haplotypes were found which defined three major genetic lineages associated with samples from Morocco, Tunisia and Europe, respectively. The same lineages were supported by nuclear data. A possible fourth lineage exists in southern Spain. Genetic distances of cytochrome b sequences between the three main lineages were in the range of 3.9–5.6%, suggesting independent evolution since the early Pliocene. Distinction of the three major lineages at the subspecies or species level is discussed to account taxonomically for the high intraspecific variation in the viperine snake. A more detailed analysis of the European samples based on genetic diversity indices and a network reconstruction suggests a complex Pleistocene history for the viperine snake in Europe. Clear differentiation was found between populations south and north of the central Iberian mountain ranges, suggesting Pleistocene glacial refugia both in the southern and northern Iberian peninsula. In the south, genetic diversity was associated with the main river valleys, whereas northern haplotypes were more broadly distributed, indicating gene flow or postglacial range expansions. Unexpectedly high levels of genetic variation in southeastern France and northwestern Italy would be compatible with the hypothesis of a glacial refugium north of the Pyrenees or in Italy. However, due to the dependence of N. maura on warm climates, the assumption of a northern refugium seems unwarranted. We believe that further sampling in northern Spain is likely to reveal genetically diverse populations which could have served as sources for postglacial recolonization of France and Italy.

Determining the origin and age of the Westland beech (Nothofagus) gap, New Zealand, using fungus beetle genetics

The formation and maintenance of the Nothofagus beech gap in the South Island, New Zealand, has been the focus of biogeographical debate since the 1920s. We examine the historical process of gap formation by investigating the population genetics of fungus beetles: Brachynopus scutellaris (Staphylinidae) inhabits logs and is absent from the beech gap, and Hisparonia hystrix (Nitidulidae) is contiguous through the gap and is found commonly on sooty mould growing on several plant species. Both species show distinctive northern and southern haplotype distributions while H. hystrix recolonized the gap as shown by definitive mixing. B. scutellaris shows two major haplotype clades with strong geographical concordance, and unlike H. hystrix, has clearly defined lineages that can be partitioned for molecular dating. Based on coalescence dating methods, disjunct lineages of B. scutellaris indicate that the gap was formed less than 200 000 years ago. Phylogenetic imprints from both species reveal similar patterns of population divergence corresponding to recent glacial cycles, favouring a glacial explanation for the origin of the gap. Post-gap colonization by H. hystrix may have been facilitated by the spread of Leptospermum scoparium host trees to the area, and they may be better at dispersing than B. scutellaris which may be constrained by fungal host and/or microhabitat. The gap-excluded species B. scutellaris is found in both beech and podocarp-broadleaf forests flanking the Westland gap and its absence in the gap may be related to incomplete recolonization following glacial retreat. We also discuss species status and an ancient polymorphism within B. scutellaris.

Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe

Domesticated cattle were one of the cornerstones of European Neolithisation and are thought to have been introduced to Europe from areas of aurochs domestication in the Near East. This is consistent with mitochondrial DNA (mtDNA) data, where a clear separation exists between modern European cattle and ancient specimens of British aurochsen. However, we show that Y chromosome haplotypes of north European cattle breeds are more similar to haplotypes from ancient specimens of European aurochsen, than to contemporary cattle breeds from southern Europe and the Near East. There is a sharp north-south gradient across Europe among modern cattle breeds in the frequencies of two distinct Y chromosome haplotypes; the northern haplotype is found in 20 out of 21 European aurochsen or early domestic cattle dated 9500-1000 BC. This indicates that local hybridization with male aurochsen has left a paternal imprint on the genetic composition of modern central and north European breeds. Surreptitious mating between aurochs bulls and domestic cows may have been hard to avoid, or may have occurred intentionally to improve the breeding stock. Rather than originating from a few geographical areas only, as indicated by mtDNA, our data suggest that the origin of domestic cattle may be far more complex than previously thought.

Mitochondrial DNA Polymerase W748S Mutation: A Common Cause of Autosomal Recessive Ataxia with Ancient European Origin

Mutations in the catalytic subunit of the mitochondrial DNA polymerase gamma (POLG) have been found to be an important cause of neurological disease. Recently, we and collaborators reported a new neurodegenerative disorder with autosomal recessive ataxia in four patients homozygous for two amino acid changes in POLG: W748S in cis with E1143G. Here, we studied the frequency of this allele and found it to be among the most common genetic causes of inherited ataxia in Finland. We identified 27 patients with mitochondrial recessive ataxia syndrome (MIRAS) from 15 Finnish families, with a carrier frequency in the general population of 1 : 125. Since the mutation pair W748S+E1143G has also been described in European patients, we examined the haplotypes of 13 non-Finnish, European patients with the W748S mutation. Haplotype analysis revealed that all the chromosomes carrying these two changes, in patients from Finland, Norway, the United Kingdom, and Belgium, originate from a common ancient founder. In Finland and Norway, long, common, northern haplotypes, outside the core haplotype, could be identified. Despite having identical homozygous mutations, the Finnish patients with this adult- or juvenile-onset disease had surprisingly heterogeneous phenotypes, albeit with a characteristic set of features, including ataxia, peripheral neuropathy, dysarthria, mild cognitive impairment, involuntary movements, psychiatric symptoms, and epileptic seizures. The high carrier frequency in Finland, the high number of patients in Norway, and the ancient European founder chromosome indicate that this newly identified ataxia should be considered in the first-line differential diagnosis of progressive ataxia syndromes.

Homozygosity Mapping of Portuguese and Japanese Forms of Ataxia-Oculomotor Apraxia to 9p13, and Evidence for Genetic Heterogeneity

Ataxia with oculomotor apraxia (AOA) is characterized by early-onset cerebellar ataxia, ocular apraxia, early areflexia, late peripheral neuropathy, slow progression, severe motor handicap, and absence of both telangiectasias and immunodeficiency. We studied 13 Portuguese families with AOA and found that the two largest families show linkage to 9p, with LOD scores of 4.13 and 3.82, respectively, at a recombination fraction of 0. These and three smaller families, all from northern Portugal, showed homozygosity and haplotype sharing over a 2-cM region on 9p13, demonstrating the existence of both a founding event and linkage to this locus, AOA1, in the five families. Three other families were excluded from this locus, demonstrating nonallelic heterogeneity in AOA. Early-onset cerebellar ataxia with hypoalbuminemia (EOCA-HA), so far described only in Japan, is characterized by marked cerebellar atrophy, peripheral neuropathy, mental retardation, and, occasionally, oculomotor apraxia. Two unrelated Japanese families with EOCA-HA were analyzed and appeared to show linkage to the AOA1 locus. Subsequently, hypoalbuminemia was found in all five Portuguese patients with AOA1 with a long disease duration, suggesting that AOA1 and EOCA-HA correspond to the same entity that accounts for a significant proportion of all recessive ataxias. The narrow localization of AOA1 should prompt the identification of the defective gene.

A Polymerase Chain Reaction–Restriction Fragment Length Polymorphism (PCR–RFLP) Assay for the Discrimination of Mitochondrial DNA from the Florida and Northern Subspecies of Largemouth Bass

Abstract Distinct mitochondrial DNA haplotypes, based on the presence or absence of a Taq I restriction site in the control region, distinguished largemouth bass Micropterus salmoides of the northern subspecies (N = 62) from the Florida subspecies (N = 28). The presence of either northern (N = 6) or Florida (N = 3) haplotypes in Lake Wateree, South Carolina, suggests that these haplotypes will be particularly useful in detecting the coexistence of these subspecies.

Genetic and Population Characteristics of Walleyes in the Mobile Drainage of Alabama

Abstract Mitochondrial DNA (mtDNA) analysis conducted on walleyes Stizostedion vitreum collected in Alabama indicated that 44 fish from the Mobile drainage were of the recently described southern haplotype, whereas all 5 fish from the Tennessee River had a northern haplotype. No successful establishment of female walleyes from Ohio stocked in the Mobile drainage between 1973 and 1985 was indicated by the mtDNA data. However, 3 of 22 loci screened by protein electrophoresis were polymorphic in Alabama walleyes, and three fish in the western portion of the Mobile drainage possessed alleles more typically seen in northern walleyes. These three fish could be descendants of stocked northern male walleyes or individuals with northern alleles that resulted from hybridizations with northern walleyes that had entered the western Mobile drainage via the Tennessee–Tombigbee Waterway. Southern walleyes in Alabama grow rapidly and reach harvestable size (356 mm) by age-2. The largest walleye collected for this study w...

POPULATION STRUCTURE OF DIPODOMYS INGENS (HETEROMYIDAE): THE ROLE OF SPATIAL HETEROGENEITY IN MAINTAINING GENETIC DIVERSITY.

The giant kangaroo rat, Dipodomys ingens (Heteromyidae), is an endangered rodent that inhabits approximately 3% of its estimated historic range. Its current distribution is centered in two geographic areas, situated about 150 km apart, in south-central California. We sequenced a 293 base-pair fragment at the 5' end of the control region in 95 giant kangaroo rats from nine localities to examine the genetic structure of extant populations. We determine that mutations in this section of the control region follow a negative binominal distribution, rather than a Poisson. However, the distance between haplotypes is small enough that the difference between a tree that corrects for the non-Poisson distribution of mutations and one that does not, is minimal. This implies that the use of methods that assume a Poisson distribution of mutations, such as those based on coalescent theory, are justified. We find that the correlation between levels of genetic diversity and estimated census size is poor. This suggests that population sizes have fluctuated over time or that populations have not been isolated from one another, or both. We also examine the hierarchical structure of populations and find that the southern populations are not genetically subdivided but that there is significant subdivision between northern and southern populations and between some northern subpopulations. The phylogeographic relationship between northern and southern populations can primarily be attributed to isolation by distance, although the time since divergence between them appears to be less than the age of either. To examine the phylogeographic relationships in more detail we construct a minimum spanning tree based on Tamura-Nei gamma-corrected distances and superimpose on it the geographic position of haplotypes. This reveals that there is more genetic distance between some northern haplotypes than between any northern and southern haplotypes, despite the geographic distance separating north from south and the larger size of the southern population. It also reveals that one northern population, in the Panoche Valley, contains old allelic lineages and shares ancestral polymorphism with several other populations. It also shows that two, small, geographically remote populations contain a surprising amount of genetic diversity, but that different population/geographic processes have affected the structure of that diversity. We estimate the average migration rate among all populations to be 7.5 per generation, and conclude that a disproportionate number of migration events involve gene flow with one northern population, the Panoche Valley. We find evidence for the hypothesis that there has been an increase in population size in the remaining populations in the north and suggest that the Panoche Valley could play a role in these expansions. Finally we discuss the probabilitiy that the genetic structure of the southern populations has been affected by fluctuations in size. These results are briefly compared to other studies on the genetic structure of rodent populations.