Southern Haplotypes Research Articles

Evidence for selection and spatially distinct patterns found in a putative zona pellucida gene in Pacific cod, and implications for management.

Genetic differentiation has been observed in marine species even when no obvious barriers to gene flow exist, and understanding such differentiation is essential for effective fisheries management. Highly differentiated outlier loci can provide information on how genetic variation might not only contribute to local adaptation but may also be affected by historical demographic events. A locus which aligned to a predicted zona pellucida sperm‐binding protein 3 gene (ZP3) in Atlantic cod (Gadus morhua) was previously identified as the highest outlier based on F ST in a RADseq study of Pacific cod (Gadus macrocephalus) across the West Coast of North America. However, because of the limited length of the RAD sequence and restricted geographic area of sampling, no conclusion on the functional significance of the observed variation was possible. In other marine species, ZP3 is involved in reproductive isolation, local adaptation, and has neofunctionalized as an antifreeze gene, and so it may provide important insights in functional population structure of Pacific cod. Here, we sequenced a 544‐bp region of ZP3 in 230 Pacific cod collected from throughout their geographic range. We observed striking patterns of spatial structuring of ZP3 haplotypes, with a sharp break near Kodiak, Alaska, USA where populations within ~200 km of each other are nearly fixed for different haplotypes, contrasting a pattern of isolation by distance at other genetic markers in this region (F ST = 0.003). Phylogenetic analysis of ZP3 haplotypes revealed that the more southern haplotypes appear to be ancestral, with the northern haplotype evolving more recently, potentially in response to a novel selective pressure as Pacific cod recolonized northern latitudes after glaciation. The sharp break in haplotype frequencies suggests strong selective pressures are operating on small spatial scales and illustrates that selection can create high divergence even in marine species with ample opportunities for gene flow.

Contact zone of two different chloroplast lineages and genetic guidelines for seed transfer in Quercus serrata and Quercus crispula

AbstractWithin their natural distribution ranges, plant species exhibit a genetic structure that has been created by global climate change and natural selection over long periods. This genetic structure needs to be conserved for sustainable use of genetic resources. To conserve local forests with different genetic structures, genetic guidelines for seed and seedling transfer in individual species are necessary. Genetic guidelines have been published for 43 Japanese tree species using population genetic data; however, for practical use, more detailed genetic borders between important genetic lineages should be clarified to inform seed collection and planting. Thus, we investigated in detail the genetic borders between two important Japanese oak species, Quercus serrata and Quercus crispula, in the Chubu region of Japan using chloroplast and nuclear DNA markers, and we discuss the factors that influenced border creation using the results of species distribution modeling (SDM). The chloroplast DNA (cpDNA) haplotype was clearly different within the Chubu region of Japan but the difference in nuclear DNA between northern and southern haplotype populations was very small, both in Q. serrata and Q. crispula. The results of SDM showed that during the last glacial maximum (LGM) Q. serrata was distributed mostly along the coastline but Q. crispula was distributed not only along the coast but also in mountainous areas further inland. The cpDNA genetic borders of these two oak species are complex and seem to have been influenced by topography and their distribution during the LGM. We propose and discuss genetic guidelines for these two oak species based on the results of this study.

Phylogeography of split kelp Hedophyllum nigripes: northern ice-age refugia and trans-Arctic dispersal

Pleistocene climate cycles greatly influenced the distributions of kelps in northern seas and gated trans-Arctic dispersals between the North (N) Pacific and N Atlantic oceans. Here, we used partial sequences of the mitochondrial DNA cytochrome oxidase I-5′ (COI) and plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit-3′ (rbcL) to resolve the phylogeography of the kelp Hedophyllum nigripes in the Gulf of Alaska and globally. In the Gulf of Alaska, genetic diversity was moderate (COI: h = 0.493 ± 0.076, n = 57; rbcL: h = 0.578 ± 0.00047, n = 54), but nucleotide diversity was small (COI: θπ = 0.00114 ± 0.00100, n = 57; rbcL: θπ = 0.0001 ± 0.00089, n = 54). Concatenated sequences showed strong haplotype-frequency differences among populations (ΦST = 0.728). The addition of previously published COI sequences from British Columbia showed a general absence of southern haplotypes in the Gulf of Alaska, supporting the conclusion of northern ice-age refugia. COI sequences in Canadian Arctic-Northwestern (NW) Atlantic populations differed by 1–2 mutation from Northeastern (NE) Pacific sequences, and unexpectedly, were marginally more closely related to populations in British Columbia than to geographically intermediate populations in the Gulf of Alaska. COI haplotypes from the Svalbard Archipelago in the NE Atlantic showed no variability and differed by 1–2 mutations from haplotypes in the NW Atlantic. Time-calibrated genetic divergences indicated trans-Arctic dispersal(s) from the N Pacific into the N Atlantic in the mid-Pleistocene.

First molecular identification of Euphlyctis ehrenbergii (Anura: Amphibia) inhabiting southwestern Saudi Arabia

The dicroglossid Euphlyctis ehrenbergii inhabiting southwestern Saudi Arabia has been identified morphologically and molecularly in this study. The morphometric measurements and their indices indicate that females are slightly bigger than males in some characters. Approximately 550 nucleotides of 16S rDNA gene were compared to the Yemeni haplotype available in the GenBank database. The phylogenetic inference revealed a strong sister relationship between the two haplotypes [bootstrap = 100% for maximum parsimony (MP), neighbor joining (NJ) and maximum likelihood (ML)]. The intra-specific genetic distance (D = 0.9%) was lower than the observed variation between southern and northern haplotypes of E. cyanophlyctis (D = 4.6%) currently ascribed to distinct lineages. Nonetheless, results suggest great intra-specific variation within E. ehrenbergii, deserving further investigation. The genetic distance between Yemeni and Saudi haplotypes of E. ehrenbergii (D = 0.9%) resembles intra-specific distances between haplotypes of E. cyanophlyctis ascribed to the same cryptic lineages (e.g. as observed within the lineages including haplotypes from southern India and Sri Lanka). More samples and molecular data from both haplotypes are needed to better clarify their phylogenetic relationships. This study adds a clue for forensic herpetology by highlighting the efficiency of 16S rDNA gene in animal barcoding.

Phylogeography of the freshwater red alga Batrachospermum viride‐brasiliense (Rhodophyta, Batrachospermales)

SUMMARYPhylogeography of B atrachospermum viride‐brasiliense was investigated using two mitochondrial regions: the cox2‐3 spacer and the barcode region of cox1 gene. Eighty‐seven individuals were analyzed from nine stream segments throughout its distribution in Brazil. Ten cox2‐3 spacer and nine cox1 haplotypes were observed among the individuals studied (87 vs. 43, respectively). Divergences among haplotypes were relatively low (≤2.4% for cox2‐3 and ≤1.8% for cox1). Most locations have a single haplotype, whereas only two locations had two haplotypes for both markers. The haplotype network for cox2‐3 showed a phylogeographic trend from the south towards the southeast with haplotypes from the southeast more closely related. For cox1 a trend from the southeast spreading towards the south and north was revealed, with the southern haplotypes more closely associated. Results clearly indicated that B . viride‐brasiliense represents a single species and the phylogeographic pattern consisted of a closely connected group of haplotypes from southern and southeastern Brazil. Levels of intra‐ and inter‐population variation were similar for the two markers with slightly higher values for cox2‐3. The trend observed in this study is similar to that in other members of Batrachospermales with little variation within a stream segment (one or two haplotypes) and more distant haplotypes showing higher divergences. This pattern could be attributed to the fact that colonization of a site might be rare by a single event with subsequent proliferation of the population. The geographic distribution of B . viride‐brasiliense was interpreted according to the biogeographic models proposed for South America being limited to three morpho‐climatic domains or biogeographic provinces: tropical Atlantic rainforest, sub‐tropical rainforest and cerrado (Brazilian savannah).

Pre-Holocene Origin for the Coronopus navasii Disjunction: Conservation Implications from Its Long Isolation.

Integration of unexpected discoveries about charismatic species can disrupt their well-established recovery plans, particularly when this requires coordinate actions among the different governments responsible. The Critically Endangered Coronopus navasii (Brassicaceae) was considered a restricted endemism to a few Mediterranean temporary ponds in a high mountain range of Southeast Spain, until a new group of populations were discovered 500 km North in 2006. Ten years after this finding, its management has not been accommodated due to limited information of the new populations and administrative inertia. In this study, DNA sequences and species distribution models are used to analyse the origin of the C. navasii disjunction as a preliminary step to reassess its recovery plan. Molecular results placed the disjunction during Miocene-Pleistocene (6.30–0.49 Mya, plastid DNA; 1.45–0.03 Mya, ribosomal DNA), which discards a putative human-mediated origin. In fact, the haplotype network and the low gene flow estimated between disjunct areas suggest long-term isolation. Dispersal is the most likely explanation for the disjunction as interpreted from the highly fragmented distribution projected to the past. Particularly, a northward dispersal from Southeast is proposed since C. navasii haplotype network is connected to the sister-group through the southern haplotype. Although the reassessment of C. navasii conservation status is more optimistic under the new extent of occurrence, its long-term survival may be compromised due to the: (1) natural fragmentation and rarity of the species habitat, (2) genetic isolation between the two disjunct areas, and (3) northward shift of suitable areas under future climate change scenarios. Several ex-situ and in-situ conservation measures are proposed for integrating Central East Spanish populations into the on-going recovery plan, which still only contemplates Southeast populations and therefore does not preserve the genetic structure and diversity of the species.

Indochinese‐Sundaic faunal transition and phylogeographical divides north of the Isthmus of Kra in Southeast Asian Bulbuls (Aves: Pycnonotidae)

AbstractAimFor terrestrial organisms, a faunal transition zone between the Indochinese and Sundaic regions is delimited north of the Isthmus of Kra on the Thai‐Malay Peninsula. We used a mitochondrial marker to test the predicted location of intraspecific north–south divides for four species of bulbuls (Pycnonotus). Phylogenetic relationships among Thai‐Malay populations and their closest relatives from the Greater Sundas were reconstructed from a multilocus data set including 35 Pycnonotus species.LocationIndochina, Thai‐Malay Peninsula, Greater Sundas.MethodsWe sampled target species along a north–south transect spanning the Isthmus of Kra and reconstructed phylogeographical patterns based on ND2 haplotype networks. Phylogenies were reconstructed using Maximum likelihood and Bayesian inference. Divergence time estimates were inferred from single‐locus and multilocus data using *beast.ResultsWe found mitochondrial north–south divides in all target species. Haplotypes of southern genetic clusters were distributed all across the Thai‐Malay Peninsula and north into Central Thailand. Local overlap of genetic lineages was confirmed at one location in one species only. In three of the focal species, the southern limits of southern haplotype clusters were restricted to the Thai‐Malay Peninsula and did not extend into the Greater Sundas. Peninsular north–south divides were dated to the late Pleistocene, whereas Indochinese‐Sundaic lineage divergence was dated to the late Pliocene.Main conclusionsPopulation boundaries did not coincide with the Isthmus of Kra, but instead were located north of the Thai‐Malay Peninsula in Central Thailand. Only one of four divides represented an Indochinese‐Sundaic transition. Different phylogeographical patterns among target species were presumably shaped by different ecological preferences in Pleistocene palaeohabitats. Pliocene Indochinese‐Sundaic lineage divergence in bulbuls coincides with strong vegetational changes on the Peninsula that shaped two phytogeographical transitions. Distribution limits of bird species roughly coincide with these transition zones and therefore the avifaunal Thai‐Malay transition represents a broad zone rather than a sharp boundary.

Lack of adult novel northern lineages of invasive green crab Carcinus maenas along much of the northern US Atlantic coast.

Introduced over 200 yr ago to the east coast of North America, Carcinus maenas now ranges from New York to Newfoundland. In the 1980s, a secondary invasion of European lineages, termed northern haplotypes, occurred in Nova Scotia. Young-of-the-year sampled in 2007 revealed that northern haplotypes were present in low frequencies at several northwestern Atlantic sites as far south as New York; a model predicted an increase in their range and frequency over time. We collected samples in 2013 and 2014 to determine the haplotypes of adult crabs from New York to Nova Scotia. Six haplotypes, encompassing previously identified northern and southern haplotypes, 1 novel southern haplotype, and 1 Scandinavian haplotype, were identified in 275 crabs sampled at 11 sites. Northern haplotypes were only found in Nova Scotia, Beals Island (Maine), and Mount Desert Island (Maine) at a frequency of 60, 8, and 24%, respectively; remaining sites were predominantly composed of a previously identified southern haplotype. Northern haplotypes are limited in adult crabs to Mount Desert Island and north, indicating that the southern haplotype is selectively favored at some point during their life history, recruitment of northern larvae is limited south of Mount Desert Island, or entire year-classes post-2007 were lost. Our results do not support the predictions of an increase in the range and frequency of northern haplotypes, at least among adults, and indicate that a more complete knowledge of factors affecting C. maenas life stages is necessary to understand the current distribution of haplotypes.

Phylogeography of the common toad (Bufo bufo, Lissamphibia: Anura) in Switzerland

WhileBufo bufois widespread in Europe, the closely relatedB. spinosusis parapatrically distributed in Western Europe and Northern Africa. The exact course of the contact zone between both taxa, however, is still unknown. 24 samples from Switzerland were analysed using mitochondrial and nuclear markers combined with 243 previously published samples from Europe and Asia. No haplotypes ofB. spinosuswere detected in Switzerland, only two mitochondrial haplotypes ofB. bufo: one north and south of the Alps, the other only north of the Alps. Both haplotypes are also widely distributed in Eastern and Central Europe. These results agree with a postglacial recolonisation of Central Europe from refugia on the Balkan Peninsula. The occurrence of one haplotype north and south of the Alps can be explained by colonisation either from the north by crossing the Alps or from the east along the southern edge of the Alps. The rapid postglacial recolonisation from Balkan refugia might have prevented the spread of southern haplotypes from Italy and ofB. spinosusfrom France.

Multiple origins of Locusta migratoria (Orthoptera: Acrididae) in the Japanese Archipelago and the presence of two major clades in the world: evidence from a molecular approach

Phylogenetic relationships among migratory locust (Locusta migratoria) populations in different climatic regions were analysed by sequencing four mitochondrial DNA regions, with special reference to the origin of Japanese populations. The populations are clearly separated into two clades: one consists of individuals from temperate and cold-temperate areas of Japan and the Chinese continent, and the other comprises those from subtropical islands of Japan, Hainan Island in China, Timol Leste, Australia, Ethiopia, France, and some individuals from Tsushima Island and Honshu of Japan. The divergence time between the two clades is estimated to be 0.86–1.89 Mya. The phylogenetic analysis revealed that Japanese L. migratoria populations were composed of individuals of six different origins: (1) Hokkaido populations possibly from the Russian continent; (2) Honshu–Kyushu populations from the Chinese continent; (3) Southwest Island populations from Hainan Island or adjacent areas; (4) Ogasawara populations that might have originated from Micronesia; (5) part of the Tsushima population that originated from somewhere in the Asian tropics; and (6) a possible relict population of ancient southern haplotypes that exists in western areas of northern Honshu. The Tsugaru Straits and Tokara Straits have acted as effective geographical barriers, as in other organisms, isolating locust populations for a few thousand years.

Finding the meeting zone: Where have the northern and southern ranges of Norway spruce overlapped?

The goal of the work was to define where migration routes of Norway spruce running from its Weichselian refuges could have intersected and formed a hybrid zone. Based on available pollen data, we have hypothesized that the central European disjunction, also called the “spruceless zone”, could be an overlapping area of boreal and southern ranges. The refugial origin of 1353 trees from 58 Norway spruce stands was determined using the maternally inherited mitochondrial nad1 b/c marker. Polymerase chain reaction-restriction fragment length polymorphism analysis of the nad1 b/c marker revealed the presence of two mtDNA variants in Poland that we designated as the “northern” and “southern” haplotypes. The geographic distribution of these haplotypes corresponds to particular Norway spruce ranges and their refugial origins. The northern haplotype was mainly found within the boreal part of the range while the southern haplotype was noted in populations from the southern portion. Co-occurrence of the two haplotypes was noted in stands from the “spruceless zone”; however, the frequency of the southern haplotype was significantly higher in those populations. Our results combined with available fossil pollen data allow us to define the area of the Middle-Polish Plains as a hybrid zone for Norway spruce originating from Carpathian and Russian refuges. The domination of Norway spruce of Carpathian origin in the hybrid zone might be attributable to its earlier expansion from this refuge in contrast to the timing of its expansion from the Russian refuge. The findings presented here together with historical sources may also help explain the modern sparse distribution of Norway spruce in the Middle-Polish Plains.

Prevalence of genetic thrombophilic polymorphisms in the Sri Lankan population — implications for association study design and clinical genetic testing services

We investigated the prevalence of genotypes/alleles of single nucleotide polymorphisms (SNP) and haplotypes defined by them in three genes in which variations are associated with venous thromboembolism in 80 Sinhalese, 80 Sri Lankan Tamils and 80 Moors in the Sri Lankan population and compared the SNP data with that of other populations in Southern India and haplotype data with that of HapMap populations. The genes and polymorphisms investigated were Methylenetetrahydrofolate reductase (MTHFR) — 677C>T (rs1801133), 1298A>C (rs1801131), 1317T>C, 1793G>A (rs2274976); Factor V (F5) — 1691G>A (rs6025) and 4070A>G (rs1800595); and prothrombin (F2) — 20210G>A (rs1799963). The polymorphisms were genotyped using PCR/RFLP methods. The prevalence of the variant alleles of each polymorphism in the Sinhalese, Tamils, and Moors was MTHFR 677T: Sinhalese — 13%, Tamils — 9%, Moors — 9%. 1317T>C: Sinhalese — 0%; Tamils — 0%; Moors — 0%. 1793A: Sinhalese — 19%, Tamils — 19%, Moors — 19%. F5 1691A: Sinhalese — 2%, Tamils — 3%, Moors — 2%. 4070G: Sinhalese — 6%, Tamils — 5%, Moors — 8%. F2 20210A: Sinhalese — 0%, Tamils — 0%, Moors — 0%. The frequencies observed were similar to data from other South Indian populations; the haplotype data showed haplotypes unique to the Sri Lankan population when compared to HapMap populations. rs9651118 was identified as a SNP that splits the haplotypes harbouring the functionally significant 677T allele in the MTHFR gene. This data would be useful in planning genetic association studies in the Sri Lankan population and in deciding on which genetic variants should be tested in a clinical genetic testing service.

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.

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.

Population genetic subdivision in the New Zealand greenshell mussel (Perna canaliculus) inferred from single-strand conformation polymorphism analysis of mitochondrial DNA.

Single-strand conformation polymorphism (SSCP) analysis of the NADH IV region of the mitochondrial DNA (mtDNA) molecule in greenshell mussels (Perna canaliculus) indicated strong population genetic structuring in this endemic New Zealand species. A northern and a southern group were differentiated by frequency shifts in common haplotypes and by the occurrence of a unique southern haplotype at approximately 20% frequency. This split occurred south of Cook Strait (the body of water between the North and the South Island) at approximately 42 degrees S latitude. Northern populations were less genetically diverse than southern populations and mussels from the west coast of the South Island were most distinct from northern mussels. We hypothesize that the unique haplotype VIII originated in the lower South Island, and that its spread northwards was obstructed by the opening of Cook Strait approximately 15 000-16 000 years ago and the subsequent establishment of present-day surface water circulation patterns in Greater Cook Strait. We suggest that present-day strong tidal flows and turbulent mixing of water masses in Cook Strait, and intense up-welling on the east and west coasts in this region, represent a barrier to gene flow between mussels located in the North Island and northern South Island vs. mussels in most of the South Island and Stewart Island.

Y-chromosome haplotype distribution in Han Chinese populations and modern human origin in East Asians

We investigated the distribution of Y-chromosome haplotype using 19 Y-SNPs in Han Chinese populations from 22 provinces of China. Our data indicate distinctive patterns of Y chromosome between southern and northern Han Chinese populations. The southern populations are much more polymorphic than northern populations. The latter has only a subset of the southern haplotypes. This result confirms the genetic difference observed between southern and northern ethnic populations in East Asia. It supports the hypothesis that the first settlement of modern humans of African origin occurred in the southern part of East Asia during the last Ice Age, and a northward migration led to the peopling of northern China.

Y-Chromosome Evidence for a Northward Migration of Modern Humans into Eastern Asia during the Last Ice Age

The timing and nature of the arrival and the subsequent expansion of modern humans into eastern Asia remains controversial. Using Y-chromosome biallelic markers, we investigated the ancient human-migration patterns in eastern Asia. Our data indicate that southern populations in eastern Asia are much more polymorphic than northern populations, which have only a subset of the southern haplotypes. This pattern indicates that the first settlement of modern humans in eastern Asia occurred in mainland Southeast Asia during the last Ice Age, coinciding with the absence of human fossils in eastern Asia, 50,000-100,000 years ago. After the initial peopling, a great northward migration extended into northern China and Siberia.

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.

The Genetic Diversity of Native, Stocked, and Hybrid Populations of Brook Trout in the Southern Appalachians

Using mitochondrial DNA (mtDNA) restriction analysis and starch‐gel electrophoresis of the CK‐A2 locus product, we examined genetic variation in 311 brook trout (Salvelinus fontinalis) from 11 native, 5 hatchery‐derived, and 8 hybrid populations in the southern Appalachian Mountains. Native southern Appalachian fish were genetically distinct from hatchery‐derived fish. Southern and hatchery‐derived fish were reliably distinguished based on three mtDNA restriction sites. Native southern haplotypes differed from hatchery‐derived haplotypes by an average of 0.84%. Northern hatchery‐derived haplotypes varied little in mtDNA compared to native southern haplotypes. Introgression of mtDNA haplotypes and the CK‐A2 locus varied among populations, and introgression of allozyme and mtDNA markers was positively correlated. Continued introductions of nonnative strains of brook trout in the southern Appalachians could simplify the genetic structure of native brook trout populations and eliminate unique genotypes.