Mitochondrial DNA Control Region Sequences Research Articles

Population genetic structure and conservation of Asian elephants (Elephas maximus) across India

This study examines the population genetic structure of Asian elephants (Elephas maximus) across India, which harbours over half the world's population of this endangered species. Mitochondrial DNA control region sequences and allele frequencies at six nuclear DNA microsatellite markers obtained from the dung of free-ranging elephants reveal low mtDNA and typical microsatellite diversity. Both known divergent clades of mtDNA haplotypes in the Asian elephant are present in India, with southern and central India exhibiting exclusively the β clade of Fernando et al. (2000), northern India exhibiting exclusively the α clade and northeastern India exhibiting both, but predominantly the α clade. A nested clade analysis revealed isolation by distance as the principal mechanism responsible for the observed haplotype distributions within the α and β clades. Analyses of molecular variance and pairwise population FST tests based on both mitochondrial and microsatellite DNA suggest that northern-northeastern India, central India, Nilgiris (in southern India) and Anamalai-Periyar (in southern India) are four demographically autonomous population units and should be managed separately. In addition, evidence for female philopatry, male-mediated gene flow and two possible historical biogeographical barriers is described.

Genetic management of the red squirrel, Sciurus vulgaris: a practical approach to regional conservation

The progressive decline in red squirrel (Sciurus vulgaris) numbers in Wales has led to conservation and reintroduction projects being established on the island of Anglesey. The recovery of the island’s remnant wild population was initially successful, however concern remained over potential loss of genetic diversity resulting from an observed demographic bottleneck. We used mitochondrial DNA (mtDNA) control region sequences and six microsatellite loci to assess current levels of genetic variation in the population. Samples were monomorphic for control region sequences and a historic specimen from the same area carrying a different haplotype demonstrated a loss of mtDNA diversity during the last 20 years. Inclusion of other Welsh haplotypes indicated phylogeographic structure in the region, in contrast to previous UK studies. Genotyping results showed allelic diversity and heterozygosity to be less than 50% of that recorded in other UK populations, with strong evidence for a recent genetic bottleneck. A parallel reintroduction programme on Anglesey included genetic analysis of individuals during the selection of captive breeding pairs. We present analysis of sequence and microsatellite data, and subsequent management decisions taken to maximise diversity in the founder and F1 generations. Population and Habitat Viability Analysis applied to both populations modelled future levels of heterozygosity and allelic diversity. Supplementation of the remnant and reintroduced populations with translocated squirrels was simulated as a potential management tool; results support use of this strategy to reduce loss of diversity and increase survival. The limitations of applying conservation genetic theory within small-scale management projects are discussed.

Mitochondrial DNA sequence data of the Cape fur seal (Arctocephalus pusillus pusillus) suggest that population numbers may be affected by climatic shifts

The Cape fur seal, Arctocephalus pusillus pusillus is distributed along the southern African coastline from northern Namibia to the south-east coast of South Africa. The species has been impacted by sealing operations since the 1600s, and historical records suggest that the taxon experienced a bottleneck prior to the 20th century. Mitochondrial DNA control region sequences were generated for 106 individuals belonging to six breeding colonies. Haplotype diversity was found to be high (0.975±0.014) whereas levels of nucleotide diversity were much lower compared to other seal species (0.011±0.006). An analysis of molecular variance indicated that the largest percentage of haplotype diversity is distributed within colonies rather than among them. This could be attributed to either extensive gene flow among colonies, a lack of substantial female site philopatry, or incomplete lineage sorting of haplotypes. Mismatch distribution and Fu’s FS test indicated that the population has experienced a historical population expansion probably between c. 37,000–18,000 YBP and this date coincides very well with the height of the last glacial maximum when food resources were abundant in the South Atlantic. These results also suggest that the recent sealing-induced bottleneck did not have a profound influence on the haplotype diversity and a historical bottleneck prior to a demographic expansion may have been severe enough to reduce nucleotide diversity substantially.

Lusitania revisited: A phylogeographic analysis of the natterjack toad Bufo calamita across its entire biogeographical range

Attempts to understand the current distributions of plants and animals require both historical and ecological information. Phylogeography has proved highly effective in elucidating historical events such as postglacial colonisations in north temperate zones. However, interesting questions still await resolution. Lusitanian distributions of fauna and flora in western Europe, for example, have puzzled biogeographers for more than 150 years. Lusitanian species have highly disjunct distributions in Ireland and in Iberia, often with few or no other populations inbetween. Despite much debate, no agreed explanation for Lusitanian distributions has yet emerged. We investigated the phylogeographic structure of one Lusitanian species, the natterjack toad Bufo calamita, using mitochondrial DNA control region sequences and allelic variation at eight microsatellite loci. Our results show that this amphibian must have survived in north European refugia, as well as in Iberia, during and since the last (Weichselian) glacial maximum around 20,000 years before present (BP). Subsequent local recolonisation after the Younger Dryas cooling around 11,000 years BP best explains the Lusitanian aspect of natterjack toad distribution.

Comparative Phylogeography between the Ermine Mustela erminea and the Least Weasel M. nivalis of Palaearctic and Nearctic Regions, Based on Analysis of Mitochondrial DNA Control Region Sequences

Phylogeography of the ermine Mustela erminea and the least weasel M. nivalis from Palaearctic and Nearctic regions were investigated based on mitochondrial DNA control region sequences. Mustela erminea exhibited a very low level of genetic variation, and geographic structures among populations were unclear. This may indicate that M. erminea recently reoccupied a wide territory in Eurasia following the last glacial retreat. In comparison with M. erminea, genetic variations within and among populations of M. nivalis were much greater. Molecular phylogenetic relationships showed that two lineages of M. nivalis occurred in the Holarctic region: one spread from the Eurasian region to North America, and the other occurred in south-eastern Europe, the Caucasus and Central Asia. The results suggest either mitochondrial DNA introgression among populations of south-eastern Europe, the Caucasus and Central Asia, or ancestral polymorphisms remaining in those populations. Contrastive phylogeographic patterns between the two mustelid species could reflect differences of their migration histories in Eurasia after the last glacial age.

EVOLUTIONARY HISTORY AND CURRENT POPULATION RELATIONSHIPS OF THE CHIRU (PANTHOLOPS HODGSONII) INFERRED FROM mtDNA VARIATION

Abstract Total population size of the chiru (Pantholops hodgsonii), a species endemic to the Tibetan plateau, has undergone a severe decline in the past several decades. This study investigates the genetic variation, evolutionary history, and current population relationships among the 3 main populations of the chiru. Samples from Xinjiang, Xizang (Tibet), and Qinghai provinces in western China were collected and mitochondrial DNA control region sequences were analyzed. Overall nucleotide diversity (π) was 2.18% and thus indicated a relatively high genetic variation. Neutrality tests suggested a significant historical population expansion (Fu's Fs = −28.152), consistent with a population decline and observed pattern of mismatch distribution. Analysis of molecular variance suggested high degrees of gene flow among all the sampled populations, of which the Xinjiang and Xizang populations were revealed to be the most genetically related. It was inferred that calving ground might play a significant role in the...

Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control

We have established a high-quality mtDNA control region sequence database for Koreans. To identify polymorphic sites and to determine their frequencies and haplotype frequencies, the complete mtDNA control region was sequenced in 593 Koreans, and major length variants of poly-cytosine tracts in HV2 and HV3 were determined in length heteroplasmic individuals by PCR analysis using fluorescence-labeled primers. Sequence comparison showed that 494 haplotypes defined by 285 variable sites were found when the major poly-cytosine tract genotypes were considered in distinguishing haplotypes, whereas 441 haplotypes were found when the poly-cytosine tracts were ignored. Statistical parameters indicated that analysis of partial mtDNA control region which encompasses the extended regions of HV1 and HV2, CA dinucleotide repeats in HV3 and nucleotide position 16497, 16519, 456, 489 and 499 (HV1ex+HV2ex+HV3CA+5SNPs) and the analysis of another partial mtDNA control region including extended regions of HV1 and HV2, HV3 region and nucleotide position 16497 and 16519 (HV1ex+HV2ex+HV3+2SNPs) can be used as efficient alternatives for the analysis of the entire mtDNA control region in Koreans. Also, we collated the basic informative SNPs, suggested the important mutation motifs for the assignment of East Asian haplogroups, and classified 592 Korean mtDNAs (99.8%) into various East Asian haplogroups or sub-haplogroups. Haplogroup-directed database comparisons confirmed the absence of any major systematic errors in our data, e.g., a mix-up of site designations, base shifts or mistypings.

Natal origin of loggerhead turtles, Caretta caretta, in the neritic habitat off the Italian coasts, Central Mediterranean

Shallow (neritic) waters close to the Italian coasts (Central Mediterranean Sea) are frequently visited by foraging loggerhead turtles, but the nesting populations which rely on this area have not been determined. To estimate the rookery origins of this feeding cohort, mitochondrial DNA control region sequences were analysed from 106 juvenile loggerhead turtles and compared to those published for key nesting populations in the Atlantic and Mediterranean regions using a Bayesian based stock analysis program. Six distinct haplotypes were detected, of which two have previously been reported from both Mediterranean and Atlantic nesting beaches and one only from Atlantic nesting populations. The remaining three haplotypes could not be assigned to a rookery of origin. Mixed stock analysis indicated that the waters along the Southern Italian coasts are utilised primarily by Mediterranean nesting populations, with approximately 68% of the individuals provided by the genetically homogeneous Greece/South eastern Mediterranean nesting aggregate and 23% by the Turkish management unit. 7% of the loggerhead turtles were assigned to Atlantic stock. Our results suggest that only a small proportion of the Atlantic juveniles which enter the Mediterranean to forage in its pelagic waters utilise also the neritic areas along the Italian coasts. This is consistent with theory of juvenile homing, according to which oceanic stage juveniles preferentially recruit to neritic developmental habitats within their natal region, and implies that the elevated human-induced mortality occurring in this area impacts almost exclusively the smaller and demographically more vulnerable Mediterranean loggerhead turtle stock.

Population genetic structure and the effect of founder events on the genetic variability of introduced sika deer, Cervus nippon, in Germany and Austria

The relationships among 214 wild-living sika deer from five locations in Germany and two in Lower Austria were examined using mitochondrial DNA (mtDNA) control region sequence. A total of 18 haplotypes are grouped consistently into two major divergent clades, A and B, which differ by a mean of 8.4% sequence divergence. Recently introduced sika deer showed a complex pattern of population structuring, which probably results from historical vicariance in at least two unknown source populations from southeastern Asia (as previously described by morphological and mtDNA findings), and subsequent population admixture as a result of human-mediated restocking. A strong genetic differentiation among populations was indicated by a global ΦST value of 0.78 reflecting mainly the differential distribution of clades A and B haplotypes. There was no association between related haplotypes and their distribution among local populations. These indicate that genealogy is a better predictor of the genetic affinity among most sika deer populations than their present-day locations. The abundant mitochondrial divergence we observed, may reflect a subspecies differentiation and could be associated with phenotypic differences among the introduced sika deer.

Mitochondrial and nuclear DNA analyses reveal fine scale geographic structure in bottlenose dolphins (Tursiops truncatus) in the Gulf of Mexico

There is a need for biological information to support current stock designations of bottlenose dolphins (Tursiops truncatus) in the Gulf of Mexico. The existence of many inshore, resident “communities” raises questions as to the relationship these dolphins may hold with dolphins inhabiting neighboring inshore and coastal areas. In this study, population subdivision was examined among four resident, inshore bottlenose dolphin stocks (Sarasota Bay, FL, Tampa Bay, FL, Charlotte Harbor, FL and Matagorda Bay, TX) and one coastal stock (1–12 km offshore) in the Gulf of Mexico. Evidence of significant population structure among all areas was found on the basis of both mitochondrial DNA (mtDNA) control region sequence data and nine nuclear microsatellite loci. Estimates of relatedness showed no population contained a significantly high number of related individuals, while separate AMOVAs for males and females indicated that both sexes exhibit a significant level of site philopatry. Results presented here provide the first genetic evidence of population subdivision between the coastal Gulf of Mexico and adjacent inshore areas along the central west coast of Florida. Such strong genetic subdivision is surprising given the short geographical distance between many of these areas and the lack of obvious geographic barriers to prevent gene flow. These findings support the current, separate identification of stocks for bottlenose dolphins inhabiting the eastern coastal and inshore areas of the Gulf of Mexico.

Worldwide structure of mtDNA diversity among Cuvier's beaked whales (Ziphius cavirostris): implications for threatened populations

We present the first description of phylogeographic structure among Cuvier's beaked whales (Ziphius cavirostris) worldwide using mitochondrial DNA (mtDNA) control region sequences obtained from strandings (n = 70), incidental fisheries takes (n = 11), biopsy (n = 1), and whale-meat markets (n = 5). Over a 290-base pair fragment, 23 variable sites defined 33 unique haplotypes among the total of 87 samples. Nucleotide diversity at the control region was relatively low (pi = 1.27%+/- 0.723%) compared to wide-ranging baleen whales, but higher than strongly matrifocal sperm, pilot and killer whales. Phylogenetic reconstruction using maximum likelihood revealed four distinct haplotype groups, each of which displayed strong frequency differences among ocean basins, but no reciprocal monophyly or fixed character differences. Consistent with this phylogeographic pattern, an analysis of molecular variance showed high levels of differentiation among ocean basins (F(ST) = 0.14, Phi ST = 0.42; P < 0.001). Estimated rates of female migration among ocean basins were low (generally < or = 2 individuals per generation). Regional sample sizes were too small to detect subdivisions within oceans except in the North Atlantic, where the Mediterranean Sea (n = 12) was highly differentiated due to the presence of two private haplotypes. One market product purchased in South Korea grouped with other haplotypes found only in the North Atlantic, suggesting a violation of current agreements banning international trade in cetacean species. Together, these results demonstrate a high degree of isolation and low maternal gene flow among oceanic, and in some cases, regional populations of Cuvier's beaked whales. This has important implications for understanding the threats of human impact, including fisheries by-catch, direct hunting, and disturbance or mortality from anthropogenic sound.

Phylogeography of colour polymorphism in the coral reef fish Pseudochromis fuscus, from Papua New Guinea and the Great Barrier Reef

Body colour has played a significant role in the evolution of coral reef fishes, but the phylogenetic level at which colour variation is expressed and the evolutionary processes driving the development and persistence of different colour patterns are often poorly understood. The aim of this study was to examine the genetic relationships between multiple colour morphs of Pseudochromis fuscus (family Pseudochromidae), both within and among geographic locations. Pseudochromis fuscus is currently described as a single species, but exhibits at least six discrete colour morphs throughout its range. In this study, P. fuscus from Papua New Guinea (PNG) and the Great Barrier Reef (GBR), Australia, formed three genetically distinct clades based on mitochondrial DNA (control region) sequence data: (1) yellow and brown morphs from the GBR and southern PNG, as well as an orange morph from southern PNG; (2) a pink morph from southern PNG; and (3) all three morphs (pink, orange and grey) found in Kimbe Bay, northern PNG. The three groups showed deep levels of divergence (d=14.6–25.4%), suggesting that P. fuscus is a complex of polychromatic species, rather than a single widespread species with many different colour morphs. Population genetic analyses indicate that the three clades have experienced unique evolutionary histories, possibly from differential effects of sea level fluctuations, barriers to gene flow and historical biogeography.

Population structure and genetic diversity in green turtles nesting at Tortuguero, Costa Rica, based on mitochondrial DNA control region sequences

The green turtle (Chelonia mydas) nesting population at Tortuguero, Costa Rica, is the largest nesting aggregation in the Atlantic, by at least an order of magnitude. Previous mitochondrial DNA (mtDNA) surveys based on limited sampling (n = 41) indicated low genetic diversity and low gene flow with other Caribbean nesting colonies. Furthermore, a survey of nuclear DNA diversity invoked the possibility of substructure within the Tortuguero rookery. To evaluate these characteristics, mtDNA control region sequences were determined for green turtles nesting at Tortuguero in 2001 (n = 157) and 2002 (n = 235). The increased sample revealed three additional haplotypes; five haplotypes are now known for Tortuguero female green turtles. Analyses of molecular variance indicated that there was no significant spatial population structure along the 30-km nesting beach. In addition, no temporal population structure was detected either between the two nesting seasons or within the nesting season. As a result of the larger sample size and additional haplotypes, estimates of genetic separation among Caribbean nesting colonies have changed and the concordance of phylogenetic and phylogeographic patterns reported in the past for green turtles in the Greater Caribbean has weakened. The five haplotypes from Tortuguero represent 36% of the haplotypes identified in green turtle nesting aggregations in the Greater Caribbean and 17% of the haplotypes known to occur in nesting or foraging aggregations in the Greater Caribbean. Haplotype diversity (0.16) and nucleotide diversity (0.0034) for the Tortuguero population are substantially lower than those for the combined rookeries in the Greater Caribbean (0.44 and 0.0078, respectively). Although comprehensive evaluation of regional genetic diversity requires nuclear DNA data, our study indicates that conserving genetic diversity in Caribbean green turtles will require careful management of the smaller rookeries in addition to the Tortuguero rookery.

Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion

Mitochondrial DNA control region sequence variation was obtained and the population history of the common hippopotamus was inferred from 109 individuals from 13 localities covering six populations in sub-Saharan Africa. In all, 100 haplotypes were defined, of which 98 were locality specific. A relatively low overall nucleotide diversity was observed (pi = 1.9%), as compared to other large mammals so far studied from the same region. Within populations, nucleotide diversity varied from 1.52% in Zambia to 1.92% in Queen Elizabeth and Masai Mara. Overall, low but significant genetic differentiation was observed in the total data set (F(ST) = 0.138; P = 0.001), and at the population level, patterns of differentiation support previously suggested hippopotamus subspecies designations (F(CT) = 0.103; P = 0.015). Evidence that the common hippopotamus recently expanded were revealed by: (i) lack of clear geographical structure among haplotypes, (ii) mismatch distributions of pairwise differences (r = 0.0053; P = 0.012) and site-frequency spectra, (iii) Fu's neutrality statistics (F(S) = -155.409; P < 0.00001) and (iv) Fu and Li's statistical tests (D* = -3.191; P < 0.01, F* = -2.668; P = 0.01). Mismatch distributions, site-frequency spectra and neutrality statistics performed at subspecies level also supported expansion of Hippopotamus amphibius across Africa. We interpret observed common hippopotamus population history in terms of Pleistocene drainage overflow and suggest recognising the three subspecies that were sampled in this study as separate management units in future conservation planning.

Evolutionary history of freshwater sculpins, genus Cottus (Teleostei; Cottidae) and related taxa, as inferred from mitochondrial DNA phylogeny

The freshwater sculpins, genus Cottus (Teleostei; Cottidae), comprise bottom-dwelling fishes that exhibit various life-history styles, having radiated throughout Northern Hemisphere freshwater habitats. The phylogenetic relationships among Cottus and related taxa were estimated from mitochondrial DNA 12S rRNA and control region (CR) sequences, the freshwater sculpins examined falling into five lineages (A–E). Lineage A consisted of Trachidermus fasciatus and C. kazika, both having a catadromous life-history. The remaining species (lineages B–E) spawn in freshwater habitats regardless of life-history (amphidromous, lacustrine or fluvial), suggesting that the various life-history types post-dated a common ancestor of lineages B–E. Molecular clock estimates suggested a Pliocene–Pleistocene radiation (or Miocene–Pliocene from the alternative clock) of lineages B–E. In eastern Eurasia, speciation with life-history changes to amphidromous or fluvial styles has apparently occurred independently in some lineages, as a general pattern. Mitochondrial DNA CR phylogeny showed the monophyletic Baikalian cottoids (Cottoidei) to be nested within Cottus and Trachidermus, suggesting that the former ecologically and morphologically divergent cottoids may have originated from a single lineage which invaded the ancient lake.

Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea

Abstract We investigated the genetic structure of blacktip shark (Carcharhinus limbatus) continental nurseries in the northwestern Atlantic Ocean, Gulf of Mexico, and Caribbean Sea using mitochondrial DNA control region sequences and eight nuclear microsatellite loci scored in neonate and young-of-the-year sharks. Significant structure was detected with both markers among nine nurseries (mitochondrial PhiST = 0.350, P < 0.001; nuclear PhiST = 0.007, P < 0.001) and sharks from the northwestern Atlantic, eastern Gulf of Mexico, western Gulf of Mexico, northern Yucatan, and Belize possessed significantly different mitochondrial DNA haplotype frequencies. Microsatellite differentiation was limited to comparisons involving northern Yucatan and Belize sharks with nuclear genetic homogeneity throughout the eastern Gulf of Mexico, western Gulf of Mexico, and northwestern Atlantic. Differences in the magnitude of maternal vs. biparental genetic differentiation support female philopatry to northwestern Atlantic, Gulf of Mexico, and Caribbean Sea natal nursery regions with higher levels of male-mediated gene flow. Philopatry has produced multiple reproductive stocks of this commercially important shark species throughout the range of this study.

Genetic differentiation and hybridization between greater and lesser spotted eagles (Accipitriformes:Aquila clanga, A. pomarina)

Greater and lesser spotted eagles (Aquila clanga, A. pomarina) are two closely related forest eagles overlapping in breeding range in east-central Europe. In recent years a number of mixed pairs have been observed, some of which fledged hybrid young. Here we use mitochondrial (control region) DNA sequences and AFLP markers to estimate genetic differentiation and possible gene flow between these species. In a sample of 83 individuals (61 pomarina, 20 clanga, 2 F1-hybrids) we found 30 mitochondrial haplotypes which, in a phylogenetic network, formed two distinct clusters differing on average by 3.0% sequence divergence. The two species were significantly differentiated both at the mitochondrial and nuclear (AFLP) genetic level. However, five individuals with pomarina phenotype possessed clanga-type mtDNA, suggesting occasional gene flow. Surprisingly, AFLP markers indicated that these “mismatched” birds (originating from Germany, E Poland and Latvia) were genetically intermediate between the samples of individuals in which mtDNA haplotype and phenotype agreed. This indicates that mismatched birds were either F1 or recent back-cross hybrids. Mitochondrial introgression was asymmetrical (no pomarina haplotype found in clanga so far), which may be due to assortative mating by size. Gene flow of nuclear markers was estimated to be about ten times stronger than for mtDNA, indicating a sex-bias in hybrid fertility in accordance with Haldane’s rule. Hybridization between the two species may be more frequent and may occur much further west than hitherto assumed. This is supported by the recent discovery of a mixed pair producing at least one fledgling in NE Germany.

Genetic structure, introgression, and a narrow hybrid zone between northern and California spotted owls (Strix occidentalis)

The northern spotted owl (Strix occidentalis caurina) is a threatened subspecies and the California spotted owl (Strix occidentalis occidentalis) is a subspecies of special concern in the western United States. Concern for their continued viability has arisen because of habitat loss caused by timber harvesting. The taxonomic status of the northern subspecies has been the subject of continuing controversy. We investigated the phylogeographical and population genetic structure of northern and California spotted owls with special reference to their region of contact. Mitochondrial DNA (mtDNA) control region sequences confirmed the existence of two well-differentiated lineages connected by a narrow hybrid zone in a region of low population density in north central California. Maximum-likelihood estimates indicated bidirectional gene flow between the lineages but limited introgression outside the region of contact. The lengths of both the mtDNA hybrid zone and the reduced density patch were similar and slightly exceeded estimates of natal dispersal distances. This suggests that the two subspecies were in secondary contact in a hybrid zone trapped by a population density trough. Consequently, the zone of interaction is expected to be geographically stable. We discovered a third, rare clade of haplotypes, which we interpreted to be a result of incomplete lineage sorting; those haplotypes result in a paraphyletic northern spotted owl with respect to the California spotted owl. A congeneric species, the barred owl (Strix varia), occasionally hybridizes with spotted owls; our results indicated an upper bound for the frequency of barred owl mtDNA haplotypes in northern spotted owl populations of 3%.

Is Homoplasy or Lineage Sorting the Source of Incongruent mtDNA and Nuclear Gene Trees in the Stiff-Tailed Ducks (Nomonyx-Oxyura)?

We evaluated the potential effects of homoplasy, ancestral polymorphism, and hybridization as obstacles to resolving phylogenetic relationships within Nomonyx-Oxyura stiff-tailed ducks (Oxyurinae; subtribe Oxyurina). Mitochondrial DNA (mtDNA) control region sequences from 94 individuals supported monophyly of mtDNA haplotypes for each of the six species and provided no evidence of extant incomplete lineage sorting or inter-specific hybridization. The ruddy ducks (O. j. jamaicensis,O. j. andina, O. j. ferruginea) are each others' closest relatives, but the lack of shared haplotypes between O. j. jamaicensis and O. j. ferruginea suggests long-standing historical isolation. In contrast, O. j. andina shares haplotypes with O. j. jamaicensis and O. j. ferruginea, which supports Todd's (1979) and Fjeldså's (1986) hypothesis that O. j. andina is an intergrade or hybrid subspecies of O. j. jamaicensis and O. j. ferruginea. Control region data and a much larger data set composed of approximately 8800 base pairs of mitochondrial and nuclear sequence for each species indicate that the two New World species, O. vittata and O. jamaicensis, branch basally within Oxyura. A clade of three Old World species (O. australis, O. maccoa, O. leucocephala) is well supported, but different loci and also different characters within the mtDNA data support three different resolutions of the Old World clade, yielding an essentially unresolved trichotomy. Fundamentally different factors limited the resolution of the mtDNA and nuclear gene trees. Gene trees for most nuclear loci were unresolved due to slow rates of mutation and a lack of informative variation, whereas uncertain resolution of the mtDNA gene tree was due to homoplasy. Within the mtDNA, approximately equal numbers of characters supported each of three possible resolutions. Parametric and nonparametric bootstrap analyses suggest that resolution of the mtDNA tree based on ~4300 bp per taxon is uncertain but that complete mtDNA sequences would yield a fully resolved gene tree. A short internode separating O. leucocephala from (O. australis, O. maccoa) in the best mtDNA tree combined with long terminal branches and substantial rate variation among nucleotide sites allowed the small number of changes occurring on the internode to be obscured by homoplasy in a significant portion of simulated data sets. Although most nuclear loci were uninformative, two loci supported a resolution of the Old World clade (O. maccoa, O. leucocephala) that is incongruent with the best mtDNA tree. Thus, incongruence between nuclear and mtDNA trees may be due to random sorting of ancestral lineages during the short internode, homoplasy in the mtDNA data, or both. The Oxyura trichotomy represents a difficult though likely common problem in molecular systematics. Given a short internode, the mtDNA tree has a greater chance of being congruent with the history of speciation because its effective population size (N(e)) is one-quarter that of any nuclear locus, but its resolution is more likely to be obscured by homoplasy. In contrast, gene trees for more slowly evolving nuclear loci will be difficult to resolve due to a lack of substitutions during the internode, and when resolved are more likely to be incongruent with the species history due to the stochastic effects of lineage sorting. We suggest that researchers consider first whether independent gene trees are adequately resolved and then whether those trees are congruent with the species history. In the case of Oxyura, the answer to both questions may be no. Complete mtDNA sequences combined with data from a very large number of nuclear loci may be the only way to resolve such trichotomies.

Parentage determination of an isolated Yangtze finless porpoise population Neophocaena phocaenoides asiaeorientalis in the Yangtze Tian-e-Zhou Baiji National Natural Reserve based on molecular data

Reproductive behaviors are poorly known for the Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis. In this study, the parentage of an isolated Yangtze finless porpoise population inhabiting the Yangtze Tian-e-Zhou Baiji National Natural Reserve is determined by analysis of microsatellite loci and mitochondrial DNA (mtDNA) control region sequences, and the porpoise's reproductive behaviors are studied. Overall 4 full parentage assignments and additional 3 single parentage assignments were determined for the population of 23 individuals. The analysis shows that their estimated reproductive cycle is shorter than that reported previously and there probably exists an overlapping between gestation and lactation period. The Study also shows that the female does not show fidelity to a particular male for breeding and vice versa, the oldest males did not monopolize mating and the dominance rank could not be so strict for the porpoise society. Moreover, the porpoise's mating pattern and relatedness among candidate parents are discussed here. These results provide important information for making guidelines of management and conservation for this protected population.