Multilocus assignment analyses reveal multiple units and rare migration events in the recently expanded yellow-eyed penguin (Megadyptes antipodes)

The identification of demographically independent populations and the recognition of management units have been greatly facilitated by the continuing advances in genetic tools. Managements units now play a key role in short-term conservation management programmes of declining species, but their importance in expanding populations receives comparatively little attention. The endangered yellow-eyed penguin ( Megadyptes antipodes ) expanded its range from the subantarctic to New Zealand's South Island a few hundred years ago and this new population now represents almost half of the species' total census size. This dramatic expansion attests to M. antipodes' high dispersal abilities and suggests the species is likely to constitute a single demographic population. Here we test this hypothesis of panmixia by investigating genetic differentiation and levels of gene flow among penguin breeding areas using 12 autosomal microsatellite loci along with mitochondrial control region sequence analyses for 350 individuals. Contrary to our hypothesis, however, the analyses reveal two genetically and geographically distinct assemblages: South Island vs. subantarctic populations. Using assignment tests, we recognize just two first-generation migrants between these populations (corresponding to a migration rate of < 2%), indicating that ongoing levels of long-distance migration are low. Furthermore, the South Island population has low genetic variability compared to the subantarctic population. These results suggest that the South Island population was founded by only a small number of individuals, and that subsequent levels of gene flow have remained low. The demographic independence of the two populations warrants their designation as distinct management units and conservation efforts should be adjusted accordingly to protect both populations.     

基于基因组SNPs的南极恩克斯堡岛阿德利企鹅繁殖种群的遗传结构

我国提议在南极恩克斯堡岛新站址北侧3 km的阿德利企鹅(Pygoscelis adeliae)聚集繁殖地建立南极特别保护区, 对保护区边界的划分, 各国尚存争议, 尤其是对南湾(South Bay)的繁殖小种群是否具有遗传独特性, 是否应将其纳入保护区是重点关注的问题。本研究采集了恩克斯堡岛海景湾(Seaview Bay)和南湾的阿德利企鹅样品, 通过全基因组重测序和种群基因组学方法, 分析了恩克斯堡岛不同区域的种群遗传结构。发现恩克斯堡岛海景湾与南湾阿德利企鹅没有显著的遗传分化, 南湾阿德利企鹅不是独特的小种群; 海景湾高海拔区域个体与低海拔区域个体之间也没有显著的遗传差异, 推测该区域阿德利企鹅繁殖群体的分布格局与冰川堆积形成的阶地不具有显著相关性。本工作为恩克斯堡岛保护区和罗斯海新站建设提供了重要科技支撑。     

企鹅珍珠贝不同地理群体遗传多样性的fAFLP 分析

为阐明企鹅珍珠贝(Pteria penguin)不同地理种群的遗传多样性机制, 采用荧光标记扩增片段长度多态性(fAFLP)技术分析了企鹅珍珠贝广西涠洲岛、广东流沙湾和海南黎安3 个不同地理群体的遗传多样性。选取7 对引物组合对90 个个体(每个群体30 个)进行fAFLP 扩增, 结果发现每个个体均能扩增出清晰的、可重复的扩增条带, 每对引物的扩增位点数在100—163 之间, 共得到895 个扩增位点, 多态位点数为865 个; 涠洲岛、流沙湾和黎安群体的多态位点比例分别为70.73%、63.13%、66.82%。Nei 遗传多样性指数为0.1634、0.1558、0.1783, Shannon 遗传多样性指数为0.2635、0.2474、0.2932。3 个群体间遗传相似度在0.9722—0.9824之间, 遗传距离在0.0177—0.0282 之间。根据遗传距离绘制UPGMA 聚类图, 但Mantel 检验结果显示企鹅珍珠贝三群体间的遗传距离与地理距离之间无显著相关。Shannon 遗传多样性指数和AMOVA 分析, 结果均显示企鹅珍珠贝的遗传变异主要来源于群体内个体间, 7.91%的遗传变异来自群体间, 92.09%的遗传变异来自群体内。分析群体的显性基因型频率分布和基因流Nm 发现3 个群体有基本相同的遗传结构, 有明显的基因交流。研究结果表明北海涠洲岛群体、湛江流沙湾群体和海南黎安群体的企鹅珍珠贝种质有较高的多态位点比例, 但未发生显著地理分化。这一结果为我国企鹅珍珠贝的良种选育以及种质资源保护措施的制定提供了参考依据。       

Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis

Australian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.

     

Genetic diversity and population parameters of sea otters, Enhydra lutris, before fur trade extirpation from 1741-1911

All existing sea otter, Enhydra lutris, populations have suffered at least one historic population bottleneck stemming from the fur trade extirpations of the eighteenth and nineteenth centuries. We examined genetic variation, gene flow, and population structure at five microsatellite loci in samples from five pre-fur trade populations throughout the sea otter's historical range: California, Oregon, Washington, Alaska, and Russia. We then compared those values to genetic diversity and population structure found within five modern sea otter populations throughout their current range: California, Prince William Sound, Amchitka Island, Southeast Alaska and Washington. We found twice the genetic diversity in the pre-fur trade populations when compared to modern sea otters, a level of diversity that was similar to levels that are found in other mammal populations that have not experienced population bottlenecks. Even with the significant loss in genetic diversity modern sea otters have retained historical structure. There was greater gene flow before extirpation than that found among modern sea otter populations but the difference was not statistically significant. The most dramatic effect of pre fur trade population extirpation was the loss of genetic diversity. For long term conservation of these populations increasing gene flow and the maintenance of remnant genetic diversity should be encouraged.     

Slow motion extinction: inbreeding,introgression, and loss in the critically endangered mangrove finch (<Emphasis Type="Italic">Camarhynchus heliobates</Emphasis>)

The critically endangered mangrove finch is now limited to one small population on the west coast of Isabela Island in the Galápagos, but 100 years ago multiple populations were found on the islands of Isabela and Fernandina. By accessing genetic datasets through museum sampling, we are able to put current levels of genetic diversity and hybridization with congenerics into a historical context for enhanced conservation. In this study, we compared neutral genetic diversity of the now extinct Fernandina population to historical and current diversity of the Isabela population using 14 microsatellite markers. We found that current genetic diversity of the last remnant population (~80–100 individuals) is far below levels 100 years ago, with only about half of the allelic diversity retained. Current genetic diversity is close to levels in the Fernandina population that went extinct by the 1970s. Bottleneck analysis did not show a strong signature of recent decline, and instead implies that this species may have consistently had low population sizes with wide fluctuations. Hybridization with congeneric woodpecker finches was found in the modern Isabela population, implying that some individuals within the few remaining breeding pairs are finding mates with woodpecker finches. Within the context of historical low population sizes and wide fluctuations, current conservation efforts may help the mangrove finch face current extinction threats and avoid the fate of the Fernandina population. However, this historically small lineage will likely continue to face challenges associated with small specialist species surrounded by a widely-distributed sister lineage producing viable hybrids.     

The influence of landscape,climate and history on spatial genetic patterns in keystone plants (Azorella) on sub‐Antarctic islands

The distribution of genetic variation in species is governed by factors that act differently across spatial scales. To tease apart the contribution of different processes, especially at intermediate spatial scales, it is useful to study simple ecosystems such as those on sub‐Antarctic oceanic islands. In this study, we characterize spatial genetic patterns of two keystone plant species, Azorella selago on sub‐Antarctic Marion Island and Azorella macquariensis on sub‐Antarctic Macquarie Island. Although both islands experience a similar climate and have a similar vegetation structure, they differ significantly in topography and geological history. We genotyped six microsatellites for 1,149 individuals from 123 sites across Marion Island and 372 individuals from 42 sites across Macquarie Island. We tested for spatial patterns in genetic diversity, including correlation with elevation and vegetation type, and clines in different directional bearings. We also examined genetic differentiation within islands, isolation‐by‐distance with and without accounting for direction, and signals of demographic change. Marion Island was found to have a distinct northwest–southeast divide, with lower genetic diversity and more sites with a signal of population expansion in the northwest. We attribute this to asymmetric seed dispersal by the dominant northwesterly winds, and to population persistence in a southwestern refugium during the Last Glacial Maximum. No apparent spatial pattern, but greater genetic diversity and differentiation between sites, was found on Macquarie Island, which may be due to the narrow length of the island in the direction of the dominant winds and longer population persistence permitted by the lack of extensive glaciation on the island. Together, our results clearly illustrate the implications of island shape and geography, and the importance of direction‐dependent drivers, in shaping spatial genetic structure.     

Isolation and characterization of macaroni penguin (Eudyptes chrysolophus) microsatellite loci and their utility in other penguin species (Spheniscidae, AVES)

We report the characterization of 25 microsatellite loci isolated from the macaroni penguin (Eudyptes chrysolophus). Thirteen loci were arranged into four multiplex sets for future genetic studies of macaroni penguin populations. All 25 loci were tested separately in each of four other penguin species [Adélie penguin (Pygoscelis adeliae), chinstrap penguin (Pygoscelis antarctica), gentoo penguin (Pygoscelis papua) and king penguin (Aptenodytes patagonicus)]. Between eight and 12 loci were polymorphic per species. These loci are expected to be useful for studies of population genetic structure in a range of penguin species.     

Genetic diversity and population structure of the serpentine endemic Ni hyperaccumulator Alyssum lesbiacum

Alyssum lesbiacum is a well-established Ni hyperaccumulator, endemic to serpentine soils of Lesbos Island (Greece). A total of 95 individuals were collected from 17 plots encompassing the only four large populations of this species. ISSR (Inter-simple sequence repeat) markers were used to assess genetic diversity and population structure of A. lesbiacum to provide initial guidance for the development of successful management and conservation measures. A total of ten primers produced 82 bands, 96.34 % being polymorphic. The largest part of total diversity was found within populations, rather than among them. AMOVA analysis partitioned the largest part of diversity within plots (66 %), while 15 % contained among plots within populations and 19 % among populations. Principal coordinates analysis along with dendrogram based on genetic distances among populations showed a high degree of genetic differentiation of the isolated population Loutra. At a smaller scale, distance was not the most significant factor influencing the patterns of genetic diversity, but topography, ecosystem types and connectivity through streams. According to our results, conservation efforts should be organized at the level of watersheds and ecosystem types, considering them as management units. For ex situ conservation and restoration, seed samplings should be representative of the different habitats and watersheds as well as the patches of large and small populations while keeping the east population of Loutra separate from the other three central populations, to avoid any loss of genetic diversity and to preserve the character of the local adapted populations.     

Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.     

Ticks Associated with Macquarie Island Penguins Carry Arboviruses from Four Genera

Macquarie Island, a small subantarctic island, is home to rockhopper, royal and king penguins, which are often infested with the globally distributed seabird tick, Ixodes uriae. A flavivirus, an orbivirus, a phlebovirus, and a nairovirus were isolated from these ticks and partial sequences obtained. The flavivirus was nearly identical to Gadgets Gully virus, isolated some 30 year previously, illustrating the remarkable genetic stability of this virus. The nearest relative to the orbivirus (for which we propose the name Sandy Bay virus) was the Scottish Broadhaven virus, and provided only the second available sequences from the Great Island orbivirus serogroup. The phlebovirus (for which we propose the name Catch-me-cave virus) and the previously isolated Precarious Point virus were distinct but related, with both showing homology with the Finnish Uukuniemi virus. These penguin viruses provided the second and third available sequences for the Uukuniemi group of phleboviruses. The nairovirus (for which we propose the name Finch Creek virus) was shown to be related to the North American Tillamook virus, the Asian Hazara virus and Nairobi sheep disease virus. Macquarie Island penguins thus harbour arboviruses from at least four of the seven arbovirus-containing genera, with related viruses often found in the northern hemisphere.     

Ancient DNA applications for wildlife conservation

Ancient DNA analyses of historical, archaeological and paleontological remains can contribute important information for the conservation of populations and species that cannot be obtained any other way. In addition to ancient DNA analyses involving a single or few individuals, population level studies are now possible. Biases inherent in estimating population parameters and history from modern genetic diversity are exaggerated when populations are small or have been heavily impacted by recent events, as is common for many endangered species. Going directly back in time to study past populations removes many of the assumptions that undermine conclusions based only on recent populations. Accurate characterization of historic population size, levels of gene flow and relationships with other populations are fundamental to developing appropriate conservation and management plans. The incorporation of ancient DNA into conservation genetics holds a lot of potential, if it is employed responsibly.     

Low MHC variation in the endangered Galápagos penguin (<Emphasis Type="Italic">Spheniscus mendiculus</Emphasis>)

The major histocompatibility complex (MHC) is one of the most polymorphic regions of the genome, likely due to balancing selection acting to maintain alleles over time. Lack of MHC variability has been attributed to factors such as genetic drift in small populations and relaxed selection pressure. The Galápagos penguin (Spheniscus mendiculus), endemic to the Galápagos Islands, is the only penguin that occurs on the equator. It relies upon cold, nutrient-rich upwellings and experiences severe population declines when ocean temperatures rise during El Niño events. These bottlenecks, occurring in an already small population, have likely resulted in reduced genetic diversity in this species. In this study, we used MHC class II exon 2 sequence data from a DRB1-like gene to characterize the amount of genetic variation at the MHC in 30 Galápagos penguins, as well as one Magellanic penguin (S. magellanicus) and two king penguins (Aptenodytes patagonicus), and compared it to that in five other penguin species for which published data exist. We found that the Galápagos penguin had the lowest MHC diversity (as measured by number of polymorphic sites and average divergence among alleles) of the eight penguin species studied. A phylogenetic analysis showed that Galápagos penguin MHC sequences are most closely related to Humboldt penguin (Spheniscus humboldti) sequences, its putative sister species based on other loci. An excess of non-synonymous mutations and a pattern of trans-specific evolution in the neighbor-joining tree suggest that selection is acting on the penguin MHC.     

青岛耐冬山茶的多样性 (Ⅱ)——居群的遗传多样性分析

采用等位酶电泳技术,检测了青岛近海岛屿--长门岩岛、大管岛和浙江普陀山的天然山茶居群的遗传状况,并与青岛植物园和杭州植物园的栽培山茶居群作了比较。分析结果表明：青岛近海岛屿山茶居群内的遗传多样性水平较高,每个位点的等位基因平均数为2.3,多态位点比率为83.3%,平均观察杂合度与期望杂合度分别为0.245及0.320,这个结果可以为青岛耐冬山茶的保护提供依据。为了探讨形态分化与等位酶变异之间的关系,对山茶居群内一些形态特殊类型的酶谱作了比较。     

Comparison of population genetic diversity between a rare, narrowly distributed species and a common, widespread species of Alnus (Betulaceae)

Comparisons of population genetic diversity between related rare and widespread species provide valuable insights to the consequences of rarity and are critical for conservation planning. Population genetic diversity of A. maritima, a rare species, was compared with its common, widespread congener A. serrulata to evaluate the impacts of small population size and high isolation on genetic diversity in A. maritima and to provide population genetic data to be used in conservation planning for A. maritima. Genetic data were also used to evaluate whether the disjunct distribution of A. maritima was due to range reduction or anthropogenic dispersal. Genetic diversity was lower in A. maritima (H(e) = 0.217) than in A. serrulata (H(e) = 0.268), and there is also higher inbreeding within A. maritima populations (f = 0.483) than A. serrulata populations (f = 0.269). The partitioning of genetic variation was also higher among A. maritima populations (Θ = 0.278), but not significantly different from that of A. serrulata (Θ = 0.197). Significant genetic differences among A. maritima populations support using local populations as seed sources for regional conservation efforts. The results also indicate that the highly disjunct distribution of A. maritima is due to natural range reduction in the past and not anthropogenic establishment of Oklahoma and Georgia populations.     

青岛耐冬山茶的多样性（Ⅱ）

采用等位酶电泳技术,检测了青岛近海岛屿———长门岩岛、大管岛和浙江普陀山的天然山茶居群的遗传状况,并与青岛植物园和杭州植物园的栽培山茶居群作了比较。分析结果表明：青岛近海岛屿山茶居群内的遗传多样性水平较高,每个位点的等位基因平均数为２３,多态位点比率为８３３％,平均观察杂合度与期望杂合度分别为０２４５及０３２０,这个结果可以为青岛耐冬山茶的保护提供依据。为了探讨形态分化与等位酶变异之间的关系,对山茶居群内一些形态特殊类型的酶谱作了比较     

Influence of translocation strategy and mating system on the genetic structure of a newly established population of island ptarmigan

Island populations and populations established by reintroductions are prone to extinction, in part because they are vulnerable to deterministic and stochastic phenomena associated with geographic isolation and small population size. As population size declines, reduced genetic diversity can result in decreased fitness and reduced adaptive potential, which may hinder short- or long-term population viability. We used 32 microsatellite markers to investigate the conservation genetics of a newly established population of Evermann’s Rock Ptarmigan (Lagopus muta evermanni) at Agattu Island, in the western Aleutian Archipelago, Alaska. We found low genetic diversity (observed heterozygosity = 0.41, allelic richness = 2.2) and a small effective population size (N _e  = 28.6), but a relatively large N _e /N ratio = 0.55, which was attributed to multiple paternity in 80% of the broods and low reproductive skew among males (λ = 0.29). Moreover, successful breeding pairs were less related to each other than random male–female pairs. For conservation efforts based on reintroductions, a mating system with high rates of multiple paternity may facilitate retention of genetic diversity, thereby reducing the potential for inbreeding in small or isolated populations. Our results underscore the importance of quantifying genetic diversity and understanding the breeding behavior of translocated populations.     

High mitochondrial and nuclear genetic diversity in one of the world’s most endangered seabirds,the Chatham Island Taiko (<Emphasis Type="Italic">Pterodroma magentae</Emphasis>)

Interpreting the levels of genetic diversity in organisms with diverse life and population histories can be difficult. The processes and mechanisms regulating this diversity are complex and still poorly understood. However, endangered species typically have low genetic variation as a consequence of the effects of genetic drift in small populations. In this study we examine genetic variation in the critically endangered Chatham Island Taiko (Tchaik, Pterodroma magentae), one of the world’s rarest seabirds. The Taiko has a very small population size of between 120 and 150 individuals, including just 8–15 breeding pairs. We report surprisingly high mitochondrial and nuclear genetic diversity in this critically endangered long-lived species. We hypothesise that the present Taiko population has retained a significant proportion of its past genetic diversity. However, it is also possible that undiscovered birds are breeding in unknown areas, which could increase the population size estimate. Importantly, from a conservation perspective, we show that the high level of variation is unlikely to be maintained in the future since chicks currently being born have only a limited number of the mitochondrial DNA haplotypes found in adults. Reduced genetic variation will mean that our ability to infer past events and the population history of Taiko using genetics could soon be lost and the power to determine, for example, parentage and other close order relationships will be diminished. Therefore, the maintenance of genetic diversity in future generations is an important consideration for conservation management of the Taiko.     

High levels of genetic variability in the moss Ceratodon purpureus from continental Antarctica, subantarctic Heard and Macquarie Islands, and Australasia

The random amplified polymorphic DNA (RAPD) technique, and DNA sequencing of the conserved nuclear ribosomal DNA internal transcribed spacer region (ITS1-5.8S-ITS2), have been used to assess levels of genetic diversity in the moss Ceratodon purpureus from several locations in Australasia, subantarctic Heard and Macquarie Islands, and continental Antarctica. Populations from Heard and Macquarie Islands and from Antarctica maintain high levels of genetic variation. Both within- and among-colony variation were observed at these locations. DNA sequence analysis showed that samples from the Ross Sea region of Antarctica were most closely related to colonies from Casey and Macquarie Island, and that one colony from Heard Island was most closely related to one from Europe. DNA sequence data separated two Australian populations from the Antarctic and subantarctic group on a dendrogram. Detailed RAPD analysis of a single colony from continental Antarctica demonstrated that mutation probably causes the high variability observed in this moss. DNA sequencing and RAPD analysis are complementary techniques for genetic investigation of Antarctic moss populations.Jenny Ninham was an integral part of this research team for several years. Unfortunately she did not live to see these results published.     

Genetic diversity in populations of Gentoo penguins (Pygoscelis papua)

RAPD analysis was used to examine the extent of genetic polymorphism in two populations of Gentoo penguin (Pygoscelis papua) from Antarctic Islands (Petermann and Livingston). The chosen two of three 10 mer oligonucleotide primers accordingly to preliminary results showed different levels of polymorphism in Gentoo penguins at Petermann Island (from 23.53 to 42.86%) and Livingston Island (from 52.94 to 57.14%). Nei's similarity coefficients were in range from 0.5606 (when Gentoo genome profiles were compared with RAPD profiles of two related penguin species: Pygoscelis adeliae (Adelie) and Pygoscelis antarctica (Chinstrep)) to 0.9281 among observed Gentoo penguin populations. Nei's distances values ranged from 0.0746 to 0.5787 among the populations and species. The obtained results will be used for further estimation of genetic diversity of Gentoo penguins and determination of their taxonomic status.