Coalescent and biophysical models of stepping‐stone gene flow in neritid snails

Marine species in the Indo‐Pacific have ranges that can span thousands of kilometres, yet studies increasingly suggest that mean larval dispersal distances are less than historically assumed. Gene flow across these ranges must therefore rely to some extent on larval dispersal among intermediate ‘stepping‐stone’ populations in combination with long‐distance dispersal far beyond the mean of the dispersal kernel. We evaluate the strength of stepping‐stone dynamics by employing a spatially explicit biophysical model of larval dispersal in the tropical Pacific to construct hypotheses for dispersal pathways. We evaluate these hypotheses with coalescent models of gene flow among high‐island archipelagos in four neritid gastropod species. Two of the species live in the marine intertidal, while the other two are amphidromous, living in fresh water but retaining pelagic dispersal. Dispersal pathways predicted by the biophysical model were strongly favoured in 16 of 18 tests against alternate hypotheses. In regions where connectivity among high‐island archipelagos was predicted as direct, there was no difference in gene flow between marine and amphidromous species. In regions where connectivity was predicted through stepping‐stone atolls only accessible to marine species, gene flow estimates between high‐island archipelagos were significantly higher in marine species. Moreover, one of the marine species showed a significant pattern of isolation by distance consistent with stepping‐stone dynamics. While our results support stepping‐stone dynamics in Indo‐Pacific species, we also see evidence for nonequilibrium processes such as range expansions or rare long‐distance dispersal events. This study couples population genetic and biophysical models to help to shed light on larval dispersal pathways.     

Habitat continuity and stepping‐stone oceanographic distances explain population genetic connectivity of the brown alga Cystoseira amentacea

Effective predictive and management approaches for species occurring in a metapopulation structure require good understanding of interpopulation connectivity. In this study, we ask whether population genetic structure of marine species with fragmented distributions can be predicted by stepping‐stone oceanographic transport and habitat continuity, using as model an ecosystem‐structuring brown alga, Cystoseira amentacea var. stricta. To answer this question, we analysed the genetic structure and estimated the connectivity of populations along discontinuous rocky habitat patches in southern Italy, using microsatellite markers at multiple scales. In addition, we modelled the effect of rocky habitat continuity and ocean circulation on gene flow by simulating Lagrangian particle dispersal based on ocean surface currents allowing multigenerational stepping‐stone dynamics. Populations were highly differentiated, at scales from few metres up to thousands of kilometres. The best possible model fit to explain the genetic results combined current direction, rocky habitat extension and distance along the coast among rocky sites. We conclude that a combination of variable suitable habitat and oceanographic transport is a useful predictor of genetic structure. This relationship provides insight into the mechanisms of dispersal and the role of life‐history traits. Our results highlight the importance of spatially explicit modelling of stepping‐stone dynamics and oceanographic directional transport coupled with habitat suitability, to better describe and predict marine population structure and differentiation. This study also suggests the appropriate spatial scales for the conservation, restoration and management of species that are increasingly affected by habitat modifications.     

Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas

Through extended survey of mitochondrial DNA (mtDNA) diversity in the Nganasan, Yukaghir, Chuvantsi, Chukchi, Siberian Eskimos, and Commander Aleuts, we filled important gaps in previously unidentified internal sequence variation within haplogroups A, C, and D, three of five (A-D and X) canonical mtDNA lineages that defined Pleistocenic extension from the Old to the New World. Overall, 515 mtDNA samples were analyzed via high-resolution SNP analysis and then complete sequencing of the 84 mtDNAs. A comparison of the data thus obtained with published complete sequences has resulted in the most parsimonious phylogenetic structure of mtDNA evolution in Siberia-Beringia. Our data suggest that although the latest inhabitants of Beringia are well genetically reflected in the Chukchi-, Eskimo-Aleut-, and Na-Dene-speaking Indians, the direct ancestors of the Paleosiberian-speaking Yukaghir are primarily drawn from the southern belt of Siberia when environmental conditions changed, permitting recolonization the high arctic since early Postglacial. This study further confirms that (1) Alaska seems to be the ancestral homeland of haplogroup A2 originating in situ approximately 16.0 thousand years ago (kya), (2) an additional founding lineage for Native American D, termed here D10, arose approximately 17.0 kya in what is now the Russian Far East and eventually spread northward along the North Pacific Rim. The maintenance of two refugial sources, in the Altai-Sayan and mid-lower Amur, during the last glacial maximum appears to be at odds with the interpretation of limited founding mtDNA lineages populating the Americas as a single migration.     

Establishing a community‐wide DNA barcode library as a new tool for arctic research

DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to‐date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology‐based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology‐based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species‐level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.     

Re‐colonization by common eiders Somateria mollissima in the Aleutian Archipelago following removal of introduced arctic foxes Vulpes lagopus

Islands provide refuges for populations of many species where they find safety from predators, but the introduction of predators frequently results in elimination or dramatic reductions in island‐dwelling organisms. When predators are removed, re‐colonization for some species occurs naturally, and inter‐island phylogeographic relationships and current movement patterns can illuminate processes of colonization. We studied a case of re‐colonization of common eiders Somateria mollissima following removal of introduced arctic foxes Vulpes lagopus in the Aleutian Archipelago, Alaska. We expected common eiders to resume nesting on islands cleared of foxes and to re‐colonize from nearby islets, islands, and island groups. We thus expected common eiders to show limited genetic structure indicative of extensive mixing among island populations. Satellite telemetry was used to record current movement patterns of female common eiders from six islands across three island groups. We collected genetic data from these and other nesting common eiders at 14 microsatellite loci and the mitochondrial DNA control region to examine population genetic structure, historical fluctuations in population demography, and gene flow. Our results suggest recent interchange among islands. Analysis of microsatellite data supports satellite telemetry data of increased dispersal of common eiders to nearby areas and little between island groups. Although evidence from mtDNA is suggestive of female dispersal among island groups, gene flow is insufficient to account for recolonization and rapid population growth. Instead, near‐by remnant populations of common eiders contributed substantially to population expansion, without which re‐colonization would have likely occurred at a much lower rate. Genetic and morphometric data of common eiders within one island group two and three decades after re‐colonization suggests reduced movement of eiders among islands and little movement between island groups after populations were re‐established. We predict that re‐colonization of an island group where all common eiders are extirpated could take decades.     

Mitochondrial DNA haplotypes indicate two postglacial re‐colonization routes of the spruce bark beetle Ips typographus through northern Europe to Scandinavia

Species in northern Europe re‐colonized the region after the last glacial maximum via several routes, which could have lingering signatures in current intraspecific trait variation. The spruce bark beetle, Ips typographus, occurs across Europe, and biological differences have been found between southern and northern Scandinavian populations. However, the postglacial history of I. typographus in Scandinavia has not been previously studied at a fine geographical scale. Therefore, we collected specimens across northern Europe and analysed the genetic variation in a quite large mitochondrial fragment (698 bp). A high genetic diversity was found in some of the most northern populations, in the Baltic States, Gotland and central Europe. Detected genetic and phylogeographic structures suggest that I. typographus re‐colonized Scandinavia via two pathways, one from the northeast and one from the south. These findings are consistent with the re‐colonization history of its host plant, Picea abies. However, we observed low haplotype and nucleotide diversity in southern Scandinavian populations of I. typographus, indicating that (unlike P. abies) it did not disperse across the Baltic Sea in multiple events. Further, the divergence among Scandinavian populations was shallow, conflicting with a scenario where I. typographus expanded concurrently with its host plant from a ‘cryptic refugium’ in the northwest.     

Fungal palaeodiversity revealed using high‐throughput metabarcoding of ancient DNA from arctic permafrost

The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty‐six sediment samples dated 16 000–32 000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 ± 3811 (mean ± SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 16 000–32 000 bp . However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one‐third of the OTUs are presumed plant‐associates (pathogens, saprotrophs and endophytes) typical of graminoid‐ and forb‐rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.     

Demography of Slate‐throated Redstarts (Myioborus miniatus): a non‐migratory Neotropical warbler

Most wood‐warblers (Parulidae) are non‐migratory residents of the Neotropics and subtropics, and the demographic characteristics of these species are poorly known. I examined the annual survival, reproductive output, dispersal, age of first breeding, and other demographic characteristics of a permanently territorial non‐migratory tropical warbler, the Slate‐throated Redstart (Myioborus miniatus), based on a 5‐yr study of a color‐banded population in Monteverde, Costa Rica. Territorial males showed strong site fidelity, but 26% of females engaged in short‐distance between‐year breeding dispersal. Estimated annual survival of territory holders, corrected for undetected female breeding dispersal, was 0.56 for males and 0.43 for females, values lower than expected and comparable to survival estimates for North American migrant warblers. The lower annual survival of females had two demographic consequences; unpaired territorial males were present in 3 of 5 yr, and some 1‐yr‐old males appeared to be floaters. Unpaired females or female floaters, however, were not observed. Mean natal dispersal distance was significantly greater for females (935 m) than males (485 m). Estimated first‐year survival was 0.29, but this is almost certainly an underestimate because of undetected long‐distance, female‐biased natal dispersal. Annual fecundity (fledglings per female) was 1.8, less than that of temperate warblers and attributable to small mean clutch sizes and a low incidence of double brooding. Estimated population growth rate (λ) was <1 for both males and females, suggesting that the study population was a demographic sink, most likely due to lower‐than‐expected adult survival.     

Mitochondrial DNA as a tool for reconstructing past life‐history traits in mammals

Reconstructing the ancestral characteristics of species is a major goal in evolutionary and comparative biology. Unfortunately, fossils are not always available and sufficiently informative, and phylogenetic methods based on models of character evolution can be unsatisfactory. Genomic data offer a new opportunity to estimate ancestral character states, through (i) the correlation between DNA evolutionary processes and species life‐history traits and (ii) available reliable methods for ancestral sequence inference. Here, we assess the relevance of mitochondrial DNA – the most popular molecular marker in animals – as a predictor of ancestral life‐history traits in mammals, using the order of Cetartiodactyla as a benchmark. Using the complete set of 13 mitochondrial protein‐coding genes, we show that the lineage‐specific nonsynonymous over synonymous substitution rate ratio (dN/dS) is closely correlated with the species body mass, longevity and age of sexual maturity in Cetartiodactyla and can be used as a marker of ancestral traits provided that the noise introduced by short branches is appropriately dealt with. Based on ancestral dN/dS estimates, we predict that the first cetartiodactyls were relatively small animals (around 20 kg). This finding is in accordance with Cope's rule and the fossil record but could not be recovered via continuous character evolution methods.     

Mitochondrial DNA from pre-Columbian Ciboneys from Cuba and the prehistoric colonization of the Caribbean

To assess the genetic affinities of extinct Ciboneys (also called Guanajuatabeys) from Cuba, 47 pre-Columbian skeletal samples belonging to this group were analyzed using ancient DNA techniques. At the time of European contact, the center and east of Cuba were occupied by agriculturalist Taino groups, while the west was mainly inhabited by Ciboneys, hunter-gatherers who have traditionally been considered a relic population descending from the initial colonization of the Caribbean. The mtDNA hypervariable region I (HVR-I) and haplogroup-specific markers were amplified and sequenced in 15 specimens using overlapping fragments; amplification from second extractions from the same sample, independent replication in different laboratories, and cloning of some PCR products support the authenticity of the sequences. Three of the five major mtDNA Amerindian lineages (A, C, and D) are present in the sample analyzed, in frequencies of 0.07, 0.60, and 0.33, respectively. Different phylogenetic analyses seem to suggest that the Caribbean most likely was populated from South America, although the data are still inconclusive, and Central American influences cannot be discarded. Our hypothesis is that the colonization of the Caribbean mainly took place in successive migration movements that emanated from the same area in South America, around the Lower Orinoco Valley: the first wave consisted of hunter-gatherer groups (ancestors of the Ciboneys), a subsequent wave of agriculturalists (ancestors of the Tainos), and a latter one of nomadic Carib warriors. However, further genetic studies are needed to confirm this scenario.     

Cavity construction by reintroduced populations of Red‐cockaded Woodpeckers (Dryobates borealis)

Although species reintroduction attempts are now common, monitoring of reintroduction attempts rarely extends beyond initial population establishment. This short timespan likely fails to document long‐term population stability, subtle changes in behavior, and the potentially larger effects that some reintroduced species may have on other species. The Red‐cockaded Woodpecker (RCW; Dryobates borealis) is an important habitat specialist and ecosystem engineer that excavates cavities in living trees. Excavation of natural RCW cavities can take years to complete, but they also persist for many years and are used by many other species. We quantified characteristics of cavity trees excavated by RCWs (n = 44) in two populations that were reintroduced to unoccupied areas more than 10 years earlier. We measured features associated with heartwood rot and used generalized linear mixed effects regression to determine whether these features differed for trees selected for cavity excavation compared with random neighboring trees. We also assessed population trends for cavity‐nesting species that commonly used RCW cavities on one of the sites. Height of first live limb was the only factor distinguishing natural RCW cavity trees from control trees. Four of six cavity‐nesting species monitored increased significantly following RCW establishment. The increases may relate to the many natural and artificial cavities created during the reintroduction effort. Future reintroductions of the RCW should lead to successful natural cavity excavation if sufficiently large trees with smaller live crowns are present. Future efforts may also benefit the broader community of cavity‐nesting birds.     

Discovery of a breeding area of the enigmatic large‐billed reed warbler Acrocephalus orinus

The present study reports the discovery of the hitherto unknown breeding grounds of the large‐billed reed warbler Acrocephalus orinus in the Badakhshan region of Tajikistan. A total of eight adult individuals were caught at three riverine woodland sites and breeding was confirmed at one locality. The identity of the birds was confirmed on the basis of partial sequences of the cytochrome b gene. Even among individuals sampled at the same locality, genetic diversity was surprisingly high. This was interpreted as the result of secondary contact between previously isolated or fragmented populations. The breeding range of the large‐billed reed warbler is likely small and the species’ habitat is under intense pressure from the collection of firewood and fodder. Consequently, the large‐billed reed warbler remains of considerable conservation concern.     

Mitochondrial DNA D‐loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens

This study sought to assess mitochondrial DNA (mtDNA) diversity and phylogeographic structure of chickens from five agro‐ecological zones of Zimbabwe. Furthermore, chickens from Zimbabwe were compared with populations from other geographical regions (Malawi, Sudan and Germany) and other management systems (broiler and layer purebred lines). Finally, haplotypes of these animals were aligned to chicken sequences, taken from GenBank, that reflected populations of presumed centres of domestication. A 455‐bp fragment of the mtDNA D‐loop region was sequenced in 283 chickens of 14 populations. Thirty‐two variable sites that defined 34 haplotypes were observed. In Zimbabwean chickens, diversity within ecotypes accounted for 96.8% of the variation, indicating little differentiation between ecotypes. The 34 haplotypes clustered into three clades that corresponded to (i) Zimbabwean and Malawian chickens, (ii) broiler and layer purebred lines and Northwest European chickens, and (iii) a mixture of chickens from Zimbabwe, Sudan, Northwest Europe and the purebred lines. Diversity among clades explained more than 80% of the total variation. Results indicated the existence of two distinct maternal lineages evenly distributed among the five Zimbabwean chicken ecotypes. For one of these lineages, chickens from Zimbabwe and Malawi shared major haplotypes with chicken populations that have a Southeast Asian background. The second maternal lineage, probably from the Indian subcontinent, was common to the five Zimbabwean chicken ecotypes, Sudanese and Northwest European chickens as well as purebred broiler and layer chicken lines. A third maternal lineage excluded Zimbabwean and other African chickens and clustered with haplotypes presumably originating from South China.     

用mtDNA控制区序列鉴定长须鲸标本

测定了采自长江口和杭州湾交汇海域的一头死亡大型须鲸骨骼标本的线粒体DNA(mt DNA)控制区序列(Control region)976 bp(登录号MF781125)、细胞色素C氧化酶Ⅰ基因(COⅠ)序列642 bp(登录号MG010134)和Cyt b序列307 bp(登录号MG010133)。通过与Gen Bank已发表的同源序列blast结果表明,与美国加利福尼亚海域长须鲸(Balaenoptera physalus)的控制区序列相似度达99%,仅在756 bp处有一个碱基T和C转换的差异;基于HKG+G模型,使用UPGMA聚类分析法和最大似然法(ML)构建的系统发育树与blast结果一致,故将标本鉴定为长须鲸,推测该个体来源于北太平洋。获取的细胞色素C氧化酶Ⅰ和Cyt b序列存在多个终止密码子,无法获取同源性较高的序列,推断可能为线粒体假基因。     

用mtDNA序列鉴定一头小布氏鲸标本

测定了采自浙江省瑞安市的一头须鲸类标本的线粒体DNA（mitochondrial DNA,mtDNA)细胞色素b(cytochrome b,cyt b)基因369bp和控制区（control region)933bp的序列,通过与已发表的须鲸类同源序列比对,发现与西太平洋和日本水域的布氏鲸的cyt b基因和控制区分别有6.78%-7.05%和13.30%－14．40％的序列差异,而与来自所罗门群岛的布氏鲸之间cyt b基因的序列完全相同,控制区的序列也仅相差一个碱基（0.28%)。提示与邻近的西太平洋和日本海的普通布氏鲸在遗传上有显著区别,而可能与所罗门群岛的布氏鲸为同一种,即小布氏鲸（Balaenoptera edeni)。同时表明,应用分子生物学手段为进行鲸肉及其制品的种类鉴定是可行和有效的。     

Mitochondrial DNA D‐loop sequence variation in maternal lineages of Iranian native horses

To understand the origin and genetic diversity of Iranian native horses, mitochondrial DNA (mtDNA) D‐loop sequences were generated for 95 horses from five breeds sampled in eight geographical locations in Iran. Sequence analysis of a 247‐bp segment revealed a total of 27 haplotypes with 38 polymorphic sites. Twelve of 19 mtDNA haplogroups were identified in the samples. The most common haplotypes were found within haplogroup X2. Within‐population haplotype and nucleotide diversities of the five breeds ranged from 0.838 ± 0.056 to 0.974 ± 0.022 and 0.011 ± 0.002 to 0.021 ± 0.001 respectively, indicating a relatively high genetic diversity in Iranian horses. The identification of several ancient sequences common between the breeds suggests that the lineage of the majority of Iranian horse breeds is old and obviously originated from a vast number of mares. We found in all native Iranian horse breeds lineages of the haplogroups D and K, which is concordant with the previous findings of Asian origins of these haplogroups. The presence of haplotypes E and K in our study also is consistent with a geographical west–east direction of increasing frequency of these haplotypes and a genetic fusion in Iranian horse breeds.