Low genetic structure and diversity of Red-billed Tropicbirds in the Mexican Pacific

Understanding genetic structure and gene flow can elucidate the mechanisms of diversification and adaptation in seabirds and help define conservation and management units. From 2012 to 2016, we collected blood and feather samples from 156 Red-billed Tropicbirds (Phaethon aethereus) from seven colonies distributed along the Gulf of California and Mexican tropical Pacific to estimate genetic diversity, genetic structure, and gene flow using microsatellite markers and mitochondrial DNA (mtDNA; control region) sequences. Nuclear and mtDNA data revealed relatively low or null levels of genetic diversity, respectively, possibly the result of a founder effect in the eastern Pacific followed by a subsequent population expansion. Nuclear data revealed significant genetic structure among the colonies, but the differences were not associated with regional grouping (i.e., Gulf of California vs. Tropical Pacific). Greater gene flow was observed from the tropical Pacific toward the Gulf of California, possibly related to shared dispersal patterns during the non-breeding season (individuals traveling north to reach warm currents with abundant prey). With the exception of one colony in the Mexican tropical Pacific, we found no evidence of recent bottleneck events. Nonetheless, the overall reduced genetic diversity suggests a high intrinsic vulnerability and risk of extinction for this species.     

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.     

Genetic variation and structure in native populations of the fire ant Solenopsis invicta: evolutionary and demographic implications

We studied population genetic variation and structure in the fire ant Solenopsis invicta using nuclear genotypic and mitochondrial DNA (mtDNA) sequence data obtained from samples collected throughout its native range. Geographic populations are strongly differentiated at both genomes, with such structure more pronounced in Brazil than in Argentina. Higher-level regional structure is evident from the occurrence of isolation-by-distance patterns among populations, the recognition of clusters of genetically similar, geographically adjacent populations by ordination analysis, and the detection of an mtDNA discontinuity between Argentina and Brazil coinciding with a previously identified landform of biogeographical relevance. Multiple lines of evidence from both genomes suggest that the ancestors of the ants we studied resembled extant northern Argentine S. invicta , and that existing Brazilian populations were established more recently by serial long-distance colonizations and/or range expansions. The most compelling evidence for this is the corresponding increase in F _K (a measure of divergence from a hypothetical ancestor) and decrease in genetic diversity with distance from the Corrientes population in northern Argentina. Relatively deep sequence divergence among several mtDNA clades, coupled with geographical partitioning of many of them, suggests prolonged occupation of South America by S. invicta in more-or-less isolated regional populations. Such populations appear, in some cases, to have come into secondary contact without regaining the capacity to freely interbreed. We conclude that nominal S. invicta in its native range comprises multiple entities that are sufficiently genetically isolated and diverged to have embarked on independent evolutionary paths.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 541–560.     

Rolling stones and stable homes: social structure,habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris)

Spinner dolphins (Stenella longirostris) exhibit different social behaviours at two regions in the Hawaiian Archipelago: off the high volcanic islands in the SE archipelago they form dynamic groups with ever‐changing membership, but in the low carbonate atolls in the NW archipelago they form long‐term stable groups. To determine whether these environmental and social differences influence population genetic structure, we surveyed spinner dolphins throughout the Hawaiian Archipelago with mtDNA control region sequences and 10 microsatellite loci (n = 505). F‐statistics, Bayesian cluster analyses, and assignment tests revealed population genetic separations between most islands, with less genetic structuring among the NW atolls than among the SE high islands. The populations with the most stable social structure (Midway and Kure Atolls) have the highest gene flow between populations (mtDNA Φ_ST < 0.001, P = 0.357; microsatellite F_ST = ?0.001; P = 0.597), and a population with dynamic groups and fluid social structure (the Kona Coast of the island of Hawai’i) has the lowest gene flow (mtDNA 0.042 < Φ_ST < 0.236, P < 0.05; microsatellite 0.016 < F_ST < 0.040, P < 0.001). We suggest that gene flow, dispersal, and social structure are influenced by the availability of habitat and resources at each island. Genetic comparisons to a South Pacific location (n = 16) indicate that Hawaiian populations are genetically depauperate and isolated from other Pacific locations (mtDNA 0.216 < F_ST < 0.643, P < 0.001; microsatellite 0.058 < F_ST < 0.090, P < 0.001); this isolation may also influence social and genetic structure within Hawai’i. Our results illustrate that genetic and social structure are flexible traits that can vary between even closely‐related populations.     

Hierarchical analysis of population genetic structure in the monogynous ant Cataglyphis cursor using microsatellite and mitochondrial DNA markers

Despite having winged queens, female dispersal in the monogynous ant Cataglyphis cursor is likely to be restricted because colonies reproduce by fission. We investigated the pattern of population genetic structure of this species using eight microsatellite markers and a mitochondrial DNA (mtDNA) sequence, in order to examine the extent of female and nuclear gene flow in two types of habitat. Sampling was carried out at a large spatial scale (16 sites from 2.5 to 120 km apart) as well as at a fine spatial scale (two 4.5-km transects, one in each habitat type). The strong spatial clustering of mtDNA observed at the fine spatial scale strongly supported a restricted effective female dispersal. In agreement, patterns of the mtDNA haplotypes observed at large and fine spatial scales suggested that new sites are colonized by nearby sites. Isolation by distance and significant nuclear genetic structure have been detected at all the spatial scales investigated. The level of local genetic differentiation for mitochondrial marker was 15 times higher than for the nuclear markers, suggesting differences in dispersal pattern between the two sexes. However, male gene flow was not sufficient to prevent significant nuclear genetic differentiation even at short distances (500 m). Isolation-by-distance patterns differed between the two habitat types, with a linear decrease of genetic similarities with distance observed only in the more continuous of the two habitats. Finally, despite these low dispersal capacities and the potential use of parthenogenesis to produce new queens, no signs of reduction of nuclear genetic diversity was detected in C. cursor populations.     

Patterns of ant species diversity and turnover across 2000 km of Amazonian floodplain forest

Aim To determine the effect and relative importance of geographic and local environmental factors on species richness and turnover of ant assemblages in floodplain forests across the Amazon basin. Location Twenty‐six mature forest sites scattered along the entire extension of the Amazon River in Brazil. The study area encompassed nearly 18° of longitude and 3.5° of latitude. Methods Systematic collections of ants were performed at each site during the low‐water season (i.e. when forests are not inundated) using three complementary sampling methods. We used variance partitioning techniques to assess the relative effects of the spatial (latitude and longitude) and environmental (rainfall, length of the dry season and flood height) variables on ant species richness and composition. Results There was a twofold variation in the number of species per site, which was largely explained by inter‐site variations in rainfall seasonality and flooding intensity. In general, there were more species at sites located in the western part of the basin, where the dry season is less severe, or near the river estuary, where precipitation is also high and flooding is less intense. Ant community composition was also affected by environmental heterogeneity. For instance, some species only occurred at those sites less affected by the river’s seasonal flooding, whereas others were mostly associated with the drier or wetter regions of the basin. In addition, the turnover of species increased significantly as geographic distances increased. Nevertheless, the rate of change was small given that many species had a broad distribution across the study area. Main conclusions Ant distribution patterns along the floodplain forests of the Amazon appear to be controlled to a relatively large extent by the current gradient in flooding intensity and – most importantly – in precipitation. Altered rainfall regimes resulting from global warming and land‐use change thus have the potential to influence these patterns.     

Phylogeographical population structure of tiger quolls Dasyurus maculatus (Dasyuridae: Marsupialia), an endangered carnivorous marsupial

Tiger quolls, Dasyurus maculatus, are the largest carnivorous marsupials still extant on the mainland of Australia, and occupy an important ecological niche as top predators and scavengers. Two allopatric subspecies are recognized, D.m. gracilis in north Queensland, and D.m. maculatus in the southeast of the mainland and Tasmania. D.m. gracilis is considered endangered while D.m. maculatus is listed as vulnerable to extinction; both subspecies are still in decline. Phylogeographical subdivision was examined to determine evolutionarily significant units (ESUs) and management units (MUs) among populations of tiger quolls to assist in the conservation of these taxa. Ninety-three tiger quolls from nine representative populations were sampled from throughout the species range. Six nuclear microsatellite loci and the mitochondrial DNA (mtDNA) control region (471 bp) were used to examine ESUs and MUs in this species. We demonstrated that Tasmanian tiger quolls are reciprocally monophyletic to those from the mainland using mtDNA analysis, but D.m. gracilis was not monophyletic with respect to mainland D.m. maculatus. Analysis of microsatellite loci also revealed significant differences between the Tasmanian and mainland tiger quolls, and between D.m. gracilis and mainland D.m. maculatus. These results indicate that Tasmanian and mainland tiger quolls form two distinct evolutionary units but that D.m. gracilis and mainland D.m. maculatus are different MUs within the same ESU. The two marker types used in this study revealed different male and female dispersal patterns and indicate that the most appropriate units for short-term management are local populations. A revised classification and management plan are needed for tiger quolls, particularly in relation to conservation of the Tasmanian and Queensland populations.     

Population boundaries and genetic diversity in the endangered Mariana crow (Corvus kubaryi)

The Mariana crow (Corvus kubaryi) is an endangered species that is restricted to the islands of Guam and Rota in the Mariana archipelago. Predation by the introduced brown tree snake (Boiga irregularis) has decimated bird populations on Guam, and the crow population there is the last wild remnant of the endemic forest avifauna. The population on Guam is critically endangered and, despite intensive management, the population has continued to decline. Additional management options include intermixing the Guam and Rota populations, but such options are best evaluated within a population genetics framework. We used three types of molecular markers to assay genetic variation in the Mariana crow: mitochondrial DNA (mtDNA) sequences, minisatellites and microsatellites. The two populations could be differentiated by mtDNA sequencing and they differed in allele frequencies at nuclear markers. Thus, the populations could be designated as evolutionarily significant units. However, the Guam population is genetically more diverse than the Rota population, and its survival probability if managed separately is very low. All markers did indicate that the two populations are closely related and separated by a shallow genealogical division. Intermixing the populations is justified by two rationales. First, the apparent population differences may result from recent human activities. Second, a greater amount of genetic information may be preserved by joint management. The translocation of birds from Rota to Guam has begun, but strategies that will ensure maintenance of the variation in the Guam population warrant further exploration.     

Genetic structure of the killifish Aphanius fasciatus, Nardo 1827 (Teleostei, Cyprinodontidae), results of mitochondrial DNA analysis

Aphanius fasciatus is a cyprinodont distributed in the salty coastal water of the central and eastern Mediterranean Sea and occasionally in internal fresh water. In this work, the authors have investigated the genetic structure of eight populations of the killifish A. fasciatus from Sardinia and Sicily. The comparison of the mtDNA control region of 237 individuals revealed a total of 49 haplotypes. Several unique haplotypes were present in each population, and no common haplotype was found among Sicilian and Sardinian populations. Almost all Sardinian populations shared a common haplotype, and indeed the four Sicilian populations examined did not share any as determined by the parsimony network analysis. The analysis of molecular variance showed that the percentage of variation among populations is much higher than within each population of A. fasciatus . The overall F _ST value is very high (0·78) and supports an extensive genetic structure of the populations. The observed genetic differentiations of A. fasciatus populations were discussed taking into account the palaeogeographic and palaeoclimatic events that interested the Mediterranean area from Miocenic to Pleistocenic age. The results provide new insight into the knowledge of the pattern of genetic structure and of evolutionary processes occurring in this species.     

Genetic diversity and connectivity of deep‐sea hydrothermal vent metapopulations

Deep‐sea hydrothermal vents provide ephemeral habitats for animal communities that depend on chemosynthetic primary production. Sporadic volcanic and tectonic events destroy local vent fields and create new ones. Ongoing dispersal and cycles of extirpation and colonization affect the levels and distribution of genetic diversity in vent metapopulations. Several species exhibit evidence for stepping‐stone dispersal along relatively linear, oceanic, ridge axes. Other species exhibit very high rates of gene flow, although natural barriers associated with variation in depth, deep‐ocean currents, and lateral offsets of ridge axes often subdivide populations. Various degrees of impedance to dispersal across such boundaries are products of species‐specific life histories and behaviours. Though unrelated to the size of a species range, levels of genetic diversity appear to correspond with the number of active vent localities that a species occupies within its range. Pioneer species that rapidly colonize nascent vents tend to be less subdivided and more diverse genetically than species that are slow to establish colonies at vents. Understanding the diversity and connectivity of vent metapopulations provides essential information for designing deep‐sea preserves in regions that are under consideration for submarine mining of precious metals.     

Geographical isolation and genetic differentiation: the case of Orestias ascotanensis (Teleostei: Cyprinodontidae), an Andean killifish inhabiting a highland salt pan

Orestias ascotanensis is a killifish endemic to the Ascotán salt pan in the Chilean Altiplano, where it inhabits 12 springs with different degrees of isolation. This species is a suitable model for studying the effect of serial geographical isolations on the differentiation process among populations. The present study examines the genetic variation and structure of the species using mitochondrial DNA control region sequences and eight microsatellite loci, analyzing populations across its distribution range. The evaluation of genetic variation revealed high levels of diversity within the species. The genetic structure analysis showed the existence of four differentiated groups: two groups were formed by the springs located in the northern and southern extremes of the salt pan and two groups were found in the centre of the salt pan. The latter two groups were formed by several springs, most likely as a consequence of the South American summer monsoon that could connect them and allow gene flow. The patterns of genetic differentiation appear to be determined based on the physical isolation of the populations. This isolation may be the result of a combination of factors, including geographical distance, a historical decrease in water levels and altitude differences in the springs of the salt pan. Therefore, this system is a rare example in which hydrological factors can explain genetic differentiation on a very small scale.     

Comparative phylogeography of sympatric sister species,Clevelandia ios and Eucyclogobius newberryi (Teleostei,Gobiidae), across the California Transition Zone

It is paradigmatic in marine species that greater dispersal ability often, but not always, results in greater gene flow and less population structure. Some of the exceptions may be attributable to studies confounded by comparison of species with dissimilar evolutionary histories, i.e. co-occurring species that are not closely related or species that are closely related but allopatric. Investigation of sympatric sister species, in contrast, should allow differences in phylogeographic structure to be attributed reliably to recently derived differences in dispersal ability. Here, using mitochondrial DNA control region sequence, we first confirm that Clevelandia ios and Eucyclogobius newberryi are sympatric sister taxa, then demonstrate considerably shallower phylogeographic structure in C. ios than in E. newberryi. This shallower phylogeographic structure is consistent with the higher dispersal ability of C. ios, which most likely results from the interaction of habitat and life-history differences between the species. We suggest that the paradigm will be investigated most rigorously by similar studies of other sympatric sister species, appended by thorough ecological studies, and by extending this sister-taxon approach to comparative phylogeographic studies of monophyletic clades of sympatric species.     

Genetic diversity and gene flow among southeastern Queensland koalas (Phascolarctos cinereus)

Habitat fragmentation and destruction associated with the rapid urban and rural development of southeast Queensland presents an immediate threat to the survival of koala populations within this region. A sensitive method combining heteroduplex analysis (HDA) with temperature gradient gel electrophoresis (TGGE) was optimized to detect within-species variation in a mitochondrial DNA (mtDNA) control-region fragment, approximately 670 bp in length, from the koala. Eight different haplotypes were characterized in koalas, of which four were novel. Analysis of mtDNA diversity in 96 koalas from five populations in southeast Queensland revealed that the number of haplotypes in a single population ranged from one to five, with an average within-population haplotype diversity of 0.379 +/- 0.016, and nucleotide diversity of 0.22 +/- 0.001%. Nucleotide divergence between populations averaged 0.09 +/- 0.001% and ranged from 0.00 to 0.14%. Significant genetic heterogeneity was observed among most populations, suggesting that koala populations may be spatially structured along matrilines, although this may not be universal. The limited distribution of the central phylogenetic haplotype suggested the possibility of historical population bottlenecks north of the Gold Coast, while the presence of two highly divergent haplotypes at the Moreton site may indicate the occurrence of one or more undocumented translocation events into this area.     

Genetic diversity,population structure and sex‐biased dispersal in three co‐evolving species

Genetic diversity and spatial structure of populations are important for antagonistic coevolution. We investigated genetic variation and population structure of three closely related European ant species: the social parasite Harpagoxenus sublaevis and its two host species Leptothorax acervorum and Leptothorax muscorum. We sampled populations in 12 countries and analysed eight microsatellite loci and an mtDNA sequence. We found high levels of genetic variation in all three species, only slightly less variation in the host L. muscorum. Using a newly introduced measure of differentiation (Jost’s D_est ), we detected strong population structuring in all species and less male‐biased dispersal than previously thought. We found no phylogeographic patterns that could give information on post‐glacial colonization routes – northern populations are as variable as more southern populations. We conclude that conditions for Thompson’s geographic mosaic of coevolution are ideal in this system: all three species show ample genetic variation and strong population structure.     

Divergence and molecular variation in common whelk Buccinum undatum (Gastropoda: Buccinidae) in Iceland: a trans‐Atlantic comparison

The dispersal and history of species affects their genetic population structure at both small and large geographical scales. The common whelk, Buccinum undatum, is a widespread subtidal gastropod in the North Atlantic that has no planktonic larvae and has thus limited dispersal capacity. The snail, which has been harvested by humans for centuries, is highly variable in morphology. To evaluate the population structure in the rich fishing grounds in western Iceland and its divergence from samples across the Atlantic, genetic patterns based on sequence variation in two mitochondrial (mt)DNA genes (COI and 16S) and five microsatellites were studied and compared with variation in populations from both sides of the Atlantic. Significant differences in allele and haplotype frequencies were found among samples separated by short distances along the coast of Iceland. Partition of the variation showed larger variance among samples obtained from distant regions than from neighbouring sites and genetic distances were correlated with geographical distance among populations in Europe. Phylogeographic patterns in mtDNA reveal different monophyletic lineages on both sides of the Atlantic, which predate the onset of the Ice Age and which may constitute cryptic species. Similar micro‐ and macrogeographical patterns were observed for the mtDNA and microsatellite markers, despite high frequencies of null alleles. Bayesian skyline reconstructions of the demographic history and mismatch distributions suggest that, although sizes of some populations were unaffected by Ice Age glaciations, others show signs of expansion after the Last Glacial Maximum. These phylogeographical patterns are consistent with patterns expected for low dispersal species that have survived in allopatric glacial refugial populations on both sides of the Atlantic and in deep‐sea refugia within each continent. The observed genetic structure has implications for conservation and sustainable management of the harvested populations. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 145–159.     

Isolation and characterization of nuclear microsatellite loci for the common green darner dragonfly Anax junius (Odonata: Aeshnidae) to constrain patterns of phenotypic and spatial diversity

Fourteen polymorphic microsatellite loci were developed from an enriched genomic library of the widely distributed migratory North American dragonfly species, the common green darner (Anax junius). For a group of 22 larvae, these loci averaged 16 alleles, with individual loci ranging from nine to 29 alleles. Observed heterozygosity averaged 0.784 per locus.     

Mitochondrial genetic diversity and population structure of a vulnerable freshwater fish,rock carp (Procypris rabaudi) in upper Yangtze River drainage

Rock carp (Procypris rabaudi (Tchang)) is an endemic species in the upper Yangtze River drainage. The genetic variability and population structure of eight populations (Mudong (MD), Hejiang (HJ), Wanzhou (WZ), Xishui (XS), Nantan (NT), Cangxi (CX), Tongjiang (TJ) and Wulong (WL)) were investigated based on mitochondrial DNA control region. According to the river dimensions, MD, HJ, WZ, WL and CX were defined as large river populations, while TJ, XS and NT were defined as small. The total genetic diversity level of rock carp was moderate (h = 0.858, π = 0.0079). Genetic differentiations among populations in small rivers were greater than those among populations in large rivers, and small rivers showed significant differentiation from large rivers. Analysis from the coalescent-based method showed that there were asymmetric gene flows among four large river populations (CX, HJ, MD and WZ). Demographic analyses suggested that the species as a whole and the WZ population experienced population expansion, while the HJ, NT, and MD populations experienced bottlenecks. The analysis of genetic diversity and population structure suggested that the WL, TJ, CX, NT and XS populations should be protected and managed separately, and that the HJ, MD and WZ populations should be considered as a genetic management unit.     

Comparative pattern of genetic structure in two Mediterranean killifishes Aphanius fasciatus and Aphanius iberus inferred from both mitochondrial and nuclear data

In this study, genetic variation was assessed in Aphanius fasciatus and Aphanius iberus characterized by similar ecological traits but with very different distribution ranges in the Mediterranean area. Five populations of A. iberus and five of A. fasciatus were analysed using five polymorphic microsatellite loci and partial mitochondrial control region (D‐loop) sequences. Congruent results were found with both nuclear and mitochondrial molecular markers. The results showed that similar levels of genetic divergence, based on mitochondrial control region sequences, are present among populations of A. iberus and among populations of A. fasciatus despite the very different geographic distance existing among the examined populations of the two species (low geographic distance in A. iberus and high in A. fasciatus). A possible explanation could be that the populations of A. iberus were isolated for a longer time than the populations of A. fasciatus supporting the hypothesis that the split in the lineage leading to A. iberus is older than the split in the lineage leading to A. fasciatus. The possibility that the wide circum‐Mediterranean distribution of A. fasciatus ensures the high connectivity of its populations, preventing, in some cases, local differentiation, however, cannot be ruled out.