Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera)

The Kuhl’s pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes.     

Microsatellite markers and cytoplasmic sequences reveal contrasting pattern of spatial genetic structure in the red algae species complex Mazzaella laminarioides

Mazzaella laminarioides is a common haploid‐diploid red alga that forms dense beds. This alga has a wide distributional range, covering 3,500 km of the Chilean coast, but is restricted to high rocky intertidal zones. Recently, the existence of three highly divergent genetic lineages was demonstrated for this taxon, and two cytoplasmic markers were used to determine that these lineages are distributed in strict parapatry. Here, using 454 next‐generation sequencing, we developed polymorphic microsatellite loci that cross amplify in all three cytoplasmic lineages. Six sites (i.e., two sites within each lineage) were analyzed using nine microsatellite loci. Our work shows that, although substantial cytoplasmic differentiation occurs within M. laminarioides, the microsatellite loci did not retrieve three nuclear genetic clusters as expected. Indeed, while the northernmost and southernmost cytoplasmic lineages form two strongly divergent nuclear groups characterized by diagnostic alleles, the third cytoplasmic lineage did not form a third nuclear independent group. It is possible that inter‐lineage gene exchange has occurred, particularly at sites along the contact zone between the different cytoplasmic lineages. This nuclear‐cytoplasmic incongruence in M. laminarioides could be explained by incomplete lineage sorting of the nuclear genes or asymmetric introgressive hybridization between the lineages. Finally, highly significant heterozygote deficiencies (suggesting occurrence of intergametophytic selfing) were observed in the three small northernmost sites while the large southernmost sites generally approached panmixia.     

Microsatellite analysis supports the existence of three cryptic species within the bumble bee <Emphasis Type="Italic">Bombus lucorum sensu lato</Emphasis>

Mitochondrial cytochrome oxidase I (COI) partial sequences are widely used in taxonomy for species identification. Increasingly, these sequence identities are combined with modelling approaches to delineate species. Yet the validity of species delineation based on such DNA ‘barcodes’ is rarely tested and may be called into question by phenomena such as ancestral polymorphisms in DNA sequences, phylogeographic divergence, mitochondrial introgression and hybridization, or distortion of mitochondrial inheritance through such factors as Wolbachia infection. The common and widespread European bumble bee Bombus lucorum s. lato contains three distinct mitochondrial DNA lineages that are assumed to represent three cryptic species, namely Bombus cryptarum, B. lucorum s. str. and B. magnus. To test whether nuclear gene pools of the three putative species were differentiated, we genotyped 304 sympatric members of the lucorum complex (54 B. cryptarum females, 168 B. lucorum s. str. females and 82 B. magnus females, as defined using mtDNA COI haplotypes) from 11 localities spread across the island of Ireland at seven nuclear microsatellite loci. Multilocus genotypes clustered into three discrete groups that largely corresponded to the three mtDNA lineages: B. cryptarum, B. lucorum s. str. and B. magnus. The good fit of mitochondrial haplotype to nuclear (microsatellite) genotypic data supports the view that these three bumble bee taxa are reproductively isolated species, as well as providing a vindication of species identity using so-called DNA barcodes.     

Invasion facilitates hybridization with introgression in the Rattus rattus species complex

Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two nuclear gene sequences (Atp5a1 and DHFR) and nine microsatellite loci to examine the distribution of three invasive black rat lineages (Rattus tanezumi, Rattus rattus I and R. rattus IV) in the United States and Asia and to determine the extent of hybridization among these taxa. Our analyses revealed two mitochondrial lineages that have spread to multiple continents, including a previously undiscovered population of R. tanezumi in the south‐eastern United States, whereas the third lineage (R. rattus IV) appears to be confined to Southeast Asia. Analyses of nuclear DNA (both sequences and microsatellites) suggested significant hybridization is occurring among R. tanezumi and R. rattus I in the United States and also suggest hybridization between R. tanezumi and R. rattus IV in Asia, although further sampling of the latter species pair in Asia is required. Furthermore, microsatellite analyses suggest unidirectional introgression from both R. rattus I and R. rattus IV into R. tanezumi. Within the United States, introgression appears to be occurring to such a pronounced extent that we were unable to detect any nuclear genetic signal for R. tanezumi, and a similar pattern was detected in Asia.     

High mitochondrial diversity in geographically widespread butterflies of Madagascar: A test of the DNA barcoding approach

The standardized use of mitochondrial cytochrome c oxidase subunit I (COI) gene sequences as DNA barcodes has been widely promoted as a high-throughput method for species identification and discovery. Species delimitation has been based on the following criteria: (1) monophyletic association and less frequently (2) a minimum 10× greater divergence between than within species. Divergence estimates, however, can be inflated if sister species pairs are not included and the geographic extent of variation within any given taxon is not sampled comprehensively. This paper addresses both potential biases in DNA divergence estimation by sampling range-wide variation in several morphologically distinct, endemic butterfly species in the genus Heteropsis, some of which are sister taxa. We also explored the extent to which mitochondrial DNA from the barcode region can be used to assess the effects of historical rainforest fragmentation by comparing genetic variation across Heteropsis populations with an unrelated forest-associated taxon Saribia tepahi. Unexpectedly, generalized primers led to the inadvertent amplification of the endosymbiont Wolbachia, undermining the use of universal primers and necessitating the design of genus-specific COI primers alongside a Wolbachia-specific PCR assay. Regardless of the high intra-specific genetic variation observed, most species satisfy DNA barcoding criteria and can be differentiated in the nuclear phylogeny. Nevertheless, two morphologically distinguishable candidate species fail to satisfy the barcoding 10× genetic distance criterion, underlining the difficulties of applying a standard distance threshold to species delimitation. Phylogeographic analysis of COI data suggests that forest fragmentation may have played an important role in the recent evolutionary diversification of these butterflies. Further work on other Malagasy taxa using both mitochondrial and nuclear data will provide better insight into the role of historical habitat fragmentation in species diversification and may potentially contribute to the identification of priority areas for conservation.     

Cytonuclear discordance in the Florida Everglades invasive Burmese python (Python bivittatus) population reveals possible hybridization with the Indian python (P. molurus)

The invasive Burmese python (Python bivittatus) has been reproducing in the Florida Everglades since the 1980s. These giant constrictor snakes have caused a precipitous decline in small mammal populations in southern Florida following escapes or releases from the commercial pet trade. To better understand the invasion pathway and genetic composition of the population, two mitochondrial (mtDNA) loci across 1,398 base pairs were sequenced on 426 snakes and 22 microsatellites were assessed on 389 snakes. Concatenated mtDNA sequences produced six haplotypes with an average nucleotide and haplotype diversity of π = 0.002 and h = 0.097, respectively. Samples collected in Florida from morphologically identified P. bivittatus snakes were similar to published cytochrome oxidase 1 and cytochrome b sequences from both P. bivittatus and Python molurus and were highly divergent (genetic distances of 5.4% and 4.3%, respectively). The average number of microsatellite alleles and expected heterozygosity were N_A = 5.50 and H_E = 0.60, respectively. Nuclear Bayesian assignment tests supported two genetically distinct groups and an admixed group, not geographically differentiated. The effective population size (N_E = 315.1) was lower than expected for a population this large, but reflected the low genetic diversity overall. The patterns of genetic diversity between mtDNA and microsatellites were disparate, indicating nuclear introgression of separate mtDNA lineages corresponding to cytonuclear discordance. The introgression likely occurred prior to the invasion, but genetic information on the native range and commercial trade is needed for verification. Our finding that the Florida python population is comprised of distinct lineages suggests greater standing variation for adaptation and the potential for broader areas of suitable habitat in the invaded range.     

DNA barcoding commercially important fish species of Turkey

DNA barcoding was used in the identification of 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. A total of 1765 DNA barcodes using a 654‐bp‐long fragment of the mitochondrial cytochrome c oxidase subunit I gene were generated for 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. These species belong to 70 genera, 40 families and 19 orders from class Actinopterygii, and all were associated with a distinct DNA barcode. Nine and 12 of the COI barcode clusters represent the first species records submitted to the BOLD and GenBank databases, respectively. All COI barcodes (except sequences of first species records) were matched with reference sequences of expected species, according to morphological identification. Average nucleotide frequencies of the data set were calculated as T = 29.7%, C = 28.2%, A = 23.6% and G = 18.6%. Average pairwise genetic distance among individuals were estimated as 0.32%, 9.62%, 17,90% and 22.40% for conspecific, congeneric, confamilial and within order, respectively. Kimura 2‐parameter genetic distance values were found to increase with taxonomic level. For most of the species analysed in our data set, there is a barcoding gap, and an overlap in the barcoding gap exists for only two genera. Neighbour‐joining trees were drawn based on DNA barcodes and all the specimens clustered in agreement with their taxonomic classification at species level. Results of this study supported DNA barcoding as an efficient molecular tool for a better monitoring, conservation and management of fisheries.     

Range‐wide population structure of European sea bass Dicentrarchus labrax

The euryhaline European sea bass Dicentrarchus labrax L., inhabiting the coasts of the eastern Atlantic Ocean and Mediterranean Sea, has had many opportunities for differentiation throughout its large natural range. However, evidence for this has been incompletely documented geographically and with an insufficient number of markers. Therefore, its full range was sampled at 22 sites and individuals were genotyped with a suite of mapped markers, including 14 microsatellite loci (N = 536) and 46 neutral or gene‐linked single nucleotide polymorphisms (SNPs; N = 644). We confirm that the Atlantic and Mediterranean basins harbour two distinct lineages. Within the Atlantic Ocean no pattern was obvious based on the microsatellite and SNP genotypes, except for a subtle difference between South‐eastern and North‐eastern Atlantic sea bass attributed to limited introgression of alleles of Mediterranean origin. SNP genotypes of the Mediterranean lineage differentiated into three groups, probably under the influence of geographical isolation. The Western Mediterranean group showed genetic homogeneity without evidence for outlier loci. The Adriatic group appeared as a distinct unit. The Eastern Mediterranean group showed a longitudinal gradient of genotypes and most interestingly an outlier locus linked to the somatolactin gene. Overall, the spatial pattern fits those observed with other taxa of between‐basin segregation and within‐basin connectivity, which concurs well with the swimming capabilities of European sea bass. Evidence from a few outlier loci in this and other studies encourages further exploration of its regional connectivity and adaptive evolution.     

Genetic variation in Tertiary relics: The case of eastern‐Mediterranean Abies (Pinaceae)

The eastern‐Mediterranean Abies taxa, which include both widely distributed species and taxa with minuscule ranges, represent a good model to study the impacts of range size and fragmentation on the levels of genetic diversity and differentiation. To assess the patterns of genetic diversity and phylogenetic relationships among eastern‐Mediterranean Abies taxa, genetic variation was assessed by eight nuclear microsatellite loci in 52 populations of Abies taxa with a focus on those distributed in Turkey and the Caucasus. Both at the population and the taxon level, the subspecies or regional populations of Abies nordmanniana s.l. exhibited generally higher allelic richness, private allelic richness, and expected heterozygosity compared with Abies cilicica s.l. Results of both the Structure analysis and distance‐based approaches showed a strong differentiation of the two A. cilicica subspecies from the rest as well as from each other, whereas the subspecies of A. nordmanniana were distinct but less differentiated. ABC simulations were run for a set of scenarios of phylogeny and past demographic changes. For A. ×olcayana, the simulation gave a poor support for the hypothesis of being a taxon resulting from a past hybridization, the same is true for Abies equi‐trojani: both they represent evolutionary branches of Abies bornmuelleriana.     

Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, COI and intron 7 of the β-fibrinogen gene in avian molecular systematics

The common raven (Corvus corax) is one of the most widely distributed and recognizable avian species in the world. Recent molecular work, however, described two mitochondrial lineages of the common raven, termed the Holarctic clade and the California clade, and questioned the monophyly of this taxon by placing the Chihuahuan raven (C. cryptoleucus) sister to the California clade. We evaluated this phylogenetic hypothesis with additional sequence data and increased taxon sampling. We used ～3.7 kb of DNA sequence data from sections of the mitochondrial coding genes COI, cyt b and ND4, a fragment of the non‐coding mitochondrial DNA control region, and the entire intron 7 of the nuclear β‐fibrinogen gene (β‐fibint 7). We combined these DNA sequence data to erect hypotheses of relationships for lineages of the common raven and related taxa. Maximum parsimony, maximum likelihood, and Bayesian methods yield a paraphyletic common raven. These analyses nest the Chihuahuan raven within the common raven, with strong support for a sister relationship between the Chihuahuan raven and the California clade. In addition, the pied crow (C. albus) is also nested within the common raven, and is sister to the Holarctic clade. Our analyses reveal the challenge of determining phylogenetic relationships and species boundaries in this morphologically conservative genus, and suggest that future molecular work with increased taxon sampling will uncover cryptic species and novel evolutionary relationships. Lastly, this survey is one of a growing number of avian phylogenetic studies to employ either β‐fibint 7 or COI, and the first to use ND4. We developed a simple procedure for comparing rates of evolution in molecular markers, and show that in Corvus the nuclear intron β‐fibint 7 is evolving at a considerably slower pace than the mitochondrial markers, while COI is evolving at a slower rate than cyt b, and ND4 approximately the same rate as cyt b. Hence, β‐fibint 7 and other individual nuclear introns may have limited utility in resolving relationships among recently evolved taxa, whereas both COI and ND4 should be useful in a wide range of avian molecular genetic investigations.     

Clonal diversity,clonal persistence and rapid taxon replacement in natural populations of species and hybrids of the Daphnia longispina complex

Hybridization is common among cyclical parthenogens, especially in zooplankton species assemblages of the genus Daphnia. To explore hybridization dynamics and the extent of clonal diversity in the Daphnia longispina complex, we analysed population structure in eight permanent lakes. Based on 15 microsatellite loci, three major taxonomic units emerged: two species, D. galeata and D. longispina and their F1 hybrids, supported by factorial correspondence analysis and two Bayesian methods. At the same time, the detection of backcross classes differed between methods. Mean clonal diversity was lowest in the F1 hybrids, as expected from the high rate of asexual reproduction. Within taxa, replicated genotypes were of clonal origin, but clonal lineages persisted in subsequent years in only one of three resampled lakes. In another lake, the taxon composition changed from being dominated by hybrids to complete dominance by one parental taxon. Such a year‐to‐year taxon replacement has not been reported for the D. longispina complex before. Our data on this hybrid complex illustrate that high‐resolution genotyping is essential for the understanding of ecological and evolutionary outcomes of hybridization in partially clonal taxa.     

Molecular patterns of introgression in a classic hybrid zone between the Australian tree frogs,Litoria ewingii and L. paraewingi: evidence of a tension zone

Hybrid zones provide a rare opportunity to explore the processes involved in reproductive isolation and speciation. The southern hybrid zone between the southeastern Australian tree frogs Litoria ewingii and L. paraewingi has been comprehensively studied over the last 40 years, primarily using reproductive compatibility experiments and male advertisement calls. We used mitochondrial DNA (mtDNA) and eight nuclear microsatellite markers to characterize this hybrid zone along a historically studied transect and to test various dispersal‐dependent and dispersal‐independent hybrid zone models. The species are genetically distinct and the level of hybridization within the contact zone is low, with the majority of admixed individuals representing later‐generation hybrids. Based on previous experimental genetic compatibility studies, we predicted that hybrids with L. paraewingi mtDNA would be more frequent than hybrids with L. ewingii mtDNA. Surprisingly, a greater proportion of the identified hybrids had L. ewingii mtDNA. Geographical cline analyses showed a sharp transition in allele frequencies across the transect, and both the mtDNA and microsatellite data showed concordant cline centres, but were best supported by a model that allowed width to vary. Overall, the L. ewingii–L. paraewingi hybrid zone is best characterized as a tension zone, due to the narrow cline width, concordant genetic clines and low levels of hybridization.     

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod

Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open‐ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite F_ST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.     

Karyological studies of some representatives of <Emphasis Type="Italic">Tanacetum</Emphasis> L. (Anthemideae-Asteraceae) from north-east Anatolia

The karyotypes of nine Tanacetum taxa distributed in north-east Anatolia, Turkey, were determined and evaluated by cluster analysis and principal-components analysis. Chromosome numbers were 2n = 2x = 18 (8 taxa) and 4x = 36 (1 taxon). Somatic chromosome numbers of two taxa and a new ploidy level in one taxon are reported for the first time. Karyotype analysis indicated that chromosomes of Tanacetum taxa have predominantly median centromeres. The taxa studied differed significantly in the size of the short arms and long arms, and the arm ratio of each pair of homologous chromosomes, indicating structural rearrangements of the chromosomes have been involved in diversification of the taxa. They were placed in 2A, 3A, and 2B of Stebbins’ karyotype classification, showing the presence of a primitive symmetrical karyotype in the genus. Several systematic and evolutionary aspects of the genus are discussed on the basis of karyological data.     

Genetic population structure of buckeye butterflies (Junonia) from Argentina

There are nine named species of buckeye butterflies (genus Junonia Hübner) in the Western Hemisphere. There is considerable geographic variation within Junonia species, and possible ongoing hybridization between species, suggesting that Junonia may be a ring species, but also making this a very difficult group to define taxonomically. We tried to determine whether two forms of Junonia from Argentina – conventionally referred to as Junonia genoveva hilaris C. & R. Felder, the light buckeye butterfly, and Junonia evarete flirtea (Fabricius), the dark buckeye butterfly – were genetically distinct species or simply colour forms of a single species using morphological characters, mitochondrial cytochrome oxidase I (COI) DNA barcodes, nuclear wingless (wg) locus DNA sequences, and anonymous nuclear Randomly Amplified Fingerprints (RAF). Phylogenetic analysis of COI identified two distinct mitochondrial haplotypes that differ by about 4% sequence divergence; one confined to light‐coloured Junonia specimens and one shared between some light‐coloured Junonia and all of dark‐coloured Junonia specimens. Analysis of nuclear wingless sequences revealed 32 alleles among 22 Junonia specimens and showed significant genetic differentiation between light‐coloured and dark‐coloured Junonia. Analysis of RAF genotypes suggests that there are actually three genetically distinct Junonia populations in Argentina: two with light wing coloration, and one with dark wing coloration. Genetic evidence of recent hybridization among these populations was also observed, consistent with the ring species hypothesis. Careful comparisons of morphological characters between Argentinian Junonia and Junonia species from elsewhere in South America suggests that the two light‐coloured populations correspond to J. genoveva and either a genetically disparate population of the same species or an undescribed cryptic Junonia species, The dark‐coloured population may correspond to J. wahlbergi Brévignon. Our data suggest that COI DNA barcodes by themselves are not very useful for studying Junonia taxonomy, population structure or evolution.     

Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates

Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island–mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long‐standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations.     

Extrinsic and intrinsic factors influence fitness in an avian hybrid zone

The effects of hybridization on evolutionary processes are primarily determined by the differential between hybrid and parental species fitness. Assessing the impacts of hybridization can be challenging, however, as determining the relationship between individual fitness and the extent of introgression in wild populations is difficult. We evaluated the fitness consequences of hybridization for pure and hybrid females in a hybrid zone between two tidal marsh birds, the saltmarsh sparrow (Ammodramus caudacutus), a salt marsh obligate, and Nelson's sparrow (A. nelsoni), which has a broader ecological niche and a much younger evolutionary association with salt marshes. Biotic stressors associated with nesting in tidal environments suggest an important role for differential adaptation in shaping hybrid zone dynamics, with saltmarsh sparrows predicted to be better adapted to nesting in salt marshes. We collected DNA samples from adults (n = 394) and nestlings (n = 431) to determine the extent of introgression using 12 microsatellite loci and tested for the influence of extrinsic (nest placement) and intrinsic (genotype) factors on female reproductive success. We monitored nests (n = 228), collected data on reproductive output, and estimated daily nest survival rates using female genotype and nest characteristics as covariates. To test for reduced survival of hybrid females, we also used capture data to assess the distribution of admixed male and female individuals across age classes. Reproductive success of females varied by genotypic class, but hybrids did not have intermediate success as predicted. Instead, we found that pure Nelson's sparrows had, on average, 33% lower hatching success than any other genotype, whereas F1/F2 hybrids, backcrossed Nelson's sparrows, and backcrossed and pure saltmarsh sparrows all had similar hatching success. We found no effect of genotype or nest placement on daily nest survival probabilities. However, hybrid individuals with a higher proportion of saltmarsh sparrow alleles exhibit nesting behaviours better suited to nesting successfully in tidal marshes. Further, while the proportion of F1/F2 individuals was similar between nestling and adult males, we found that the proportion of F1/F2 individuals was 2.3 times greater in nestling females compared with adult females, indicating reduced survival of F1 females. We conclude that differences in reproductive success among pure and admixed individuals coupled with intrinsic mechanisms (reduced survival in F1 females) shape hybrid zone dynamics in this system.     

Delineating closely related species with DNA barcodes for routine biological monitoring

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Microsatellite loci for the critically endangered Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) and other Ambystoma taxa

The imperiled Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) is a geographically isolated lineage of the long-toed salamander species complex. Recovery of this taxon requires understanding its population genetic structure, which is necessary to identify critical habitat. To assess the population structure of A. m. croceum, I developed primers for 17 microsatellite loci and evaluated their performance. Polymorphism ranged from 3 to 10 alleles per locus, with an average of 6.3 per locus. Mean observed and expected heterozygosity were similar (H _O = 0.678; H _E = 0.708), with one locus demonstrating heterozygote deficiency. The performance of these and previously identified microsatellite loci were also characterized for two other long-toed salamander lineages, as well as two other species of Ambystoma. The utility of these markers has similar and overlapping applications for conservation and population genetics studies of other Ambystoma taxa, and will provide a basis for revising the recovery plan for A. m. croceum, particularly for designating corridors among interacting breeding populations and upland areas, and identifying areas where gene flow should be restored.