Delimiting species boundaries and the conservation genetics of the endangered maritime ringlet butterfly (Coenonympha nipisiquit McDunnough)

Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies

We studied the evolutionary relationship of two widely distributed parapatric butterfly species, Melitaea athalia and Melitaea celadussa, using the ddRAD sequencing approach, as well as genital morphology and mtDNA data. M. athalia was retrieved as paraphyletic with respect to M. celadussa. Several cases of mito-nuclear discordance and morpho-genetic mismatch were found in the contact zone. A strongly diverged and marginally sympatric clade of M. athalia from the Balkans was revealed. An in-depth analysis of genomic structure detected high levels of admixture between M. athalia and M. celadussa at the contact zone, though not reaching the Balkan clade. The demographic modelling of populations supported the intermediate genetic make-up of European M. athalia populations with regards to M. celadussa and the Balkan clade. However, the dissimilarity matrix of genotype data (PCoA) suggested the Balkan lineage having a genetic component that is unrelated to the athalia-celadussa group. Although narrowly sympatric, almost no signs of gene flow were found between the main M. athalia group and the Balkan clade. We propose two possible scenarios on the historical evolution of our model taxa and the role of the last glacial maximum in shaping their current distribution. Finally, we discuss the complexities regarding the taxonomic delimitation of parapatric taxa.

Lepidoptera of Canada

The known Lepidoptera (moths and butterflies) of the provinces and territories of Canada are summarised, and current knowledge is compared to the state of knowledge in 1979. A total of 5405 species are known to occur in Canada in 81 families, and a further 50 species have been reported but are unconfirmed. This represents an increase of 1348 species since 1979. The DNA barcodes available for Canadian Lepidoptera are also tabulated, based on a dataset of 148,314 specimens corresponding to 5842 distinct clusters. A further yet-undiscovered 1400 species of Lepidoptera are estimated to occur in Canada. The Gelechioidea are the most poorly known major lineage of Lepidoptera in Canada. Nunavut, Prince Edward Island, and British Columbia are thought to show the greatest deficit in our knowledge of Lepidoptera. The unglaciated portions of the Yukon (Beringia), and the Pacific Maritime, Montane Cordillera, and Western Interior Basin ecozones of British Columbia are also identified as hotbeds of undescribed biodiversity.

Ecological Factors Affecting the Flight Phenology of the Endangered Coenonympha nipisiquit (Lepidoptera: Nymphalidae)

Coenonympha nipisiquit McDunnough (Lepidoptera: Nymphalidae) is an endemic butterfly species that has been recorded only in 10 salt marshes of eastern Canada. Despite obtaining the endangered status and benefiting from a conservation program, the populations of this species appear to be declining. However, a lack of information about the ecology of the species and current demographics undermines potential in-situ conservation efforts. To identify the environmental factors affecting the emergence phenology and flight period of this species, daily visual counts of adult C. nipisiquit were carried out on a daily basis from 2011 to 2015 during the flight period along transects in four marshes where the butterfly maintains a continuous presence. A series of environmental parameters was collected during the monitoring. Additive modeling indicated that the accumulation of degree-days above 7 °C from mid-May contributed to the synchronization of adult emergence and flight in C. nipisiquit and identified a number of abiotic factors having an impact on the activity and monitoring of this insect. Data also indicated that some demographic aspects of this butterfly differ between sites and confirmed that C. nipisiquit has been declining from 2011 to 2015. In conclusion, this study not only generated information critical to the adjustment of the conservation program for C. nipisiquit, but also indicated that the extirpation of this species from its natural range should remain a concern.

Deceptive single-locus taxonomy and phylogeography: Wolbachia-associated divergence in mitochondrial DNA is not reflected in morphology and nuclear markers in a butterfly species

The satyrine butterfly Coenonympha tullia (Nymphalidae: Satyrinae) displays a deep split between two mitochondrial clades, one restricted to northern Alberta, Canada, and the other found throughout Alberta and across North America. We confirm this deep divide and test hypotheses explaining its phylogeographic structure. Neither genitalia morphology nor nuclear gene sequence supports cryptic species as an explanation, instead indicating differences between nuclear and mitochondrial genome histories. Sex-biased dispersal is unlikely to cause such mito-nuclear differences; however, selective sweeps by reproductive parasites could have led to this conflict. About half of the tested samples were infected by Wolbachia bacteria. Using multilocus strain typing for three Wolbachia genes, we show that the divergent mitochondrial clades are associated with two different Wolbachia strains, supporting the hypothesis that the mito-nuclear differences resulted from selection on the mitochondrial genome due to selective sweeps by Wolbachia strains.

High latitudes and high genetic diversity: phylogeography of a widespread boreal bird, the gray jay (Perisoreus canadensis)

We describe range-wide phylogeographic variation in gray jays (Perisoreus canadensis), a boreal Nearctic corvid that occurs today primarily in recently glaciated regions. Phylogenetic analysis of mitochondrial DNA (1041 base pairs ND2 gene; N=205, 50 localities) revealed four reciprocally monophyletic groups. One widespread clade occurs across the North American boreal zone, from Newfoundland to Alaska and southwest into Utah. Three other clades occur at lower latitudes in the montane West in Colorado, the northern Rocky Mountains, and the Pacific Northwest respectively. The geographic distribution of clades in gray jays corresponds with a general pattern that is emerging for boreal taxa, having one widespread northern clade and one or more geographically restricted southwestern clades. Population genetic analyses indicate that the larger boreal clade is genetically structured and harbors significantly more genetic diversity than those clades occurring at lower latitudes. Species distribution modeling (SDM) revealed multiple putative Pleistocene refugia including several occurring at higher latitudes. We suggest that multiple post-glacial colonization routes, some of which originate from these northern refugia, are responsible for the relatively high genetic diversity at high latitudes. Conversely, lower latitude clades show little variation, probably as a result of historical restriction to smaller geographical areas with smaller long-term population sizes. This 'upside-down' pattern of genetic diversity contrasts with the conventional view that populations of north-temperate species occupying previously glaciated habitats should possess lower levels of diversity than their southern counterparts.

An earthworm riddle: systematics and phylogeography of the Spanish lumbricid Postandrilus

Background

As currently defined, the genus Postandrilus Qui and Bouché, 1998, (Lumbricidae) includes six earthworm species, five occurring in Majorca (Baleares Islands, western Mediterranean) and another in Galicia (NW Spain). This disjunct and restricted distribution raises some interesting phylogeographic questions: (1) Is Postandrilus distribution the result of the separation of the Baleares-Kabylies (BK) microplate from the proto-Iberian Peninsula in the Late Oligocene (30–28 Mya) – vicariant hypothesis? (2) Did Postandrilus diversify in Spain and then colonize the Baleares during the Messinian salinity crisis (MSC) 5.96–5.33 Mya – dispersal hypothesis? (3) Is the distribution the result of a two-step process – vicariance with subsequent dispersal?

Methodology/Principal Findings

To answer these questions and assess Postandrilus evolutionary relationships and systematics, we collected all of the six Postandrilus species (46 specimens – 16 locations) and used Aporrectodea morenoe and three Prosellodrilus and two Cataladrilus species as the outgroup. Regions of the nuclear 28S rDNA and mitochondrial 16S rDNA, 12S rDNA, ND1, COII and tRNA genes (4,666 bp) were sequenced and analyzed using maximum likelihood and Bayesian methods of phylogenetic and divergence time estimation. The resulting trees revealed six new Postandrilus species in Majorca that clustered with the other five species already described. This Majorcan clade was sister to an Iberian clade including A. morenoe (outgroup) and Postandrilus bertae. Our phylogeny and divergence time estimates indicated that the split between the Iberian and Majorcan Postandrilus clades took place 30.1 Mya, in concordance with the break of the BK microplate from the proto-Iberian Peninsula, and that the present Majorcan clade diversified 5.7 Mya, during the MSC.

Conclusions

Postandrilus is highly diverse including multiple cryptic species in Majorca. The genus is not monophyletic and invalid as currently defined. Postandrilus is of vicariant origin and its radiation began in the Late Oligocene.

Genetic signature of reproductive manipulation in the phylogeography of the bat fly, Trichobius major

The bat fly (Trichobius major) is a blood-feeding ectoparasite of the cave myotis (Myotis velifer). A recent mitochondrial DNA (mtDNA) study examining population structure of T. major in the South Central United States detected a single haplotype from all individuals examined (N = 48 from 12 different caves), representing one of only a few known examples of such widespread mtDNA uniformity. We examined nuclear genetic diversity using amplified fragment length polymorphism and detected high levels of nuclear genetic diversity in all populations sampled. Amplified fragment length polymorphism analyses indicated significant levels of gene flow among caves >700 km apart, suggesting the absence of mtDNA diversity in T. major is the result of a selective sweep, not a demographic event (i.e., a recent bottleneck). One mechanism by which mtDNA sweeps occur in arthropods is through bacterial parasites that manipulate host reproduction and mtDNA inheritance. We used PCR to test for the presence of all known reproductive parasites and detected a widespread infection (91.33% infection rate) of T. major with a novel Arsenophonus bacterium, as well as the infection of 2 individuals (1.16% infection rate) with a novel strain of Rickettsia. We discuss the implications for T. major phylogeography and the necessity of a bigenomic approach in arthropod population genetics.

Phylogeographic structure of jack pine (Pinus banksiana; Pinaceae) supports the existence of a coastal glacial refugium in northeastern North America

PREMISE OF THE STUDY

The genetic structure of jack pine (Pinus banksiana Lamb.), a North American boreal conifer with large longitudinal distribution, was investigated to test for the possible existence of a genetically distinct lineage in the Maritimes region in northeastern North America, which could be indicative of a mid-latitude coastal refuge during the last glaciation. •

METHODS

One maternally inherited mitochondrial DNA (mtDNA) minisatellite marker and four paternally inherited chloroplast DNA (cpDNA) microsatellite markers were used to assess the range-wide geographical structure of jack pine populations with particular focus on northeastern North America. •

KEY RESULTS

The populations from the Maritimes region presented a unique mtDNA background characterized by very low diversity and the preponderance of a distinctive mitotype. The distribution of cpDNA diversity was not spatially structured, though three chlorotypes were restricted to the east. •

CONCLUSIONS

MtDNA data suggest that populations from the Maritimes region derive from a genetically depauperated north-coastal refugium. Contrastingly, the much higher geographical uniformity observed for cpDNA variation indicates that gene flow by pollen had been much more effective than seed gene flow at homogenizing population structure.

Species delimitation: a case study in a problematic ant taxon

Species delimitation has been invigorated as a discipline in systematics by an influx of new character sets, analytical methods, and conceptual advances. We use genetic data from 68 markers, combined with distributional, bioclimatic, and coloration information, to hypothesize boundaries of evolutionarily independent lineages (species) within the widespread and highly variable nominal fire ant species Solenopsis saevissima, a member of a species group containing invasive pests as well as species that are models for ecological and evolutionary research. Our integrated approach uses diverse methods of analysis to sequentially test whether populations meet specific operational criteria (contingent properties) for candidacy as morphologically cryptic species, including genetic clustering, monophyly, reproductive isolation, and occupation of distinctive niche space. We hypothesize that nominal S. saevissima comprises at least 4-6 previously unrecognized species, including several pairs whose parapatric distributions implicate the development of intrinsic premating or postmating barriers to gene flow. Our genetic data further suggest that regional genetic differentiation in S. saevissima has been influenced by hybridization with other nominal species occurring in sympatry or parapatry, including the quite distantly related Solenopsis geminata. The results of this study illustrate the importance of employing different classes of genetic data (coding and noncoding regions and nuclear and mitochondrial DNA [mtDNA] markers), different methods of genetic data analysis (tree-based and non-tree based methods), and different sources of data (genetic, morphological, and ecological data) to explicitly test various operational criteria for species boundaries in clades of recently diverged lineages, while warning against over reliance on any single data type (e.g., mtDNA sequence variation) when drawing inferences.