Divergent Mitochondrial Lineages Research Articles

Completing a taxonomic puzzle: integrative review of geckos of the Paroedura bastardi species complex (Squamata, Gekkonidae)

The Paroedura bastardi clade, a subgroup of the Madagascan gecko genus Paroedura, currently comprises four nominal species: P. bastardi, supposedly widely distributed in southern and western Madagascar, P. ibityensis, a montane endemic, and P. tanjaka and P. neglecta, both restricted to the central west region of the island. Previous work has shown that Paroedura bastardi is a species complex with several strongly divergent mitochondrial lineages. Based on one mitochondrial and two nuclear markers, plus detailed morphological data, we undertake an integrative revision of this species complex. Using a representative sampling for seven nuclear and five mitochondrial genes we furthermore propose a phylogenetic hypothesis of relationships among the species in this clade. Our analyses reveal at least three distinct and independent evolutionary lineages currently referred to P. bastardi. Conclusive evidence for the species status of these lineages comes from multiple cases of syntopic occurrence without genetic admixture or morphological intermediates, suggesting reproductive isolation. We discuss the relevance of this line of evidence and the conditions under which concordant differentiation in unlinked loci under sympatry provides a powerful approach to species delimitation, and taxonomically implement our findings by (1) designating a lectotype for Paroedura bastardi, now restricted to the extreme South-East of Madagascar, (2) resurrecting of the binomen Paroedura guibeae Dixon & Kroll, 1974, which is applied to the species predominantly distributed in the South-West, and (3) describing a third species, Paroedura rennerae sp. nov., which has the northernmost distribution within the species complex.

Revision of the Litoria watjulumensis (Anura: Pelodryadidae) group from the Australian monsoonal tropics, including the resurrection of L. spaldingi.

We show that the Wotjulum frog, Litoria watjulumensis (Copland, 1957), comprises two deeply divergent mitochondrial DNA lineages that are also reciprocally monophyletic for a nuclear gene locus and have discrete distributions. The taxa are differentiated in multivariate analysis of shape but show no appreciable differences in colour and pattern. The two taxa differ substantially in the degree of female biased sexual size dimorphism, with the western taxon showing considerably more pronounced dimorphism. We subsequently resurrect Litoria (Hyla) spaldingi (Hosmer, 1964) for populations from east of the Daly River system in the Northern Territory through to western Queensland and restrict L. watjulumensis to populations from the Kimberley region of north-western Australia and the Victoria River system of the western Northern Territory. The complex advertisement call of L. spaldingi is described for the first time.

A multidisciplinary approach to identify priority areas for the monitoring of a vulnerable family of fishes in Spanish Marine National Parks

BackgroundSyngnathid fishes (Actinopterygii, Syngnathidae) are flagship species strongly associated with seaweed and seagrass habitats. Seahorses and pipefishes are highly vulnerable to anthropogenic and environmental disturbances, but most species are currently Data Deficient according to the IUCN (2019), requiring more biological and ecological research. This study provides the first insights into syngnathid populations in the two marine Spanish National Parks (PNIA—Atlantic- and PNAC—Mediterranean). Fishes were collected periodically, marked, morphologically identified, analysed for size, weight, sex and sexual maturity, and sampled for stable isotope and genetic identification. Due the scarcity of previous information, habitat characteristics were also assessed in PNIA.ResultsSyngnathid diversity and abundance were low, with two species identified in PNIA (Hippocampus guttulatus and Syngnathus acus) and four in PNAC (S. abaster, S. acus, S. typhle and Nerophis maculatus). Syngnathids from both National Parks (NP) differed isotopically, with much lower δ15N in PNAC than in PNIA. The dominant species were S. abaster in PNAC and S. acus in PNIA. Syngnathids preferred less exposed sites in macroalgal assemblages in PNIA and Cymodocea meadows in PNAC. The occurrence of very large specimens, the absence of small-medium sizes and the isotopic comparison with a nearby population suggest that the population of Syngnathus acus (the dominant syngnathid in PNIA) mainly comprised breeders that migrate seasonally. Mitochondrial cytochrome b sequence variants were detected for H. guttulatus, S. acus, and S. abaster, and a novel 16S rDNA haplotype was obtained in N. maculatus. Our data suggest the presence of a cryptic divergent mitochondrial lineage of Syngnathus abaster species in PNAC.ConclusionsThis is the first multidisciplinary approach to the study of syngnathids in Spanish marine NPs. Habitat preferences and population characteristics in both NPs differed. Further studies are needed to assess the occurrence of a species complex for S. abaster, discarding potential misidentifications of genus Syngnathus in PNAC, and evaluate migratory events in PNIA. We propose several preferential sites in both NPs for future monitoring of syngnathid populations and some recommendations for their conservation.

A new fanged frog in the Limnonectes kuhlii complex (Anura: Dicroglossidae) from northeastern Cambodia.

The Limnonectes kuhlii complex is a group of morphologically similar species of fanged frogs distributed across much of mainland and insular Southeast Asia. Many new species in this complex have been described in recent years, primarily on the basis of mitochondrial DNA divergence corroborated by differences in linear measurements and qualitative characters. Males in this species complex develop enlarged heads at sexual maturity, but the degree of head enlargement varies among mature males, even within the same population. We evaluated the utility of body length (snout-vent length minus head length) in descriptive statistics and in size-adjusting measurements for traditional morphometric analysis, as well as a landmark-based geometric morphometric analysis of male head shape, in Indochinese species of the L. kuhlii complex. The analyses supported quantitative and qualitative morphological distinction of a divergent mitochondrial lineage of the L. kuhlii complex in northeastern Cambodia, and the lineage is described as a new species. Limnonectes fastigatus sp. nov. differs from its closest relatives and from geographically proximate members of the complex by having the combination of elongated, slender odontoids; nuptial pads on the first finger; immaculate belly; significantly different body length-adjusted measurements in both sexes; and a significantly different male head shape. The new species is the only member of the L. kuhlii complex known from Cambodia.

Locomotor responses to salt stress in native and invasive mud-tidal gastropod populations (Batillaria).

Plasticity in salt tolerance can be crucial for successful biological invasions of novel habitats by marine gastropods. The intertidal snail Batillaria attramentaria, which is native to East Asia but invaded the western shores of North America from Japan 80 years ago, provides an opportunity to examine how environmental salinity may shape behavioral and morphological traits. In this study, we compared the movement distance of four B. attramentaria populations from native (Korea and Japan) and introduced (United States) habitats under various salinity levels (13, 23, 33, and 43 PSU) during 30 days of exposure in the lab. We sequenced a partial mitochondrial CO1 gene to infer phylogenetic relationships among populations and confirmed two divergent mitochondrial lineages constituting our sample sets. Using a statistical model‐selection approach, we investigated the effects of geographic distribution and genetic composition on locomotor performance in response to salt stress. Snails exposed to acute low salinity (13 PSU) reduced their locomotion and were unable to perform at their normal level (the moving pace of snails exposed to 33 PSU). We did not detect any meaningful differences in locomotor response to salt stress between the two genetic lineages or between the native snails (Japan vs. Korea populations), but we found significant locomotor differences between the native and introduced groups (Japan or Korea vs. the United States). We suggest that the greater magnitude of tidal salinity fluctuation at the US location may have influenced locomotor responses to salt stress in introduced snails.

Conservation units and historical matrilineal structure in the tequila bat (Leptonycteris yerbabuenae)

The tequila bat (Leptonycteris yerbabuenae) has been the focus of intense research over the last 20 years. Its close relationship to economically important plants used in the production of tequila and mezcal has raised awareness of its importance as both a keystone mutualist and a mobile link between habitats. The study of its migratory habits has shed light on patterns of movement and routes that animals follow, and how these movements affect the genetic composition of its populations. Delimiting the boundaries of breeding populations is of great importance for conservation, however, determining these boundaries has been difficult for L. yerbabuenae. Understanding the demographic history of the species could provide additional insight into current differences of its migratory behaviour and reproductive asynchrony. Here, we report evidence of historical matrilineal structure by comparing partial sequences of mtDNA cytochrome b (bp 306) and Control Region (497 bp) and inferred patterns of differentiation across the distribution of L. yerbabuenae in Mexico. Our population-based statistical analysis suggests panmixia among colonies with low genetic differentiation between north-western and south-eastern colonies. Neutrality tests of the Control Region indicate the presence of two divergent mitochondrial lineages in the south-east and the north-west of Mexico. Our results corroborate recent population expansion events, possibly due to the influence of physical barriers to migration and historical population demography. We recognize one single population but two Conservation Units (CUs) based on differences in reproductive phenology, migratory behaviour and the evidence of two matrilineal lineages as found in this study. We recommend the use of large-scale genomic datasets to better delimit fine-scale population structure in the future.

Lineage diversity, morphological and genetic divergence in Daphnia magna (Crustacea) among Chinese lakes at different altitudes

The biogeography and genetic structure of aquatic zooplankton populations remains understudied in the Eastern Palearctic, especially the Qinghai-Tibetan Plateau. Here, we explored the population-genetic diversity and structure of the cladoceran waterflea Daphnia magna found in eight (out of 303 investigated) waterbodies across China. The three Tibetan D. magna populations were detected within a small geographical area, suggesting these populations have expanded from refugia. We detected two divergent mitochondrial lineages of D. magna in China: one was restricted to the Qinghai-Tibetan Plateau and the other was present in lowland China. Several different haplotypes in the Qinghai-Tibetan Plateau were most similar to those from various parts of Siberia, suggesting that as a source region. We also found substantial genetic differentiation between D. magna populations from the Qinghai-Tibetan Plateau and those from lowland China. Moreover, significant morphological differences were identified: D. magna from the Qinghai-Tibetan Plateau had a larger head length, body length and body width than did those from lowland China. Geographical and environmental factors were correlated with the observed morphological variation and genetic divergence of D. magna in China. Our data offer an insight into the divergence of freshwater zooplankton due to the uplift of the Qinghai-Tibetan Plateau.

Mitochondrial ghost lineages blur phylogeography and taxonomy of Natrix helvetica and N. natrix in Italy and Corsica

AbstractGrass snakes are widely distributed across the Western Palearctic. Recent phylogeographic studies provided evidence that three distinct parapatric species exist. Two of these occur in Italy, Natrix helvetica and N. natrix, and a contact zone between both taxa has been suggested for north‐eastern Italy. Moreover, previous investigations revealed for the Italian Peninsula a complex phylogeographic structure. Using mtDNA sequences and microsatellite loci, we examined the situation for mainland Italy, Sicily, Sardinia, and Corsica. Our study confirmed the occurrence of N. natrix in north‐eastern Italy. Cline analyses revealed limited gene flow between N. helvetica and N. natrix across a narrow hybrid zone. Within N. helvetica, conflicting patterns of mitochondrial and nuclear genomic differentiation were revealed. Three nuclear genomic clusters were found; one of them corresponded to no fewer than five distinct and, in part, deeply divergent and ancient mitochondrial lineages from mainland Italy and Sicily. This cluster was paraphyletic with respect to the two remaining mitochondrial lineages, each of which matched with another nuclear genomic cluster (one from Corsica plus Sardinia and another one from western Europe north of the Alps). This unexpected pattern most likely results from mainly male‐mediated gene flow and female philopatry combined with population‐density‐dependent processes such as ‘high‐density blocking’. With respect to taxonomy, we propose to synonymize N. h. lanzai Kramer, 1970 with N. h. sicula (Cuvier, 1829), acknowledging their lacking nuclear genomic differentiation. The studied hybrid zone of N. h. helvetica and N. h. sicula in Italy is wide, with a smooth cline for nuclear markers, supporting their subspecies status. We found no evidence for the distinctiveness of the two subspecies from Corsica (N. h. corsa) and Sardinia (N. h. cetti), suggesting their synonymy, but refrain from taxonomic conclusions because of small sample sizes and the endangered status of the Sardinian taxon.

A new species of Cyrtodactylus (Squamata, Gekkonidae) from Cambodia's Prey Lang Wildlife Sanctuary.

Cyrtodactylusphnomchiensissp. nov. is described from Phnom Chi, an isolated mountain in Prey Lang Wildlife Sanctuary, Kampong Thom Province, Cambodia. The new species is recognized by having a unique combination of morphological characters, including snout-vent length 76.1–80.7 mm; paravertebral tubercles 31–36; ventral scales 45–54; enlarged femoral scales 0–8, without pores; enlarged precloacal scales 7–10, bearing pores 4–5 in males, pits 1–7 in females; the posterior border of nuchal loop unbroken and pointed, bordered anteriorly and posteriorly by a broad yellow or yellowish white band; and yellow spots on top of head. The new species also represents a divergent mitochondrial DNA lineage within the C.irregularis complex that is closely related to C.ziegleri, but the phylogenetic relationships among the new species and two divergent mitochondrial subclades within C.ziegleri are not resolved based on available sequence data. Cyrtodactylusphnomchiensissp. nov. is the only member of the C.irregularis complex known to occur west of the Mekong River. The new species may be endemic to Phnom Chi, and likely faces imminent conservation threats.

Arriving at the correct taxonomy: a comment on “A new and highly divergent mitochondrial lineage in the Small Five-toed Jerboa, Scarturus elater, from Iran”

We reanalyzed 657 base pairs of mitochondrial cytochrome b (cytb) sequences of the Small Five-toed jerboas Scarturus from Iran, which had been published as Allactaga by Mohammadi et al. (2016) in the Zoology in the Middle East. We show that taxonomic names are available for the three main clusters they recognized: S. hotsoni, S. elater, and S. toussi. The last two species each contained two lineages, both in our analysis as well in those published earlier. We recommend the taxonomic identification of specimens in molecular analyses and call for deposition of voucher material in responsible public collections.

Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude.

Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed freshwater shrimp in eastern Australia. The species has been considered as an important stream organism for studying genetics, dispersal, biology, behaviour and evolution in atyids and is a major food source for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of nine highly divergent mitochondrial DNA lineages. Previous studies in southeast Queensland showed that “lineage 4” favours upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify putative selection and population structure between high elevation and low elevation populations of this lineage at relatively small spatial scales. Sample localities were selected from three streams: Booloumba Creek, Broken Bridge Creek and Obi Obi Creek in the Conondale Range, southeast Queensland. Six sample localities, consisting of 142 individuals in total were sequenced using double digest Restriction Site Associated DNA-sequencing (ddRAD-seq) technique. Among the 142 individuals, 131 individuals shared 213 loci. Outlier analysis on 213 loci showed that 27 loci were putatively under selection between high elevation and low elevation populations. Outlier analysis on individual streams was also done to test for parallel patterns of adaptation, but there was no evidence of a parallel pattern. Population structure was observed using both the 27 outliers and 186 neutral loci and revealed similar population structure in both cases. Therefore, we cannot differentiate between selection and drift here. The highest genetic differentiation was observed between high elevation and low elevation populations of Booloumba Creek, with small levels of differentiation in the other two streams.

Variable phylogeographic histories of five forest birds with populations in Upper and Lower Guinea: implications for taxonomy and evolutionary conservation

This study evaluates phylogeographic structure in selected forest bird species distributed on either side of the Dahomey Gap in West Africa to extend analyses of avian diversification across the Guineo-Congolean forest. Mitochondrial DNA sequence data were collected for five species, including four with a break in distribution across the Dahomey Gap and one with a more continuous distribution. Data for the five focal species were included in a single analysis along with appropriate outgroup taxa, allowing estimates of divergence time on a common timescale. Both phylogeographic patterns and estimated divergence times were highly variable. In two cases (Green Hylia Hylia prasina and Yellow-whiskered Greenbul Eurillas latirostris), samples from east and west of the Dahomey Gap belong to divergent mitochondrial lineages, but with substantially older divergence in Eurillas (∼4.1 MY). In Western Bluebill Spermophaga haematina, relatively divergent eastern and western lineages (∼1.1 MY) were sampled in the same locality in eastern Ghana, suggesting east to west gene flow across the gap following earlier vicariance. In Forest Robin Stiphrornis erythrothorax, birds sampled within Ghana were from two highly divergent lineages (∼1.9 MY), one of which is more closely related to birds from Cameroon and Equatorial Guinea, such that divergence across the Dahomey Gap was comparatively recent (∼0.36 MY). For both Hylia and Stiphrornis, we corroborate recent studies documenting multiple divergent lineages within each genus, some of which may represent distinct species. Consistent with previous studies, our analysis shows that the Dahomey Gap can be a significant barrier to gene flow for species restricted to forest habitats. At the same time, individual species exhibit a broad range of divergence times and phylogeographic histories of variable complexity. We discuss the taxonomic implications of our results for each focal species.

Description of the lucky Cophyla (Microhylidae, Cophylinae), a new arboreal frog from MarojejyNational Park in north-eastern Madagascar.

We describe a new species of arboreal microhylid frog from northern Madagascar. The new species is assigned to the genus Cophyla based on molecular phylogeny and morphological similarities to other species of this genus. Molecular phylogenetic analysis resolved Cophyla fortuna sp. nov. as closely related to C. noromalalae. However, the two species were reciprocally monophyletic both in a tree reconstructed from a combination of mitochondrial genes, and in a tree based on the nuclear RAG-1 gene. The new species, previously identified as candidate species Cophyla sp. Ca4, occurs in lowland bamboo forests around the Marojejy Massif in northeastern Madagascar. It differs from the allopatric C. noromalalae, so far only known from the Montagne d'Ambre Massif in northern Madagascar, by slightly smaller body size and shorter duration and higher spectral frequency of advertisement calls. Several additional genetically divergent mitochondrial lineages of Cophyla, related to the C. fortuna/noromalalae complex and to C. phyllodactyla, occur in intervening areas between Montagne d'Ambre and Marojejy, and their status requires further study.

Origins, Divergence, and Contrasting Invasion History of the Sweet Potato Weevil Pests Cylas formicarius (Coleoptera: Brentidae) and Euscepes batatae (Coleoptera: Curculionidae) in the Asia-Pacific.

Cylas formicarius F. and Euscepes batatae Waterhouse are the most damaging sweet potato insect pests globally. Both weevils are thought to have invaded the Pacific alongside the movement of sweet potato (Ipomoea batatas (L.) Lam. Convolvulaceae), with C. formicarius having originated in India and E. batatae in Central or South America. Here we compare the genetic relationships between populations of the pests, primarily in the Asia-Pacific, to understand better their contemporary population structure and their historical movement relative to that of sweet potato. Cylas formicarius has divergent mitochondrial lineages that indicate a more complex biogeographic and invasive history than is presently assumed for this insect, suggesting it was widespread across the Asia-Pacific before the arrival of sweet potato. Cylas formicarius must have originally fed on Ipomoea species other than I. batatas but the identity of these species is presently unknown. Cylas formicarius was formerly designated as three species or subspecies and the genetic data presented here suggests that these designations should be reinvestigated. Euscepes batatae has very low genetic diversity which is consistent with its historical association with sweet potato and a recent introduction to the Asia-Pacific from the Americas. The distribution of E. batatae may be narrower than that of C. formicarius in the Asia-Pacific because it has relied relatively more on human-assisted movement. Consequently, E. batatae may become more widespread in the future. Investigating the invasion history of both species will help to understand the probability and nature of future invasions.

A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris

Mitochondrial DNA (mtDNA) sequencing has led to an unprecedented rise in the identification of cryptic species. However, it is widely acknowledged that nuclear DNA (nuDNA) sequence data are also necessary to properly define species boundaries. Next generation sequencing techniques provide a wealth of nuclear genomic data, which can be used to ascertain both the evolutionary history and taxonomic status of putative cryptic species. Here, we focus on the intriguing case of the butterfly Thymelicus sylvestris (Lepidoptera: Hesperiidae). We identified six deeply diverged mitochondrial lineages; three distributed all across Europe and found in sympatry, suggesting a potential case of cryptic species. We then sequenced these six lineages using double-digest restriction-site associated DNA sequencing (ddRADseq). Nuclear genomic loci contradicted mtDNA patterns and genotypes generally clustered according to geography, i.e., a pattern expected under the assumption of postglacial recolonization from different refugia. Further analyses indicated that this strong mtDNA/nuDNA discrepancy cannot be explained by incomplete lineage sorting, sex-biased asymmetries, NUMTs, natural selection, introgression or Wolbachia-mediated genetic sweeps. We suggest that this mitonuclear discordance was caused by long periods of geographic isolation followed by range expansions, homogenizing the nuclear but not the mitochondrial genome. These results highlight T.sylvestris as a potential case of multiple despeciation and/or lineage fusion events. We finally argue, since mtDNA and nuDNA do not necessarily follow the same mechanisms of evolution, their respective evolutionary history reflects complementary aspects of past demographic and biogeographic events.

Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe.

Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.

Divergent mitochondrial lineages arose within a large, panmictic population of the Savannah sparrow (Passerculus sandwichensis).

Unusual patterns of mtDNA diversity can reveal interesting aspects of a species' biology. However, making such inferences requires discerning among the many alternative scenarios that could underlie any given mtDNA pattern. Next-generation sequencing methods provide large, multilocus data sets with increased power to resolve unusual mtDNA patterns. A mtDNA-based phylogeography of the Savannah sparrow (Passerculus sandwichensis) previously identified two sympatric, but divergent (~2%) clades within the nominate subspecies group and a third clade that consisted of birds sampled from northwest Mexico. We revisited the phylogeography of this species using a population genomic data set to resolve the processes leading to the evolution of sympatric and divergent mtDNA lineages. We identified two genetic clusters in the genomic data set corresponding to (a) the nominate subspecies group and (b) northwestern Mexico birds. Following divergence, the nominate clade maintained a large, stable population, indicating that divergent mitochondrial lineages arose within a panmictic population. Simulations based on parameter estimates from this model further confirmed that this demographic history could produce observed levels of mtDNA diversity. Patterns of divergent, sympatric mtDNA lineages are frequently interpreted as admixture of historically isolated lineages. Our analyses reject this interpretation for Savannah sparrows and underscore the need for genomic data sets to resolve the evolutionary mechanisms behind anomalous, locus-specific patterns.

Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate

Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (FST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.

Isolation by elevation: mitochondrial divergence among sky island populations of Sacramento Mountain salamander (Aneides hardii)

The Sacramento Mountain salamander (Aneides hardii) is a fully terrestrial plethodontid endemic to mountains in south-central New Mexico. This species is of conservation concern but there is scant knowledge regarding the degree of genetic divergence among populations. This information is vital for developing an appropriate species management strategy. To address this issue, we generated sequence data from the mitochondrial cytochrome b gene and four nuclear loci to explore population demographic history. Cytochrome b data revealed three deeply divergent (2.3–2.8%) mitochondrial lineages corresponding to distinct mountains (Capitan, White, and Sacramento). Divergence dates suggest separation since the early Pleistocene, and signatures of population expansion in the mid to late Pleistocene. Of 25 haplotypes identified, none were shared among mountains, but genetic diversity differed among mitochondrial lineages and suggested different demographic histories within lineages. A single microsatellite locus identified private alleles in each of the three lineages. Other nuclear loci screened were invariant within and among populations, which corresponds to a lower mutation rate compared with mtDNA. Together these results indicate that each mountain population of A. hardii represents a demographically and genetically distinct management unit.

Transcriptomic analysis confirms differences among nuclear genomes of cryptic earthworm lineages living in sympatry

BackgroundMany earthworm species demonstrate significant cryptic diversity, with several highly diverged mitochondrial lineages found within most of the taxa studied to date. The status of differences between these lineages on the nuclear level is still unclear. Because of widespread polyploidy in earthworms, most studies were limited to two nuclear loci, the ribosomal and the histone clusters. Here we attempted to elucidate the status of a set of genetic lineages within Eisenia nordenskioldi nordenskioldi, an earthworm species from Northern Asia with high intraspecific diversity. We performed RNA-seq on an IonTorrent platform for five specimens of this species belonging to five genetic lineages, as well as two outgroups from the family Lumbricidae, the congenetic E. andrei, and Lumbricus rubellus.ResultsWe de novo assembled transcriptomes and constructed datasets of genes present in all seven specimens using broad (ProteinOrtho; 809 genes) and narrow (HaMStR; 203 genes) ortholog assignment. The majority of orthologs had identical amino acid sequences in all studied specimens, which we believe was due to strong bias towards the most conserved genes. However, for the rest of genes the differences among the lineages were lower than those between them and the congeneric E. andrei. Both datasets yielded phylogenetic trees with the same topology. E. n. nordenskioldi was found to be monophyletic. The differences on the genetic level had no concordance with geography, implying complex history of dispersal.ConclusionsWe found that genetic lineages of E. n. nordenskioldi are genetically distinct on nuclear level and probably diverged long ago. Current data implies that they might even represent distinct species within the E. nordenskioldi species complex.