Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.

An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia

Cambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup classification and phylogenetic reconstruction. The application of diverse phylogenetic algorithms revealed an exciting picture of the genetic diversity of Cambodia, especially in relation to populations from Southeast Asia and from the whole world. A total of 224 unique haplotypes were identified, which were mostly classified under haplogroups B5a1, F1a1, or categorized as newly defined basal haplogroups or basal sub-branches of R, N and M clades. The presence of autochthonous maternal lineages could be confirmed as reported in previous studies. The exceptional homogeneity observed between and within the three investigated Cambodian ethnic groups indicates genetic isolation of the whole population. Between ethnicities, genetic barriers were not detected. The mtDNA data presented here increases the phylogenetic resolution in Cambodia significantly, thereby highlighting the need for an update of the current human mtDNA phylogeny.

Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group)

Background The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. Results The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene. Conclusion The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

Systematics and Phylogeography of The Non-Ethiopian Speckled-Pelage Brush-Furred Rats (Lophuromys Flavopunctatus Group) Inferred From Integrative Genetics and Morphometry

Background: The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) has been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys.Results: The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agreed with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene.Conclusion: The phylogenetic associations and divergence times of the L. flavopunctatus group conform to demonstrated hypotheses surrounding the paleoclimatic and ecosystem refugium impacts on the evolutionary radiation of rodents dependent on stably humid conditions in the East Africa region. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

Scavenging amphipods from the Wallaby-Zenith Fracture Zone: Extending the hadal paradigm beyond subduction trenches

Our understanding of the ecology of the hadal zone (> 6000 m depth) is based solely on subduction trenches, leaving other geomorphological features, such as fracture zones, troughs, and basins, understudied. To address this knowledge gap, the Wallaby-Zenith Fracture Zone, Indian Ocean (WZFZ; ~ 22°S, 102°E; maximum depth 6625 m measured during Expedition SO258) was studied using free-fall baited landers. We assessed the amphipod distribution and community assemblage of this non-subduction hadal feature and compared it to subduction hadal features. Eleven species were identified across the abyssal-hadal transition zone using a paired morphological and DNA barcoding approach. The community composition was found to change gradually from abyssal to hadal depths, which contrasts with the ecotone shift characteristic of subduction trenches. A large population of Bathycallisoma schellenbergi (Birstein & Vinogradov, 1958), a quintessential hadal amphipod, was present at the flat bottom of the WZFZ. Further, an mtDNA phylogeny resolved a degree of phylogeographic structure between the B. schellenbergi WZFZ population and four previously sampled Pacific Ocean subduction trench populations, indicating these features are not interconnected through ongoing gene flow. Combined, these data indicate that some amphipods have far broader distributions than previously understood, with some species present in both hadal subduction trenches and non-subduction fracture zones and basins interspersed across the abyssal plains. This initial exploration highlights that whilst non-subduction features are an overlooked minor fraction of the total hadal area, they are essential to our understanding of the ecological and evolutionary dynamics across the hadal zone.

Evidence for Miocene overwater colonization in CaribbeanCyrtognathaspiders

Island systems provide excellent arenas to test evolutionary hypotheses pertaining to gene flow and diversification of dispersal-limited organisms. Here we focus on an orbweaver spider genusCyrtognatha(Tetragnathidae) from the Caribbean, with the aims to reconstruct its evolutionary history, describe its biogeographic history in the archipelago, and to estimate the timing and route of Caribbean colonization. Specifically, we test ifCyrtognathabiogeographic history is consistent with an ancient vicariant scenario (the GAARlandia landbridge hypothesis) or overwater dispersal. We reconstructed a species level phylogeny based on one mitochondrial (CO1) and one nuclear (28S) marker. We then used this topology to constrain a time-calibrated mtDNA phylogeny, for subsequent biogeographical analyses of over 100 originally sampledCyrtognathaindividuals. Our results suggest a monophyletic radiation of CaribbeanCyrtognatha, containing 11 to 14 species that are exclusively single island endemics. Our analyses refute vicariance and instead support an overwater colonization to the Caribbean in mid-Miocene. Having colonized Hispaniola first,Cyrtognathasubsequently dispersed to, and diversified on, the other islands of the Greater, and Lesser Antilles.

Cutthroat Trout: Evolutionary Biology and Taxonomy

<em>Abstract</em>.—North American trout have undergone a long and complicated taxonomic history and this holds for taxonomic designations of Cutthroat Trout <em>Oncorhynchus clarkii</em>. Current Cutthroat Trout taxonomy recognizes a monophyletic species comprising 11–16 subspecies. The complex geological and climatic history of western North America is postulated to have strongly influenced differentiation among Cutthroat Trout subspecies. Early studies relied on morphological and meristic data in conjunction with fossil data and known aquatic connections within and among hydrological basins to infer the phylogenetic history of Cutthroat Trout. More recently, molecular studies incorporating karyotypes, allozymes, restriction fragment length polymorphisms, and mitochondrial DNA (mtDNA) sequence data have tested these early phylogenetic hypotheses and yielded additional insights into Cutthroat Trout evolution, although some phylogenetic relationships remain unresolved. In this study, we analyzed DNA sequence data from approximately half of the mitochondrial genome (8,057 base pairs) to better resolve phylogenetic relationships and estimate divergence times among Cutthroat Trout lineages. Herein, we present a well-resolved mtDNA phylogeny and discuss Cutthroat Trout evolution in a phylogeographic framework, as well as clarify current taxonomic implications and make recommendations for future research directions.

A new species of Isthmura (Caudata: Plethodontidae) from the montane cloud forest of central Veracruz, Mexico

We describe a new plethodontid salamander species of the genus Isthmura, known only from one locality in the mountainous region of central Veracruz, Mexico. Like its congeners, Isthmura corrugata sp. nov. has a large and robust body, but it is easily distinguished from the other species in the genus by the absence of any spot or mark on the dorsum (except by dull reddish brown coloration on eyelids) and by extremely well-marked costal grooves separated by very pronounced costal folds. Based on an mtDNA phylogeny, the new species is most closely related to the geographically distant I. boneti and I. maxima but occurs very near I. naucampatepetl and I. gigantea on the eastern slope of Cofre de Perote, Veracruz. The region where I. corrugata occurs contains a high number of plethodontid salamander species and is threatened by human activity.

Isolation and Gene Flow in a Speciation Continuum in Newts

Because reproductive isolation often evolves gradually, differentiating lineages may retain the potential for genetic exchange for prolonged periods, providing an opportunity to quantify and understand the fundamental role of gene flow during speciation. Here we delimit taxa, reconstruct the phylogeny and infer gene flow in newts of the Lissotriton vulgaris species complex based on 74 nuclear markers sampled from 127 localities. We demonstrate that distinct lineages along the speciation continuum in newts exchange nontrivial amounts of genes, affecting their evolutionary trajectories. By integrating a wide array of methods, we delimit nine taxa and show that two principle factors have driven their genetic differentiation: time since the last common ancestor determining levels of shared ancestral polymorphism, and shifts in geographic distributions determining the extent of secondary contact. Post-divergence gene flow, indicative of evolutionary non-independence, has been most extensive between sister and non-sister taxa in Central Europe, while four southern European lineages have acquired the population genetic hallmarks of independent species (L. graecus, L. kosswigi, L. lantzi, L. schmidtleri). We obtained strong statistical support for widespread mtDNA introgression, previously suggested by discordance between mtDNA phylogeny and morphology. Our study suggests that long-term evolution in structured populations that may periodically exchange genes may be common: although some of these populations may become extinct or fuse, others will acquire complete reproductive isolation and will carry signatures of this complex history in their genomes.

High regional genetic diversity and lack of host-specificity in Ostrinia nubilalis (Lepidoptera: Crambidae) as revealed by mtDNA variation

The European corn borer (Ostrinia nubilalis) infests a wide array of host plants and is considered one of the most serious pests of maize in Europe. Recent studies suggest that individuals feeding on maize in Europe should be referred to O. nubilalis (sensu nov.), while those infesting dicots as Ostrinia scapulalis (sensu nov.). We test if the clear genetic distinctiveness among individuals of O. nubilalis living on maize vs. dicots is tracked by mitochondrial DNA (mtDNA). We used fragments of COI and COII genes of 32 individuals traditionally recognized as O. nubilalis collected on three host plants, maize, mugwort and hop, growing in different parts of Poland. In addition, we reconstructed the mtDNA phylogeny of Ostrinia species based on our data and sequences retrieved from GenBank to assess host and/or biogeographic patterns. We also compared haplotype variation found in Poland (east-central Europe) with other regions (Anatolia, Eastern Europe, Balkans, Far East, North America). Our study showed high mtDNA diversity of O. nubilalis in Poland in comparison with other regions and revealed rare haplotypes likely of Asian origin. We did not find distinct mtDNA haplotypes in larvae feeding on maize vs. dicotyledonous plants. Phylogenetic analyses showed an apparent lack of mtDNA divergence among putatively distinct lineages belonging to the O. nubilalis group as identical haplotypes are shared by Asian and European individuals. We argue that human-mediated dispersal, hybridization and sporadic host jumps are likely responsible for the lack of a geographic pattern in mtDNA variation.