Search Results (14)

Lodgepole pine (Pinus contorta Dougl.) exhibits pronounced morphological variation across its range, historically attributed to allopatric differentiation during the Wisconsin glaciation. However, whether genetic divergence aligns with morphological differentiation—a fundamental prediction of allopatric speciation theory—remains untested. We conducted a comprehensive phylogeographic analysis of chloroplast DNA (trnL intron and trnL/trnF spacer) and mitochondrial DNA (nad1 b/c intron) across 31 populations representing all four recognized subspecies to test hypotheses of refugial isolation and to evaluate the genetic basis of current taxonomic classification. Contrary to predictions of allopatric divergence, both organellar genomes showed striking genetic uniformity (π = 0.000178–0.000186; intersubspecific genetic distances: 1.06 × 10⁻⁴ to 3.96 × 10⁻⁴) with no phylogenetic structure corresponding to morphological boundaries. Significant negative neutrality test values (Tajima’s D = −2.26, p < 0.02; Fu and Li’s D* = −4.52, p < 0.02) suggest recent demographic expansion rather than equilibrium divergence. A distinctive 5 bp indel in coastal populations provides molecular evidence for a northern Pacific refugium, and its occurrence in interior populations is consistent with post-glacial pollen-mediated gene flow, though this directionality remains inferential pending nuclear genomic confirmation. These findings suggest that morphological divergence reflects rapid adaptive evolution in heterogeneous environments rather than deep phylogenetic divisions. This pattern exemplifies gene flow-selection balance, in which divergent selection maintains local adaptation despite extensive gene flow—supporting an ecotypic rather than a phylogenetic interpretation of intraspecific diversity. The persistence of morphological variation despite genetic homogeneity indicates strong selection on ecologically important traits, likely driven by variation in fire regimes, differential seed predation, and climate gradients. These results have critical implications for understanding adaptive evolution rates in widespread conifers and for developing conservation strategies that emphasize adaptive processes over taxonomic categories. Full article

The Mongolian racerunner, Eremias argus, is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt b gene revealed eight lineages that were unbounded by geographic region. The genetic structure of E. argus was mainly determined by geographic distance. Divergence dating indicated that E. argus and E. brenchleyi diverged during the Mid-Pliocene Warm Period. E. argus was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of E. argus. The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, E. argus barbouri most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia. Full article

A range-wide phylogenetic/phylogeographic study of the three-toed jerboas of the genus Stylodipus is conducted using the mitochondrial cytb gene and fragments of several nuclear genes. The genus has been believed to include three species: S. telum (W Central Asia, SE Europe), S. andrewsi (E Central Asia), and S. sungorus (Dzungar basin). Our data support the dichotomy between S. andrewsi and the other taxa forming S. telum species group. Within the latter, both mtDNA and nuclear loci indicate a species-level divergence between S. telum and the S. t. birulae lineage (Zaisan depression, NE Kazakhstan), previously considered a subspecies of S. telum and here elevated to full species. S. sungorus is recovered as a close sister group to S. birulae on the basis of nuclear data but clustered with S. telum in the mitochondrial tree. The latter taxon is the most variable and includes two closely related eastern and western sublineages, separated by the Volga-Ural sands and joined by a more divergent S. t. karelini lineage (E Kazakhstan). The observed mitonuclear discordance is hypothesized to occur due to mtDNA introgression resulting from hybridization between S. sungorus and S. t. karelini, which highlights the important role of reticulations in the evolution of Dipodidae. Full article

Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021–January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed “Deltacron”, was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation—a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus’s local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus’s epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic’s dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation. Full article

Andaman and Nicobar Islands, a part of South-East Asia, is enriched with the presence of native breeds of livestock (cattle, pig, goat) and poultry. There are two native goat breeds, viz., Andaman local goat and Teressa goat in Andaman and Nicobar Islands. However, to date, the origin and genetic makeup of these two breeds have not been detailed. Therefore, the present study describes the genetic makeup of Andaman goats through analysis of mitochondrial D-loop sequence for sequence polymorphism, phylogeographical signaling and population expansion events. The genetic diversity of the Teressa goat was less compared to the Andaman local goat due to its sole presence on Teressa Island. Out of 38 well-defined haplotypes of Andaman goats, the majority of haplotypes belonged to haplogroup A followed by haplogroup B and haplogroup D. The result of mismatch distribution and neutrality tests indicated no population expansion event of haplogroup A and B. Finally, based on poor geographical signaling, we hypothesize that Andaman goats have been imported to these Islands either through multidirectional diffusion or unidirectional diffusion. We justify our hypothesis of multidirectional diffusion on the basis of observation of the haplotype and nucleotide diversity of Andaman goats. Simultaneously, the probability of unidirectional diffusion of goats in these islands from the Indian subcontinent in different spells of domestication events through maritime routes cannot be ignored. Full article

Mepraia is a genus (Triatominae) endemic to Chile and a vector of Trypanosoma cruzi. Alternative phylogeographic hypotheses have been suggested for Mepraia. We tested different colonization routes hypothesized using mitochondrial sequences and phylogeographic approaches to select the best-supported hypothesis. Our results suggest that, after the split from the sister genus Triatoma at ~4.3 Mya, Mepraia formed two main clades at ~2.1 Mya. The northern clade diverged from Mepraia sp. ~1.7 Mya, giving rise to M. parapatrica and M. gajardoi about ~1.4 Mya. The southern clade originated M. spinolai ~1.68 Mya. We suggest that Mepraia had an origin in the north-central Andes along with orogenic processes, reinforced by hyperaridity during the Pliocene. The hyperarid cycle would have separated the southern and northern clades. Then, in the northern clade, dispersal occurred north and south from the centre through corridors during the Pleistocene Climatic Oscillations. Climate changes may have induced a major speciation process in the Atacama Desert, while the more homogeneous habitat colonized by the southern clade led to only one, but structured, species. Full article

Tocantins is a state in the cross-section between the Central-West, North and Northeast regions of Brazilian territory; it is a gathering point for travelers and transportation from the whole country. In this study, 9493 genome sequences, including 241 local SARS-CoV-2 samples (collected from 21 December 2020, to 16 December 2021, and sequenced in the MinION platform) were analyzed with the following aims: (i) identify the relative prevalence of SARS-CoV-2 lineages in the state of Tocantins; (ii) analyze them phylogenetically against global SARS-CoV-2 sequences; and (iii) hypothesize the viral dispersal routes of the two most abundant lineages found in our study using phylogenetic and phylogeographic approaches. The performed analysis demonstrated that the majority of the strains sequenced during the period belong to the Gamma P.1.7 (32.4%) lineage, followed by Delta AY.99.2 (27.8%), with the first detection of VOC Omicron. As expected, there was mainly a dispersion of P.1.7 from the state of São Paulo to Tocantins, with evidence of secondary spreads from Tocantins to Goiás, Mato Grosso, Amapá, and Pará. Rio de Janeiro was found to be the source of AY.99.2 and from then, multiple cluster transmission was observed across Brazilian states, especially São Paulo, Paraiba, Federal District, and Tocantins. These data show the importance of trade routes as pathways for the transportation of the virus from Southeast to Northern Brazil. Full article

Almost a year after the COVID-19 pandemic had begun, new lineages (B.1.1.7, B.1.351, P.1, and B.1.617.2) associated with enhanced transmissibility, immunity evasion, and mortality were identified in the United Kingdom, South Africa, and Brazil. The previous most prevalent lineages in the state of Rio Grande do Sul (RS, Southern Brazil), B.1.1.28 and B.1.1.33, were rapidly replaced by P.1 and P.2, two B.1.1.28-derived lineages harboring the E484K mutation. To perform a genomic characterization from the metropolitan region of Porto Alegre, we sequenced viral samples to: (i) identify the prevalence of SARS-CoV-2 lineages in the region, the state, and bordering countries/regions; (ii) characterize the mutation spectra; (iii) hypothesize viral dispersal routes by using phylogenetic and phylogeographic approaches. We found that 96.4% of the samples belonged to the P.1 lineage and approximately 20% of them were assigned as the novel P.1.2, a P.1-derived sublineage harboring signature substitutions recently described in other Brazilian states and foreign countries. Moreover, sequences from this study were allocated in distinct branches of the P.1 phylogeny, suggesting multiple introductions in RS and placing this state as a potential diffusion core of P.1-derived clades and the emergence of P.1.2. It is uncertain whether the emergence of P.1.2 and other P.1 clades is related to clinical or epidemiological consequences. However, the clear signs of molecular diversity from the recently introduced P.1 warrant further genomic surveillance. Full article

The phylogeny and taxonomy of freshwater mussels of the genus Castalia in South America is complicated by issues of morphological plasticity and limited molecular genetic data. We present field data on the distributions of the nominal Castalia ambigua and C. inflata in the upper Paraguay River basin in Brazil based on original occurrence data at 23 sample sites and on historical records. The upper basin has distinct highland and lowland regions, the latter including the Pantanal wetland, where “C. ambigua” occurs in the highlands and “C. inflata” occurs in both regions. At Baixo Stream in the highlands, we observed individuals with shell morphologies of either C. ambigua or C. inflata, and also individuals with intermediate shell morphology. DNA sequence variation in the upland Baixo Stream and two representative lowland populations were screened. Two mitochondrial and three nuclear genes were sequenced to test hypotheses regarding the number of species-level phylogenetic lineages present. Reported individual DNA sequences from Amazon-basin C. ambigua and other Castalia and outgroup species were included in the analysis as outgroups. Individuals from the Paraguay River basin exhibited 17 haplotypes at the mitochondrial cytochrome oxidase I (COI) gene and nine at mitochondrial 16S rRNA. Analysis of haplotype networks and phylogenetic trees of combined COI + 16S rRNA sequences among individuals with the respective shell morphologies supported the hypothesis that C. ambigua and C. inflata from the Paraguay River basin belong to the same species and one phylogenetic lineage. No variation was observed at the nuclear 18S rRNA internal transcribed spacer, 28S rRNA, or H3NR histone genes among individuals used in this study. Across all markers, less variation was observed among Paraguay basin populations than between Paraguay and Amazon basin populations. Our results collectively suggest that: (1) “C. ambigua”, “C. inflata”, and morphologically intermediate individuals within the upper Paraguay drainage represent one phylogenetic lineage, (2) a phylogeographic divide exists between Castalia populations occurring in the Paraguay and Amazon River basins, and (3) the evolutionary and taxonomic uncertainties that we have identified among Castalia species should be thoroughly assessed across their distribution using both morphological and molecular characters. Full article

North American freshwaters are among the world’s most threatened ecosystems, and freshwater mussels are among the most imperiled inhabiting these systems. A critical aspect of conservation biology is delineating patterns of genetic diversity, which can be difficult when a taxon has been extirpated from a significant portion of its historical range. In such cases, evaluating conservation and recovery options may benefit by using surrogate species as proxies when assessing overall patterns of genetic diversity. Here, we integrate the premise of surrogate species into a comparative phylogeographic framework to hypothesize genetic relationships between extant and extirpated populations of Potamilus inflatus by characterizing genetic structure in co-distributed congeners with similar life histories and dispersal capabilities. Our mitochondrial and nuclear sequence data exhibited variable patterns of genetic divergence between Potamilus spp. native to the Mobile and Pascagoula + Pearl + Pontchartrain (PPP) provinces. However, hierarchical Approximate Bayesian Computation indicated that the diversification between Mobile and PPP clades was synchronous and represents a genetic signature of a common history of vicariance. Recent fluctuations in sea-level appear to have caused Potamilus spp. in the PPP to form a single genetic cluster, providing justification for using individuals from the Amite River as a source of brood stock to re-establish extirpated populations of P. inflatus. Future studies utilizing eDNA and genome-wide molecular data are essential to better understand the distribution of P. inflatus and establish robust recovery plans. Given the imperilment status of freshwater mussels globally, our study represents a useful methodology for predicting relationships among extant and extirpated populations of imperiled species. Full article

It is assumed that complex life cycles in cnidarian parasites belonging to the Myxozoa result from incorporation of vertebrates into simple life cycles exploiting aquatic invertebrates. However, nothing is known about the driving forces and implementation of this event, though it fostered massive diversification. We performed a comprehensive search for myxozoans in evolutionary ancient fishes (Chondrichthyes), and more than doubled existing 18S rDNA sequence data, discovering seven independent phylogenetic lineages. We performed cophylogenetic and character mapping methods in the largest monophyletic dataset and demonstrate that host and parasite phylogenies are strongly correlated, and that tectonic changes may explain phylogeographic clustering in recent skates and softnose skates, in the Atlantic. The most basal lineages of myxozoans inhabit the bile of chondrichthyans, an immunologically privileged site and protective niche, easily accessible from the gut via the bile duct. We hypothesize that feed-integration is a likely mechanism of host acquisition, an idea supported by feeding habits of chimaeras and ancient sharks and by multiple entries of different parasite lineages from invertebrates into the new host group. We provide exciting first insights into the early evolutionary history of ancient metazoan parasites in a host group that embodies more evolutionary distinctiveness than most other vertebrates. Full article

Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Molecular Ecology 1998, 7, 499–517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels. Full article

A prediction in phylogeographic studies is that patterns of lineage diversity and timing will be similar within the same landscape under the assumption that these lineages have responded to past environmental changes in comparable ways. Eight invertebrate taxa from four different orders were included in this study of mainland New Zealand and Chatham Islands lineages to explore outcomes of island colonization. These comprised two orthopteran genera, one an endemic forest-dwelling genus of cave weta (Rhaphidophoridae, Talitropsis) and the other a grasshopper (Acrididae, Phaulacridum) that inhabits open grassland; four genera of Coleoptera including carabid beetles (Mecodema), stag beetles (Geodorcus), weevils (Hadramphus) and clickbeetles (Amychus); the widespread earwig genus Anisolabis (Dermaptera) that is common on beaches in New Zealand and the Chatham Islands, and an endemic and widespread cockroach genus Celatoblatta (Blattodea). Mitochondrial DNA data were used to reconstruct phylogeographic hypotheses to compare among these taxa. Strikingly, despite a maximum age of the Chathams of ~4 million years there is no concordance among these taxa, in the extent of genetic divergence and partitioning between Chatham and Mainland populations. Some Chatham lineages are represented by insular endemics and others by haplotypes shared with mainland populations. These diverse patterns suggest that combinations of intrinsic (taxon ecology) and extrinsic (extinction and dispersal) factors can result in apparently very different biogeographic outcomes. Full article

Phylogeography contributes to our knowledge of regional biotas by integrating spatial and genetic information. In New Zealand, comprising two main islands and hundreds of smaller ones, phylogeography has transformed the way we view our biology and allowed comparison with other parts of the world. Here we review studies on New Zealand terrestrial and freshwater invertebrates. We find little evidence of congruence among studies of different taxa; instead there are signatures of partitioning in many different regions and expansion in different directions. A number of studies have revealed unusually high genetic distances within putative species, and in those where other data confirm this taxonomy, the revealed phylogeographic structure contrasts with northern hemisphere continental systems. Some taxa show a signature indicative of Pliocene tectonic events encompassing land extension and mountain building, whereas others are consistent with range expansion following the last glacial maximum (LGM) of the Pleistocene. There is some indication that montane taxa are more partitioned than lowland ones, but this observation is obscured by a broad range of patterns within the sample of lowland/forest taxa. We note that several geophysical processes make similar phylogeographic predictions for the same landscape, rendering confirmation of the drivers of partitioning difficult. Future multi-gene analyses where applied to testable alternative hypotheses may help resolve further the rich evolutionary history of New Zealand’s invertebrates. Full article