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1.
J Infect Dev Ctries ; 16(8): 1258-1268, 2022 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-36099368

RESUMO

INTRODUCTION: Since the COVID-19 pandemic began in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved with many variants of concern emerging across the world. METHODOLOGY: In order to monitor the evolution of these variants in Morocco, we analyzed a total of 2130 genomes of the delta variant circulating around the world. We also included 164 Moroccan delta variant sequences in our analysis. RESULTS: Our findings suggest at least four introductions from multiple international sources and a rise of a dominant delta sub-lineage AY.33 in Morocco. Moreover, we report three mutations in the N-terminal domain of the S protein specific to the Moroccan AY.33 isolates, T29A, T250I and T299I. The effect of these mutations on the secondary structure and the dynamic behavior of the S protein N-terminal domain was further determined. CONCLUSIONS: We conclude that these mutations might have functional consequences on the S protein of SARS-CoV-2.


Assuntos
COVID-19 , SARS-CoV-2 , COVID-19/epidemiologia , Genômica , Humanos , Marrocos/epidemiologia , Pandemias , Filogeografia , SARS-CoV-2/genética
2.
Nat Commun ; 13(1): 5477, 2022 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-36115862

RESUMO

Human herpes simplex virus 2 (HSV-2) is a ubiquitous, slowly evolving DNA virus. HSV-2 has two primary lineages, one found in West and Central Africa and the other found worldwide. Competing hypotheses have been proposed to explain how HSV-2 migrated out-of-Africa (i)HSV-2 followed human migration out-of-Africa 50-100 thousand years ago, or (ii)HSV-2 migrated via the trans-Atlantic slave trade 150-500 years ago. Limited geographic sampling and lack of molecular clock signal has precluded robust comparison. Here, we analyze newly sequenced HSV-2 genomes from Africa to resolve geography and timing of divergence events within HSV-2. Phylogeographic analysis consistently places the ancestor of worldwide dispersal in East Africa, though molecular clock is too slow to be detected using available data. Rates 4.2 × 10-8-5.6 × 10-8 substitutions/site/year, consistent with previous age estimates, suggest a worldwide dispersal 22-29 thousand years ago. Thus, HSV-2 likely migrated with humans from East Africa and dispersed after the Last Glacial Maximum.


Assuntos
Genoma , Herpesvirus Humano 2 , Adulto , África , Sequência de Bases , Herpesvirus Humano 2/genética , Humanos , Filogeografia , Adulto Jovem
3.
Int J Mol Sci ; 23(17)2022 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-36077190

RESUMO

Since the beginning of the 21st century, humans have experienced three coronavirus pandemics, all of which were transmitted to humans via animals. Recent studies have found that porcine deltacoronavirus (PDCoV) can infect humans, so swine enteric coronavirus (SeCoV) may cause harm through cross-species transmission. Transmissible gastroenteritis virus (TGEV) and PDCoV have caused tremendous damage and loss to the pig industry around the world. Therefore, we analyzed the genome sequence data of these two SeCoVs by evolutionary dynamics and phylogeography, revealing the genetic diversity and spatiotemporal distribution characteristics. Maximum likelihood and Bayesian inference analysis showed that TGEV could be divided into two different genotypes, and PDCoV could be divided into four main lineages. Based on the analysis results inferred by phylogeography, we inferred that TGEV might originate from America, PDCoV might originate from Asia, and different migration events had different migration rates. In addition, we also identified positive selection sites of spike protein in TGEV and PDCoV, indicating that the above sites play an essential role in promoting membrane fusion to achieve adaptive evolution. In a word, TGEV and PDCoV are the past and future of SeCoV, and the relatively smooth transmission rate of TGEV and the increasing transmission events of PDCoV are their respective transmission characteristics. Our results provide new insights into the evolutionary characteristics and transmission diversity of these SeCoVs, highlighting the potential for cross-species transmission of SeCoV and the importance of enhanced surveillance and biosecurity measures for SeCoV in the context of the COVID-19 epidemic.


Assuntos
COVID-19 , Doenças dos Suínos , Vírus da Gastroenterite Transmissível , Animais , Teorema de Bayes , Deltacoronavirus , Humanos , Filogeografia , Suínos , Doenças dos Suínos/epidemiologia , Vírus da Gastroenterite Transmissível/genética
4.
Sci Rep ; 12(1): 15726, 2022 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-36130954

RESUMO

Studying the population-genetic and phylogeographic structures of a representative species of a particular geographical region can not only provide us with information regarding its evolutionary history, but also improve our understanding of the evolutionary processes underlying the patterns of species diversity in that area. By analysing eight highly polymorphic microsatellite loci and two chloroplast DNA regions, we have investigated the influence of Pleistocene climate fluctuations on the evolutionary history of Salvia officinalis L. (common sage). The populations with the highest genetic diversity were located in the central parts of the Balkan distribution range. A large group of closely related haplotypes was distributed throughout the Balkans and the central Apennines, while the private lineage occupied the southern Apennines. In addition, two highly differentiated lineages were scattered only over the Balkans. The results suggest that a single refugium of the studied species from the last glacial period was located in the central part of the range in the Balkans. Numerous microrefugia, probably spanning several glaciation cycles, were scattered across the Balkans, while colonisation of the Apennines from the Balkans occurred at least on two occasions.


Assuntos
Salvia officinalis , Península Balcânica , DNA de Cloroplastos/genética , DNA Mitocondrial/genética , Variação Genética , Haplótipos , Repetições de Microssatélites/genética , Filogenia , Filogeografia , Salvia officinalis/genética
5.
Genes (Basel) ; 13(8)2022 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-36011332

RESUMO

In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds' differentiation level (Wright's fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies.


Assuntos
Variação Genética , Carneiro Doméstico , Animais , Variação Genética/genética , Genótipo , Humanos , Repetições de Microssatélites , Filogeografia , Ovinos/genética , Carneiro Doméstico/genética
6.
Genes (Basel) ; 13(8)2022 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-36011336

RESUMO

Leymus is a perennial genus that belongs to the tribe Triticeae (Poaceae) which has an adaptive capacity to ecological conditions and strong resistance to cold, drought, and salinity. Most Leymus species are fine herbs that can be used for agriculture, conservation, and landscaping. Due to confusion taxonomy within genera, the complete chloroplast (cp) genome of 13 Leymus species was sequenced, assembled, and compared with those of three other previously published Leymus species (Leymus condensatus, Leymus angustus, and Leymus mollis) to clarify the issue. Overall, the whole cp genome size ranged between 135,057 (L. condensatus) and 136,906 bp (Leymus coreanus) and showed a typical quadripartite structure. All studied species had 129 genes, including 83 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. In total, 800 tandem repeats and 707 SSR loci were detected, most of which were distributed in the large single-copy region, followed by the inverted repeat (IR) and small single-copy regions. The sequence identity of all sequences was highly similar, especially concerning the protein-coding and IR regions; in particular, the protein-coding regions were significantly similar to those in the IR regions, regardless of small sequence differences in the whole cp genome. Moreover, the coding regions were more conserved than the non-coding regions. Comparisons of the IR boundaries showed that IR contraction and expansion events were reflected in different locations of rpl22, rps19, ndhH, and psbA genes. The close phylogenetic relationship of Leymus and Psathyrostachys indicated that Psathyrostachys possibly is the donor of the Ns genome sequence identified in Leymus. Altogether, the complete cp genome sequence of Leymus will lay a solid foundation for future population genetics and phylogeography studies, as well as for the analysis of the evolution of economically valuable plants.


Assuntos
Genoma de Cloroplastos , Tamanho do Genoma , Genoma de Cloroplastos/genética , Filogenia , Filogeografia , Poaceae/genética
7.
Nature ; 609(7926): 313-319, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-36045297

RESUMO

The vertebrate lineages that would shape Mesozoic and Cenozoic terrestrial ecosystems originated across Triassic Pangaea1-11. By the Late Triassic (Carnian stage, ~235 million years ago), cosmopolitan 'disaster faunas' (refs. 12-14) had given way to highly endemic assemblages12,13 on the supercontinent. Testing the tempo and mode of the establishment of this endemism is challenging-there were few geographic barriers to dispersal across Pangaea during the Late Triassic. Instead, palaeolatitudinal climate belts, and not continental boundaries, are proposed to have controlled distribution15-18. During this time of high endemism, dinosaurs began to disperse and thus offer an opportunity to test the timing and drivers of this biogeographic pattern. Increased sampling can test this prediction: if dinosaurs initially dispersed under palaeolatitudinal-driven endemism, then an assemblage similar to those of South America4,19-21 and India19,22-including the earliest dinosaurs-should be present in Carnian deposits in south-central Africa. Here we report a new Carnian assemblage from Zimbabwe that includes Africa's oldest definitive dinosaurs, including a nearly complete skeleton of the sauropodomorph Mbiresaurus raathi gen. et sp. nov. This assemblage resembles other dinosaur-bearing Carnian assemblages, suggesting that a similar vertebrate fauna ranged high-latitude austral Pangaea. The distribution of the first dinosaurs is correlated with palaeolatitude-linked climatic barriers, and dinosaurian dispersal to the rest of the supercontinent was delayed until these barriers relaxed, suggesting that climatic controls influenced the initial composition of the terrestrial faunas that persist to this day.


Assuntos
Dinossauros , Ecossistema , Animais , Clima , Fósseis , História Antiga , Filogenia , Filogeografia , Densidade Demográfica , Dinâmica Populacional , Esqueleto , Zimbábue
8.
Mol Phylogenet Evol ; 176: 107592, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-35926825

RESUMO

Hyb-Seq and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for plant phylogenomic studies. Each method has its own pros and cons. The choice between them is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms in plants. In this study, we employed RAD-seq and Hyb-Seq of Angiosperms353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian (EA) -eastern North American (ENA) disjunct distribution, and compared them side by side. Our results showed congruences in phylogenetic inference and divergence time dating between the two data sets obtained through our customized procedures of library preparation and sequence trimming, although they differed in the number of loci and informative sites, the amount of missing data, and sampling within species. We provide recommendations regarding the selection of the two methods for phylogenomic study at generic level based on fund availability and sampling scale. If funds and time are not constrained, we recommend Hyb-Seq. If funds and time are somewhat limited and sampling is large, we recommend RAD-seq. However, we found greater conflict among gene trees from the RAD-seq data due to the short sequences per locus. Therefore, species tree building and network detecting with the RAD-seq data with short RAD-seq loci (e.g., <150 bp) should avoid using analytical methods relying on gene trees of individual locus, but using site-based methods such as SVDQuartets and D-statistic method. Our phylogenetic analyses of RAD-seq and Hyb-Seq data resulted in well-resolved species relationships. Analyses of the data using the D-statistic test and PhyloNet revealed ancient introgressions in both genera. Biogeographic analyses including fossil data using total evidence-based dated tree and DEC model applying specific inter-area dispersal probabilities revealed a complicated history for each genus, indicating multiple interareal dispersals and local extinctions within and outside areas of the taxa's modern ranges in both the Paleogene and Neogene. The study demonstrates the importance of including fossil taxa for a more accurate reconstruction of biogeographic histories of taxa to understand the EA and ENA floristic disjunction. Our results support a widespread ancestral range in EA-western North America (WNA) followed by early diversification in EA and expansion to North America (NA) and Europe for Castanea and a more widespread ancestral range in EA-ENA-WNA for Hamamelis. The origins of the modern EA-ENA disjunction in both genera were suggested to be the result of vicariance from widespread ancestors in Eurasia-ENA of the mid-Miocene and in EA-NA of the late Oligocene, respectively.


Assuntos
Fósseis , Hamamelis , Biodiversidade , Evolução Biológica , Filogenia , Filogeografia , Plantas
9.
Int J Mol Sci ; 23(16)2022 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-36012483

RESUMO

Despite the importance of ancient DNA for understanding human prehistoric dispersals, poor survival means that data remain sparse for many areas in the tropics, including in Africa. In such instances, analysis of contemporary genomes remains invaluable. One promising approach is founder analysis, which identifies and dates migration events in non-recombining systems. However, it has yet to be fully exploited as its application remains controversial. Here, we test the approach by evaluating the age of sub-Saharan mitogenome lineages sampled outside Africa. The analysis confirms that such lineages in the Americas date to recent centuries-the time of the Atlantic slave trade-thereby validating the approach. By contrast, in North Africa, Southwestern Asia and Europe, roughly half of the dispersal signal dates to the early Holocene, during the "greening" of the Sahara. We elaborate these results by showing that the main source regions for the two main dispersal episodes are distinct. For the recent dispersal, the major source was West Africa, but with two exceptions: South America, where the fraction from Southern Africa was greater, and Southwest Asia, where Eastern Africa was the primary source. These observations show the potential of founder analysis as both a supplement and complement to ancient DNA studies.


Assuntos
DNA Mitocondrial , Pessoas Escravizadas , África ao Sul do Saara , Mudança Climática , DNA Antigo , DNA Mitocondrial/genética , Humanos , Filogenia , Filogeografia
10.
Sci Rep ; 12(1): 14609, 2022 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-36028749

RESUMO

The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985-4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467-2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.


Assuntos
Galinhas , DNA Mitocondrial , Animais , Variação Genética , Haplótipos , Filogenia , Filogeografia , Polimorfismo Genético , Dinâmica Populacional
11.
Sci Rep ; 12(1): 14716, 2022 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-36042258

RESUMO

Trichiurus nanhaiensis is one of the most important commercial fish species in the South China Sea. This study aimed to investigate the level of genetic variation and population genetic structure of T. nanhaiensis in the South China Sea for the first time, using 281 individuals collected from seven locations along the coast of mainland China, Taiwan, and Hainan Island. A high level of haplotype diversity and low nucleotide diversity were detected in the mitochondrial DNA cyt b gene and nuDNA RYR 3 gene. The overall expected heterozygosity (He = 0.693) among the seven populations ranged from 0.681 to 0.706 in microsatellite DNA data, which revealed high levels of genetic diversity. Significant genetic differentiation was found in Taidong populations in Taiwan, revealing the prevention of gene flow caused by the Kuroshio Current. Two major lineages based on the cyt b gene suggested that the Taiwan Strait acted as a geographic barrier for T. nanhaiensis during the glacier periods in the late Pleistocene. The Bayesian skyline plot also revealed that population demographic expansion of T. nanhaiensis was estimated to have occurred in 0.1 Mya. Our results indicated that all populations of T. nanhaiensis had experienced a recent genetic bottleneck following recent expansion based on ABC analysis.


Assuntos
Citocromos b , Perciformes , Animais , Teorema de Bayes , China , Citocromos b/genética , DNA Mitocondrial/genética , Demografia , Variação Genética , Haplótipos , Masculino , Perciformes/genética , Filogenia , Filogeografia
12.
Sci Rep ; 12(1): 14192, 2022 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-35987816

RESUMO

Elucidating the processes responsible for maintaining the population connectivity of marine benthic species mediated by larval dispersal remains a fundamental question in marine ecology and fishery management. Understanding these processes becomes particularly important in areas with a biogeographic break and unidirectional water movement along the sides of the break. Based on variability at 4209 single-nucleotide polymorphisms in 234 individuals, we determine the genetic structure, temporal genetic stability, and gene flow among populations of the commercially important mola rock crab Metacarcinus edwardsii in a system in southern Chile with a biogeographic break at latitude 42°S. Specimens were collected at eight sites within its geographic distribution, with collection at four of these sites was performed twice. Using population genetic approaches, we found no evidence of geographic or temporal population differentiation. Similarly, we found no evidence of an effect on gene flow of the biogeographic break caused by the the West Wind Drift Current. Moreover, migration analyses supported gene flow among all sites but at different rates for different pairs of sites. Overall, our findings indicate that M. edwardsii comprises a single large population with high levels of gene flow among sites separated by over 1700 km and demonstrate temporal stability in its genetic structure.


Assuntos
Braquiúros , Genoma , Animais , Braquiúros/genética , Fluxo Gênico , Variação Genética , Genética Populacional , Filogeografia
13.
Parasitol Res ; 121(10): 2803-2816, 2022 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-35918454

RESUMO

Studying the genetic diversity of nematode parasite populations is crucial to gaining insight into parasite infection dynamics and informing parasite phylogeography. Anisakiasis is a zoonotic disease caused by the consumption of infectious third-stage larvae (L3) of Anisakis spp. carried by marine fish. In the present study, a total of 206 mitochondrial DNA sequences (cytochrome c oxidase 2, cox2) were used to study the genetic diversity, genetic structure, and historical demography of twelve A. pegreffii populations from Trichiurus japonicas along the coast of mainland China and Taiwan. Two distinct evolutionary lineages of A. pegreffii and no significant genealogical structures corresponding to sampling localities suggested that isolation in the marginal seas shaped their patterns of phylogeographic distribution along the coast of mainland China and Taiwan during glaciation with lower sea levels. Furthermore, pairwise FST values and AMOVA did not indicate any significant genetic differentiation among groups with no relation to the geographic area, which might be attributed to fewer barriers to gene flow as well as large population sizes. The results of the neutrality test, mismatch distribution, and Bayesian skyline plot analyses showed that entire population underwent population expansion during the late Pleistocene. Analysis of the demographic history revealed that A. pegreffii underwent historical lineage diversification and admixture due to secondary contact based on ABC analysis. The present research represents the first definitive population structure and demographic history across sampling locations of A. pegreffii along the coast of mainland China and Taiwan.


Assuntos
Anisaquíase , Anisakis , Perciformes , Animais , Anisaquíase/parasitologia , Anisaquíase/veterinária , Anisakis/genética , Teorema de Bayes , China , Demografia , Variação Genética , Perciformes/parasitologia , Filogeografia , Taiwan
14.
PLoS Comput Biol ; 18(8): e1010422, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35984849

RESUMO

Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between populations shapes the genealogical history of sampled individuals and thereby structures genetic variation within and between populations. However, in the presence of recombination an individual may inherit different regions of their genome from different parents, resulting in a mosaic of genealogical histories across the genome, which can be represented by an Ancestral Recombination Graph (ARG). In this case, different genomic regions may have different ancestral histories and so different histories of movement between populations. Recombination therefore poses an additional challenge to phylogeographic methods that aim to reconstruct the movement of individuals from genealogies, although also a potential benefit in that different loci may contain additional information about movement. Here, we introduce the Structured Coalescent with Ancestral Recombination (SCAR) model, which builds on recent approximations to the structured coalescent by incorporating recombination into the ancestry of sampled individuals. The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates. Using the SCAR model, we explore the potential and limitations of phylogeographic inference using full ARGs. We then apply the SCAR to lineages of the recombining fungus Aspergillus flavus sampled across the United States to explore patterns of recombination and migration across the genome.


Assuntos
Genoma , Modelos Genéticos , Genética Populacional , Humanos , Filogeografia , Densidade Demográfica , Recombinação Genética/genética
15.
BMC Ecol Evol ; 22(1): 100, 2022 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-35971061

RESUMO

BACKGROUND: Contemporary species distribution, genetic diversity and evolutionary history in many taxa are shaped by both historical and current climate as well as topography. The Himalayas show a huge variation in topography and climatic conditions across its entire range, and have experienced major climatic fluctuations in the past. However, very little is known regarding how this heterogenous landscape has moulded the distribution of Himalayan fauna. A recent study examined the effect of these historical events on the genetic diversity of the Himalayan langurs in Nepal Himalaya. However, this study did not include the samples from the Indian Himalayan region (IHR). Therefore, here we revisit the questions addressed in the previous study with a near complete sampling from the IHR, along with the samples from the Nepal Himalaya. We used the mitochondrial Cytochrome-b (Cyt-b, 746 bp) region combined with multiple phylogeographic analyses and palaeodistribution modelling. RESULTS: Our dataset contained 144 sequences from the IHR as well as the Nepal Himalaya. Phylogenetic analysis showed a low divergent western clade nested within high divergent group of eastern lineages and in the network analysis we identified 22 haplotypes over the entire distribution range of the Himalayan langurs. Samples from the Nepal Himalaya showed geographically structured haplotypes corresponding to different river barriers, whereas samples from IHR showed star-like topology with no structure. Our statistical phylogeography analysis using diyABC supported the model of east to west colonisation of these langurs with founder event during colonisation. Analysis of demographic history showed that the effective population size of the Himalayan langurs decreased at the onset of last glacial maximum (LGM) and started increasing post LGM. The palaeodistribution modelling showed that the extent of suitable habitat shifted from low elevation central Nepal, and adjoining parts of north India, during LGM to the western Himalaya at present. CONCLUSION: The current genetic diversity and distribution of Himalayan langurs in the Nepal Himalaya has been shaped by river barriers, whereas the rivers in the IHR had relatively less time to act as a strong genetic barrier after the recent colonisation event. Further, the post LGM expansion could have had confounding effect on Himalayan langur population structure in both Nepal Himalaya and IHR.


Assuntos
Presbytini , Animais , Estruturas Genéticas , Variação Genética/genética , Filogenia , Filogeografia
16.
Proc Natl Acad Sci U S A ; 119(32): e2205495119, 2022 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-35914141

RESUMO

Jensen's inequality predicts that the response of any given system to average constant conditions is different from its average response to varying ones. Environmental fluctuations in abiotic conditions are pervasive on Earth; yet until recently, most ecological research has addressed the effects of multiple environmental drivers by assuming constant conditions. One could thus expect to find significant deviations in the magnitude of their effects on ecosystems when environmental fluctuations are considered. Drawing on experimental studies published during the last 30 years reporting more than 950 response ratios (n = 5,700), we present a comprehensive analysis of the role that environmental fluctuations play across the tree of life. In contrast to the predominance of interactive effects of global-change drivers reported in the literature, our results show that their cumulative effects were additive (58%), synergistic (26%), and antagonistic (16%) when environmental fluctuations were present. However, the dominant type of interaction varied by trophic level (autotrophs: interactive; heterotrophs: additive) and phylogenetic group (additive in Animalia; additive and positive antagonism in Chromista; negative antagonism and synergism in Plantae). In addition, we identify the need to tackle how complex communities respond to fluctuating environments, widening the phylogenetic and biogeographic ranges considered, and to consider other drivers beyond warming and acidification as well as longer timescales. Environmental fluctuations must be taken into account in experimental and modeling studies as well as conservation plans to better predict the nature, magnitude, and direction of the impacts of global change on organisms and ecosystems.


Assuntos
Mudança Climática , Ecossistema , Filogenia , Animais , Processos Autotróficos , Processos Heterotróficos , Filogeografia , Plantas
17.
Sci Rep ; 12(1): 13579, 2022 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-35945429

RESUMO

Contact zones are considered as windows into the evolutionary process, allowing identification of factors influencing the evolutionary forces. Here, we combined phylogenetic and morphometric analyses to explore the evolutionary process affecting the taxonomic pattern of two subspecies of Testudo graeca (T. g. buxtoni and T. g. zarudnyi) across their contact zone in Central Iran. Our results showed high levels of phylogeographic and phenotypic variation in the contact zone. Two monophyletic clades including, clade 1 (T. g. zarudnyi) and clade 2 (T. g. buxtoni) were identified. Furthermore, four distinct subclades were found in T. g. buxtoni, across a wide geographic range. Divergence time analysis suggests that the two subspecies diverged from one another after the uplifting of the Zagros Mountains during the early Pliocene. Using neutrality tests and mismatch distribution analysis, we found no evidence of recent population expansion. Morphological associations among geographical populations in the contact zone found more distinctions, with some significant adaptive and non-adaptive morphological variations in these populations. These distinctive morphological populations can be considered as management units (MUs) to conserve the evolutionary potential of this species. Finer scale evolutionary studies are required to address the southern part of the Zagros mountain range, where the overlapping of mitochondrial clades and subclades has occurred. Such information is essential for effective conservation of T. graeca populations, preventing translocation or mixing of individuals without comprehensive genetic and morphological assessment.


Assuntos
DNA Mitocondrial , Tartarugas , Animais , DNA Mitocondrial/genética , Variação Genética , Haplótipos , Humanos , Irã (Geográfico) , Filogenia , Filogeografia , Tartarugas/genética
18.
Proc Natl Acad Sci U S A ; 119(32): e2112853119, 2022 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-35914165

RESUMO

The Bantu expansion transformed the linguistic, economic, and cultural composition of sub-Saharan Africa. However, the exact dates and routes taken by the ancestors of the speakers of the more than 500 current Bantu languages remain uncertain. Here, we use the recently developed "break-away" geographical diffusion model, specially designed for modeling migrations, with "augmented" geographic information, to reconstruct the Bantu language family expansion. This Bayesian phylogeographic approach with augmented geographical data provides a powerful way of linking linguistic, archaeological, and genetic data to test hypotheses about large language family expansions. We compare four hypotheses: an early major split north of the rainforest; a migration through the Sangha River Interval corridor around 2,500 BP; a coastal migration around 4,000 BP; and a migration through the rainforest before the corridor opening, at 4,000 BP. Our results produce a topology and timeline for the Bantu language family, which supports the hypothesis of an expansion through Central African tropical forests at 4,420 BP (4,040 to 5,000 95% highest posterior density interval), well before the Sangha River Interval was open.


Assuntos
Idioma , Floresta Úmida , África Central , Teorema de Bayes , Negros , Migração Humana , Humanos , Filogeografia , Rios
19.
Zool Res ; 43(5): 706-718, 2022 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-35927393

RESUMO

Evolutionary biologists are always interested in deciphering the geographic context of diversification, therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms that contribute to shared genetic structures among organisms from the same region. Here, we used multi-locus genetic data along with environmental data to investigate shared phylogeographic patterns among three Asian-endemic newt genera, Cynops, Paramesotriton and Pachytriton, which occurred in montane/submontane streams or ponds in southern China. Our 222 samples from 78 localities covered the entire range of the three genera and represented the largest dataset of this group to date. We reconstructed matrilineal genealogies from two protein-coding, mitochondrial genes, and gene network from two nuclear genes. We also estimated divergence times of major cladogenetic events and used occurrence data to evaluate niche difference and similarity between lineages. Our results revealed a common basal split in all three genera that corresponds to the separation of two geographic terrains of southern China. Those ancient divergence occurred during middle to late Miocene and likely correlate with paleoclimatic fluctuations caused by the uplift of the Qinghai-Xizang (Tibet) Plateau (QTP). Particularly, the strengthening and weakening of Asian summer monsoons during the Miocene may have profoundly impacted southern China and led to repeatedly vicariance in those newts. However, despite differences in realized niches between lineages, there is no evidence for divergence of fundamental niches. Preservation of old newt matriline lineages in mountains of southern China suggests that the region acts as both museums and cradles of speciation. Based on those results, we advocate a multi-pronged protection strategy for newts in the three genera.


Assuntos
Variação Genética , Salamandridae , Animais , Teorema de Bayes , China , Filogenia , Filogeografia , Salamandridae/genética
20.
Sci Rep ; 12(1): 12013, 2022 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-35853951

RESUMO

Rivers are known to act as biogeographic barriers in several strictly terrestrial taxa, while possibly serving as conduits of dispersal for freshwater-tolerant or -dependent species. However, the influence of river systems on genetic diversity depends on taxa-specific life history traits as well as other geographic factors. In amphibians, several studies have demonstrated that river systems have only minor influence on their divergence. Here, we assess the role of the paleodrainage systems of the Sunda region (with a focus on the island of Sumatra) in shaping the evolutionary history of two genera of frogs (Sumaterana and Wijayarana) whose tadpoles are highly dependent on cascading stream habitats. Our phylogenetic results show no clear association between the genetic diversification patterns of both anurans genera and the existence of paleodrainage systems. Time-calibrated phylogenies and biogeographical models suggest that these frogs colonized Sumatra and diversified on the island before the occurrence of the Pleistocene drainage systems. Both genera demonstrate phylogenetic structuring along a north-south geographic axis, the temporal dynamics of which coincide with the geological chronology of proto Sumatran and -Javan volcanic islands. Our results also highlight the chronic underestimation of Sumatran biodiversity and call for more intense sampling efforts on the island.


Assuntos
Biodiversidade , Evolução Biológica , Animais , Anuros/genética , Larva/genética , Filogenia , Filogeografia
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