Using ddRAD-seq phylogeography to test for genetic effects of headwater river capture in suckermouth armored catfish (Loricariidae: Hypostomus) from the central Brazilian Shield

River capture is a geological process of potentially great importance in shaping the genetic diversity, distributions, and community composition of freshwater taxa. Using phylogeographic analyses of ddRAD-seq data from suckermouth armored catfish (Hypostomus sp. 2) populations, we tested for predicted genetic effects of headwater river capture events in central Brazil, previously supported by geological and community ecological data. We analyzed 227 ddRAD tags (3829 SNP loci) across 42 samples. Molecular results strongly supported six Hypostomus genetic clusters/lineages, with the deepest divergence ~1.25 million years ago in the early Pleistocene between a clade from the Upper Paraná and Upper São Francisco river basins versus all other lineages. Consistent with the 'Paraná Capture Hypothesis', several lines of evidence supported mid-Pleistocene colonization and vicariant isolation of Hypostomus populations from an ancestral Upper Paraná population, including: (1) significant phylogeographic structure, with predicted phylogenetic patterns, (2) higher Paraná lineage diversity, (3) ancestral geographic locations reconstructed in the Paraná basin, and (4) non-random interdrainage dispersal and vicariance events, indicating river captures primarily into the Tocantins and Upper São Francisco basins c. ~220,000-145,500 years ago. Phylogeographic inference was complicated by lack of lineage monophyly across loci and lineages distributed in multiple basins, the latter of which lent support to the non-mutually exclusive 'Frequent Interdrainage Dispersal Hypothesis'. However, species tree and demographic modeling results suggested these were artefacts of incomplete sorting of alleles in large ancestral populations over a geologically recent timeframe of divergence. Qualitative and quantitative sensitivity analyses demonstrated that our downstream genetic results were robust to effects of varying ddRAD-seq assembly parameters, which heavily influenced the number of output loci. We predict that codistributed freshwater taxa in Central Brazil may not exhibit phylogeographic patterns similar to Hypostomus sp. 2 due to complex patterns of superimposed river capture events, or if smaller ancestral population sizes have allowed more complete lineage sorting in other taxa.

Download Full-text

Cytonuclear discordance in the crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrys: a mitochondrial selective sweep?

10.1101/2020.08.20.259549 ◽

2020 ◽

Author(s):

Rebecca S. Taylor ◽

Ashley C. Bramwell ◽

Rute Clemente-Carvalho ◽

Nicholas A. Cairns ◽

Frances Bonier ◽

...

Keyword(s):

Mitochondrial Dna ◽

Environmental Changes ◽

Incomplete Lineage Sorting ◽

Mitochondrial Gene ◽

Nuclear Gene ◽

Phylogeographic Structure ◽

Gene Trees ◽

Lineage Sorting ◽

Reciprocal Monophyly ◽

Mitochondrial Introgression

ABSTRACTThe golden-crowned (Zonotrichia atricapilla) and white-crowned (Z. leucophrys) sparrows have been presented as a compelling case for rapid speciation. They display divergence in song and plumage with overlap in their breeding ranges implying reproductive isolation, but have almost identical mitochondrial genomes. Previous research proposed hybridization and subsequent mitochondrial introgression as an alternate explanation, but lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting. We test for signatures of these processes between Z. atricapilla and Z. leucophrys, and investigate the relationships among Z. leucophrys subspecies, using mitochondrial sequencing and a reduced representation nuclear genomic dataset. Contrary to the paraphyly evident in mitochondrial gene trees, we confirmed the reciprocal monophyly of Z. atricapilla and Z. leucophrys using large panels of single nucleotide polymorphism (SNPs). The pattern of cytonuclear discordance is consistent with limited, historical hybridization and mitochondrial introgression, rather than a recent origin and incomplete lineage sorting between recent sister species. We found evidence of nuclear phylogeographic structure within Z. leucophrys with two distinct clades. Altogether, our results support the true species status of Z. atricapilla and Z. leucophrys, and indicate deeper divergences between the two species than inferred using mitochondrial markers. Our results demonstrate the limitations of relying solely on mitochondrial DNA for taxonomy, and raise questions about the possibility of selection on the mitochondrial genome during temperature oscillations (e.g. during the Pleistocene). Historical mitochondrial introgression facilitated by past environmental changes could cause erroneous dating of lineage splitting in other taxa when based on mitochondrial DNA alone.

Download Full-text

Ecological drivers of African swine fever virus persistence in wild boar populations: insight for control

10.1101/2019.12.13.875682 ◽

2019 ◽

Author(s):

Kim M. Pepin ◽

Andrew J. Golnar ◽

Zaid Abdo ◽

Tomasz Podgórski

Keyword(s):

Wild Boar ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Host Density ◽

Fever Virus ◽

Sensitivity Analyses ◽

Relative Role ◽

Primary Role ◽

Direct Transmission ◽

Ecological Data

AbstractEnvironmental sources of infection can play a primary role in shaping epidemiological dynamics, however the relative impact of environmental transmission on host-pathogen systems is rarely estimated. We developed and fit a spatially-explicit model of African swine fever virus (ASFV) in wild boar to estimate what proportion of carcass-based transmission is contributing to the low-level persistence of ASFV in Eastern European wild boar. Our model was developed based on ecological insight and data from field studies of ASFV and wild boar in Eastern Poland. We predicted that carcass-based transmission would play a substantial role in persistence, especially in low-density host populations where contact rates are low. By fitting the model to outbreak data using Approximate Bayesian Computation, we inferred that between 53 to 66% of transmission events were carcass-based – i.e., transmitted through contact of a live host with a contaminated carcass. Model fitting and sensitivity analyses showed that the frequency of carcass-based transmission increased with decreasing host density, suggesting that management policies should emphasize the removal of carcasses and consider how reductions in host densities may drive carcass-based transmission. Sensitivity analyses also demonstrated that carcass-based transmission is necessary for the autonomous persistence of ASFV under realistic parameters. Autonomous persistence through direct transmission alone required high host densities; otherwise re-introduction of virus periodically was required for persistence when direct transmission probabilities were moderately high. We quantify the relative role of different persistence mechanisms for a low-prevalence disease using readily collected ecological data and viral surveillance data. Understanding how the frequency of different transmission mechanisms vary across host densities can help identify optimal management strategies across changing ecological conditions.

Download Full-text

Concordant patterns of mtDNA and nuclear phylogeographic structure reveal Pleistocene vicariant event in the green crab Carcinus aestuarii across the Siculo-Tunisian Strait

Mediterranean Marine Science ◽

10.12681/mms.1562 ◽

2016 ◽

Vol 17 (2) ◽

pp. 533 ◽

Cited By ~ 8

Author(s):

T. DELI ◽

N. CHATTI ◽

K. SAID ◽

C. D SCHUBART

Keyword(s):

Genetic Structure ◽

Demographic History ◽

Time Estimation ◽

Mediterranean Coast ◽

Green Crab ◽

Early Pleistocene ◽

Phylogeographic Structure ◽

Secondary Contact ◽

Mediterranean Populations ◽

Vicariant Event

This study focuses on the population genetic structure of the green crab Carcinus aestuarii along part of the African Mediterranean coast, with the main target to confirm genetic subdivision across the well documented genetic boundary of the Siculo-Tunisian Strait. For this purpose, the mitochondrial COI (cytochrome oxidase I) gene and five polymorphic microsatellite loci were analysed in 144 and 120 specimens, respectively. Our results show the existence of two distinct haplogroups, separated by 16 mutational steps and revealed a non random distribution of the genetic variation along the African Mediterranean coast. Dating analyses, based on the use of different molecular clock models and rates, placed the divergence among both haplogroups at 1.91 Myr (95% HPD: 1.11–2.68 Myr) to 0.69 Myr (95% HPD: 0.44–0.98 Myr). This range of divergence time estimation corresponds to the Early Pleistocene. The particular pattern of genetic divergence among Eastern and Western African Mediterranean populations of C. aestuarii, detected by 2-level AMOVA at the mitochondrial level, was consistent with that inferred from microsatellite analysis and suggests a vicariant event in C. aestuarii. Demographic reconstruction, inferred from mismatch distribution and BSP analyses, yielded different patterns of demographic history between both African Mediterranean groups. The distribution pattern of the two haplogroups across the African Mediterranean coast, along with results of Bayesian analysis of genetic structure revealing an intermediate geographic group between the two divergent groups of the African coast, support the hypothesis of a secondary contact between two historically isolated groups. Although this hypothetical contact zone, thought to be located near the Siculo-Tunisian Strait, still needs to be verified, the asymmetric gene flow from Western to Eastern African Mediterranean, as inferred by the results of a MIGRATE analysis, reinforces the previously mentioned results.

Download Full-text

Investigating the causal effect of maternal vitamin B12 and folate levels on offspring birthweight

10.1101/2020.01.21.914655 ◽

2020 ◽

Author(s):

Gunn-Helen Moen ◽

Robin N Beaumont ◽

Christine Sommer ◽

Beverley M. Shields ◽

Deborah A Lawlor ◽

...

Keyword(s):

Vitamin B12 ◽

Genetic Variants ◽

Observational Studies ◽

Genome Wide Association Study ◽

Causal Effect ◽

Meta Analysis ◽

Serum Vitamin ◽

Genetic Effects ◽

Sensitivity Analyses ◽

A Genome

AbstractLower maternal serum vitamin B12 (B12) and folate levels have been associated with lower offspring birthweight in observational studies. The aim of this study was to investigate whether this relationship is causal.We performed two-sample Mendelian Randomization (MR) using summary data on associations between genotype-B12 (10 genetic variants) or genotype-folate (4 genetic variants) levels from a genome-wide association study of 45,576 individuals (sample 1) and maternal-specific genetic effects on offspring birthweight from the latest EGG consortium meta-analysis with 297,356 individuals reporting their own birthweight and 210,248 women reporting their offspring’s birthweight (sample 2). To investigate the effect of offspring’s own B12 or folate levels on their own birthweight, we performed two-sample MR using the fetal-specific genetic effects from the latest EGG consortium meta-analysis. We used the inverse variance weighted method, and sensitivity analyses to account for pleiotropy, in addition to sensitivity analyses excluding a potentially pleiotropic variant in the FUT2 gene for B12.We did not find evidence for a causal effect of maternal B12 on offspring birthweight, nor evidence for an effect of offspring B12 on their own birthweight using the fetal-specific genetic effect. The results were consistent across the different methods and in sensitivity analyses excluding the FUT2 variant. We found a positive effect of maternal folate on offspring birthweight (0.146 [0.065, 0.227], which corresponds to an increase in birthweight of 71g per 1SD higher folate). We found some evidence for a small inverse effect of fetal folate on their own birthweight (−0.051 [−0.100, −0.003]).In conclusion, our results are consistent with evidence from randomized controlled trials that increased maternal folate levels increase offspring birthweight. We did not find evidence for a causal effect of B12 on offspring birthweight, suggesting previous observational studies may have been due to confounding.

Download Full-text

Species limits and cryptic biogeographic structure in a widespread complex of Australian monsoon tropics trees (broad-leaf paperbarks: Melaleuca, Myrtaceae)

Australian Systematic Botany ◽

10.1071/sb18032 ◽

2018 ◽

Cited By ~ 1

Author(s):

Robert D. Edwards ◽

Michael D. Crisp ◽

Lyn G. Cook

Keyword(s):

Incomplete Lineage Sorting ◽

Phylogeographic Structure ◽

Lineage Sorting ◽

Species Limits ◽

Widespread Species ◽

Australian Monsoon ◽

Network Analyses ◽

The North ◽

Broad Leaf ◽

Drying Trend

The Australian monsoon tropics are currently dominated by savanna and tropical woodland biomes that have arisen in response to a cooling and drying trend within the past ~3 million years. It is expected that organisms well adapted to these conditions have expanded into available habitats, leading to the differentiation of populations and species across this landscape, a process that could be magnified by the presence of several biogeographic barriers. The broad-leaved paperbark (Melaleuca leucadendra (L.) L.) complex is one such group of plants, with 14 poorly morphologically differentiated species occupying large overlapping distributions across the region, and across several recognised biogeographic barriers. Using phylogenetic and network analyses of nuclear and plastid sequences, we tested species limits among currently described species within the complex and for phylogeographic structure within species across seven of these barriers. Overall, our data suggested patterns of differentiation among species consistent with the early to middle stages of incomplete lineage sorting, and evidence for an idiosyncratic cryptic response of species to biogeographic barriers. Unexpectedly, we found a deep molecular split across all species, broadly coinciding with the northern part of the Great Dividing Range, a feature not typically considered to be a barrier to dispersal. Our study has offered one of the first insights into the dynamics within and among widespread species across the north of Australia, suggesting considerably more geographic structure than was previously recognised.

Download Full-text

Conservation units and phylogeographic structure of an arboreal marsupial, the yellow-bellied glider (Petaurus australis)

Australian Journal of Zoology ◽

10.1071/zo06034 ◽

2006 ◽

Vol 54 (5) ◽

pp. 305 ◽

Cited By ~ 25

Author(s):

Meredeth Brown ◽

Huw Cooksley ◽

Susan M. Carthew ◽

Steven J. B. Cooper

Keyword(s):

South Australia ◽

Type Specimen ◽

Disjunct Distribution ◽

Phylogeographic Structure ◽

Restricted Gene Flow ◽

Ecological Data ◽

Isolated Populations ◽

Conservation Units ◽

Evolutionarily Significant Unit ◽

Petaurus Australis

Subspecific status has often been used as a surrogate for conservation unit, but does not always reflect intraspecific lineages with different evolutionary histories. One contentious case of subspecific classification occurs in the yellow-bellied glider (Petaurus australis), a marsupial species showing considerable decline in population size and requiring conservation management. Our aim was to assess the current subspecific status of populations and define units of conservation using a combination of phylogeographical analyses of mitochondrial DNA and morphological analyses. Analyses of the mitochondrial ND4 gene provided evidence for significant phylogeographic structure within P. australis. Isolated populations in north Queensland (NQ) and Victoria/South Australia were genetically distinct from populations in New South Wales and southern Queensland. Morphological analyses provided little evidence for discrimination of populations, although NQ specimens were generally smaller in size than southern forms. Our analyses do not support the classification of subspecies P. a. reginae for the original type specimen from southern Queensland. Taking into account other behavioural and ecological data, and the disjunct distribution of NQ populations from southern populations, we propose that the NQ population represents a distinct Evolutionarily Significant Unit, a lineage showing highly restricted gene flow from the rest of the species.

Download Full-text

Systematic revision ofPlatantherain the Azorean archipelago: not one but three species, including arguably Europe’s rarest orchid

PeerJ ◽

10.7717/peerj.218 ◽

2013 ◽

Vol 1 ◽

pp. e218 ◽

Cited By ~ 18

Author(s):

Richard M. Bateman ◽

Paula J. Rudall ◽

Mónica Moura

Keyword(s):

Endemic Species ◽

Geographic Origin ◽

Morphological Characters ◽

Habitat Destruction ◽

Ancestral Population ◽

Ecological Data ◽

Systematic Revision ◽

Taxonomic Descriptions ◽

Speciation Event ◽

Macaronesian Islands

Background and Aims.The Macaronesian islands represent an excellent crucible for exploring speciation. This dominantly phenotypic study complements a separate genotypic study, together designed to identify and circumscribePlatantheraspecies (butterfly-orchids) on the Azores, and to determine their geographic origin(s) and underlying speciation mechanism(s).Methods.216 individuals ofPlatantherafrom 30 Azorean localities spanning all nine Azorean islands were measured for 38 morphological characters, supported by light and scanning electron microscopy of selected flowers. They are compared through detailed multivariate and univariate analyses with four widespread continental European relatives in theP. bifolia-chloranthaaggregate, represented by 154 plants from 25 populations, and with the highly misleading original taxonomic descriptions. Physiographic and ecological data were also recorded for each study population.Key Results.Despite limited genetic divergence, detailed phenotypic survey reveals not one or two but three discrete endemic species ofPlatantherathat are readily distinguished using several characters, most floral:P. pollostantha(newly named, formerlyP. micrantha) occupies the widest range of habitats and altitudes and occurs on all nine islands;P. micrantha(formerlyP. azorica) occurs on eight islands but is restricted to small, scattered populations in laurisilva scrub; the trueP. azoricaappears confined to a single volcanigenic ridge on the central island of São Jorge.Conclusions.Although hybridity seems low, the excess of phenotypic over genotypic divergence suggests comparatively recent speciation. The most probable of several credible scenarios is that AzoreanPlatantheras represent a single migration to the archipelago of airborne seed from ancestral population(s) located in southwest Europe rather than North America, originating from within theP. bifolia-chloranthaaggregate. We hypothesise that an initial anagenetic speciation event, aided by the founder effect, was followed by the independent origins of at least one of the two rarer endemic species from within the first-formed endemic species, via a cladogenetic speciation process that involved radical shifts in floral development, considerable phenotypic convergence, and increased mycorrhizal specificity. The recent amalgamation by IUCN of AzoreanPlatantherasinto a single putative species on their Red List urgently requires overruling, as (a)P. azoricais arguably Europe’s rarestbona fideorchid species and (b) the almost equally rareP. micranthais one of the best indicators of semi-natural laurisilva habitats remaining on the Azores. Both species are threatened by habitat destruction and invasive alien plants. These orchids constitute a model system that illustrates the general advantages of circumscribing species by prioritising field-based over herbarium-based morphological approaches.

Download Full-text

Remote spatial analysis lacking ethnographic grounding mischaracterizes sustainability of Indigenous burning regime

Biota Neotropica ◽

10.1590/1676-0611-bn-2021-1220 ◽

2022 ◽

Vol 22 (1) ◽

Author(s):

James R. Welch ◽

Eduardo S. Brondizio ◽

Carlos E. A. Coimbra Jr.

Keyword(s):

Spatial Analysis ◽

Fire Regimes ◽

Ecological Data ◽

Anthropogenic Fire ◽

Central Brazil ◽

Fire Scar ◽

Indigenous Territories ◽

Indigenous Burning ◽

Indigenous Land

Abstract: Scientific research that purports to evaluate Indigenous fire regimes in the absence of ethnographically contextualized ecological data runs the risk of exacerbating the fire blame game and providing evidence to support distorted narratives advanced by anti-Indigenous advocates. Spatial analysis of fire scars in Indigenous territories can be an effective tool for characterizing cultural fire regimes in terms of distribution and frequency, especially when qualified by linkages to different local ecosystems. A recently published article drew on fire scar mapping from satellite imagery to assess anthropogenic fire distribution and frequency in the Pimentel Barbosa Indigenous Land, Central Brazil. The authors use their findings to characterize A'uwẽ (Xavante) use of fire as unmanaged and a model of unsustainable use of cerrado resources. In this article, we discuss Aguiar & Martins's recent paper in light of our long-term research on A'uwẽ hunting with fire in the Pimentel Barbosa Indigenous Land, arguing that A'uwẽ hunters do burn according to established cultural protocols, manage their use of fire for conservationist purposes, and do not cause environmental degradation by burning.

Download Full-text

Molecular phylogeny and phylogeography of the freshwater-fish genus Pethia (Teleostei: Cyprinidae) in Sri Lanka

BMC Ecology and Evolution ◽

10.1186/s12862-021-01923-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Hiranya Sudasinghe ◽

Tharindu Ranasinghe ◽

Jayampathi Herath ◽

Kumudu Wijesooriya ◽

Rohan Pethiyagoda ◽

...

Keyword(s):

Sri Lanka ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Morphological Diversity ◽

Phylogeographic Structure ◽

Sri Lankan ◽

Lineage Sorting ◽

Multiple Sources ◽

Reciprocal Monophyly ◽

Wet Zone

Abstract Background Sri Lanka is a continental island separated from India by the Palk Strait, a shallow-shelf sea, which was emergent during periods of lowered sea level. Its biodiversity is concentrated in its perhumid south-western ‘wet zone’. The island’s freshwater fishes are dominated by the Cyprinidae, characterized by small diversifications of species derived from dispersals from India. These include five diminutive, endemic species of Pethia (P. bandula, P. cumingii, P. melanomaculata, P. nigrofasciata, P. reval), whose evolutionary history remains poorly understood. Here, based on comprehensive geographic sampling, we explore the phylogeny, phylogeography and morphological diversity of the genus in Sri Lanka. Results The phylogenetic analyses, based on mitochondrial and nuclear loci, recover Sri Lankan Pethia as polyphyletic. The reciprocal monophyly of P. bandula and P. nigrofasciata, and P. cumingii and P. reval, is not supported. Pethia nigrofasciata, P. cumingii, and P. reval show strong phylogeographic structure in the wet zone, compared with P. melanomaculata, which ranges across the dry and intermediate zones. Translocated populations of P. nigrofasciata and P. reval in the Central Hills likely originate from multiple sources. Morphological analyses reveal populations of P. nigrofasciata proximal to P. bandula, a narrow-range endemic, to have a mix of characters between the two species. Similarly, populations of P. cumingii in the Kalu basin possess orange fins, a state between the red-finned P. reval from Kelani to Deduru and yellow-finned P. cumingii from Bentara to Gin basins. Conclusions Polyphyly in Sri Lankan Pethia suggests two or three colonizations from mainland India. Strong phylogeographic structure in P. nigrofasciata, P. cumingii and P. reval, compared with P. melanomaculata, supports a model wherein the topographically complex wet zone harbors greater genetic diversity than the topographically uniform dry-zone. Mixed morphological characters between P. bandula and P. nigrofasciata, and P. cumingii and P. reval, and their unresolved phylogenies, may suggest recent speciation scenarios with incomplete lineage sorting, or hybridization.

Download Full-text

Fragmentación y expansión demográfica en las poblaciones mexicanas de Pinus ayacahuite var. ayacahuite

Botanical Sciences ◽

10.17129/botsci.1786 ◽

2017 ◽

pp. 25

Author(s):

Alejandra Ortíz-Medrano ◽

Alejandra Moreno-Letelier ◽

Daniel Piñero

Keyword(s):

Genetic Diversity ◽

Spatial Analysis ◽

Cold Period ◽

Early Pleistocene ◽

Phylogeographic Structure ◽

Chloroplast Microsatellites ◽

Nested Clade Analysis ◽

Analysis Of Molecular Variance ◽

Molecular Variance ◽

Mexican Populations

This study explores the phylogeographic structure and the demographic hi story of the Mexican populations of Pinus ayacahuite var. ayacahuite. Three chloroplast microsatellites were amplified in 198 individuals from 14 populations. Twelve haplotypes were found and an average genetic diversity (He) of 0.705. Two maximally differentiated groups were determined with a spatial analysis of molecular variance. A significant correlation was detected between the genetic and geographic distances between these two groups, but not within them. A significant phylogeographic structure was found, produced by the existence of the two groups. Two demographic expansions were detected, the first in the entire species, the second only in the southernmost populations. Additionally, a nested clade analysis was pe1formed to complement our observations. The results showed that the Tehuantepec Isthmus was a corridor for species of temperate affinities in a cold period in early Pleistocene, and later acted as a barrier

Download Full-text