Quaternary climate changes as speciation drivers in the Amazon floodplains

The role of climate as a speciation driver in the Amazon has long been discussed. Phylogeographic studies have failed to recover synchronous demographic responses across taxa, although recent evidence supports the interaction between rivers and climate in promoting speciation. Most studies, however, are biased toward upland forest organisms, while other habitats are poorly explored and could hold valuable information about major historical processes. We conducted a comparative phylogenomic analysis of floodplain forest birds to explore the effects of historical environmental changes and current connectivity on population differentiation. Our findings support a similar demographic history among species complexes, indicating that the central portion of the Amazon River basin is a suture zone for taxa isolated across the main Amazonian sub-basins. Our results also suggest that changes in the fluvial landscape induced by climate variation during the Mid- and Late Pleistocene drove population isolation, leading to diversification with subsequent secondary contact.

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Neogene and Quaternary climate changes shaped the lineage differentiation and demographic history of Fokienia hodginsii (Cupressaceae s.l.), a Tertiary relict in East Asia

Journal of Systematics and Evolution ◽

10.1111/jse.12582 ◽

2020 ◽

Author(s):

Qian‐Yi Yin ◽

Qiang Fan ◽

Pan Li ◽

DoVan Truong ◽

Wan‐Yi Zhao ◽

...

Keyword(s):

East Asia ◽

Climate Changes ◽

Demographic History ◽

Lineage Differentiation ◽

Quaternary Climate ◽

History Of ◽

Quaternary Climate Changes

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Environmental Changes at Lake Cheshi, Zambia Since 40,000 Years B.P.

Quaternary Research ◽

10.1016/0033-5894(88)90071-3 ◽

1988 ◽

Vol 29 (1) ◽

pp. 54-65 ◽

Cited By ~ 37

Author(s):

J. Curt Stager

Keyword(s):

Climate Changes ◽

Environmental Changes ◽

Late Quaternary ◽

Central Africa ◽

Testate Amoeba ◽

Lake Levels ◽

Quaternary Climate ◽

South Central ◽

Arid Conditions ◽

Quaternary Climate Changes

Sediment and microfossil analyses of a 7.5-m core from Lake Cheshi suggest that south-central Africa experienced late Quaternary climate changes similar to those in East Africa. The lake formed around 34,000 yr B.P., after a prelacustrine phase of at least 6000 yr, from climatic or tectonic causes. Ratios of precipitation to evaporation were probably similar to those of today until a decline about 15,000–13,000 yr B.P. when the lake shrank and became chemically concentrated. Maximal lake levels occurred between 8000 and 4000 yr B.P., and were followed by a low stand under presumably arid conditions about 3500 yr B.P. Encroachment of sudd vegetation contributed to shallowing during the last 3000 yr. A phase of microfossil dilution may reflect human activity in the basin, or climatic or hydrological changes. Melosira valve morphology seems to reflect mixing regimes. Sponge and testate amoeba remains were most numerous relative to diatoms during low-water phases.

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Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz077 ◽

2019 ◽

Vol 128 (1) ◽

pp. 149-169 ◽

Cited By ~ 2

Author(s):

Drew R Schield ◽

Blair W Perry ◽

Richard H Adams ◽

Daren C Card ◽

Tereza Jezkova ◽

...

Keyword(s):

Gene Flow ◽

Demographic History ◽

Secondary Contact ◽

Tree Model ◽

Crotalus Viridis ◽

Species Complexes ◽

Isolating Mechanisms ◽

Allopatric Divergence ◽

History Of ◽

Study Population

Abstract The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically.

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Late Miocene origin and recent population collapse of the Malagasy savanna olive tree (Noronhia lowryi)

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz164 ◽

2019 ◽

Vol 129 (1) ◽

pp. 227-243 ◽

Cited By ~ 6

Author(s):

Jordi Salmona ◽

Jill K Olofsson ◽

Cynthia Hong-Wa ◽

Jacqueline Razanatsoa ◽

Franck Rakotonasolo ◽

...

Keyword(s):

Environmental Changes ◽

Abiotic Factors ◽

Demographic History ◽

Olive Tree ◽

Nuclear Data ◽

Chloroplast Microsatellites ◽

Population Genetic Analysis ◽

Central Plateau ◽

Habitat Mosaics

Abstract Debates regarding the origin of tropical savannas have attempted to disentangle the role of human, biotic and abiotic factors. Understanding the origins of savanna remains essential to identifying processes that gave rise to habitat mosaics, particularly those found in the Central Plateau of Madagascar. Documenting the evolutionary history and demography of native trees occurring in open habitats may reveal footprints left by past and recent environmental changes. We conducted a population genetic analysis of an endangered Malagasy shrub (Noronhia lowryi, Oleaceae) of the Central Plateau. Seventy-seven individuals were sampled from three sites and genotyped at 14 nuclear and 24 chloroplast microsatellites. We found a highly contrasting nuclear and plastid genetic structure, suggesting that pollen-mediated gene flow allows panmixia, while seed-based dispersal may rarely exceed tens of metres. From a phylogeny based on full plastomes, we dated the surprisingly old crown age of maternal lineages back to ~6.2 Mya, perhaps co-occurring with the global expansion of savanna. In contrast, recent demographic history inferred from nuclear data shows a bottleneck signature ~350 generations ago, probably reflecting an environmental shift during the Late Pleistocene or the Holocene. Ancient in situ adaptation and recent demographic collapse of an endangered woody plant highlight the unique value and vulnerability of the Malagasy savannas.

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Faculty Opinions recommendation of Quaternary climate changes explain diversity among reptiles and amphibians.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1101201.557206 ◽

2008 ◽

Author(s):

Roland Jansson

Keyword(s):

Climate Changes ◽

Quaternary Climate ◽

Quaternary Climate Changes

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Demographic history and genomic response to environmental changes in a rapid radiation of wild rats

Molecular Biology and Evolution ◽

10.1093/molbev/msaa334 ◽

2021 ◽

Author(s):

Deyan Ge ◽

Anderson Feijó ◽

Zhixin Wen ◽

Alexei V Abramov ◽

Liang Lu ◽

...

Keyword(s):

Environmental Changes ◽

Demographic History ◽

Terrestrial Ecosystems ◽

Tibet Plateau ◽

Global Changes ◽

Rapid Radiation ◽

Protein Functions ◽

Wild Rats ◽

Qinghai Tibet Plateau ◽

Genomic Response

Abstract For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau (QHTP) was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.

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Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex

BMC Plant Biology ◽

10.1186/s12870-021-03099-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhi Wang ◽

Caihong Zhong ◽

Dawei Li ◽

Chunlin Yan ◽

Xiaohong Yao ◽

...

Keyword(s):

Environmental Changes ◽

Demographic History ◽

Wide Distribution ◽

Historical Demography ◽

Actinidia Chinensis ◽

Ecological Niche Models ◽

Subtropical China ◽

Modeling Tools ◽

Climatic Fluctuations ◽

Ploidy Levels

Abstract Background Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. Results The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties’ ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). Conclusions Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.

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