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1. Genetic insights into the evolution of genera with the eastern Asia–eastern North America floristic disjunction: a transcriptomics analysis

   https://doi.org/10.1002/ajb2.1579  

   Melton, Anthony E. ; Chen, Shichao ; Zhao, Yunpeng ; Fu, Chengxin ; Xiang, Qiu‐Yun ; Cheng, Shifeng ; Wong, Gane K. ‐S. ; Soltis, Pamela S. ; Soltis, Douglas E. ; Gitzendanner, Matthew A. ( December 2020 , American Journal of Botany)

   Large disjunctions in species distributions provide excellent opportunities to study processes that shape biogeographic patterns. One such disjunction is the eastern Asia–eastern North America (EA‐ENA) floristic disjunction. For many genera with this disjunction, species richness is greater in EA than in ENA; this pattern has been attributed, in part, to higher rates of molecular evolution and speciation in EA. Longer branch lengths have been found in some EA clades, relative to their ENA sister clades, suggesting that the EA lineages have evolved at a higher rate, possibly due to environmental heterogeneity, potentially contributing to the species richness anomaly.

   To evaluate whether rates of molecular evolution are elevated in EA relative to ENA, we used transcriptomes from species in 11 genera displaying this disjunction. Rates of molecular evolution were estimated for up to 385 orthologous nuclear loci per genus.

   No statistically significant differences were identified in pairwise comparisons between EA and ENA sister species, suggesting equal rates of molecular evolution for both species; the data also suggest similar selection pressures in both regions. For larger genera, evidence likewise argues against more species‐rich clades having higher molecular evolutionary rates, regardless of region. Our results suggest that genes across multiple gene ontology categories are evolving at similar rates under purifying selection in species in both regions.

   Our data support the hypothesis that greater species richness in EA than ENA is due to factors other than an overall increase in rates of molecular evolution in EA.

    

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2. Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North American Nyssa (Nyssaceae)

   https://doi.org/10.1111/jse.12599  

   Zhou, Wenbin ; Xiang, Qiu‐Yun ; Wen, Jun ( June 2020 , Journal of Systematics and Evolution)

   Nyssa(Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian–eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographical history, and investigate the evolution of morphology and ecological niches, aiming at a better understanding of the well‐known EA–ENA floristic disjunction. Results showed that the Central American (CAM)Nyssa talamancanawas sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographical history suggested thatNyssahad an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central AmericanN. talamancanarepresents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals ofNyssaand the Neogene dispersals, respectively, as well as the role of Central America as refugia of the Paleogene flora. The total‐evidence‐based dated phylogeny suggested that the pattern of macroevolution ofNyssacoincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA–ENA disjunct, supporting the ecological selection driving trait evolutions after geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene, but “out of Asia” migrations in the Neogene, to explain the present disjunct distribution ofNyssain EA and ENA.

    

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3. Climatic niche evolution in turtles is characterized by phylogenetic conservatism for both aquatic and terrestrial species

   https://doi.org/10.1111/jeb.13395  

   Rodrigues, João Fabrício M. ; Villalobos, Fabricio ; Iverson, John B. ; Diniz‐Filho, José Alexandre F. ( November 2018 , Journal of Evolutionary Biology)

   Understanding how the climatic niche of species evolved has been a topic of high interest in current theoretical and applied macroecological studies. However, little is known regarding how species traits might influence climatic niche evolution. Here, we evaluated patterns of climatic niche evolution in turtles (tortoises and freshwater turtles) and whether species habitat (terrestrial or aquatic) influences these patterns. We used phylogenetic, climatic and distribution data for 261 species to estimate their climatic niches. Then, we compared whether niche overlap between sister species was higher than between random species pairs and evaluated whether niche optima and rates varied between aquatic and terrestrial species. Sister species had higher values of niche overlap than random species pairs, suggesting phylogenetic climatic niche conservatism in turtles. The climatic niche evolution of the group followed an Ornstein–Uhlenbeck model with different optimum values for aquatic and terrestrial species, but we did not find consistent evidence of differences in their rates of climatic niche evolution. We conclude that phylogenetic climatic niche conservatism occurs among turtle species. Furthermore, terrestrial and aquatic species occupy different climatic niches but these seem to have evolved at similar evolutionary rates, reinforcing the importance of habitat in understanding species climatic niches and their evolution.

    

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4. Niche conservatism over deep timescales and diverse niche axes in land vertebrates

   https://doi.org/10.1111/geb.13715  

   Saban, Kristen E. ; Qu, Yan‐Fu ; Wiens, John J. ( June 2023 , Global Ecology and Biogeography)

   There has been considerable interest in niche conservatism, the idea that ecological variables are similar among related species. Much research has focused on climatic niches of recently diverged species, rather than deeper timescales or non‐climatic niche axes. Furthermore, it has been suggested that conservatism disappears over deeper timescales, and is greater in alpha niche traits (like diet and microhabitat) than beta niche variables (like climate). Here, we test these latter two ideas by comparing patterns of phylogenetic conservatism among 10 niche variables across major clades of land vertebrates.

   Global.

   Present to 350 million years ago.

   Tetrapods, including amphibians, mammals, lepidosaurs (including lizards and snakes), turtles, crocodilians and birds.

   The 10 niche variables included four alpha niche components (diet, diel activity, habitat, body temperature) and six beta niche components (related to climatic temperature and precipitation). We analysed these variables on time‐calibrated phylogenies with similar taxon sampling (~1700 species), using phylogenetic signal (lambda) to estimate conservatism, along with theDstatistic and estimates of evolutionary rates.

   Phylogenetic signal was generally strong across all variables, with lambda generally >0.80 (with 1.0 representing maximum signal). Nevertheless, mean phylogenetic signal was lower in beta niche traits than alpha niche traits (based on lambda and especially theDstatistic), and alpha niche traits showed significantly slower rates of evolution.

   We address two long‐held views in the literature on niche conservatism, rejecting one but supporting the other. We show that phylogenetic signal does not disappear over deep timescales for many important niche variables, even over 350 million years. We also generally support greater conservatism in alpha niche traits than beta niche traits over hundreds of millions of years, a pattern that was previously suggested (but not explicitly tested) based on closely related species.

    

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5. Out of the temperate zone: A phylogenomic test of the biogeographical conservatism hypothesis in a contrarian clade of ants

   https://doi.org/10.1111/jbi.14462  

   Branstetter, Michael G. ; Longino, John T. ; Reyes‐López, Joaquín L. ; Brady, Seán G. ; Schultz, Ted R. ( July 2022 , Journal of Biogeography)

   The standard latitudinal diversity gradient (LDG), in which species richness decreases from equator to pole, is a pervasive pattern observed in most organisms. Some lineages, however, exhibit inverse LDGs. Seemingly problematic, documenting and studying contrarian groups can advance understanding of LDGs generally. Here, we identify one such contrarian clade and use a historical approach to evaluate alternative hypotheses that might explain the group's atypical diversity pattern. We focus on the biogeographical conservatism hypothesis (BCH) and the diversification rate hypothesis (DRH).

   Global.

   Ants (Hymenoptera: Formicidae: Stenammini).

   We examined the shape of the LDG in Stenammini by plotting latitudinal midpoints for all extant, described species. We inferred a robust genome‐scale phylogeny using UCE data. We estimated divergence dates using beast2 and tested several biogeographical models inBioGeoBEARS. To examine diversification rates and test for a correlation between rate and latitude, we used the programs BAMM and STRAPP, respectively.

   Stenammini has a skewed inverse LDG with a richness peak in the northern temperate zone. Phylogenomic analyses revealed five major clades and several instances of non‐monophyly among genera (Goniomma,Aphaenogaster). Stenammini and all its major lineages arose in the northern temperate zone. The tribe originated ~51 Ma during a climatic optimum and then diversified and dispersed southward as global climate cooled. Stenammini invaded the tropics at least seven times, but these events occurred more recently and were not linked with increased diversification. There is evidence for a diversification rate increase in HolarcticAphaenogaster + Messor, but we found no significant correlation between latitude and diversification rate generally.

   Our results largely support the BCH as an explanation for the inverse latitudinal gradient in Stenammini. The clade originated in the Holarctic and likely became more diverse there due to center‐of‐origin, time‐for‐speciation and niche conservatism effects, rather than latitudinal differences in diversification rate.

    

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