Biology subjects

Kates, H. R.

Publications and source records attributed to Kates, H. R..

6 recordsLinked to original sources

bioRxiv2023

Phylogenetic diversity and regionalization of root nodule symbiosis

AimHere we determine centers of species richness (SR), relative phylogenetic diversity (RPD) and centers of paleo- and neo-endemism, and regionalizations of phylogenetic diversity in the mimosoid clade of the legumes to understand the distribution and environmental associates of mimosoids lacking RNS (root nodule symbiosis). LocationGlobal. Time periodPresent. Major taxa studiedMimosoid legumes. MethodsWe built a phylogenetic tree of 1313 species and high-quality species distribution models for 1128 species representing the phylogenetic breadth of the mimosoid clade to identify the geographic distribution of RNS. Centers of significant RPD and endemism were identified using a randomization approach, the latter using CANAPE. Phylogenetic regionalization used a distance-based phylogenetic beta-diversity approach. ResultsWe recognized nine areas of contiguous high SR as distinct SR hotspots. Non-RNS species occur mainly outside hotspots but are closely correlated with high RPD. Absence of RNS was best predicted by high precipitation, and represents multiple independent phylogenetic assemblages in different biogeographic areas. Main conclusionsSR hotspots are partly incongruent with centers of RPD and phylogenetic endemism. Lineages lacking RNS are distributed in SR hotspots in Africa and the Americas, belong to biogeographically separate species assemblages, and are, in most cases, associated with relatively moist tropical environments with low temperature seasonality and high available soil nitrogen.

ecology↗

bioRxiv2023

Rapid in-situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

O_LIThe macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. C_LIO_LIWe integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. C_LIO_LIOur results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in-situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. C_LIO_LIThe proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in-situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in-situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales. C_LI

evolutionary biology↗

bioRxiv2023

Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus

Astragalus (Fabaceae), with more than 3,000 species, represents a successful radiation of morphologically highly similar species found across the Northern Hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness. Here, for the first time using extensive taxonomic sampling in a phylogenetic analysis, we ask whether (1) Astragalus is uniquely characterized by bursts of radiation or is instead similar to related taxa. Then we test whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats or (3) particular soils. Finally, we test (4) whether Astragalus originated in central Asia as proposed and (5) whether niche evolutionary shifts were associated with the colonization of other continents. Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but attributable to no abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. We find strong evidence for a central Asian origin and direct dispersals from this region responsible for much of the present-day distribution, highlighting the importance of central Asia as a biogeographic gateway. In contrast to diversification shifts, biogeographic shifts have a strong association with the abiotic environment. Our most important result was a fundamental divide in soil types and diurnal temperature variation between the Eastern and Western Hemisphere species; this divergence does not reflect differences in available habitat among these biogeographic domains but may reflect unique local gains of edaphic and abiotic stress adaptations. While large clades are logistically difficult to tackle, our investigation shows the importance of phylogenetic and evolutionary studies of "mega-radiations." Our findings reject any simple key innovation behind the dominance and richness of Astragalus and underline the often nuanced, multifactorial processes leading to species-rich clades.

plant biology↗

bioRxiv2023

Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae)

AO_SCPLOWBSTRACTC_SCPLOWOaks (Quercus), one of the most species-rich and ecologically dominant woody plant clades in the Northern Hemisphere, are well known for their propensity to hybridize and form syngameons, complexes where alleles are readily exchanged among closely related species. While hybridization has been extensively studied towards the tips of the oak phylogeny, the extent, timeline, and evolutionary scenarios of hybridization during the early radiation of oaks and related genera (Quercoideae) remain poorly known. Using an expansive new dataset of nuclear and chloroplast sequences (including up to 431 spp.), we conducted a multifaceted phylogenomic investigation of Quercus aimed at characterizing gene-tree and cytonuclear (chloroplast-nuclear) discordance and identifying ancient reticulation in the early evolution of the group. We document extensive nuclear gene-tree and cytonuclear discordance at deep nodes in Quercus and Quercoideae, with Quercus recovered as non-monophyletic in the chloroplast phylogeny. Analyses recovered clear signatures of gene flow against a backdrop of incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and Quercoideae during their initial radiation, dated to the early-middle Eocene. Ancestral reconstructions including fossil data suggest that the ancestors of Castanea+Castanopsis, Lithocarpus, and the Old World oak clade co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Following this initial phase of radiation and reticulation, we detected multiple niche shifts in Quercus and other Quercoideae genera that likely facilitated their expansion into new habitats arising from post-Eocene climatic changes. Our study shows that hybridization--perhaps in the form of ancient syngameons similar to those seen today--has been a common and important process throughout the evolutionary history of oaks and their close relatives.

evolutionary biology↗

bioRxiv2023

Fagalean phylogeny in a nutshell: Chronicling the diversification history of Fagales

Reconstructing the biogeographical history and timing of the diversification of temperate forests is essential for understanding their history and resolving uncertainties about how flowering plants emerged from their deep tropical origins to dominate in todays freezing terrestrial environments. The angiosperm order Fagales, comprising iconic components of temperate forests worldwide with an extensive fossil record, are an excellent plant system in which to apply a fossil-aware paradigm, such as the fossilized birth-death (FBD) process, for investigating the macroevolution of temperate forest biomes. Here, we improve upon previous efforts to resolve phylogeny and incorporate fossils in Fagales using low-copy nuclear loci and an expanded morphological matrix to reevaluate the Fagales fossil record and: (1) infer the phylogenetic relationships and the time of origin of the clade using the FBD model as implemented in RevBayes, (2) provide a framework for evaluating the climatic and biogeographic history of Fagales, and (3) investigate how the inclusion of fossils via the FBD method influences ancestral reconstruction and diversification estimation. The phylogenetic relationships we recovered are conventional except for the position of Nothofagaceae, while our inferred ages support older timelines than previously proposed, with a mid-Cretaceous date for the most recent common ancestor (MRCA) of the order. Biogeographical analysis shows an origin of Fagales consistent with an ancestral circumboreal temperate distribution corroborated by ancestral niche reconstructions. While distributions today largely reflect the general conservatism of temperate forests, we identified two episodes of high diversification, one at the mid-Cretaceous origin of the clade and the other continuing from the Miocene to the present. Removing fossil taxa from the tree reveals a different story, shifting the origin of extant families from North America to East Asia, reflecting refugial distributions in this biodiversity "museum" and implying a general bias towards low extinction areas in biogeographic reconstruction. Likewise, without fossil data, diversification estimates were higher and unable to detect an early diversification burst. Based on our analyses, we close with recommendations regarding the interpretation of estimates of diversification and ancestral state reconstruction using phylogenetic trees with only extant species as tips.

plant biology↗

bioRxiv2022

Testing the evolutionary drivers of nitrogen-fixing symbioses in challenging soil environments

O_LIWhile the importance of root nodular symbioses (RNS) in plants has long been recognized, the ecological and evolutionary factors maintaining RNS remain obscure. RNS is associated with environmental stressors such as aridity and nitrogen-poor soils; the ability to tolerate harsh environments may provide ecological opportunities for diversification, yet, nodulators are also diverse outside these environments. C_LIO_LIWe test several environmental determinants of increased survival and enhanced diversification of RNS species, using an explicitly phylogenetic approach for the first time. We assembled the largest phylogeny of the nitrogen-fixing clade to date and a comprehensive set of abiotic niche estimates and nodulation data. We used comparative phylogenetic tools to test environmental and diversification associations. C_LIO_LIWe found that RNS is associated with warm, arid, and nitrogen-poor habitats. However, RNS was gained long before lineages entered these habitats. RNS is associated with accelerated diversification, but diversification rates are heterogeneous among nodulators, and non-legume nodulators do not show elevated diversification. C_LIO_LIOur findings undermine the interpretation that RNS directly drove the invasion of challenging habitats, and do not support a direct relationship between soil or climate and the diversity of nodulators. Still, RNS may have been an important exaptation allowing further niche evolution. C_LI

plant biology↗