Recent radiation and dispersal of an ancient lineage: The case of Fouquieria (Fouquiericeae, Ericales) in North American deserts

Phylogeography and population genetics of a widespread cold-adapted ant, Prenolepis imparis

As species arise, evolve, and diverge, they are shaped by forces that unfold across short and long time scales and at both local and vast geographic scales. It is rare, however, to be able document this history across broad sweeps of time and space in a single species. Here, we report the results of a continental-scale phylogenomic analysis across the entire range of a widespread species. We analyzed sequences of 1,402 orthologous Ultraconserved Element (UCE) loci from 75 individuals to identify population genetic structure and historical demographic patterns across the continent-wide range of a cold-adapted ant, the winter ant, Prenolepis imparis. We recovered five well-supported, genetically isolated clades representing lineages that diverged from 8.2-2.2 million years ago. These include: 1) an early diverging lineage located in Florida, 2) a lineage that spans the southern United States, 3) populations that extend across the midwestern and northeastern United States, 4) populations from the western United States, and 5) populations in southwestern Arizona and Mexico. Population genetic analyses revealed little or no gene flow among these lineages, but patterns consistent with more recent gene flow among populations within lineages, and localized structure with migration in the western United States. High support for five major geographic lineages and lack of evidence of contemporary gene flow indicate in situ diversification across the species' range, producing relatively ancient lineages that persisted through subsequent climate change and glaciation during the Quaternary.

Phylogeography and genetic structure of an iconic tree of the Sonoran Desert, the Cirio (Fouquieria columnaris), based on chloroplast DNA

We have examined the phylogeographical distribution of chloroplast DNA (cpDNA) lineages of Fouquieria columnaris (Kellogg) Kellogg ex Curran (Fouquieriaceae) in the Sonoran Desert, to understand how historical climatic and/or geological changes have influenced genetic patterns in the species. Using two chloroplast intergenic DNA spacers (psbJ-petA and ndhF-rpl32), we found low levels of nucleotide diversity (π = 0.0025) but high levels of haplotype diversity (h = 0.9339). Analysis of 28 haplotypes revealed four lineages, one belonging to the continental massif and three to the peninsula of Baja California. This structure may be explained and dated by three events: (1) formation of the Gulf of California during the late Miocene (7.24 Mya), (2) activity of the Tres Vírgenes volcanic field (1.20 Mya) and (3) opening of the mid-peninsula seaway during the late Pleistocene (1.53 Mya). Furthermore, the cpDNA lineages show evidence for population contraction during the Last Glacial Maximum, with a subsequent population expansion in the Holocene.

Phylogenomics in Cactaceae: A case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts

PREMISE

Although numerous phylogenetic studies have been conducted in Cactaceae, whole-plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age, and morphological evolution.

METHODS

We developed a plastome dataset for most known diploid members of the chollas (42 taxa) as well as for other members of Cylindropuntieae. Paired-end, raw reads from genome skimming were reference-mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, and were used to build our plastome dataset, which was analyzed using various methods.

RESULTS

Our plastome dataset resolved the phylogeny of the chollas, including most interspecific and intraspecific relationships. Tribe Cylindropuntieae arose ~18 mya, during the early Miocene in southern South America, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series in Cylindropuntia (e.g., spiny fruit) are mostly homoplasious.

CONCLUSIONS

This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although the chollas s.l. are widespread throughout western North American deserts, their most recent common ancestor likely arose in the Chihuahuan Desert region during the mid-Miocene, with much of their species diversity arising in the early to mid-Pliocene, a pattern strikingly similar to those found in other western North American desert groups.

Crassula, insights into an old, arid-adapted group of southern African leaf-succulents

The Crassulaceae is an important family in the Greater Cape Floristic Region of southern Africa and is the seventh largest family in the arid Succulent Karoo Biome. After the Aizoaceae it is the largest group of leaf-succulents in southern Africa. This is the first investigation of a broad selection (68%) of the ±170 species of Crassula. We used data from three chloroplast and two nuclear gene-regions, which yielded many informative characters and provided good resolution among the species. We show that only five of the 20 sections in Crassula are monophyletic. However, the clades recovered show close correlation with the two subgenera that were once recognized. Crassula contains more than 25 succulent annual species which are not closely related to each other but form early-diverging branches in each of the three major clades. One of these major clades contains far more perennial species than the others and is the greatest diversification within Crassula. This diversification mostly arose within the last 10 million years (my) and spread across much of southern Africa. Members of the smaller two major clades are often soft- and flat-leaved perennials (many with basic chromosome number x = 8, with high levels of polyploidy). Those in the largest diversification (where a basic chromosome number of x = 7 predominates) show other arid-adaptations (more highly succulent leaves with a dense covering of hairs or papillae or a smooth xeromorphic epidermis). Their flowers are also more variable in shape and bee-, moth- and butterfly-pollinated species are known among them. We establish that Crassula arose in the Greater Cape Floristic Region of southern Africa. While much of its diversity has evolved in the last 10 my, Crassula nevertheless contains species that are much older and itself arose ±46 my ago. Since all its species are succulent it is possible that they are part of an early arid-adapted flora that contributed to the Succulent Karoo Biome in the western part of southern Africa. Consequently this Biome may not be assembled only from 'young lineages' as is usually thought to be the case.