Phylogeography of Pinus subsection Australes in the Caribbean Basin

Impacts of habitat fragmentation on the genetic diversity of the endangered Guatemalan fir (Abies guatemalensis Rehder)

Abies guatemalensis Rehder, an endangered conifer endemic to Central American highlands, is ecologically vital in upper montane forests. It faces threats from habitat fragmentation, unsustainable logging, and illegal Christmas tree harvesting. While previous genetic studies on mature trees from eighteen populations showed high within-population diversity and limited among-population differentiation, the genetic impact of recent anthropogenic pressures on younger generations has yet to be discovered. Understanding these effects is crucial for developing effective conservation strategies for this vulnerable species. We sampled 170 young trees (< 15 years old) from seven populations across Guatemala. Seven microsatellite markers were used to analyse genetic diversity, population structure, and recent demographic history. Moderate levels of genetic diversity were observed within populations (mean Shannon diversity index = 4.97, mean Simpson's index = 0.51, mean allelic richness = 11.59, mean observed heterozygosity = 0.59). Although genetic structure broadly aligned with mountain corridors, substantial admixture patterns suggest historical connectivity across all populations. Most populations showed evidence of recent bottlenecks (p < 0.05) and inbreeding. The results suggest a potential decline in genetic diversity and increased population structuring (ΦST = 0.274, p < 0.01) over the past decades compared to the previous study on old trees. The observed genetic patterns indicate ongoing impacts of habitat fragmentation and anthropogenic pressures on A. guatemalensis. Conservation efforts should prioritise expanding effective population sizes and facilitating gene flow, particularly for isolated populations. While restoration efforts may be logistically easier within mountain ranges, genetic evidence suggests that increasing overall population connectivity could benefit this species. Management strategies should implement systematic seed collection protocols to maintain genetic diversity in future populations. These findings highlight the urgent need for conservation measures to preserve remaining genetic diversity and promote connectivity among A. guatemalensis populations.

Species distribution modelling and cpSSR reveal population history of the Neotropical annual herb Tithonia rotundifolia (Asteraceae)

The impacts of the historical geologic and climatic events on the diversity and genetic structure of Neotropical taxa have recently become a subject of study. However, annual plants associated with tropical dry forests remain under-studied. The exploration of additional taxa in contrasting environments will improve the current understanding of responses of the Neotropical biota to these events. Here, we explore the species distribution and geographic structure of the annual herb Tithonia rotundifolia. We sampled 175 individuals from 19 populations of T. rotundifolia. Species distribution modelling and six microsatellite chloroplast loci were used to infer its population history. We identified areas of historical climate suitability and then tested if there is genetic structuring among these areas. Haplotypes showed strong phylogeographic structure. Historical climatic suitability areas were found along the Pacific coast; however, a gap was found at the Isthmus of Tehuantepec (IT). Although Bayesian analysis showed population structuring, amova revealed that the IT is not its main driver. Instead, a subdivision into a higher number of regions had higher F_CT values. Also, populations to the east of the IT showed evidence of recent population expansion and migration in a south-north direction. Pleistocene climate fluctuations partially explain the geographic structure of T. rotundifolia. However, life-history characteristics such as limited seed dispersal and the patchy distribution of suitable habitats explain the high haplotype diversity and population sub-structuring and diversity. Lastly, the absence of geographic structure of some haplotypes may indicate long-distance dispersal, or hybridisation with the closely related T. tubaeformis.

Multi-locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

PREMISE OF THE STUDY

Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long-lived, wind-pollinated plants with large population sizes and weak reproductive barriers.

METHODS

We used solution hybridization for targeted enrichment and massive parallel sequencing to characterize low-copy-number nuclear genes and high-copy-number plastomes (Hyb-Seq) in 74 individuals of Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance. We inferred relationships using methods that account for both incomplete lineage sorting and reticulation.

KEY RESULTS

Concatenation- and coalescent-based trees inferred from nuclear genes mainly agreed with one another, but they contradicted the plastid DNA tree in recovering the Attenuatae (the California closed-cone pines) and Oocarpae (the egg-cone pines of Mexico and Central America) as monophyletic and the Australes sensu stricto (the southern yellow pines) as paraphyletic to the Oocarpae. The plastid tree featured some relationships that were discordant with morphological and geographic evidence and species limits. Incorporating gene flow into the coalescent analyses better fit the data, but evidence supporting the hypothesis that hybridization explains the non-monophyly of the Attenuatae in the plastid tree was equivocal.

CONCLUSIONS

Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.

Appropriate homoplasy metrics in linked SSRs to predict an underestimation of demographic expansion times

BACKGROUND

Homoplasy affects demographic inference estimates. This effect has been recognized and corrective methods have been developed. However, no studies so far have defined what homoplasy metrics best describe the effects on demographic inference, or have attempted to estimate such metrics in real data. Here we study how homoplasy in chloroplast microsatellites (cpSSR) affects inference of population expansion time. cpSSRs are popular markers for inferring historical demography in plants due to their high mutation rate and limited recombination.

RESULTS

In cpSSRs, homoplasy is usually quantified as the probability that two markers or haplotypes that are identical by state are not identical by descent (Homoplasy index, P). Here we propose a new measure of multi-locus homoplasy in linked SSR called Distance Homoplasy (DH), which measures the proportion of pairwise differences not observed due to homoplasy, and we compare it to P and its per cpSSR locus average, which we call Mean Size Homoplasy (MSH). We use simulations and analytical derivations to show that, out of the three homoplasy metrics analyzed, MSH and DH are more correlated to changes in the population expansion time and to the underestimation of that demographic parameter using cpSSR. We perform simulations to show that Approximate Bayesian Computation (ABC) can be used to obtain reasonable estimates of MSH and DH. Finally, we use ABC to estimate the expansion time, MSH and DH from a chloroplast SSR dataset in Pinus caribaea. To our knowledge, this is the first time that homoplasy has been estimated in population genetic data.

CONCLUSIONS

We show that MSH and DH should be used to quantify how homoplasy affects estimates of population expansion time. We also demonstrate how ABC provides a methodology to estimate homoplasy in population genetic data.

Phylogeography of a good Caribbean disperser: Argiope argentata (Araneae, Araneidae) and a new 'cryptic' species from Cuba

The Caribbean islands harbor rich biodiversity with high levels of single island endemism. Stretches of ocean between islands represent significant barriers to gene-flow. Yet some native species are widespread, indicating dispersal across oceans, even in wingless organisms like spiders. Argiopeargentata (Fabricius, 1775) is a large, charismatic, and widespread species of orb-weaving spider ranging from the United States to Argentina and is well known to balloon. Here we explore the phylogeography of Argiopeargentata in the Caribbean as a part of the multi-lineage CarBio project, through mtDNA haplotype and multi-locus phylogenetic analyses. The history of the Argiopeargentata lineage in the Caribbean goes back 3-5 million years and is characterized by multiple dispersal events and isolation-by-distance. We find a highly genetically distinct lineage on Cuba which we describe as Argiopebutchkosp. n. While the argentata lineage seems to readily balloon shorter distances, stretches of ocean still act as filters for among-island gene-flow as evidenced by distinct haplotypes on the more isolated islands, high F^ST values, and strong correlation between intraspecific (but not interspecific) genetic and geographic distances. The new species described here is clearly genetically diagnosable, but morphologically cryptic, at least with reference to the genitalia that typically diagnose spider species. Our results are consistent with the intermediate dispersal model suggesting that good dispersers, such as our study species, limit the effect of oceanic barriers and thus diversification and endemism.

Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads

Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group.

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors hundreds of mitochondria and plastids. Hence, assembly of the 123-kb plastid and 5.9-Mb mitochondrial genomes were accomplished by analyzing data sets primarily representing low coverage of the nuclear genome. The assembled organellar genomes were annotated for their coding genes, ribosomal RNA, and transfer RNA. Transcript abundances of the mitochondrial genes were quantified in three developmental tissues and five mature tissues using data from RNA-seq experiments. C-to-U RNA editing was observed in the majority of mitochondrial genes, and in four genes, editing events were noted to modify ACG codons to create cryptic AUG start codons. The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data.

A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)

PREMISE OF THE STUDY

Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. •

METHODS

Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences of ycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. •

RESULTS

The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. •

DISCUSSION

The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group.