skip to main content


Title: Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta) in relation to taxonomy and geography
Premise

TheSphagnum recurvumcomplex comprises a group of closely related peat mosses that are dominant components of many northern wetland ecosystems. Taxonomic hypotheses for the group range from interpreting the whole complex as one polymorphic species to distinguishing 6–10 species. The complex occurs throughout the Northern Hemisphere, and some of the putative species have intercontinental ranges. Our goals were to delimit the complex and assess its phylogenetic structure in relation to morphologically defined species and intercontinental geography.

Methods

RADseq analyses were applied to a sample of 384 collections from Europe, North America, and Asia. The data were subjected to maximum likelihood phylogenetic analyses and analyses of genetic structure using the software STRUCTURE and multivariate ordination approaches.

Results

TheS. recurvumcomplex includesS. angustifolium,S. fallax,S. flexuosum,S. pacificum, andS. recurvumas clades with little evidence of admixture. We also resolved an unnamed clade that is referred to here asS. “pseudopacificum.” We confirm thatS. balticumandS. obtusumare nested within the complex. Species with bluntly acute to obtuse stem leaf apices are sister to those with acute to apiculate leaves. Most of the species exhibit some differentiation between intraspecific population systems disjunct on different continents.

Conclusions

We recognize seven species in the amendedS. recurvumcomplex, includingS. balticumandS. obtusum, in addition to the informal cladeS. “pseudopacificum.” Although we detected some geographically correlated phylogenetic structure within widespread morphospecies, our RADseq data support the interpretation that these species have intercontinental geographic ranges.

 
more » « less
Award ID(s):
1928514
NSF-PAR ID:
10456446
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
American Journal of Botany
Volume:
107
Issue:
9
ISSN:
0002-9122
Page Range / eLocation ID:
p. 1283-1295
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Background and Aims

    Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with ~300–500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. We assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites.

    Methods

    Four hundred and five samples of the four species, representing 57 populations, were subjected to restriction site-associated DNA sequencing (RADseq). Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Difference in fitness between genets was estimated as the numbers of ramets each genet comprised. Degrees of clonality [numbers of genets/numbers of ramets (samples)] within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex.

    Key Results

    All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but two to eight ramets were dsumbers ansd text etected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets and sexes were not detected. Within S. divinum, however, female gametophytes harboured two to three times the number of microbial taxa as males.

    Conclusions

    These four Sphagnum species all exhibit similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns, where genets abut one another but do not extensively mix because of limited ramet fragmentation, and the guerrilla patterns, where extensive genet fragmentation and dispersal result in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.

     
    more » « less
  2. Abstract Objectives

    Long‐tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long‐tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long‐tailed macaques using low‐coverage nuclear DNA (nDNA) data from museum specimens.

    Methods

    We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long‐tailed macaque museum specimens from localities throughout Southeast Asia.

    Results

    We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades withinM. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island‐living individuals, including those from southern Sumatra.

    Conclusions

    Overall, we demonstrate that low‐coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.

     
    more » « less
  3. Abstract Aim

    We used genome‐scale sampling to assess the phylogeography of a group of topminnows in theFundulus notatusspecies complex. Two of the species have undergone extensive range expansions resulting in broadly overlapping distributions, and sympatry within drainages has provided opportunities for hybridization and introgression. We assessed the timing and pattern of range expansion in the context of late Pleistocene–Holocene drainage events and evaluated the evidence for introgressive hybridization between species.

    Location

    Central and southern United States including drainages of the Gulf of Mexico Coastal Plain and portions of the Mississippi River drainage in and around the Central Highlands.

    Taxon

    Topminnows, GenusFundulus, subgenusZygonectesFundulus notatus, Fundulus olivaceus, Fundulus euryzonus.

    Methods

    We sampled members of theF. notatusspecies complex throughout their respective ranges, including numerous drainage systems where species co‐occur. We collected genome‐wide single nucleotide polymorphisms (SNPs) using the genotype‐by‐sequencing (GBS) method and subjected data to population genetic analyses to infer the population histories of both species, including explicit tests for admixture and introgression. The methods employed includedSTRUCTURE, principal coordinates analysis, TreeMix and approximate Bayesian computation.

    Results

    Genetic data are presented for 749 individuals sampled from 14F. notatus, 20F. olivaceusand 2F. euryzonuspopulations. Members of the species complex differed in phylogeographic structure, withF. notatusexhibiting geographic clusters corresponding to Pleistocene coastal drainages andF. olivaceuscomparatively lacking in phylogeographic structure. Evidence for interspecific introgression varied by drainage.

    Main conclusions

    Populations ofF. notatusandF. olivaceusexhibited contrasting patterns of lineage diversity among coastal drainages, indicating interspecific differences in their Pleistocene southern refugia. Phylogeographic patterns in both species indicated that range expansions into the northern limits of contemporary distributions coincided with and continued subsequent to the Last Glacial Maximum. There was evidence of introgression between species in some, but not all drainages where the species co‐occur, in a pattern that is correlated with previous estimates of hybridization rates.

     
    more » « less
  4. Abstract Premise

    The ~140 species ofLoniceraare characterized by variously fused leaves, bracteoles, and ovaries, making it a model system for studying the evolution and development of organ fusion. However, previous phylogenetic analyses, based mainly on chloroplast DNA markers, have yielded uncertain and conflicting results. A well‐supported phylogeny ofLonicerawill allow us to trace the evolutionary history of organ fusion.

    Methods

    We inferred the phylogeny ofLonicerausing restriction site–associated DNA sequencing (RADSeq), sampling all major clades and 18 of the 23 subsections. This provided the basis for inferring the evolution of five fusion‐related traits.

    Results

    RADSeq data yielded a well‐resolved and well‐supported phylogeny. The two traditionally recognized subgenera (PericlymenumandChamaecerasus), three of the four sections (Isoxylosteum,Coeloxylosteum, andNintooa), and half of the subsections sampled were recovered as monophyletic. However, the large and heterogeneous sectionIsikawas strongly supported as paraphyletic.Nintooa, a clade of ~22 mostly vine‐forming species, includingL. japonica, was recovered in a novel position, raising the possibility of cytonuclear discordance. We document the parallel evolution of fused leaves, bracteoles, and ovaries, with rare reversals. Most strikingly, complete cupules, in which four fused bracteoles completely enclose two unfused ovaries, arose at least three times. Surprisingly, these appear to have evolved directly from ancestors with free bracteoles instead of partial cupules.

    Conclusions

    We provide the most comprehensive and well‐supported phylogeny ofLonicerato date. Our inference of multiple evolutionary shifts in organ fusion provides a solid foundation for in depth developmental and functional analyses.

     
    more » « less
  5. Abstract Aim

    Periodic lowering of sea levels and formation of land bridges can reshape phylogeographic patterns of insular biotas. Using archipelago‐wide sampling, we aimed to test if phylogeography of an old‐endemic bat lineage reflected Pleistocene land bridges.

    Location

    Solomon Islands and Papua New Guinea.

    Taxon

    MelonycterisandNesonycterisbats (Pteropodidae).

    Methods

    We sequenced genome‐wide RADseq data for 49 specimens from 15 islands. We assessed phylogenetic relationships using maximum likelihood inRAxMLand quartet‐based methods inSVDquartets, population structure usingStructure, and admixture using maximum likelihood methods inTreeMix. We tested for genetic and geographic distance correlations using distance‐based redundancy analyses (dbRDA), identifying best‐fit models using stepwise model selection.

    Results

    Phylogenetic analyses identified fiveNesonycterisclades corresponding to Greater Bukida, Guadalcanal, Makira, Malaita and New Georgia group. Makira samples were sister to remainingNesonycteris.Structureidentified four populations: New IrelandMelonycteris melanops; andNesonycterisfrom Greater Bukida (including Guadalcanal); Malaita and Makira; and New Georgia group. Genetic backgrounds of Mono, Ngella and Guadalcanal separated from remaining Greater Bukida islands. Makira and Malaita separated into two populations. New Georgia group lacked structure, and genetic and geographic distances were not correlated. The best‐fit geographic distance models forNesonycterisand a Greater Bukida subset were least shore‐to‐shore distance; and Euclidean and least‐cost distances respectively.

    Main Conclusions

    Influences of modern and Pleistocene island isolation and connectivity were evident in the overall Phylogeography ofNesonycteris. The lack of structure or geographic distance correlations within the New Georgia group indicated all islands were interconnected during the Last Glacial Maximum or contemporary oceanic divides are ineffective barriers. Conversely, genetic divergence across Greater Bukida islands reflected land‐bridge constrained dispersal. A Makira clade sister to allNesonycterispossibly indicates an origin on Makira. Alternately it reflects Makira's long‐isolated geographic status, as similar results exist for a range of taxa.

     
    more » « less