A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity

Abstract

Premise: Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives.

Methods: To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution.

Results: Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species.

Conclusions: The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.

Keywords: Banksia; DArTseq; Proteaceae; cpDNA; genome-wide analysis; last glacial maximum; single nucleotide polymorphism; species boundaries; taxonomy; threatened species.

Figure 1

Morphological diversity of the hairpin banksia species complex. (A) B. vincentia from Vincentia, NSW. (B) B. cunninghamii from Blackheath, NSW. (C) B. neoanglica from Girraween National Park, Qld. (D) Banksia spinulosa from Glenbrook National Park, NSW. (E) B. collina from Kungala, NSW. (F) B. spinulosa from Isla Gorge National Park, NSW. Images not to scale. Image credits: A, K. Coutts‐McClelland; B, J. Allen; C and D, T.C. Wilson; E and F, P. H. Weston. Scale = 25 mm.

Figure 2

Hairpin banksia complex distribution based on specimen records acquired from the Atlas of Living Australia website (http://www.ala.org.au [accessed 25 April 2020]). Five species are distinguished according to Stimpson et al. (2016): B. collina (green circles), B. cunninghamii (blue squares), B. spinulosa (yellow circles), B. neoanglica (red squares), B. vincentia (V). Dotted lines indicate approximate area of major biogeographic barrier sensu Bryant and Krosch (2016): Brisbane Valley Barrier (BVB), Hunter River Corridor (HRC), Saint Lawrence Gap (SLG), Southern Transition Zone (STZ). State capitals are Adelaide (A), Brisbane (B), Darwin (D), Hobart (H), Melbourne (M), Perth (P), Sydney (S).

Figure 3

SplitsTree network analysis of 1384 SNP loci for 597 specimens sampled from across the Banksia spinulosa complex using B. ericifolia and B. paludosa as outgroups. The network clusters members of the hairpin banksia complex into two distinct groups/clades: B. cunninghamii clade (B. cunninghamii, B. neoanglica and B. vincentia) and B. spinulosa clade (B. collina and B. spinulosa). The network indicates (1) relative amounts of reticulation through the width of the branches between clusters of samples: extensive reticulation is evident between B. cunninghamii, B. neoanglica, and B. vincentia subclusters, and (2) wild‐sourced specimens of B. neoanglica, B. spinulosa, and B. ericifolia and cultivated seedlings of B. vincentia (Australian Botanic Gardens, ABG) are placed between major species clusters, which is indicative of a hybrid genome

Figure 4

TreeMix maximum likelihood tree of the relationships among representative populations of the hairpin banksia complex indicating one migration event and its direction between sympatric species at the Lamington site. Migration events are modelled for populations that do not fit well into the bifurcating tree model, because they have ancestry from multiple parental populations, and they are indicated as edges. The number of migration events presented is based on an examination of the progressive improvement in fit (Appendix S18). The color of the edges reflects the relative weight of migration, i.e., the fraction of alleles in the descendant population that originated in each parental population (m = 0 → 1, yellow: small fraction of alleles, red: large fraction). Bootstrap support values below 50% are not reported. Refer to Appendix S1 for detailed locality data.

Figure 5

Sampling and genomic analysis of the Banksia cunninghamii clade for B. cunninghamii (8–14, 16–23), B. neoanglica (1–7), and B. vincentia (15) across southeastern Australia. (A) Pie charts represent averaged snmf Q values according to three ancestral populations (K = 3) for each population. (B) Network analysis of the chloroplast genome where each hash on a branch represents a mutational change and color corresponds to results from snmf analysis. (C) SVDQ quartets coalescent tree, with total incompatible quartets = 20475 (20.475%), branch tips representing a population of up to six individuals, bootstrap support values >70% placed above branches and green circles indicating inclusion in the chloroplast genomic dataset; Mount Mitchel (5) and Medway (12) were not included; proximally located specimens were amalgamated as one population in two places: Secret River (19) and Shipwreck Creek (20) as “Croajingalong NP”, and Girraween NP (2) and Boonoo Boonoo NP (2) as “Girraween/Boonoo”. Refer to Appendices S7–S10 for cross entropy vs. number of ancestral populations and corresponding averaged Q values, Appendix S1 for detailed locality and sampling information for all analyses, and Bryant and Kosch (2016) for description of the Hunter Valley Corridor (HRC) and Southern Transition Zone (STZ) biogeographical barriers.

Figure 6

Sampling and nuclear and plastid genomic analysis of the Banksia spinulosa clade for B. collina (1–36) and B. spinulosa (37–49) across eastern Australia. (A) Pie charts represent averaged snmf Q values according to four ancestral populations (K = 4) for each population. (B) Network analysis of the chloroplast genome. Hashes on a branch represent number of mutational changes, and color indicates species (B. collina = green; B. spinulosa = yellow). Populations are organized as two discrete haplogroups based on 59 mutational changes, the smallest haplogroup consisting of seven haplotypes (more northern populations) and the largest consisting of southern populations with a large central haplotype joined to numerous satellite haplotypes. (C) SVDQ quartets coalescent tree, with total incompatible quartets = 42,964 (45.923%), branch tips representing a population of up to six individuals, bootstrap support values >70% placed above branches, and green circles indicating inclusion in the chloroplast genomic data set; Banksia spinulosa is rendered paraphyletic with respect to B. collina. Lamington (20) was not included in phylogeny or chloroplast; Wallaroo and Barren Grounds (B) were included with Limeburners (27) and Carrington Falls (45) for snmf, respectively; Parr (31a = NSW1033917, 31b = NSW1033272, 31c = NSW1033274, 31d = NSW1033541) and Yengo (28a = NSW1033276, 28b = NSW1033944, 28c = NSW1033269) samples were not recovered together in the network; Coondella (N), Mogo (G), Ulladulla (U), Katoomba (K), McMahons (M), Tewantin (T) samples were only included in network analysis; the central chloroplast network haplotype (C) consisted of Wallaroo, Mooloolah River (10), Glasshouse Mountains (11), Helidon Hills (15), Russel Island (17), Kungala (23), Scotts Head (26), Limeburners Creek (27), Parr (31d), Forrester's Beach (34), Bouddi (36), Evan's Lookout (38) and Bournda (49). Refer to Appendices S7–S10 for cross entropy vs. number of ancestral populations and corresponding averaged Q values and Appendix S1 for all locality and sampling information.

Figure 7

Last glacial maximum (LGM) and present environmental niche modeling projections provided for the samples of the hairpin banksia B. cunninghamii clade nDNA data set, with B. vincentia removed and augmented with specimen records from the Atlas of Living Australia website (http://www.ala.org.au [accessed 25 April 2020]). Modelling was provided for the (T) total data set and for the three groups of populations identified from analysis of the nDNA data set: (N) northern group found north of the Hunter river in New South Wales; (S) southern group found south of the Towamba River in southern New South Wales; (C) central group found between the Hunter river and Towamba River. The total data set showed a present‐day optimal climatic envelope similar to its southeastern Australia range but extending much farther south. The highest optimality occurred away from the coast along most of the eastern side of the continent, along the southern coast of the mainland, and extensively throughout the island of Tasmania. When the data set was restricted to southern, central, or northern groups, the projected optimality envelope was generally similar to the current distribution, although it extended north of the Hunter River corridor for the central group, and south to the north coast of the island of Tasmania for the southern group. Projections of each data set for the LGM were all provided a lower suitability, although the range of suitability was more extensive by latitude.