Phylogenetic divergence of island biotas: Molecular dates, extinction, and "relict" lineages

Fossil-calibrated phylogenies of Southern cave wētā show dispersal and extinction confound biogeographic signal

The biota of continents and islands are commonly considered to have a source-sink relationship, but small islands can harbour distinctive taxa. The distribution of four monotypic genera of Orthoptera on young subantarctic islands indicates a role for long-distance dispersal and extinction. Phylogenetic relationships were inferred from whole mtDNA genomes and nuclear sequences (45S cassette; four histones). We used a fossil and one palaeogeographic event to calibrate molecular clock analysis. We confirm that neither the Australian nor Aotearoa-New Zealand Rhaphidophoridae faunas are monophyletic. The radiation of Macropathinae may have begun in the late Jurassic, but trans-oceanic dispersal is required to explain the current distribution of some lineages within this subfamily. Dating the most recent common ancestor of seven island endemic species with their nearest mainland relative suggests that each existed long before their island home was available. Time estimates from our fossil-calibrated molecular clock analysis suggest several lineages have not been detected on mainland New Zealand, Australia, or elsewhere most probably due to their extinction, providing evidence that patterns of extinction, which are not consistently linked to range size or lineage age, confound biogeographic signal.

Genomics reveals repeated landlocking of diadromous fish on an isolated island

Landlocking of diadromous fish in freshwater systems can have significant genomic consequences. For instance, the loss of the migratory life stage can dramatically reduce gene flow across populations, leading to increased genetic structuring and stronger effects of local adaptation. These genomic consequences have been well-studied in some mainland systems, but the evolutionary impacts of landlocking in island ecosystems are largely unknown. In this study, we used a genotyping-by-sequencing (GBS) approach to examine the evolutionary history of landlocking in common smelt (Retropinna retropinna) on Chatham Island, a small isolated oceanic island 800 kilometres east of mainland New Zealand. We examined the relationship between Chatham Island and mainland smelt and used coalescent analyses to test the number and timing of landlocking events on Chatham Island. Our genomic analysis, based on 21,135 SNPs across 169 individuals, revealed that the Chatham Island smelt was genomically distinct from the mainland New Zealand fish, consistent with a single ancestral colonisation event of Chatham Island in the Pleistocene. Significant genetic structure was also evident within the Chatham Island smelt, with a diadromous Chatham Island smelt group, along with three geographically structured landlocked groups. Coalescent demographic analysis supported three independent landlocking events, with this loss of diadromy significantly pre-dating human colonisation. Our results illustrate how landlocking of diadromous fish can occur repeatedly across a narrow spatial scale, and highlight a unique system to study the genomic basis of repeated adaptation.

Diversification and historical demography of Rhampholeon spectrum in West-Central Africa

Pygmy Chameleons of the genus Rhampholeon represent a moderately diverse, geographically circumscribed radiation, with most species (18 out of 19 extant taxa) limited to East Africa. The one exception is Rhampholeon spectrum, a species restricted to West-Central African rainforests. We set out to characterize the geographic basis of genetic variation in this disjunctly distributed Rhampholeon species using a combination of multilocus Sanger data and genomic sequences to explore population structure and range-wide phylogeographic patterns. We also employed demographic analyses and niche modeling to distinguish between alternate explanations to contextualize the impact of past geological and climatic events on the present-day distribution of intraspecific genetic variation. Phylogenetic analyses suggest that R. spectrum is a complex of five geographically delimited populations grouped into two major clades (montane vs. lowland). We found pronounced population structure suggesting that divergence and, potentially, speciation began between the late Miocene and the Pleistocene. Sea level changes during the Pleistocene climatic oscillations resulted in allopatric divergence associated with dispersal over an ocean channel barrier and colonization of Bioko Island. Demographic inferences and range stability mapping each support diversification models with secondary contact due to population contraction in lowland and montane refugia during the interglacial period. Allopatric divergence, congruent with isolation caused by geologic uplift of the East African rift system, the "descent into the Icehouse," and aridification of sub-Saharan Africa during the Eocene-Oligocene are identified as the key events explaining the population divergence between R. spectrum and its closely related sister clade from the Eastern Arc Mountains. Our results unveil cryptic genetic diversity in R. spectrum, suggesting the possibility of a species complex distributed across the Lower Guinean Forest and the Island of Bioko. We highlight the major element of species diversification that modelled today's diversity and distributions in most West-Central African vertebrates.

Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)

The biogeographical origins of the endemic birds of New Zealand (Aotearoa) are of great interest, particularly Palaeogene lineages such as Callaeidae, a passerine family characterized by brightly coloured wattles behind the beak and, in some cases, extreme sexual dimorphism in bill size and shape. Ancestral representatives of Callaeidae are thought to have split from their closest relatives outside New Zealand in the Oligocene, but little is known about the timing of divergences within the family. We present a fully dated molecular phylogeny of Callaeidae mitogenomes and discuss the biogeographical implications. Our results suggest that formation of Pliocene marine seaways, such as the Manawatu Strait, are likely to have played a significant role in the differentiation of North Island and South Island kōkako (Callaeas spp.) and saddlebacks/tīeke (Philesturnus spp.).

Assessing population genetic structure of three New Zealand stream insects using mitochondrial and nuclear DNA markers

Assessing genetic differentiation among natural populations can aid understanding of dispersal patterns and connectivity among habitats. Several molecular markers have become increasingly popular in determining population genetic structure for this purpose. Here, we compared the resolution of mitochondrial cytochrome c oxidase subunit I (COI) and nuclear single nucleotide polymorphism (SNP) markers for detecting population structure among stream insects at small spatial scales. Individuals of three endemic taxa - Coloburiscus humeralis (Ephemeroptera), Zelandobius confusus (Plecoptera), and Hydropsyche fimbriata (Trichoptera) - were collected from forested streams that flow across open pasture in the North Island of New Zealand. Both COI and SNP data indicated limited population structure across the study area, and small differences observed among these species were likely related to their putative dispersal abilities. For example, fine-scale genetic differentiation between and among neighbouring stream populations for H. fimbriata suggests that gene flow, and hence dispersal, may be more limited for this species relative to the others. Based on the generally similar results provided by both types of markers, we suggest that either COI or SNP markers can provide suitable initial estimates of fine-scale population genetic differentiation in stream insects.

Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions

Thirty years ago, DNA sequences were obtained from an extinct Aotearoa New Zealand animal for the first time. Since then, ancient DNA research has provided many - often unexpected - insights into the origins of New Zealand's terrestrial and marine vertebrate fauna. Because recent human activities in New Zealand have caused the decline or extinction of many endemic plant, bird, reptile, and marine mammal species, ancient DNA has been instrumental in reconstructing their identities and origins. However, most ancient DNA studies focusing on New Zealand species have been restricted to vertebrates, with small sample sizes, and/or relatively few genetic markers. This has limited their power to infer fine-scale biogeographic patterns, including (pre)historic distributions and range-shifts driven by past climate and environmental change. Recently, 'next-generation' methodological and technological advances have broadened the range of hypotheses that can feasibly be tested with ancient DNA. These advances represent an exciting opportunity for further exploring New Zealand biogeography using ancient DNA, but their promise has not yet been fully realised. In this review, we summarise the last 30 years of ancient DNA research into New Zealand faunal biogeography and highlight key objectives, challenges, and possibilities for the next 30 years and beyond.

Eco-evolutionary priority and the assembly of the New Zealand flora

Eco-evolutionary priority effects, in which early arriving taxa pre-empt environmental niches and evolve to exclude or marginalise later arriving taxa, have been claimed to have influenced current vegetation communities in New Zealand. We here critically assess this claim. An examination of the entire New Zealand conifer and angiosperm flora shows that early arriving lineages do not have more species than later arriving lineages, and do not dominate regional species pools. A nationwide forest plot data set shows no influence of lineage age on tree dominance. Woody species with wide latitudinal ranges tend to be older, but plant height and biotically dispersed fruit exert a stronger influence. Range extent is not influenced by lineage age in the alpine zone. The New Zealand studies on which the original claim for eco-evolutionary priority effects is based are flawed as they sample only a small fraction of the flora and plant communities and base their conclusions on a few selected lineages. The large climatic and landscape alterations of the last 50 million years, changes in the type and number of immigrant taxa establishing, and extinction are likely to have been much more influential than arrival times in shaping the extant New Zealand flora.

Insights into Aotearoa New Zealand's biogeographic history provided by the study of natural hybrid zones

Hybridisation is commonly observed in geographical zones of contact between distinct lineages. These contact zones have long been of interest for biogeographers because they provide insight into the evolutionary and ecological processes that influence the distribution of species as well as the process of speciation. Here we review research on hybrid zones and zones of past introgression, both terrestrial and marine, in Aotearoa New Zealand. Many of New Zealand's hybrid zones occur between lineages or species that diverged prior to the Last Glacial Maximum (LGM), with numerous divergences dating to the early Pleistocene or Pliocene. Few secondary contact zones have been detected in terrestrial plants and in marine taxa. This may reflect a lack of the intensive sampling required to detect hybrid zones in these groups but for plants may also indicate widespread Pleistocene survival across the country. Lastly, we suggest avenues for research into New Zealand hybrid zones that are likely to be fruitful.

Ancient DNA from the extinct Haitian cave-rail (Nesotrochis steganinos) suggests a biogeographic connection between the Caribbean and Old World

Worldwide decline in biodiversity during the Holocene has impeded a comprehensive understanding of pre-human biodiversity and biogeography. This is especially true on islands, because many recently extinct island taxa were morphologically unique, complicating assessment of their evolutionary relationships using morphology alone. The Caribbean remains an avian hotspot but was more diverse before human arrival in the Holocene. Among the recently extinct lineages is the enigmatic genus Nesotrochis, comprising three flightless species. Based on morphology, Nesotrochis has been considered an aberrant rail (Rallidae) or related to flufftails (Sarothruridae). We recovered a nearly complete mitochondrial genome of Nesotrochis steganinos from fossils, discovering that it is not a rallid but instead is sister to Sarothruridae, volant birds now restricted to Africa and New Guinea, and the recently extinct, flightless Aptornithidae of New Zealand. This result suggests a widespread or highly dispersive most recent common ancestor of the group. Prior to human settlement, the Caribbean avifauna had a far more cosmopolitan origin than is evident from extant species.

Comparative phylogeography of two Agarophyton species in the New Zealand archipelago

Molecular studies have reported the coexistence of two species of Agarophyton in New Zealand: the newly described A.transtasmanicum with an apparently restricted distribution to some sites in the North Island, and the more widespread A.chilense. Here, we compared the distribution, genetic diversity, and structure of both Agarophyton species throughout the archipelago using sequences of the nuclear Internal Transcribed Spacer 2 (ITS2) marker. Agarophyton chilense's distribution was continuous and extensive along the North and South Islands, Stewart Island, and Chatham Island, and the genetic clusters were mostly concordant with boundaries between biogeographic regions. In contrast, specimens of A.transtasmanicum were collected in four sites broadly distributed in both the North and South Islands, with no clear spatial structure of the genetic diversity. Populations, where the species co-occurred, tended to display similar levels in genetic diversity for the two species. Demographic inferences supported a postglacial demographic expansion for two A.chilense genetic clusters, one present in the South Island and the eastern coast of the North Island, and the other present in northern South Island. A third genetic cluster located on the western coast of the North Island had a signature of long-term demographic stability. For A.transtasmanicum, the skyline plot also suggested a postglacial demographic expansion. Last, we developed a new molecular tool to quickly and easily distinguish between the two Agarophyton species, which could be used to ease future fine-scale population studies, especially in areas where the two species coexist.